High‐density genome‐wide association mapping implicates an <scp>F</scp>‐box encoding gene in <i><scp>M</scp>edicago truncatula</i> resistance to <i><scp>A</scp>phanomyces euteiches</i>

Bonhomme, Maxime; Olivier, André; Badis, Yacine; Ronfort, Joëlle; Burgarella, Concetta; Chantret, Nathalie; Prosperi, J.M.; Briskine, Roman; Mudge, Joann; Debelle, Frédéric; Navier, Hélène; Miteul, Henri; Hajri, Ahmed; Baranger, Alain; Tiffin, Peter; Dumas, Bernard; Pilet‐Nayel, Marie‐Laure; Young, Nevin D.; Jacquet, Christophe

doi:10.1111/nph.12611

Cited by 83 publications

(121 citation statements)

References 82 publications

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“…Examples of where LD mapping has been applied for identification of both novel and previously characterized genes responsible for agronomic traits include genome‐wide association studies (GWAS) in model legume Medicago truncatula (Stanton‐Geddes et al, ), common bean (Kamfwa, Cichy, & Kelly, ; Moghaddam et al, ), and soybean (Contreras‐Soto et al, ; Zhou et al, ). GWAS has also proven to be successful in identifying candidate genes for ascochyta blight resistance (Li et al, ) and heat and drought tolerant loci in chickpea (Thudi, Upadhyaya, et al, ), and Aphanomyces euteiches resistance in Medicago truncatula (Bonhomme et al, ). Applying GWAS in a population comprising 292 pigeonpea accessions using data over several years enabled identification of association between candidate genes and traits, including 100‐seed weight, days to 50% flowering, and plant height (Varshney et al, ).…”

Section: Finding Adaptive Genes and Adaptive Traitsmentioning

confidence: 99%

Adapting legume crops to climate change using genomic approaches

Mousavi‐Derazmahalleh

Bayer

Hane

et al. 2018

Plant Cell & Environment

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Our agricultural system and hence food security is threatened by combination of events, such as increasing population, the impacts of climate change, and the need to a more sustainable development. Evolutionary adaptation may help some species to overcome environmental changes through new selection pressures driven by climate change. However, success of evolutionary adaptation is dependent on various factors, one of which is the extent of genetic variation available within species. Genomic approaches provide an exceptional opportunity to identify genetic variation that can be employed in crop improvement programs. In this review, we illustrate some of the routinely used genomics-based methods as well as recent breakthroughs, which facilitate assessment of genetic variation and discovery of adaptive genes in legumes. Although additional information is needed, the current utility of selection tools indicate a robust ability to utilize existing variation among legumes to address the challenges of climate uncertainty.

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Section: Finding Adaptive Genes and Adaptive Traitsmentioning

confidence: 99%

Adapting legume crops to climate change using genomic approaches

Mousavi‐Derazmahalleh

Bayer

Hane

et al. 2018

Plant Cell & Environment

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“…These results have been corroborated by genetic studies. A major locus associated with resistance to A. euteiches , namely AER1 , has been identified (Pilet‐Nayel et al ., ) and confirmed by a genome‐wide association study, which identified two major independent loci on top of chromosome 3, one of which co‐localized with prAe1 (formerly named AER1) (Bonhomme et al ., ). The functional role of the prAe1 locus has been investigated recently (Badis et al ., ) using two near‐isogenic lines, NR and NS, partially resistant and susceptible, respectively, differing in the allelic state of prAe1.…”

Section: Introductionmentioning

confidence: 97%

Nitrogen modulation of Medicago truncatula resistance to Aphanomyces euteiches depends on plant genotype

Thalineau

Fournier

Gravot

et al. 2017

Molecular Plant Pathology

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Nitrogen (N) availability can impact plant resistance to pathogens by the regulation of plant immunity. To better understand the links between N nutrition and plant defence, we analysed the impact of N availability on Medicago truncatula resistance to the root pathogen Aphanomyces euteiches. This oomycete is considered to be the most limiting factor for legume production. Ten plant genotypes were tested in vitro for their resistance to A. euteiches in either complete or nitrate-deficient medium. N deficiency led to enhanced or reduced susceptibility depending on the plant genotype. Focusing on four genotypes displaying contrasting responses, we determined the impact of N deficiency on plant growth and shoot N concentration, and performed expression analyses on N- and defence-related genes, as well as the quantification of soluble phenolics and different amino acids in roots. Our analyses suggest that N modulation of plant resistance is not linked to plant response to N deprivation or to mechanisms previously identified to be involved in plant resistance. Furthermore, our studies highlight a role of glutamine in mediating the susceptibility to A. euteiches in M. truncatula.

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“…(2011) as a potential contributor to climate-specific survival in A. thaliana, and an M. truncatula homolog of the A. thaliana CPR30 has been shown to confer resistance to the oomycete Aphanomyces euteiches (Bonhomme et al 2014). Bonhomme et al also speculated that this M. truncatula F-box gene may play a direct role in response to abiotic stress.…”

Section: Functional Roles Of Candidatesmentioning

confidence: 99%

Genomic Signature of Adaptation to Climate in Medicago truncatula

et al. 2014

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Local adaptation and adaptive clines are pervasive in natural plant populations, yet the effects of these types of adaptation on genomic diversity are not well understood. With a data set of 202 accessions of Medicago truncatula genotyped at almost 2 million single nucleotide polymorphisms, we used mixed linear models to identify candidate loci responsible for adaptation to three climatic gradientsannual mean temperature (AMT), precipitation in the wettest month (PWM), and isothermality (ITH)-representing the major axes of climate variation across the species' range. Loci with the strongest association to these climate gradients tagged genome regions with high sequence similarity to genes with functional roles in thermal tolerance, drought tolerance, or resistance to herbivores of pathogens. Genotypes at these candidate loci also predicted the performance of an independent sample of plant accessions grown in climatecontrolled conditions. Compared to a genome-wide sample of randomly drawn reference SNPs, candidates for two climate gradients, AMT and PWM, were significantly enriched for genic regions, and genome segments flanking genic AMT and PWM candidates harbored less nucleotide diversity, elevated differentiation between haplotypes carrying alternate alleles, and an overrepresentation of the most common haplotypes. These patterns of diversity are consistent with a history of soft selective sweeps acting on loci underlying adaptation to climate, but not with a history of long-term balancing selection. L OCAL and clinal adaptation is widespread in natural populations (Clausen et al. 1941;Leimu and Fischer 2008), which, by definition, results from selection that varies across a species' range. Most methods to search for the targets of adaptation are designed to identify gene regions that have experienced "hard" selective sweeps, in which selection acts on new mutations that confer a selective advantage across the entire range of a sample (Maynard Smith and Haigh 1974;Nielsen 2005;Pritchard and Di Rienzo 2010;Kelly et al. 2013). These methods are not designed to identify targets of adaptation to selective environments that vary across the range of sampled populations. The targets of locally variable selection either may be maintained as stable polymorphisms or experience partial, or "soft," sweeps either because local adaptation involves fixation of different alleles in different portions of a species' range or because selection acts on standing variation (Hermisson and Pennings 2005;Pavlidis et al. 2012;Messer and Petrov 2013).Identifying the molecular targets of clinal adaptation offers an opportunity not only to identify functionally important genes, but also to further our understanding of adaptation itself. If the selective environment that drives clinal adaptation is stable, and alleles responsible for adaptation are at stable equilibria, then the loci responsible for adaptation may bear population genetic signatures of balancing selection: elevated differentiation between haplotypes linked to the ...

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High‐density genome‐wide association mapping implicates an F‐box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches

Cited by 83 publications

References 82 publications

Adapting legume crops to climate change using genomic approaches

Adapting legume crops to climate change using genomic approaches

Nitrogen modulation of Medicago truncatula resistance to Aphanomyces euteiches depends on plant genotype

Genomic Signature of Adaptation to Climate in Medicago truncatula

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