ORCID Profile
0000-0001-7506-2589
Current Organisations
R&D Certainty Pty Ltd
,
University of Adelaide
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
In Research Link Australia (RLA), "Research Topics" refer to ANZSRC FOR and SEO codes. These topics are either sourced from ANZSRC FOR and SEO codes listed in researchers' related grants or generated by a large language model (LLM) based on their publications.
Agricultural Biotechnology | Plant Cell and Molecular Biology | Agricultural Biotechnology not elsewhere classified | Crop and Pasture Improvement (Selection and Breeding)
Publisher: Elsevier
Date: 2003
Publisher: Springer Science and Business Media LLC
Date: 12-2021
Publisher: Scientific Societies
Date: 1995
DOI: 10.1094/PD-79-0461
Publisher: Springer Science and Business Media LLC
Date: 14-09-2017
Publisher: Oxford University Press (OUP)
Date: 2018
Abstract: In crop plant genetics, linkage maps provide the basis for the mapping of loci that affect important traits and for the selection of markers to be applied in crop improvement. In outcrossing species such as almond (Prunus dulcis Mill. D. A. Webb), application of a double pseudotestcross mapping approach to the F1 progeny of a biparental cross leads to the construction of a linkage map for each parent. Here, we report on the application of genotyping by sequencing to discover and map single nucleotide polymorphisms in the almond cultivars “Nonpareil” and “Lauranne.” Allele-specific marker assays were developed for 309 tag pairs. Application of these assays to 231 Nonpareil × Lauranne F1 progeny provided robust linkage maps for each parent. Analysis of phenotypic data for shell hardness demonstrated the utility of these maps for quantitative trait locus mapping. Comparison of these maps to the peach genome assembly confirmed high synteny and collinearity between the peach and almond genomes. The marker assays were applied to progeny from several other Nonpareil crosses, providing the basis for a composite linkage map of Nonpareil. Applications of the assays to a panel of almond clones and a panel of rootstocks used for almond production demonstrated the broad applicability of the markers and provide subsets of markers that could be used to discriminate among accessions. The sequence-based linkage maps and single nucleotide polymorphism assays presented here could be useful resources for the genetic analysis and genetic improvement of almond.
Publisher: Public Library of Science (PLoS)
Date: 12-11-2015
Publisher: Elsevier BV
Date: 05-2013
Publisher: Springer New York
Date: 2014
DOI: 10.1007/978-1-4939-0446-4_2
Abstract: Once the sequence is known for a gene of interest, it is usually possible to design markers to detect polymorphisms within the gene. Such markers can be particularly useful in plant breeding, especially if they detect the causal polymorphism within the gene and are diagnostic of the phenotype. In this chapter, we (1) discuss how gene sequences are obtained and aligned and how polymorphic sites can be identified or predicted (2) explain the principles of PCR primer design and PCR lification and provide guidelines for their application in the design and testing of markers (3) discuss detection methods for presence/absence (dominant) polymorphisms, length polymorphisms and single nucleotide polymorphisms (SNPs) and (4) outline some of the factors that affect the utility of markers in plant breeding and explain how markers can be evaluated (validated) for use in plant breeding.
Publisher: Oxford University Press (OUP)
Date: 05-1993
Publisher: Scientific Societies
Date: 1996
DOI: 10.1094/PHYTO-86-110
Publisher: Oxford University Press (OUP)
Date: 10-2019
DOI: 10.1105/TPC.19.00272
Publisher: Wiley
Date: 1998
Publisher: Springer Science and Business Media LLC
Date: 18-01-2019
Publisher: International Society for Horticultural Science (ISHS)
Date: 2019
Publisher: CSIRO Publishing
Date: 2015
DOI: 10.1071/CP15013
Abstract: Durum wheat production in southern Australia is limited when water deficit occurs immediately before and during anthesis. This study was conducted to determine the effect of genotypic variation on various yield, morphological and physiological responses to pre-anthesis water-deficit stress by evaluating 20 durum wheat (Triticum turgidum L. ssp. durum) genotypes over 2 years of glasshouse experiments. Grain number was the major yield component that affected yield under pre-anthesis water-deficit stress. Genotypes with less yield reduction also had less reduction in chlorophyll content, relative water content and leaf water potential, suggesting that durum genotypes tolerant of water-deficit stress maintain a higher photosynthetic rate and leaf water status. Weak to moderate positive correlations of morphological traits, including plant height and fertile tiller number, with grain number and biomass make the evaluation of high-yielding genotypes in rainfed conditions possible. Morphological traits (such as plant height and tiller number) and physiological traits (such as chlorophyll content, relative water content and leaf water potential) could therefore be considered potential indicators for indirect selection of durum wheat with water-deficit stress tolerance under Mediterranean conditions.
Publisher: Elsevier BV
Date: 03-2004
Publisher: Springer Science and Business Media LLC
Date: 08-2002
DOI: 10.1007/S00122-002-0941-1
Abstract: The suitability of barley ( Hordeum vulgare L.) grain for malting depends on many criteria, including the size, shape and uniformity of the kernels. Here, image analysis was used to measure kernel size and shape attributes (area, perimeter, length, width, F-circle and F-shape) in grain s les of 140 doubled-haploid lines from a two-rowed (cv Harrington) by six-rowed (cv Morex) barley cross. Interval mapping was used to map quantitative trait loci (QTLs) affecting the means and within-s le standard deviations of these attributes using a 107-marker genome map. Regions affecting one or more kernel size and shape traits were detected on all seven chromosomes. These included one near the vrs1 locus on chromosome 2 and one near the int-c locus on chromosome 4. Some, but not all, of the QTLs exhibited interactions with the environment and some QTLs affected the within-s le variability of kernel size and shape without affecting average kernel size and shape. When QTL analysis was conducted using data from only the two-rowed lines, the region on chromosome 2 was not detected but QTLs were detected elsewhere in the genome, including some that had not been detected in the analysis of the whole population. Analysis of only the six-rowed lines did not detect any QTLs affecting kernel size and shape attributes. QTL alleles that made kernels larger and/or rounder also tended to improve malt quality and QTL alleles that increased the variability of kernel size were associated with poor malt quality.
Publisher: Oxford University Press (OUP)
Date: 09-05-2013
Publisher: Wiley
Date: 03-1997
Publisher: Elsevier BV
Date: 09-2008
Publisher: Canadian Science Publishing
Date: 12-1988
DOI: 10.1139/G88-135
Abstract: Ratios of the phenotypic values of two traits may be used as selection criteria in animal and plant breeding to improve the ratio traits themselves or to effect changes in their two component (numerator and denominator) traits. Prediction of genetic responses to ratio-based selection would facilitate quantitative analysis and evaluation of selection based on ratios. Methods for predicting such responses are derived and presented here. They employ expressions for the truncation value of a ratio and for the phenotypic selection differentials of the numerator and denominator traits. The derivation of these expressions is based upon the assumption that the phenotypic values of each of these traits are normally distributed. Worked ex les relating to livestock and crop improvement are included to demonstrate how responses to selection for ratios may be predicted.Key words: ratio selection criterion, selection differential, genetic response.
Publisher: Wiley
Date: 03-2009
Publisher: EDP Sciences
Date: 04-2018
DOI: 10.1051/0004-6361/201731169
Abstract: Context. The large jet kinetic power and non-thermal processes occurring in the microquasar SS 433 make this source a good candidate for a very high-energy (VHE) gamma-ray emitter. Gamma-ray fluxes above the sensitivity limits of current Cherenkov telescopes have been predicted for both the central X-ray binary system and the interaction regions of SS 433 jets with the surrounding W50 nebula. Non-thermal emission at lower energies has been previously reported, indicating that efficient particle acceleration is taking place in the system. Aim. We explore the capability of SS 433 to emit VHE gamma rays during periods in which the expected flux attenuation due to periodic eclipses ( P orb ~ 13.1 days) and precession of the circumstellar disk ( P pre ~ 162 days) periodically covering the central binary system is expected to be at its minimum. The eastern and western SS 433/W50 interaction regions are also examined using the whole data set available. We aim to constrain some theoretical models previously developed for this system with our observations. Methods. We made use of dedicated observations from the Major Atmospheric Gamma Imaging Cherenkov telescopes (MAGIC) and High Energy Spectroscopic System (H.E.S.S.) of SS 433 taken from 2006 to 2011. These observation were combined for the first time and accounted for a total effective observation time of 16.5 h, which were scheduled considering the expected phases of minimum absorption of the putative VHE emission. Gamma-ray attenuation does not affect the jet/medium interaction regions. In this case, the analysis of a larger data set amounting to ~40–80 h, depending on the region, was employed. Results. No evidence of VHE gamma-ray emission either from the central binary system or from the eastern/western interaction regions was found. Upper limits were computed for the combined data set. Differential fluxes from the central system are found to be ≲ 10 −12 –10 −13 TeV −1 cm −2 s −1 in an energy interval ranging from ~few × 100 GeV to ~few TeV. Integral flux limits down to ~ 10 −12 –10 −13 ph cm −2 s −1 and ~ 10 −13 –10 −14 ph cm −2 s −1 are obtainedat 300 and 800 GeV, respectively. Our results are used to place constraints on the particle acceleration fraction at the inner jetregions and on the physics of the jet/medium interactions. Conclusions. Our findings suggest that the fraction of the jet kinetic power that is transferred to relativistic protons must be relatively small in SS 433, q p ≤ 2.5 × 10 −5 , to explain the lack of TeV and neutrino emission from the central system. At the SS 433/W50 interface, the presence of magnetic fields ≳10 μ G is derived assuming a synchrotron origin for the observed X-ray emission. This also implies the presence of high-energy electrons with E e − up to 50 TeV, preventing an efficient production of gamma-ray fluxes in these interaction regions.
Publisher: Wiley
Date: 11-2005
Publisher: Oxford University Press (OUP)
Date: 09-1996
Publisher: CSIRO Publishing
Date: 2008
DOI: 10.1071/AR08074
Abstract: Black point and kernel discoloration of barley both appear to occur under conditions of high humidity at grain fill. Both of these traits are likely to result from the enzymatic oxidation of phenolic compounds to quinones and the transformation of those oxidation products to brown or black pigments during high humidity. However, even though black point symptoms are quite distinct from other types of kernel discoloration, black point of barley has not previously been the sole focus of environmental studies or quantitative trait locus (QTL) analysis. We have evaluated black point tolerance in doubled haploid progeny of Alexis/Sloop and mapped QTLs on chromosomes 2H and 3H. We have also established that the occurrence of low vapour pressure deficit, high humidity, and low temperatures is associated with the formation of black point in susceptible varieties. These environmental conditions probably create a moist environment during grain development so that the developing grain cannot dry out. Stress or wounding to the embryo caused by this environment might then lead to black point formation. The results of this study will enable the use of comprehensive genetic and biochemical approaches to develop a more detailed understanding of this disorder.
Publisher: Informa UK Limited
Date: 03-1994
Publisher: Scientific Societies
Date: 1993
DOI: 10.1094/PD-77-1248
Publisher: Elsevier BV
Date: 03-1999
Publisher: Springer Science and Business Media LLC
Date: 1996
DOI: 10.1007/BF00033098
Publisher: Wiley
Date: 07-1999
Publisher: Springer Science and Business Media LLC
Date: 02-2015
Publisher: Canadian Science Publishing
Date: 12-2002
DOI: 10.1139/G02-089
Abstract: Marker genotype data and grain and malt quality phenotype data from three barley (Hordeum vulgare L.) mapping populations were used to investigate the feasibility of selective genotyping for detection of quantitative trait loci (QTLs). With selective genotyping, only in iduals with high and low phenotypic values for the trait of interest are genotyped. Here, genotyping of 10 to 70% of each population (i.e., 5 to 35% in each tail of the phenotypic distribution) was considered. Genomic positions detected by selective genotyping were compared to QTL position estimates from interval mapping analysis using marker genotype data from the entire population. Selective genotyping reliably detected almost all of the mapped QTLs, often with only 10% of the population genotyped. Selective genotyping also detected spurious QTLs in regions of the genome where no significant QTL had been mapped. Even with additional genotyping to verify putative QTLs, the total genotyping effort for detection of QTLs for a single trait by selective genotyping was usually less than 30% of that required for conventional interval mapping. Simultaneous investigation of two or more traits by selective genotyping would require additional genotyping effort, but could still be worthwhile.Key words: selective genotyping, quantitative trait loci, barley.
Publisher: Public Library of Science (PLoS)
Date: 08-07-2015
Publisher: Canadian Science Publishing
Date: 06-1994
DOI: 10.1139/G94-070
Abstract: Molecular markers linked to loci of interest can be used for fine mapping a particular area of a genome or for marker-assisted selection. We present an approach for screening in idual plants with polymorphic markers that facilitates phenotyping in large populations. Polymorphic DNA fragments, lified by PCR, are labelled with digoxigenin and used as probes on slot blots of lified DNA from the in idual plants to be tested. DNA is obtained by a simple two-tube purification method. The colorimetric detection of alleles on the blots is more reliable, and more amenable to automation, than conventional staining of electrophoresis gels.Key words: molecular markers, RAPD, genetic mapping, breeding.
Publisher: Elsevier BV
Date: 11-1994
Publisher: Elsevier BV
Date: 03-2009
Publisher: Cold Spring Harbor Laboratory
Date: 03-04-2020
DOI: 10.1101/2020.04.01.020750
Abstract: Enset ( Ensete ventricosum (Welw.) Cheesman) is a drought tolerant, vegetatively propagated crop that was domesticated in Ethiopia. It is a staple food for more than 20 million people in Ethiopia. Despite its current importance and immense potential, enset is among the most genetically understudied and underexploited food crops. We collected 230 enset wild and cultivated accessions across the main enset producing regions in Ethiopia and applied lified fragment length polymorphism and genotype by sequencing (GBS) methods to these accessions. Wild and cultivated accessions were clearly separated from each other, with 89 genes found to harbour SNPs that separated wild from cultivated accessions. Among these, 17 genes are thought to be involved in flower initiation and seed development. Among cultivated accessions, differentiation was mostly associated with geographical location and with proximity to wild populations. Our results indicate that vegetative propagation of elite clones has favoured capacity for vegetative growth at the expense of capacity for sexual reproduction. This is consistent with previous reports that cultivated enset tends to produce non-viable seeds and flowers less frequent than wild enset.
Publisher: Oxford University Press (OUP)
Date: 03-1994
Publisher: Springer Science and Business Media LLC
Date: 15-10-2009
DOI: 10.1007/S00122-008-0904-2
Abstract: Selective genotyping of one or both phenotypic extremes of a population can be used to detect linkage between markers and quantitative trait loci (QTL) in situations in which full-population genotyping is too costly or not feasible, or where the objective is to rapidly screen large numbers of potential donors for useful alleles with large effects. Data may be subjected to 'trait-based' analysis, in which marker allele frequencies are compared between classes of progeny defined based on trait values, or to 'marker-based' analysis, in which trait means are compared between progeny classes defined based on marker genotypes. Here, bidirectional and unidirectional selective genotyping were simulated, using population sizes and selection intensities relevant to cereal breeding. Control of Type I error was usually adequate with marker-based analysis of variance or trait-based testing using the normal approximation of the binomial distribution. Bidirectional selective genotyping was more powerful than unidirectional. Trait-based analysis and marker-based analysis of variance were about equally powerful. With genotyping of the best 30 out of 500 lines (6%), a QTL explaining 15% of the phenotypic variance could be detected with a power of 0.8 when tests were conducted at a marker 10 cM from the QTL. With bidirectional selective genotyping, QTL with smaller effects and (or) QTL farther from the nearest marker could be detected. Similar QTL detection approaches were applied to data from a population of 436 recombinant inbred rice lines segregating for a large-effect QTL affecting grain yield under drought stress. That QTL was reliably detected by genotyping as few as 20 selected lines (4.5%). In experimental populations, selective genotyping can reduce costs of QTL detection, allowing larger numbers of potential donors to be screened for useful alleles with effects across different backgrounds. In plant breeding programs, selective genotyping can make it possible to detect QTL using even a limited number of progeny that have been retained after selection.
Publisher: Wiley
Date: 1984
Publisher: Springer Science and Business Media LLC
Date: 30-07-2018
DOI: 10.1007/S00122-018-3146-Y
Abstract: Novel QTL for salinity tolerance traits have been detected using non-destructive and destructive phenotyping in bread wheat and were shown to be linked to improvements in yield in saline fields. Soil salinity is a major limitation to cereal production. Breeding new salt-tolerant cultivars has the potential to improve cereal crop yields. In this study, a doubled haploid bread wheat mapping population, derived from the bi-parental cross of Excalibur × Kukri, was grown in a glasshouse under control and salinity treatments and evaluated using high-throughput non-destructive imaging technology. Quantitative trait locus (QTL) analysis of this population detected multiple QTL under salt and control treatments. Of these, six QTL were detected in the salt treatment including one for maintenance of shoot growth under salinity ( QG (1 – 5) .asl - 7A ), one for leaf Na + exclusion ( QNa.asl - 7A ) and four for leaf K + accumulation ( QK.asl - 2B.1 , QK.asl - 2B.2 , QK.asl - 5A and QK:Na.asl - 6A ). The beneficial allele for QG (1 – 5) .asl - 7A (the maintenance of shoot growth under salinity) was present in six out of 44 mainly Australian bread and durum wheat cultivars. The effect of each QTL allele on grain yield was tested in a range of salinity concentrations at three field sites across 2 years. In six out of nine field trials with different levels of salinity stress, lines with alleles for Na + exclusion and/or K + maintenance at three QTL ( QNa.asl - 7A , QK.asl - 2B.2 and QK:Na.asl - 6A ) excluded more Na + or accumulated more K + compared to lines without these alleles. Importantly, the QK.asl - 2B.2 allele for higher K + accumulation was found to be associated with higher grain yield at all field sites. Several alleles at other QTL were associated with higher grain yields at selected field sites.
Publisher: Wiley
Date: 1999
Publisher: Springer Science and Business Media LLC
Date: 28-05-2014
DOI: 10.1007/S00122-014-2322-Y
Abstract: Genetic analysis of the yield and physical quality of wheat revealed complex genetic control, including strong effects of photoperiod-sensitivity loci. Environmental conditions such as moisture deficit and high temperatures during the growing period affect the grain yield and grain characteristics of bread wheat (Triticum aestivum L.). The aim of this study was to map quantitative trait loci (QTL) for grain yield and grain quality traits using a Drysdale/Gladius bread wheat mapping population grown under a range of environmental conditions in Australia and Mexico. In general, yield and grain quality were reduced in environments exposed to drought and/or heat stress. Despite large effects of known photoperiod-sensitivity loci (Ppd-B1 and Ppd-D1) on crop development, grain yield and grain quality traits, it was possible to detect QTL elsewhere in the genome. Some of these QTL were detected consistently across environments. A locus on chromosome 6A (TaGW2) that is known to be associated with grain development was associated with grain width, thickness and roundness. The grain hardness (Ha) locus on chromosome 5D was associated with particle size index and flour extraction and a region on chromosome 3B was associated with grain width, thickness, thousand grain weight and yield. The genetic control of grain length appeared to be largely independent of the genetic control of the other grain dimensions. As expected, effects on grain yield were detected at loci that also affected yield components. Some QTL displayed QTL-by-environment interactions, with some having effects only in environments subject to water limitation and/or heat stress.
Publisher: Informa UK Limited
Date: 09-1992
Publisher: Springer Science and Business Media LLC
Date: 26-02-2015
DOI: 10.1007/S00122-015-2482-4
Abstract: The research identified rye chromosome 4R arms associated with good pollinator traits, and demonstrated possible use of rye genetic resources to develop elite pollinators for hybrid wheat breeding. Bread wheat (Triticum aestivum) is a predominantly self-pollinating plant which has relatively small-sized anthers and produces a low number of pollen grains. These features limit the suitability of most wheat lines as pollinators for hybrid seed production. One strategy for improving the pollination ability of wheat is to introgress cross-pollination traits from related species. One such species is rye (Secale cereale L.), which has suitable traits such as high anther extrusion, long anthers containing large amounts of pollen and long pollen viability. Therefore, introducing these traits into wheat is of great interest in hybrid wheat breeding. Here, we investigated wheat-rye chromosome addition lines for the effects of rye chromosomes on anther and pollen development in wheat. Using a single nucleotide polymorphism genotyping array, we detected 984 polymorphic markers that showed expected syntenic relationships between wheat and rye. Our results revealed that the addition of rye chromosomes 1R or 2R reduced pollen fertility, while addition of rye chromosome 4R increased anther size by 16% and pollen grain number by 33%. The effect on anther length was associated with increases in both cell size and the number of endothecium cells and was attributed to the long arm of chromosome 4R. In contrast, the effect on pollen grain number was attributed to the short arm of chromosome 4R. These results indicate that rye chromosome 4R contains at least two genetic factors associated with increased anther size and pollen grain number that can favourably affect pollination traits in wheat.
Publisher: Springer Science and Business Media LLC
Date: 22-09-2012
DOI: 10.1007/S00122-011-1708-3
Abstract: Bread is one of the major constituents of the human diet and wheat (Triticum aestivum L.) is the most important cereal for bread making. The gluten proteins (glutenins and gliadins) are recognised as important components affecting the processing quality of wheat flour. In this research, we investigated a particular glutenin subunit allele in an Australian cultivar, H45. Based on protein and DNA assays, the Glu-B1 allele of H45 seems to be Glu-B1al, an allele that includes a functional duplication of a gene encoding an x-type high-molecular-weight glutenin subunit, and is thought to increase dough strength through overexpression of that subunit. Yet H45 does not have the dough properties that would be expected if it carries the Glu-B1al allele. After confirming that H45 overexpresses Bx subunits and that it has relatively low un-extractable polymeric protein (an indicator of weak dough), we cloned and sequenced two Bx genes from H45. The sequences of the two genes differ from each other, and they each differ by four single-nucleotide polymorphisms (SNPs) from the sequence that has been reported for the Glu-B1al x-type glutenin genes of the Canadian wheat cultivar Glenlea. One of the SNPs leads to an extra cysteine residue in one of the subunits. The presence of this additional cysteine may explain the dough properties of H45 through effects on cross-linkage within or between glutenin subunits. We propose that the Glu-B1 allele of H45 be designated Glu-B1br, and we present evidence that Glu-B1br is co-inherited with low un-extractable polymeric protein.
Publisher: Canadian Science Publishing
Date: 12-1994
DOI: 10.1139/G94-141
Abstract: In an F 2 population, the alleles at two loci with a recombination fraction r 0.5 are in linkage disequilibrium. If r is small, then a pool of DNA from k diploid in iduals that are fixed at one locus has a relatively high probability (P = (1 − r) 2k ) of containing only the coupled allele at the second locus. Based on this principle, several methods have been described to detect linkage (using one or two pools) or to estimate r (using a group of n pools). This report compares maximum likelihood and approximate estimators of r for use in pooled-DNA analysis and illustrates the use of this analysis for dominant markers. Expected values and expected mean squares for estimators of r were computed for varying levels of r, k, and n. Both estimators were biased, but the bias and variability were slightly smaller for the maximum-likelihood estimator. Bias was not severe except when k was large relative to r and (or) n. Methods for optimizing k are discussed relative to several criteria: minimizing variance, minimizing bias, minimizing the probability that linkage cannot be detected, and minimizing the number of s les that must be screened.Key words: pooled DNA, linkage analysis, molecular markers, RAPD, genetic mapping.
Publisher: Oxford University Press (OUP)
Date: 15-10-2011
DOI: 10.1093/JXB/ERQ311
Abstract: Theoretical considerations suggest that wheat yield potential could be increased by up to 50% through the genetic improvement of radiation use efficiency (RUE). However, to achieve agronomic impacts, structural and reproductive aspects of the crop must be improved in parallel. A Wheat Yield Consortium (WYC) has been convened that fosters linkage between ongoing research platforms in order to develop a cohesive portfolio of activities that will maximize the probability of impact in farmers' fields. Attempts to increase RUE will focus on improving the performance and regulation of Rubisco, introduction of C(4)-like traits such as CO(2)-concentrating mechanisms, improvement of light interception, and improvement of photosynthesis at the spike and whole canopy levels. For extra photo-assimilates to translate into increased grain yield, reproductive aspects of growth must be tailored to a range of agro-ecosystems to ensure that stable expression of a high harvest index (HI) is achieved. Adequate partitioning among plant organs will be critical to achieve favourable expression of HI, and to ensure that plants with heavier grain have strong enough stems and roots to avoid lodging. Trait-based hybridization strategies will aim to achieve their simultaneous expression in elite agronomic backgrounds, and wide crossing will be employed to augment genetic ersity where needed for ex le, to introduce traits for improving RUE from wild species or C(4) crops. Genomic selection approaches will be employed, especially for difficult-to-phenotype traits. Genome-wide selection will be evaluated and is likely to complement crossing of complex but complementary traits by identifying favourable allele combinations among progeny. Products will be delivered to national wheat programmes worldwide via well-established international nursery systems and are expected to make a significant contribution to global food security.
Publisher: CSIRO Publishing
Date: 2014
DOI: 10.1071/FP14060
Abstract: High temperatures during grain filling can reduce the yield of wheat and affect its grain protein concentration. The Gpc-B1 locus of wheat also affects grain protein concentration, but it is not known whether its effects interact with those of heat. The aim of this study was to investigate the effects of high temperature in lines with and without functional (high-protein) alleles at Gpc-B1. A highly replicated experiment was conducted in a glasshouse under control conditions (24/18°C, 14/10 h day/night), with half of the plants of each line or cultivar put into a heat chamber (37/27°C, 14/10 h day/night) at 15 days after anthesis for 3 days. Backcross derivatives with the Gpc-B1 introgression segment differed from their recurrent parents more than those without that segment. In some respects, the effects of the Gpc-B1 introgression were similar to those of the heat treatment: both could accelerate peduncle senescence, increase grain protein content and increase the percentage of unextractable polymeric protein. Unlike the heat treatment, Gpc-B1 did not reduce grain weight, indicating that factors that hasten senescence do not necessarily limit grain size. The presence of the Gpc-B1 segment did not exacerbate the effects of heat stress on any trait.
Publisher: Springer Science and Business Media LLC
Date: 23-09-2005
DOI: 10.1007/S00122-005-0043-Y
Abstract: The limited population sizes used in many quantitative trait locus (QTL) detection experiments can lead to underestimation of QTL number, overestimation of QTL effects, and failure to quantify QTL interactions. We used the barley/barley stripe rust pathosystem to evaluate the effect of population size on the estimation of QTL parameters. We generated a large (n = 409) population of doubled haploid lines derived from the cross of two inbred lines, BCD47 and Baronesse. This population was evaluated for barley stripe rust severity in the Toluca Valley, Mexico, and in Washington State, USA, under field conditions. BCD47 was the principal donor of resistance QTL alleles, but the susceptible parent also contributed some resistance alleles. The major QTL, located on the long arm of chromosome 4H, close to the Mlo gene, accounted for up to 34% of the phenotypic variance. Subpopulations of different sizes were generated using three methods-res ling, selective genotyping, and selective phenotyping-to evaluate the effect of population size on the estimation of QTL parameters. In all cases, the number of QTL detected increased with population size. QTL with large effects were detected even in small populations, but QTL with small effects were detected only by increasing population size. Selective genotyping and/or selective phenotyping approaches could be effective strategies for reducing the costs associated with conducting QTL analysis in large populations. The method of choice will depend on the relative costs of genotyping versus phenotyping.
Publisher: CSIRO Publishing
Date: 2011
DOI: 10.1071/CP10154
Abstract: A genetic map of barley (Hordeum vulgare L.) with 163 lified fragment length polymorphism and 69 simple sequence repeat (SSR) markers was constructed using a population of 178 doubled haploid lines from a cross between the varieties ‘Baudin’ and ‘AC Metcalfe’. Linkage groups were assigned to barley chromosomes using published map locations of SSR markers as reference points. The total length of the map was 1307.2 cM with an average interval length of 5.6 cM between markers. The genetic map was used to locate quantitative trait loci (QTLs) for several disease resistance traits. The population was tested for spot type net blotch, caused by Pyrenophora teres f. maculata, and net type net blotch, caused by Pyrenophora teres f. teres, in greenhouse experiments and in a range of field environments in Western Australia and Queensland. The response of the lines to leaf rust (caused by Puccinia hordei L.) at adult plant growth stages was evaluated in Western Australia. Significant marker–trait associations were found for seedling resistance and symptom severity in adult plants to these diseases. A new locus conferring resistance to P. teres f. maculata at both seedling and adult plant stages was detected on the short arm of chromosome 6H. From the seedling testing against P. teres f. teres, five highly repeatable QTLs were detected, on chromosomes 2HS, 2HL, 3HS, 4HL, and 6HS. For leaf rust, one highly significant QTL was detected on chromosome 2HL. The markers within these QTL regions present an opportunity for marker-assisted selection for these traits in barley-breeding programs.
Publisher: Wiley
Date: 05-2005
Publisher: Springer Science and Business Media LLC
Date: 12-2013
Publisher: Public Library of Science (PLoS)
Date: 04-02-2019
Publisher: Canadian Science Publishing
Date: 08-2006
DOI: 10.1139/G06-055
Abstract: Using pseudomolecules of assembled genomic sequence, we computed the frequencies of 6 to 24 bp oligonucleotide (oligo) "words" across the genome of rice (Oryza sativa L. subsp. japonica). All oligos of 10 or fewer basepairs were repeated at least 12 times in the genome. The percentage of unique (non-repeated) oligos ranged from 0.1% for 12 bp oligos to 76.0% for 24 bp oligos. For three 200 kb regions, we annotated each nucleotide position with the genome-wide frequency of the 18 bp oligo starting at that position. These frequencies formed landscapes consisting of high- and low-frequency zones. Low-frequency zones contained occasional high-frequency spikes these may represent footprints of RIM2 transposon activity. BLASTn searches of high-frequency non-SSR (simple sequence repeat) 18 bp oligos returned few sequences from species other than rice. These results demonstrate that, in rice, words are not randomly used between different regions within the same genome, and indicate that words that are frequently repeated within the rice genome tend to be unique to rice.Key words: oligonucleotide, sequence repetition, word match frequency, rice.
Publisher: Springer Science and Business Media LLC
Date: 11-04-2023
DOI: 10.1007/S00425-023-04131-1
Abstract: The cumulative action of combinations of alleles at several loci on the wheat genome is associated with different levels of resistance to late maturity α-amylase in bread wheat. Resistance to late maturity α-amylase (LMA) in bread wheat ( Triticum aestivum L.) involves a complex interaction between the genotype and the environment. Unfortunately, the incidence and severity of LMA expression is difficult to predict and once the trait has been triggered an unacceptably low falling number, high grain α-amylase may be the inevitable consequence. Wheat varieties with different levels of resistance to LMA have been identified but whilst some genetic loci have been reported, the mechanisms involved in resistance and the interaction between resistance loci requires further research. This investigation was focused on mapping resistance loci in populations derived by inter-crossing resistant wheat varieties or crossing resistant lines with a very susceptible line and then mapping quantitative trait loci. In addition to the previously reported locus on chromosome 7B for which a candidate gene has been proposed, loci were mapped on chromosomes 1B, 2A, 2B, 3A, 3B, 4A, 6A and 7D. These loci have limited effects on their own but have a cumulative effect in combination with each other. Further research will be required to determine the nature of the causal genes at these loci, to develop diagnostic markers and determine how the genes fit into the pathway that leads to the induction of α-AMY1 transcription in the aleurone of developing wheat grains. Depending on the target environmental conditions, different combinations of alleles may be required to achieve a low risk of LMA expression.
Publisher: Canadian Science Publishing
Date: 04-2006
DOI: 10.1139/G06-051
Publisher: Informa UK Limited
Date: 12-1992
Publisher: Informa UK Limited
Date: 26-07-2014
DOI: 10.3109/09593985.2013.816894
Abstract: Barriers and enablers of physical activity have been investigated, but it remains unclear what middle-aged adults' physical activity preferences are. Two physical activity interventions were compared to determine barriers, enablers and preferences for physical activity format in sedentary, community-dwelling 50- to 65-year-olds. Using mixed methods, 37 Physical Activity at Home (PAAH) participants took part in focus groups at the end of the intervention period and completed the Active Australia Survey (AAS). Participants were ided into three sub-groups: (1) group exercise attendees (GA, n = 14) (2) group exercise non-attendees (GNA, n = 9) and (3) physiotherapist-led home-based physical activity program attendees (HB, n = 14). Focus groups were audio-taped, transcribed, coded and analysed using an inductive thematic approach. Thirty-seven exit telephone calls with GNA were included in the analysis. Cost, self-efficacy, work and carer commitments were major themes identified for GA and GNA. HB participants reported fewer barriers and a number of enablers, including flexibility of the program and physiotherapist instruction. HB and GNA were younger than GA (p< 0.05), more likely to be in paid employment and GNA participants were insufficiently active (p ≤ 0.01). All participants preferred some home-based physical activity, although a variety of formats was indicated. The barriers, enablers and preferences indicate that the physiotherapist-led home-based physical activity program with initial face-to-face contact and telephone support may increase the adoption and maintenance of physical activity in middle-aged adults, particularly for those not interested in, or unable to attend, group exercise.
Publisher: WORLD SCIENTIFIC
Date: 26-02-2018
DOI: 10.1142/10986
Publisher: Springer Science and Business Media LLC
Date: 1997
Publisher: Canadian Science Publishing
Date: 10-1996
DOI: 10.4141/CJPS96-128
Abstract: Seven selected doubled haploid lines, from each of three cycles (C0, C1, C2) of a diallel recurrent selection program, the seven original parents and two check cultivars were evaluated in replicated hill and row plots at two locations in Ontario in 1988 and 1989. Comparison of hill and row plots using means ranges, coefficient of variation, repeatability and correlations among traits indicated that grain yield, days to heading plant height and powdery mildew resistance could be evaluated with similar accuracy and precision using either of the methods. Regression of row plot yield on hill plot yield was positive and highly significant showing a strong relationship between the two plot types for grain yield. Selection efficiency in hill plots was high for all the traits. The percentage of lines with similar performance for yield in both the plot types was high. The hill plot method appears to be a useful technique for evaluating homozygous lines for yield and other agronomic traits in a doubled haploid recurrent selection program in six-row barley. Key words:Hordeum vulgare L., barley, breeding methods, yield, powdery mildew, doubled haploid, recurrent selection
Publisher: Oxford University Press (OUP)
Date: 22-07-2004
DOI: 10.1093/BIOINFORMATICS/BTH413
Abstract: Summary: EC_oligos designs oligonucleotides (oligos) from exons of annotated genomic sequence information. It can automatically and rapidly select oligos that are conserved between two sets of sequence data, and can pair up oligos for use as PCR primers. It can do this on a whole-genome scale and according to user-defined criteria. Availability: The source code, executable program and user manual are available at ftp://ftp.ebi.ac.uk ub/software/dos/EC_oligos/.
Publisher: Informa UK Limited
Date: 2002
Publisher: Wiley
Date: 07-1996
Publisher: Elsevier BV
Date: 04-2005
Publisher: Informa UK Limited
Date: 12-1997
Publisher: CSIRO Publishing
Date: 2007
DOI: 10.1071/AR06203
Abstract: Selection for malting quality traits is a major breeding objective for barley breeding programs. With molecular markers linked to loci affecting these traits, this selection can be undertaken at an earlier stage of the breeding program than is possible using conventional tests. Quantitative trait loci (QTLs) associated with malting quality traits were mapped in 2 populations derived from parents with elite malting quality. Progeny from an Arapiles/Franklin population grown in 4 environments and an Alexis/Sloop population grown in 5 environments were tested for grain protein percentage, α-amylase activity, diastatic power, hot water extract, wort viscosity, wort β-glucan, β-glucanase, and free α-amino acids. QTL analysis was performed using a one-stage approach, which allowed for modelling of spatial variation in the field, and in each phase of the malting quality analysis in the laboratory. QTLs for malting quality traits were detected on all chromosomes and for both populations. Few of these QTLs were significant in all of the environments, indicating that QTL × environment interactions were important. There were many coincident QTLs for traits that are expected to be related such as diastatic power and α-amylase activity, wort β-glucan and wort viscosity and for some traits that are not expected to be related such as hot water extract and malt viscosity.
Publisher: Wiley
Date: 05-1998
Publisher: CSIRO Publishing
Date: 2010
DOI: 10.1071/CP09140
Abstract: The identification of genetic variation using molecular markers is fundamental to modern plant breeding and research. The present study was undertaken to develop a resource of informative single nucleotide polymorphism (SNP) markers for molecular characterisation of Australian barley germplasm. In total, 190 SNP markers were developed and characterised using 88 elite barley lines and varieties, s ling genetic ersity relevant to Australian breeding programs, and a core set of 48 SNPs for distinguishing among the barley lines was identified. The utility of the core 48-SNP set for distinguishing barley lines and varieties using DNA extracted from grain s les was also assessed. Finally, the 48 SNPs in the core set were converted into simple PCR markers to enable co-dominant SNP genotyping on agarose gel. The SNP markers developed, and in particular the core 48-SNP set, provide a useful marker resource for assessing genetic relationships between in iduals and populations of current Australian barley germplasm. They are also useful for identity and purity testing of inbred lines in research, breeding, and commercial applications.
Publisher: Canadian Science Publishing
Date: 2001
Publisher: Springer Science and Business Media LLC
Date: 1993
DOI: 10.1007/BF00023465
Publisher: Springer Science and Business Media LLC
Date: 03-01-2021
DOI: 10.1007/S00299-020-02641-W
Abstract: Resistance conferred by the Cre8 locus of wheat prevents cereal cyst nematode feeding sites from reaching and invading root metaxylem vessels. Cyst nematodes develop syncytial feeding sites within plant roots. The success of these sites is affected by host plant resistance. In wheat (Triticum aestivum L.), 'Cre' loci affect resistance against the cereal cyst nematode (CCN) Heterodera avenae. To investigate how one of these loci (Cre8, on chromosome 6B) confers resistance, CCN-infected root tissue from susceptible (-Cre8) and resistant (+Cre8) wheat plants was examined using confocal microscopy and laser ablation tomography. Confocal analysis of transverse sections showed that feeding sites in the roots of -Cre8 plants were always adjacent to metaxylem vessels, contained many intricate 'web-like' cell walls, and sometimes 'invaded' metaxylem vessels. In contrast, feeding sites in the roots of +Cre8 plants were usually not directly adjacent to metaxylem vessels, had few inner cell walls and did not 'invade' metaxylem vessels. Models based on data from laser ablation tomography confirmed these observations. Confocal analysis of longitudinal sections revealed that CCN-induced xylem modification that had previously been reported for susceptible (-Cre8) wheat plants is less extreme in resistant (+Cre8) plants. Application of a lignin-specific stain revealed that secondary thickening around xylem vessels in CCN-infected roots was greater in +Cre8 plants than in -Cre8 plants. Collectively, these results indicate that Cre8 resistance in wheat acts by preventing cyst nematode feeding sites from reaching and invading root metaxylem vessels.
Publisher: Springer Science and Business Media LLC
Date: 2021
DOI: 10.1007/S00425-020-03518-8
Abstract: Dormancy in white-grained wheat is conditioned by the cumulative effects of several QTL that delay the onset of the capacity to germinate during ripening and after-ripening. Grain dormancy at harvest-ripeness is a major component of resistance to preharvest sprouting in wheat (Triticum aestivum L.) and an important trait in regions where rain is common during the harvest period. Breeding lines developed in Australia maintained their dormancy phenotype over multiple seasons and during grain ripening, the time between anthesis and the acquisition of the capacity to germinate, dormancy release, increased in line with the strength of dormancy. Genetic dissection of two dormant lines indicated that dormancy was due to the cumulative action of between one and three major genetic loci and several minor loci. This presents a significant challenge for breeders targeting environments with a high risk of sprouting where strong dormancy is desirable. Only around half of the difference in dormancy between the dormant lines and a non-dormant variety could be attributed to the major genetic loci on chromosomes 4A and 3A. A QTL that was mapped on chromosome 5A may be an orthologue of a minor QTL for dormancy in barley. At each locus, the dormancy allele increased the time to dormancy release during ripening. In combination, these alleles had cumulative effects. Embryo sensitivity to abscisic acid was related to the dormancy phenotype of the whole caryopsis, however, changes in concentrations of abscisic acid and gibberellins in embryo sections and de-embryonated grains during ripening and after-ripening could not be linked to the timing of dormancy release.
Publisher: Springer Science and Business Media LLC
Date: 12-12-2013
DOI: 10.1007/S00726-012-1441-5
Abstract: The quality of wheat (Triticum aestivum L.) for making bread is largely due to the strength and extensibility of wheat dough, which in turn is due to the properties of polymeric glutenin. Polymeric glutenin consists of high- and low-molecular-weight glutenin protein subunits linked by disulphide bonds between cysteine residues. Glutenin subunits differ in their effects on dough mixing properties. The research presented here investigated the effect of a specific, recently discovered, glutenin subunit on dough mixing properties. This subunit, Bx7.1, is unusual in that it has a cysteine in its repetitive domain. With site-directed mutagenesis of the gene encoding Bx7.1, a guanine in the repetitive domain was replaced by an adenine, to provide a mutant gene encoding a subunit (MutBx7.1) in which the repetitive-domain cysteine was replaced by a tyrosine residue. Bx7.1, MutBx7.1 and other Bx-type glutenin subunits were heterologously expressed in Escherichia coli and purified. This made it possible to incorporate each in idual subunit into wheat flour and evaluate the effect of the cysteine residue on dough properties. The Bx7.1 subunit affected dough mixing properties differently from the other subunits. These differences are due to the extra cysteine residue, which may interfere with glutenin polymerisation through cross-linkage within the Bx7.1 subunit, causing this subunit to act as a chain terminator.
Publisher: Springer Science and Business Media LLC
Date: 17-01-2020
DOI: 10.1038/S41598-020-57498-6
Abstract: In many plant species, self-incompatibility systems limit self-pollination and mating among relatives. This helps maintain genetic ersity in natural populations but imposes constraints in agriculture and plant breeding. In almond [ Prunus dulcis (Mill.) D.A. Webb], the specificity of self-incompatibility is mainly determined by stylar ribonuclease (S-RNase) and S -haplotype-specific F-box (SFB) proteins, both encoded within a complex locus, S . Prior to this research, a nearly complete sequence was available for one S -locus haplotype. Here, we report complete sequences for four haplotypes and partial sequences for 11 haplotypes. Haplotypes vary in sequences of genes (particularly S-RNase and SFB ), distances between genes and numbers and positions of long terminal repeat transposons. Haplotype variation outside of the S-RNase and SFB genes may help maintain functionally important associations between S-RNase and SFB alleles. Fluorescence-based assays were developed to distinguish among some S-RNase alleles. With three-dimensional modelling of five S-RNase proteins, conserved active sites were identified and variation was observed in electrostatic potential and in the numbers, characteristics and positions of secondary structural elements, loop anchoring points and glycosylation sites. A hypervariable region on the protein surface and differences in the number, location and types of glycosylation sites may contribute to determining S-RNase specificity.
Publisher: Springer Science and Business Media LLC
Date: 1999
Publisher: Wiley
Date: 20-03-2014
DOI: 10.1111/PBI.12183
Publisher: MDPI AG
Date: 20-05-2021
Abstract: Preservation of lutein concentrations in wheat-based end-products during processing is important both for product quality and nutritional value. A key constituent involved in lutein degradation is endogenous lipoxygenase. Lutein and lutein ester concentrations were compared at intervals during storage of noodle sheets prepared from flour of wheat varieties representing a range in lipoxygenase activity, as well as in different mill streams and in different grain tissues. Higher lipoxygenase concentration was associated with an increased loss of free lutein and lutein mono-esters whereas lutein diesters appeared to be more resistant to degradation. Lutein degradation was reduced in the presence of a lipoxygenase inhibitor, when noodle sheets were heated to destroy enzyme activity or when pH was increased. In addition, three populations were used to investigate the genetic control of lipoxygenase. A previously reported mutation of Lpx-B1.1 was associated with a reduction in activity from high to intermediate whilst a new locus on chromosome 4D was associated with variation between intermediate and near-zero. The gene underlying the 4D locus is a putative lipoxygenase. Stability of lutein could be improved by deployment of the mutations at the 4B and 4D loci and/or by post-harvest storage of grain under conditions that promote esterification.
Publisher: Springer Science and Business Media LLC
Date: 03-06-2020
DOI: 10.1038/S41598-020-66080-Z
Abstract: Cyst nematodes induce host-plant root cells to form syncytia from which the nematodes feed. Comprehensive histological investigation of these feeding sites is complicated by their variable shape and their positions deep within root tissue. Using tissue clearing and confocal microscopy, we examined thick (up to 150 μm) sections of wheat roots infected by cereal cyst nematodes ( Heterodera avenae ). This approach provided clear views of feeding sites and surrounding tissues, with resolution sufficient to reveal spatial relationships among nematodes, syncytia and host vascular tissues at the cellular level. Regions of metaxylem vessels near syncytia were found to have deviated from classical developmental patterns. Xylem vessel elements in these regions had failed to elongate but had undergone radial expansion, becoming short and plump rather than long and cylindrical. Further investigation revealed that vessel elements cease to elongate shortly after infection and that they later experience delays in secondary thickening (lignification) of their outer cell walls. Some of these elements were eventually incorporated into syncytial feeding sites. By interfering with a developmental program that normally leads to programmed cell death, H. avenae may permit xylem vessel elements to remain alive for later exploitation by the parasite.
Publisher: Springer Science and Business Media LLC
Date: 12-2009
Abstract: Many research and diagnostic applications rely upon the assay of in idual single nucleotide polymorphisms (SNPs). Thus, methods to improve the speed and efficiency for single-marker SNP genotyping are highly desirable. Here, we describe the method of temperature-switch PCR (TSP), a biphasic four-primer PCR system with a universal primer design that permits lification of the target locus in the first phase of thermal cycling before switching to the detection of the alleles. TSP can simplify assay design for a range of commonly used single-marker SNP genotyping methods, and reduce the requirement for in idual assay optimization and operator expertise in the deployment of SNP assays. We demonstrate the utility of TSP for the rapid construction of robust and convenient endpoint SNP genotyping assays based on allele-specific PCR and high resolution melt analysis by generating a total of 11,232 data points. The TSP assays were performed under standardised reaction conditions, requiring minimal optimization of in idual assays. High genotyping accuracy was verified by 100% concordance of TSP genotypes in a blinded study with an independent genotyping method. Theoretically, TSP can be directly incorporated into the design of assays for most current single-marker SNP genotyping methods. TSP provides several technological advances for single-marker SNP genotyping including simplified assay design and development, increased assay specificity and genotyping accuracy, and opportunities for assay automation. By reducing the requirement for operator expertise, TSP provides opportunities to deploy a wider range of single-marker SNP genotyping methods in the laboratory. TSP has broad applications and can be deployed in any animal and plant species.
Publisher: Springer Science and Business Media LLC
Date: 28-07-2018
Publisher: Springer Science and Business Media LLC
Date: 12-07-2009
DOI: 10.1007/S00122-009-1101-7
Abstract: Simple molecular marker assays underpin routine plant breeding and research activities in many laboratories worldwide. With the rapid growth of single nucleotide polymorphism (SNP) resources for many important crop plants, the availability of routine, low-tech marker assays for genotyping SNPs is of increased importance. In this study, we demonstrate that temperature-switch PCR (TSP) supports the rapid development of robust, allele-specific PCR markers for codominant SNP genotyping on agarose gel. A total of 87 TSP markers for assessing gene ersity in barley were developed and used to investigate the efficacy for marker development, assay reliably and genotyping accuracy. The TSP markers described provide good coverage of the barley genome, are simple to use, easy to interpret and score, and are amenable to assay automation. They provide a resource of informative SNP markers for assessing genetic relationships among in iduals, populations and gene pools of cultivated barley (Hordeum vulgare L.) and its wild relative H. spontaneum K. Koch. TSP markers provide opportunities to use available SNP resources for marker-assisted breeding and plant genetic research, and to generate information that can be integrated with SNP data from different sources and studies. TSP markers are expected to provide similar advantages for any animal or plant species.
Publisher: Springer Science and Business Media LLC
Date: 22-04-2016
Publisher: Springer Science and Business Media LLC
Date: 30-12-2014
Publisher: Springer Science and Business Media LLC
Date: 02-1993
DOI: 10.1007/BF00215037
Publisher: Springer Science and Business Media LLC
Date: 2005
Publisher: Oxford University Press (OUP)
Date: 11-2020
DOI: 10.1038/S41438-020-00409-7
Abstract: Enset ( Ensete ventricosum (Welw.) Cheesman) is a drought tolerant, vegetatively propagated crop that was domesticated in Ethiopia. It is a staple food for more than 20 million people in Ethiopia. Despite its current importance and immense potential, enset is among the most genetically understudied and underexploited food crops. We collected 230 enset wild and cultivated accessions across the main enset producing regions in Ethiopia and applied lified fragment length polymorphism (AFLP) and genotype by sequencing (GBS) analyses to these accessions. Wild and cultivated accessions were clearly separated from each other, with 89 genes found to harbour SNPs that separated wild from cultivated accessions. Among these, 17 genes are thought to be involved in flower initiation and seed development. Among cultivated accessions, differentiation was mostly associated with geographical location and with proximity to wild populations. Our results indicate that vegetative propagation of elite clones has favoured capacity for vegetative growth at the expense of capacity for sexual reproduction. This is consistent with previous reports that cultivated enset tends to produce non-viable seeds and flowers less frequently than wild enset.
Publisher: MDPI AG
Date: 07-12-2022
Abstract: Para rubber trees (Hevea brasiliensis) are the largest major source of natural rubber in the world. Its major pathogens are Phytophthora spp., Corynespora cassiicola, and Colletotrichum spp. A rubber ersity panel of 116 clones using over 12,000 single nucleotide polymorphisms (SNPs) from DArTSeq genotyping revealed clear phylogenetic differences in clones that originated from different geographical regions of the world. An integrated linkage map constructed with an F1 progeny of 86 from an interspecific cross between H. brasiliensis and H. benthamiana using 23,978 markers [10,323 SNPs and 13,655 SilicoDArTs] spanned 3947.83 cM with 0.83 cM average marker-interval. The genome scaffolds that were anchored to the linkage map, covering 1.44 Gb of H. brasiliensis reference genome, revealed a high level of collinearity between the genetic map and reference genome. Association analysis identified 12 SNPs significantly associated with the resistance against Phytophthora, Corynespora, and Colletotrichum in six linkage groups: 2, 6, 12, 14, 17, and 18. Kompetitive Allele-Specific PCR marker assays were developed for those 12 SNPs, screened with 178 in iduals, and detected clear separation between two genotypes. Within the proximity to those SNPs, 41 potentially key genes that have previously been reported to associate with plant disease resistance were predicted with high confidence.
Publisher: Springer Science and Business Media LLC
Date: 1997
Publisher: Frontiers Media SA
Date: 21-12-2020
Abstract: Representative, broad and erse collections are a primary resource to dissect genetic ersity and meet pre-breeding and breeding goals through the identification of beneficial alleles for target traits. From 2,500 tetraploid wheat accessions obtained through an international collaborative effort, a Global Durum wheat Panel (GDP) of 1,011 genotypes was assembled that captured 94–97% of the original ersity. The GDP consists of a wide representation of Triticum turgidum ssp. durum modern germplasm and landraces, along with a selection of emmer and primitive tetraploid wheats to maximize ersity. GDP accessions were genotyped using the wheat iSelect 90K SNP array. Among modern durum accessions, breeding programs from Italy, France and Central Asia provided the highest level of genetic ersity, with only a moderate decrease in genetic ersity observed across nearly 50 years of breeding (1970–2018). Further, the breeding programs from Europe had the largest sets of unique alleles. LD was lower in the landraces (0.4 Mbp) than in modern germplasm (1.8 Mbp) at r 2 = 0.5. ADMIXTURE analysis of modern germplasm defined a minimum of 13 distinct genetic clusters ( k ), which could be traced to the breeding program of origin. Chromosome regions putatively subjected to strong selection pressure were identified from fixation index ( F st ) and ersity reduction index ( DRI ) metrics in pairwise comparisons among decades of release and breeding programs. Clusters of putative selection sweeps (PSW) were identified as co-localized with major loci controlling phenology ( Ppd and Vrn ), plant height ( Rht ) and quality (gliadins and glutenins), underlining the role of the corresponding genes as driving elements in modern breeding. Public seed availability and deep genetic characterization of the GDP make this collection a unique and ideal resource to identify and map useful genetic ersity at loci of interest to any breeding program.
Publisher: Elsevier BV
Date: 04-2015
DOI: 10.1016/J.PLANTSCI.2015.01.008
Abstract: Mapping of quantitative trait loci associated with levels of in idual metabolites (mQTL) was combined with the mapping of agronomic traits to investigate the genetic basis of variation and co-variation in metabolites, agronomic traits, and plant phenology in a field-grown bread wheat population. Metabolome analysis was performed using liquid chromatography-mass spectrometry resulting in identification of mainly polar compounds, including secondary metabolites. A total of 558 metabolic features were obtained from the flag leaves of 179 doubled haploid lines, of which 197 features were putatively identified, mostly as alkaloids, flavonoids and phenylpropanoids. Coordinated genetic control was observed for several groups of metabolites, such as organic acids influenced by two loci on chromosome 7A. Five major phenology-related loci, which were introduced as cofactors in the analyses, differed in their impact upon metabolic and agronomic traits with QZad-aww-7A having more impact on the expression of both metabolite and agronomic QTL than Ppd-B1, Vrn-A1, Eps, and QZad-aww-7D. This QTL study validates the utility of combining agronomic and metabolomic traits as an approach to identify potential trait enhancement targets for breeding selection and reinforces previous results that demonstrate the importance of including plant phenology in the assessment of useful traits in this wheat mapping population.
Publisher: Scientific Societies
Date: 1996
DOI: 10.1094/PD-80-0081
Publisher: Springer Science and Business Media LLC
Date: 07-06-2008
DOI: 10.1007/S00122-008-0811-6
Abstract: Fructans (fructo-oligosaccharides) are prebiotics that are thought to selectively promote the growth of colonic bifidobacteria, thereby improving human gut health. Fructans are present in the grain of wheat, a staple food crop. In the research reported here, we aimed to detect and map loci affecting grain fructan concentration in wheat using a doubled-haploid population derived from a cross between a high-fructan breeding line, Berkut, and a low-fructan cultivar, Krichauff. Fructan concentration was measured in grain s les grown at two locations in Australia and one in Kazakhstan. Fructan concentration varied widely within the population, ranging from 0.6 to 2.6% of grain dry weight, and was quite repeatable, with broad-sense heritability estimated as 0.71. With a linkage map of 528 molecular markers, quantitative trait loci (QTLs) were detected on chromosomes 2B, 3B, 5A, 6D and 7A. Of these, the QTLs on chromosomes 6D and 7A had the largest effects, explaining 17 and 27% of the total phenotypic variance, respectively, both with the favourable (high-fructan concentration) alleles contributed from Berkut. These chromosome regions had similar effects in another mapping population, Sokoll/Krichauff, with the favourable alleles contributed from Sokoll. It is concluded that grain fructan concentration of wheat can be improved by breeding and that molecular markers could be used to select effectively for favourable alleles in two regions of the wheat genome.
Publisher: Springer Science and Business Media LLC
Date: 06-1991
DOI: 10.1007/BF00039658
Publisher: Elsevier BV
Date: 07-2015
Publisher: Springer Science and Business Media LLC
Date: 20-12-2013
DOI: 10.1007/S00122-012-2015-3
Abstract: Improved mapping, multi-environment quantitative trait loci (QTL) analysis and dissection of allelic effects were used to define a QTL associated with grain yield, thousand grain weight and early vigour on chromosome 3BL of bread wheat (Triticum aestivum L.) under abiotic stresses. The QTL had pleiotropic effects and showed QTL x environment interactions across 21 erse environments in Australia and Mexico. The occurrence and the severity of water deficit combined with high temperatures during the growing season affected the responsiveness of this QTL, resulting in a reversal in the direction of allelic effects. The influence of this QTL can be substantial, with the allele from one parent (RAC875) increasing grain yield by up to 12.5 % (particularly in environments where both heat and drought stress occurred) and the allele from the other parent (Kukri) increasing grain yield by up to 9 % in favourable environments. With the application of additional markers and the genotyping of additional recombinant inbred lines, the genetic map in the QTL region was refined to provide a basis for future positional cloning.
Publisher: Wiley
Date: 11-1998
Publisher: Oxford University Press (OUP)
Date: 05-1993
Publisher: Elsevier BV
Date: 07-2015
Publisher: Springer Science and Business Media LLC
Date: 20-01-2012
Publisher: Frontiers Media SA
Date: 03-08-2021
Abstract: Kushen root, from the woody legume Sophora flavescens , is a traditional Chinese medicine that is a key ingredient in several promising cancer treatments. This activity is attributed in part to two quinolizidine alkaloids (QAs), oxymatrine and matrine, that have a variety of therapeutic activities in vitro . Genetic selection is needed to adapt S. flavescens for cultivation and to improve productivity and product quality. Genetic ersity of S. flavescens was investigated using genotyping-by-sequencing (GBS) on 85 plants grown from seeds collected from 9 provinces of China. DArTSeq provided over 10,000 single nucleotide polymorphism (SNP) markers, 1636 of which were used in phylogenetic analysis to reveal clear regional differences for S. flavescens . One accession from each region was selected for PCR-sequencing to identify gene-specific SNPs in the first two QA pathway genes, lysine decarboxylase (LDC) and copper amine oxidase (CAO). To obtain SfCAO sequence for primer design we used a targeted transcript capture and assembly strategy using publicly available RNA sequencing data. Partial gene sequence analysis of SfCAO revealed two recently duplicated genes, SfCAO1 and SfCAO2 , in contrast to the single gene found in the QA-producing legume Lupinus angustifolius . We demonstrate high efficiency converting SNPs to Kompetitive Allele Specific PCR (KASP) markers developing 27 new KASP markers, 17 from DArTSeq data, 7 for SfLDC , and 3 for SfCAO1 . To complement this genetic ersity analysis a field trial site has been established in South Australia, providing access to erse S. flavescens material for morphological, transcriptomic, and QA metabolite analysis. Analysis of dissected flower buds revealed that anthesis occurs before buds fully open suggesting a potential for S. flavescens to be an inbreeding species, however this is not supported by the relatively high level of heterozygosity observed. Two plants from the field trial site were analysed by quantitative real-time PCR and levels of matrine and oxymatrine were assessed in a variety of tissues. We are now in a strong position to select erse plants for crosses to accelerate the process of genetic selection needed to adapt kushen to cultivation and improve productivity and product quality.
Publisher: Oxford University Press (OUP)
Date: 13-06-2019
DOI: 10.1093/JXB/ERZ271
Abstract: Soil biota have important effects on crop productivity, but can be difficult to study in situ. Laser ablation tomography (LAT) is a novel method that allows for rapid, three-dimensional quantitative and qualitative analysis of root anatomy, providing new opportunities to investigate interactions between roots and edaphic organisms. LAT was used for analysis of maize roots colonized by arbuscular mycorrhizal fungi, maize roots herbivorized by western corn rootworm, barley roots parasitized by cereal cyst nematode, and common bean roots damaged by Fusarium. UV excitation of root tissues affected by edaphic organisms resulted in differential autofluorescence emission, facilitating the classification of tissues and anatomical features. S les were spatially resolved in three dimensions, enabling quantification of the volume and distribution of fungal colonization, western corn rootworm damage, nematode feeding sites, tissue compromised by Fusarium, and as well as root anatomical phenotypes. Owing to its capability for high-throughput s le imaging, LAT serves as an excellent tool to conduct large, quantitative screens to characterize genetic control of root anatomy and interactions with edaphic organisms. Additionally, this technology improves interpretation of root–organism interactions in relatively large, opaque root segments, providing opportunities for novel research investigating the effects of root anatomical phenes on associations with edaphic organisms.
Start Date: 08-2020
End Date: 07-2023
Amount: $486,000.00
Funder: Australian Research Council
View Funded Activity