WhoGEM: an admixture-based prediction machine accurately predicts quantitative functional traits in plants

Gentzbittel, Laurent; Ben, Cécile; Mazurier, Mélanie; Shin, Min-Gyoung; Lorenz, Todd C.; Rickauer, Martina; Marjoram, Paul; Nuzhdin, Sergey V.; Tatarinova, Tatiana V.

doi:10.1186/s13059-019-1697-0

Cited by 12 publications

(15 citation statements)

References 113 publications

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“…• C and 25/15 • C). Different letters indicate significant differences among year for each temperature (Fisher's LSD test, α = 0.05), Table S1: List of tested Medicago accessions with calculated seed dormancy traits and extracted environmental variables, Table S2: Basic descriptive statistics of 23 bioclimatic variables and 10 soil variables of sites of accessions origin, Table S3: Classification of 176 M. truncatula accessions in four cluster based on environmental and climatic conditions, Table S4: Pearson coefficients-probabilities between dormancy traits and bioclimatic variables, Table S5: Regression coefficient (r2) between environmental variables and plasticity index by macroecological and genetic clusters [106], Table S6: Complete list of QTN identified by GWA studies for each dormancy trait, Table S7: Over-representation analysis of the 136 candidate genes potentially involved in dormancy traits.…”

Section: Discussionmentioning

confidence: 99%

Physical Dormancy Release in Medicago truncatula Seeds Is Related to Environmental Variations

Renzi

Duchoslav

Brus

et al. 2020

Plants

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Seed dormancy and timing of its release is an important developmental transition determining the survival of individuals, populations, and species in variable environments. Medicago truncatula was used as a model to study physical seed dormancy at the ecological and genetics level. The effect of alternating temperatures, as one of the causes releasing physical seed dormancy, was tested in 178 M. truncatula accessions over three years. Several coefficients of dormancy release were related to environmental variables. Dormancy varied greatly (4–100%) across accessions as well as year of experiment. We observed overall higher physical dormancy release under more alternating temperatures (35/15 °C) in comparison with less alternating ones (25/15 °C). Accessions from more arid climates released dormancy under higher experimental temperature alternations more than accessions originating from less arid environments. The plasticity of physical dormancy can probably distribute the germination through the year and act as a bet-hedging strategy in arid environments. On the other hand, a slight increase in physical dormancy was observed in accessions from environments with higher among-season temperature variation. Genome-wide association analysis identified 136 candidate genes related to secondary metabolite synthesis, hormone regulation, and modification of the cell wall. The activity of these genes might mediate seed coat permeability and, ultimately, imbibition and germination.

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Section: Discussionmentioning

confidence: 99%

Physical Dormancy Release in Medicago truncatula Seeds Is Related to Environmental Variations

Renzi

Duchoslav

Brus

et al. 2020

Plants

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“…We compared the genetic 5 3 0 groups identified by Gentzbittel et al (2019) to our study macroclimatic clusters and found 5 3 1 significant correspondence (r 2 =0.582**, Table S5). As discussed in Gentzbittel et al (2019),…”

Section: 8mentioning

confidence: 89%

“…Regression coefficient (r 2 ) between environmental variables and plasticity index by macroecological and genetic clusters ofGentzbittel et al (2019).…”

mentioning

confidence: 99%

Plasticity ofMedicago truncatulaseed dormancy relates to large-scale environment variation

Renzi

Duchoslav

Brus

et al. 2019

Preprint

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Seed dormancy and timing of its release is important developmental transition determining the survival of individual as well as population and species. We used Medicago truncatula as model to study legume seed dormancy in ecological and genomics context. The effect of oscillating temperatures as one of the dormancy release factor was tested over the period of 88 days on the set of 178 accessions originating from variable environmental conditions of Mediterranean basin. Phenotypic plasticity of final dormancy was significantly correlated with increased aridity, suggesting that plastic responses to external stimuli provide seeds with strong bet-hedging capacity and the potential to cope with high levels of environmental heterogeneity. Genome-wide association analysis identified candidate genes associated with dormancy release related to secondary metabolites synthesis, hormone regulation and modification of the cell wall likely mediating seed coat permeability and ultimately imbibition and germination.HighlightMedicago seed dormancy was correlated with increased aridity of the environment, suggesting that plastic responses provide seeds with a bet-hedging capacity. Genome-wide association analysis identified candidate genes associated with release from dormancy.

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“…While MAS/MABC has been successfully used for product development, HBB has shown huge potential for trait improvement in rice ( Abbai et al, 2019 ) and pigeonpea ( Sinha et al, 2020 ). During recent years the accuracy and prediction of predicting phenotypes in genomics selection has been improved extensively through approaches including (i) estimating global GEBVs while considering interaction of marker and environment covariates (G × E) ( Jarquín et al, 2014 ; Crossa et al, 2017 ), (ii) estimating haplotype/bin- based local GEBVs ( Voss-Fels et al, 2019 ), (iii) WhoGEM approach that explores the relationships between phenotypes and admixture components, land types, admixture components × environment interactions, and controls for the environment ( Gentzbittel et al, 2019 ), and (iv) optimal contribution selection method that enables simultaneous trait improvement and enriching the genetic base ( Woolliams et al, 2015 ; Cowling et al, 2017 ). In case, a causal gene is available for a trait, gene editing approach can be used for the trait improvement ( Zhang et al, 2018b ).…”

Section: Future Perspectivesmentioning

confidence: 99%

Genomic resources in plant breeding for sustainable agriculture

Thudi

Ramesh

Schnable

et al. 2021

Journal of Plant Physiology

112

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Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965−85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.

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WhoGEM: an admixture-based prediction machine accurately predicts quantitative functional traits in plants

Cited by 12 publications

References 113 publications

Physical Dormancy Release in Medicago truncatula Seeds Is Related to Environmental Variations

Physical Dormancy Release in Medicago truncatula Seeds Is Related to Environmental Variations

Plasticity ofMedicago truncatulaseed dormancy relates to large-scale environment variation

Genomic resources in plant breeding for sustainable agriculture

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