Population Genomics for Understanding Adaptation in Wild Plant Species

Weigel, Detlef; Nordborg, Magnus

doi:10.1146/annurev-genet-120213-092110

Cited by 85 publications

(91 citation statements)

References 164 publications

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“…Genome-wide association studies (GWAS) are another approach to decipher the genetic architecture of traits (Weigel and Nordborg, 2015). Recently, two flowering-time GWAS in B. distachyon identified nine and five associated peaks, none of which overlap with the QTLs identified in this study (Tyler et al, 2016;Wilson et al, 2015).…”

Section: Discussionmentioning

confidence: 57%

“…Recently, two flowering-time GWAS in B. distachyon identified nine and five associated peaks, none of which overlap with the QTLs identified in this study (Tyler et al, 2016;Wilson et al, 2015). Thus, the QTL identified in our RIL population may represent rare alleles that do not surface in GWAS, or the GWAS that was conducted contains too few accessions or compounding population structures (issues that are common when conducting GWAS in in-breeding species; Weigel and Nordborg 2015). For example, initial GWAS flowering studies in Arabidopsis had difficulty identifying FLOWERING LOCUS C and FRIGIDA, two genes responsible for much of the flowering-time variation among accessions of Arabidopsis.…”

Section: Discussionmentioning

confidence: 99%

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Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

et al. 2016

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The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time. A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.Proper timing of flowering is a major developmental decision in the life history of plants, and the genetic manipulation of flowering time has played a crucial role in the domestication and spread of cereal crops such as wheat (Triticum spp.), barley (Hordeum vulgare L.), rice (Oryza sativa), and maize (Zea mays; Greenup et al., 2009;Hung et al., 2012). Moreover, the modulation of flowering time has been important in the diversification of temperate (pooid) grasses into higher latitudes with colder winters (Woods et al., 2016;Fjellheim et al., 2014). An important environmental cue that often affects flowering is day (d) length (photoperiod; Song et al., 2015). Many plants adapted to temperate regions flower in response to increasing day lengths (long-d plants), in contrast to many plants from the tropics that flower as day length decreases (short-d plants). In addition, some plants adapted to temperate climates have taken on a biennial/winter annual life history strategy in which plants become established in the fall, then overwinter and flower rapidly in the spring as day lengths increase (Amasino 2010). Essential to this strategy is the prevention of flowering before winter because cold temperatures could damage delicate floral structures, preventing reproduction. Thus, plants have evolved ways to repress flowering in the fall and alleviate this repression by sensing the passing of winter to establish competence to flower. This process, by which the block to flowering is alleviated by exposure to prolonged time in cold temperatures, is known as vernalization (Chouard 1960).Many varieties of wheat, barley, oats (Avena sativa), and rye (Secale cereale) requ...

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Section: Discussionmentioning

confidence: 57%

Section: Discussionmentioning

confidence: 99%

Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

et al. 2016

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“…GWA screens can complement QTL studies by identification of loci that do not have segregating alleles in the two RIL founder populations (Gibson 2012; Weigel and Nordborg 2015). We used 64 of the 98 accessions we had screened previously for a GWA study (see Table S3) because whole-genome resequencing data were available for them (http://1001genomes.org; 1001 Genomes Consortium 2016).…”

Section: Resultsmentioning

confidence: 99%

Effector-Triggered Immune Response in Arabidopsis thaliana Is a Quantitative Trait

et al. 2016

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We identified loci responsible for natural variation in Arabidopsis thaliana (Arabidopsis) responses to a bacterial pathogen virulence factor, HopAM1. HopAM1 is a type III effector protein secreted by the virulent Pseudomonas syringae strain Pto DC3000. Delivery of HopAM1 from disarmed Pseudomonas strains leads to local cell death, meristem chlorosis, or both, with varying intensities in different Arabidopsis accessions. These phenotypes are not associated with differences in bacterial growth restriction. We treated the two phenotypes as quantitative traits to identify host loci controlling responses to HopAM1. Genome-wide association (GWA) of 64 Arabidopsis accessions identified independent variants highly correlated with response to each phenotype. Quantitative trait locus (QTL) mapping in a recombinant inbred population between Bur-0 and Col-0 accessions revealed genetic linkage to regions distinct from the top GWA hits. Two major QTL associated with HopAM1-induced cell death were also associated with HopAM1-induced chlorosis. HopAM1-induced changes in Arabidopsis gene expression showed that rapid HopAM1-dependent cell death in Bur-0 is correlated with effector-triggered immune responses. Studies of the effect of mutations in known plant immune system genes showed, surprisingly, that both cell death and chlorosis phenotypes are enhanced by loss of EDS1, a regulatory hub in the plant immune-signaling network. Our results reveal complex genetic architecture for response to this particular type III virulence effector, in contrast to the typical monogenic control of cell death and disease resistance triggered by most type III effectors.

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“…Thirdly, the lower the selective pressure, the greater the accumulation of mutations, and mutated allelic sites in genic regions are usually easily swept away under the relatively greater selective pressure in these regions. Finally, some variable regions result from adaptative pressures, whereby mutations in genes related to adaptive capacity are more likely to be retained, as variability may increase survival probabilities with exposure to environmental stress (Hayward et al, 2015; Weigel and Nordborg, 2015). …”

Section: Discussionmentioning

confidence: 99%

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

Zhou

Zheng

et al. 2017

Front. Plant Sci.

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Single Nucleotide Polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism, and hence make highly favorable markers for genetic map construction and genome-wide association studies. In this study, a total of 300 rapeseed accessions (278 representative of Chinese germplasm, plus 22 outgroup accessions of different origins and ecotypes) were collected and sequenced using Specific-Locus Amplified Fragment Sequencing (SLAF-seq) technology, obtaining 660.25M reads with an average sequencing depth of 6.27 × and a mean Q30 of 85.96%. Based on the 238,711 polymorphic SLAF tags a total of 1,197,282 SNPs were discovered, and a subset of 201,817 SNPs with minor allele frequency >0.05 and integrity >0.8 were selected. Of these, 30,877 were designated SNP “hotspots,” and 41 SNP-rich genomic regions could be delineated, with 100 genes associated with plant resistance, vernalization response, and signal transduction detected in these regions. Subsequent analysis of genetic diversity, linkage disequilibrium (LD), and population structure in the 300 accessions was carried out based on the 201,817 SNPs. Nine subpopulations were observed based on the population structure analysis. Hierarchical clustering and principal component analysis divided the 300 varieties roughly in accordance with their ecotype origins. However, spring-type varieties were intermingled with semi-winter type varieties, indicating frequent hybridization between spring and semi-winter ecotypes in China. In addition, LD decay across the whole genome averaged 299 kb when r2 = 0.1, but the LD decay in the A genome (43 kb) was much shorter than in the C genome (1,455 kb), supporting the targeted introgression of the A genome from progenitor species B. rapa into Chinese rapeseed. This study also lays the foundation for genetic analysis of important agronomic traits using this rapeseed population.

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Population Genomics for Understanding Adaptation in Wild Plant Species

Cited by 85 publications

References 164 publications

Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

Genetic Architecture of Flowering-Time Variation in Brachypodium distachyon

Effector-Triggered Immune Response in Arabidopsis thaliana Is a Quantitative Trait

Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

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