ORCID Profile
0000-0003-3972-7058
Current Organisations
University of Melbourne
,
Agriculture Victoria
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Publisher: MDPI AG
Date: 27-09-2021
Abstract: Advancements in high-throughput genotyping and sequencing technologies are enabling the development of a vast range of genomic tools and resources for a new revolution in plant breeding. Several genotyping-by-sequencing (GBS) methods including capture-based, genome complexity reduction and sequencing of cDNA (GBS-t) are available for application in trait dissection, association mapping, and genomic selection (GS) in crop plants. The aims of this study were to identify genomic regions conferring resistance to Ascochyta blight (AB) introgressed from the wild Cicer echinospernum into the domesticated C. arietinum, through a conventional recombinant inbred population genotyped using a variety of GBS methods. Evaluation of GBS methods revealed that capture-based approaches are robust and reproducible while GBS-t is rapid and flexible. A genetic linkage map consisting of 5886 polymorphic loci spanning 717.26 cM was generated. Using field phenotyping data from two years, a single genomic region on LG4 was identified with quantitative trait loci (QTL) mapping. Both GBS methods reported in this study are well suited for applications in genomics assisted plant breeding. Linked markers for AB resistance, identified in the current study, provide an important resource for the deployment into chickpea breeding programs for marker-assisted selection (MAS).
Publisher: Wiley
Date: 05-07-2018
DOI: 10.1111/PBR.12608
Publisher: Springer Science and Business Media LLC
Date: 08-03-2023
DOI: 10.1038/S41586-023-05791-5
Abstract: Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of bio ersity 1 . However, plant protein production is h ered by the lack of a cool-season legume equivalent to soybean in agronomic value 2 . Faba bean ( Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of lification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.
Publisher: MDPI AG
Date: 22-08-2022
DOI: 10.3390/JOF8080884
Abstract: Ascochyta Blight (AB) is a major disease of many cool-season legumes globally. In field pea, three fungal pathogens have been identified to be responsible for this disease in Australia, namely Peyronellaea pinodes, Peyronellaea pinodella and Phoma koolunga. Limited genomic resources for these pathogens have been generated, which has h ered the implementation of effective management strategies and breeding for resistant cultivars. Using Oxford Nanopore long-read sequencing, we report the first high-quality, fully annotated, near-chromosome-level nuclear and mitochondrial genome assemblies for 18 isolates from the Australian AB complex. Comparative genome analysis was performed to elucidate the differences and similarities between species and isolates using phylogenetic relationships and functional ersity. Our data indicated that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic. More homology and orthologous gene clusters are shared between P. pinodes and P. pinodella compared to P. koolunga. The analysis of the repetitive DNA content showed differences in the transposable repeat composition in the genomes and their expression in the transcriptomes. Significant repeat expansion in P. koolunga’s genome was seen, with strong repeat-induced point mutation (RIP) activity being evident. Phylogenetic analysis revealed that genetic ersity can be exploited for species marker development. This study provided the much-needed genetic resources and characterization of the AB species to further drive research in key areas such as disease epidemiology and host–pathogen interactions.
Publisher: Public Library of Science (PLoS)
Date: 18-02-2022
DOI: 10.1371/JOURNAL.PONE.0262857
Abstract: Heterosis is defined as increased performance of the F 1 hybrid relative to its parents. In the current study, a cohort of populations and parents were created to evaluate and understand heterosis across generations (i.e., F 1 to F 3 ) in lentil, a self-pollinated annual diploid (2n = 2× = 14) crop species. Lentil plants were evaluated for heterotic traits in terms of plant height, biomass fresh weight, seed number, yield per plant and 100 grain weight. A total of 47 selected lentil genotypes were cross hybridized to generate 72 F 1 hybrids. The F 1 hybrids from the top five crosses exhibited between 31%–62% heterosis for seed number with reference to the better parent. The five best performing heterotic crosses were selected with a negative control for evaluation at the subsequent F 2 generation and only the tails of the distribution taken forward to be assessed in the F 3 generation as a sub selection. Overall, heterosis decreases across the subsequent generations for all traits studied. However, some in idual genotypes were identified at the F 2 and sub-selected F 3 generations with higher levels of heterosis than the best F 1 mean value (hybrid mimics). The phenotypic data for the selected F 2 and sub selected F 3 hybrids were analysed, and the study suggested that 100 grain weight was the biggest driver of yield followed by seed number. A genetic ersity analysis of all the F 1 parents failed to correlate genetic distance and ergence among parents with heterotic F 1 ’s. Therefore, genetic distance was not a key factor to determine heterosis in lentil. The study highlights the challenges associated with different breeding systems for heterosis (i.e., F 1 hybrid-based breeding systems and/or via hybrid mimics) but demonstrates the potential significant gains that could be achieved in lentil productivity.
Publisher: Cold Spring Harbor Laboratory
Date: 26-09-2022
DOI: 10.1101/2022.09.23.509015
Abstract: Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emission and loss of bio ersity. However, plant protein production is h ered by the lack of a cool-season legume equivalent to soybean in agronomic value. Faba bean ( Vicia faba L.) has a high yield potential and is well-suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has grown to a massive 13 Gb in size through an imbalance between the rates of lification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, though with significant copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association (GWA) analysis to dissect the genetic basis of hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate improvement of sustainable protein production across Mediterranean, subtropical, and northern temperate agro-ecological zones.
No related grants have been discovered for Sukhjiwan Kaur.