ORCID Profile
0000-0001-7959-6959
Current Organisations
École Polytechnique Fédérale de Lausanne
,
University of Saskatchewan
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.
Biological Mathematics | Plant Biology | Plant Physiology | Population, Ecological and Evolutionary Genetics | Intellectual Property Law
Expanding Knowledge in the Agricultural and Veterinary Sciences | Expanding Knowledge in Law and Legal Studies | Expanding Knowledge in the Mathematical Sciences |
Publisher: Wiley
Date: 25-10-2022
DOI: 10.1002/TPG2.20269
Abstract: Adaptation constraints within crop species have resulted in limited genetic ersity in some breeding programs and areas where new crops have been introduced, for ex le, for lentil ( Lens culinaris Medik.) in North America. An improved understanding of the underlying genetics involved in phenology‐related traits is valuable knowledge to aid breeders in overcoming limitations associated with unadapted germplasm and expanding their genetic ersity by introducing new, exotic material. We used a large, 18 site‐year, multienvironment dataset phenotyped for phenology‐related traits across nine locations and over 3 yr along with accompanying latent variable phenotypes derived from a photothermal model and principal component analysis (PCA) of days from sowing to flower (DTF) data for a lentil ersity panel (324 accessions), which has also been genotyped with an exome capture array. Genome‐wide association studies (GWAS) on DTF across multiple environments helped confirm associations with known flowering‐time genes and identify new quantitative trait loci (QTL), which may contain previously unknown flowering time genes. Additionally, the use of latent variable phenotypes, which can incorporate environmental data such as temperature and photoperiod as both GWAS traits and as covariates, strengthened associations, revealed additional hidden associations, and alluded to potential roles of the associated QTL. Our approach can be replicated with other crop species, and the results from our GWAS serve as a resource for further exploration into the complex nature of phenology‐related traits across the major growing environments for cultivated lentil.
Publisher: Wiley
Date: 09-02-2021
DOI: 10.1002/NBM.4484
Abstract: The translation of MRS to clinical practice has been impeded by the lack of technical standardization. There are multiple methods of acquisition, post‐processing, and analysis whose details greatly impact the interpretation of the results. These details are often not fully reported, making it difficult to assess MRS studies on a standardized basis. This h ers the reviewing of manuscripts, limits the reproducibility of study results, and complicates meta‐analysis of the literature. In this paper a consensus group of MRS experts provides minimum guidelines for the reporting of MRS methods and results, including the standardized description of MRS hardware, data acquisition, analysis, and quality assessment. This consensus statement describes each of these requirements in detail and includes a checklist to assist authors and journal reviewers and to provide a practical way for journal editors to ensure that MRS studies are reported in full.
Publisher: Cold Spring Harbor Laboratory
Date: 12-03-2022
DOI: 10.1101/2022.03.10.483676
Abstract: Adaptation constraints within crop species have resulted in limited genetic ersity in some breeding programs and/or areas where new crops have been introduced, e.g., lentil (Lens culinaris Medik.) in North America. An improved understanding of the underlying genetics involved in phenology-related traits is valuable knowledge to aid breeders in overcoming limitations associated with unadapted germplasm and expanding their genetic ersity by introducing new, exotic material. We used a large, 18 site-year, multi-environment dataset, phenotyped for phenology-related traits across nine locations and over three years, along with accompanying latent variable phenotypes derived from a photothermal model and principal component analysis (PCA) of days from sowing to flower (DTF) data for a lentil ersity panel (324 accessions) which has also been genotyped with an exome capture array. Genomewide association studies (GWAS) on DTF across multiple environments helped confirm associations with known flowering time genes and identify new quantitative trait loci (QTL), which may contain previously unknown flowering time genes. Additionally, the use of latent variable phenotypes, which can incorporate environmental data such as temperature and photoperiod as both GWAS traits and as covariates, strengthened associations, revealed additional hidden associations, and alluded to potential roles of the associated QTL. Our approach can be replicated with other crop species, and the results from our GWAS serve as a resource for further exploration into the complex nature of phenology-related traits across the major growing environments for cultivated lentil.
Publisher: Wiley
Date: 23-09-2021
DOI: 10.1111/TPJ.15472
Abstract: Food legumes are crucial for all agriculture‐related societal challenges, including climate change mitigation, agrobio ersity conservation, sustainable agriculture, food security and human health. The transition to plant‐based diets, largely based on food legumes, could present major opportunities for adaptation and mitigation, generating significant co‐benefits for human health. The characterization, maintenance and exploitation of food‐legume genetic resources, to date largely unexploited, form the core development of both sustainable agriculture and a healthy food system. INCREASE will implement, on chickpea ( Cicer arietinum ), common bean ( Phaseolus vulgaris ), lentil ( Lens culinaris ) and lupin ( Lupinus albus and L. mutabilis ), a new approach to conserve, manage and characterize genetic resources. Intelligent Collections , consisting of nested core collections composed of single‐seed descent‐purified accessions (i.e., inbred lines), will be developed, exploiting germplasm available both from genebanks and on‐farm and subjected to different levels of genotypic and phenotypic characterization. Phenotyping and gene discovery activities will meet, via a participatory approach, the needs of various actors, including breeders, scientists, farmers and agri‐food and non‐food industries, exploiting also the power of massive metabolomics and transcriptomics and of artificial intelligence and smart tools. Moreover, INCREASE will test, with a citizen science experiment, an innovative system of conservation and use of genetic resources based on a decentralized approach for data management and dynamic conservation. By promoting the use of food legumes, improving their quality, adaptation and yield and boosting the competitiveness of the agriculture and food sector, the INCREASE strategy will have a major impact on economy and society and represents a case study of integrative and participatory approaches towards conservation and exploitation of crop genetic resources.
Publisher: Wiley
Date: 13-10-2021
DOI: 10.1002/TPG2.20144
Abstract: The continued success of lentil ( Lens culinaris Medik.) genetic improvement relies on the availability of broad genetic ersity, and new alleles need to be identified and incorporated into the cultivated gene pool. Availability of robust and predictive markers greatly enhances the precise transfer of genomic regions from unadapted germplasm. Quantitative trait loci (QTL) for key phenological traits in lentil were located using a recombinant inbreed line (RIL) population derived from a cross between an Ethiopian landrace (ILL 1704) and a northern temperate cultivar (CDC Robin). Field experiments were conducted at Sutherland research farm in Saskatoon and at Rosthern, Saskatchewan, Canada during 2018 and 2019. A linkage map was constructed using 21,634 single nucleotide polymorphisms (SNPs) located on seven linkage groups (LGs), which correspond to the seven haploid chromosomes of lentil. Eight QTL were identified for six phenological traits. Flowering‐related QTL were identified at two regions on LG6. FLOWERING LOCUS T ( FT ) genes were annotated within the flowering time QTL interval based on the lentil reference genome. Similarly, a major QTL for postflowering developmental processes was located on LG5 with several senescence‐associated genes annotated within the QTL interval. The flowering time QTL was validated in a different genetic background indicating the potential use of the identified markers for marker‐assisted selection to precisely transfer genomic regions from exotic germplasm into elite crop cultivars without disrupting adaptation.
Publisher: Cold Spring Harbor Laboratory
Date: 24-07-2021
DOI: 10.1101/2021.07.23.453237
Abstract: Understanding the genomic relationship between wild and cultivated genomes would facilitate access to the untapped variability found in crop wild relatives. We developed genome assemblies of a cultivated lentil ( Lens culinaris ) as well as a wild relative ( L. ervoides ). Comparative analyses revealed large-scale structural rearrangements and additional repetitive DNA in the cultivated genome, resulting in regions of reduced recombination, segregation distortion and permanent heterozygosity in the offspring of a cross between the two species. These novel findings provide plant breeders with better insight into how best to approach accessing the novel variability available in wild relatives.
Publisher: Wiley
Date: 28-03-2019
DOI: 10.1002/MRM.27742
Publisher: Cold Spring Harbor Laboratory
Date: 16-08-2021
DOI: 10.1101/2021.08.16.456438
Abstract: Reproductive phenology is well known to be a key feature of crop adaptation to erse ecogeographic variation and management practices. Lentil is one of the founder pulse crops of middle-eastern Neolithic agriculture, and the modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian and northern temperate, which correspond approximately to the major global production environments. Understanding the molecular basis of these adaptations is crucial to maximise efficiency of breeding programs. Here, we use a QTL approach to dissect the earliness that is characteristic of the South Asian pilosae ecotype, and that suits it to the typically short winter cropping season. We identified two loci, DTF6a and DTF6b , at which dominant alleles confer early flowering. We show that, although these loci can interact in an additive manner, DTF6a alone is sufficient to confer early flowering even in extremely short photoperiods. Comparisons with closely related legume species confirmed the presence of a conserved cluster of three FT orthologs among potential candidate genes in the region, and expression analysis in near-isogenic material showed that the early dtf6a allele is associated with a strong derepression of the FTa1 gene in particular. Analysis of sequence variation revealed the presence of a 7.4 kb deletion in the FTa1 - FTa2 intergenic region in the pilosae parent, and a wide survey of over 400 accessions with erse origin showed that the dtf6a allele is dominant in South Asia material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.
Publisher: Cold Spring Harbor Laboratory
Date: 15-02-2021
DOI: 10.1101/2021.02.14.429948
Abstract: Flowering time is important due to its roles in adaptation to different environments and subsequent formation of crop yield. Changes in light quality affect a range of developmental processes including flowering time, however little is known about light quality induced flowering time control in lentil. This study aims to investigate the genetic basis for differences in flowering response to light quality in lentil. We explored variation in flowering time caused by changes in red/far-red related light quality environments of a lentil interspecific recombinant inbred line population developed from a cross between Lens culinaris cv. Lupa and L. orientalis accession BGE 016880. A genetic linkage map was constructed and then used for identifying QTL associated with flowering time regulation under different light quality environments. Differential gene expression analysis through transcriptomic study and RT-qPCR were used to identify potential candidate genes. QTL mapping located 13 QTLs controlling flower time under different light quality environments, with phenotypic variance explained ranging from 1.7 to 62.9%. Transcriptomic profiling and gene expression analysis for both parents of this interspecific RIL population identified flowering-related genes showing environment-specific differential expression (flowering DEGs). One of these, a member of the florigen gene family FTa1 ( LcFTa1 ) was located close to 3 major QTLs. Furthermore, gene expression results suggests two other florigen genes ( LcFTb1 and LcFTb2 ), MADS-box transcription factors like LcAGL6/13d, LcSVPb, LcSOC1b and LcFULb , as well as bHLH transcription factor LcPIF6 and Gibberellin 20 oxidase LcGA20oxC,G , may be involved in the light quality response as well. Our results show that a major component of flowering time sensitivity to light quality is tightly linked to LcFTa1 and associated with changes in its expression. This work provides a foundation for crop improvement of lentil with better adaptation to variable light environments.
Publisher: Oxford University Press (OUP)
Date: 15-03-2022
DOI: 10.1093/JXB/ERAC107
Abstract: Modern-day domesticated lentil germplasm is generally considered to form three broad adaptation groups: Mediterranean, South Asian, and northern temperate, which correspond to the major global production environments. Reproductive phenology plays a key role in lentil adaptation to this erse ecogeographic variation. Here, we dissect the characteristic earliness of the pilosae ecotype, suited to the typically short cropping season of South Asian environments. We identified two loci, DTF6a and DTF6b, at which dominant alleles confer early flowering, and we show that DTF6a alone is sufficient to confer early flowering under extremely short photoperiods. Genomic synteny confirmed the presence of a conserved cluster of three florigen (FT) gene orthologues among potential candidate genes, and expression analysis in near-isogenic material showed that the early allele is associated with a strong derepression of the FTa1 gene in particular. Sequence analysis revealed a 7.4 kb deletion in the FTa1–FTa2 intergenic region in the pilosae parent, and a wide survey of & accessions with erse origin showed that the dtf6a allele is predominant in South Asian material. Collectively, these results contribute to understanding the molecular basis of global adaptation in lentil, and further emphasize the importance of this conserved genomic region for adaptation in temperate legumes generally.
Location: Switzerland
Start Date: 12-2020
End Date: 12-2027
Amount: $35,000,000.00
Funder: Australian Research Council
View Funded Activity