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Molecular ecology and selection in the drought-related Asr gene polymorphisms in wild and cultivated common bean (Phaseolus vulgaris L.).

Cortés AJ, Chavarro MC, Madriñán S, This D, Blair MW - BMC Genet. (2012)

Bottom Line: These patterns were more notable in wild beans than in cultivated common beans indicting that natural selection has played a role over long time periods compared to farmer selection since domestication.Together these results suggested the importance of Asr1 in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits.Furthermore, one of our major successes was to find that wild common bean is a reservoir of genetic variation and selection signatures at Asr genes, which may be useful for breeding drought tolerance in cultivated common bean.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Biologia, Universidad de los Andes, Carrera 1 N° 18A - 12, J302 Bogotá, Colombia. andres.cortes@ebc.uu.se

ABSTRACT

Background: The abscisic acid (ABA) pathway plays an important role in the plants' reaction to drought stress and ABA-stress response (Asr) genes are important in controlling this process. In this sense, we accessed nucleotide diversity at two candidate genes for drought tolerance (Asr1 and Asr2), involved in an ABA signaling pathway, in the reference collection of cultivated common bean (Phaseolus vulgaris L.) and a core collection of wild common bean accessions.

Results: Our wild population samples covered a range of mesic (semi-arid) to very dry (desert) habitats, while our cultivated samples presented a wide spectrum of drought tolerance. Both genes showed very different patterns of nucleotide variation. Asr1 exhibited very low nucleotide diversity relative to the neutral reference loci that were previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, Asr2 exhibited higher levels of nucleotide diversity, which is indicative of adaptive selection. These patterns were more notable in wild beans than in cultivated common beans indicting that natural selection has played a role over long time periods compared to farmer selection since domestication.

Conclusions: Together these results suggested the importance of Asr1 in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits. Furthermore, one of our major successes was to find that wild common bean is a reservoir of genetic variation and selection signatures at Asr genes, which may be useful for breeding drought tolerance in cultivated common bean.

Show MeSH
Comparison of Asr genes to Phaseolus vulgaris general nucleotide diversity. π (E-2)statistic from the wild collection was computed. The background distribution was estimated by Cortés et al.[45]. Asr1 and Asr2 are indicated by arrows in the corresponding classes. Population structure and adaptive selection are associated with a high π values, but bottlenecks and directional selection is associated with low π value.
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Figure 2: Comparison of Asr genes to Phaseolus vulgaris general nucleotide diversity. π (E-2)statistic from the wild collection was computed. The background distribution was estimated by Cortés et al.[45]. Asr1 and Asr2 are indicated by arrows in the corresponding classes. Population structure and adaptive selection are associated with a high π values, but bottlenecks and directional selection is associated with low π value.

Mentions: π values for Asr1 and Asr2 were compared against the background distribution from Cortés et al.[45] for non-drought related genes. Despite this selection of random genes, the background distribution was not neutral and tended to inflate π values, as would be expected where some of the random genes were important for sub-population selection. Asr2 fell within the range of random genes. However, Asr1 presented extreme lower values in relation with the evolutionary background, accounting for a p-value less than 0.001 (Figure2). This shows that like the background distribution of SNPs, the present SNPs accounted for the gene pool structure.


Molecular ecology and selection in the drought-related Asr gene polymorphisms in wild and cultivated common bean (Phaseolus vulgaris L.).

Cortés AJ, Chavarro MC, Madriñán S, This D, Blair MW - BMC Genet. (2012)

Comparison of Asr genes to Phaseolus vulgaris general nucleotide diversity. π (E-2)statistic from the wild collection was computed. The background distribution was estimated by Cortés et al.[45]. Asr1 and Asr2 are indicated by arrows in the corresponding classes. Population structure and adaptive selection are associated with a high π values, but bottlenecks and directional selection is associated with low π value.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3473318&req=5

Figure 2: Comparison of Asr genes to Phaseolus vulgaris general nucleotide diversity. π (E-2)statistic from the wild collection was computed. The background distribution was estimated by Cortés et al.[45]. Asr1 and Asr2 are indicated by arrows in the corresponding classes. Population structure and adaptive selection are associated with a high π values, but bottlenecks and directional selection is associated with low π value.
Mentions: π values for Asr1 and Asr2 were compared against the background distribution from Cortés et al.[45] for non-drought related genes. Despite this selection of random genes, the background distribution was not neutral and tended to inflate π values, as would be expected where some of the random genes were important for sub-population selection. Asr2 fell within the range of random genes. However, Asr1 presented extreme lower values in relation with the evolutionary background, accounting for a p-value less than 0.001 (Figure2). This shows that like the background distribution of SNPs, the present SNPs accounted for the gene pool structure.

Bottom Line: These patterns were more notable in wild beans than in cultivated common beans indicting that natural selection has played a role over long time periods compared to farmer selection since domestication.Together these results suggested the importance of Asr1 in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits.Furthermore, one of our major successes was to find that wild common bean is a reservoir of genetic variation and selection signatures at Asr genes, which may be useful for breeding drought tolerance in cultivated common bean.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Biologia, Universidad de los Andes, Carrera 1 N° 18A - 12, J302 Bogotá, Colombia. andres.cortes@ebc.uu.se

ABSTRACT

Background: The abscisic acid (ABA) pathway plays an important role in the plants' reaction to drought stress and ABA-stress response (Asr) genes are important in controlling this process. In this sense, we accessed nucleotide diversity at two candidate genes for drought tolerance (Asr1 and Asr2), involved in an ABA signaling pathway, in the reference collection of cultivated common bean (Phaseolus vulgaris L.) and a core collection of wild common bean accessions.

Results: Our wild population samples covered a range of mesic (semi-arid) to very dry (desert) habitats, while our cultivated samples presented a wide spectrum of drought tolerance. Both genes showed very different patterns of nucleotide variation. Asr1 exhibited very low nucleotide diversity relative to the neutral reference loci that were previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, Asr2 exhibited higher levels of nucleotide diversity, which is indicative of adaptive selection. These patterns were more notable in wild beans than in cultivated common beans indicting that natural selection has played a role over long time periods compared to farmer selection since domestication.

Conclusions: Together these results suggested the importance of Asr1 in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits. Furthermore, one of our major successes was to find that wild common bean is a reservoir of genetic variation and selection signatures at Asr genes, which may be useful for breeding drought tolerance in cultivated common bean.

Show MeSH