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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.

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Geographic distribution of wild common bean accessions. Geographic distribution of wild common bean accessions considering genetic polymorphism and precipitation of driest period for a) Asr1_161 (in significant linkage disequilibrium with Asr1_233) and b) for the two major haplotypes of Asr2. Different circle sizes correspond to different allele or haplotypes. Mexico and Ecuador-Northern Peru regions are detailed in each case.
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Figure 4: Geographic distribution of wild common bean accessions. Geographic distribution of wild common bean accessions considering genetic polymorphism and precipitation of driest period for a) Asr1_161 (in significant linkage disequilibrium with Asr1_233) and b) for the two major haplotypes of Asr2. Different circle sizes correspond to different allele or haplotypes. Mexico and Ecuador-Northern Peru regions are detailed in each case.

Mentions: A qualitative evaluation of the possible association between population structure, drought tolerance, and haplotype and nucleotide diversity of candidate genes was made by comparing the allelic diversity with ecological variation for drought tolerance (Figure4). Median Joining Networks aided in this inspection in this way, it was possible to identify genetic variation correlated with estimated habitat drought index and drought severity index for the wild and cultivated genotypes, respectively. In particular, the combination of estimated habitat drought stress, drought severity index, population structure, and candidate gene haplotypes in a qualitative analysis revealed four main categories of relationships, as described below.


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)

Geographic distribution of wild common bean accessions. Geographic distribution of wild common bean accessions considering genetic polymorphism and precipitation of driest period for a) Asr1_161 (in significant linkage disequilibrium with Asr1_233) and b) for the two major haplotypes of Asr2. Different circle sizes correspond to different allele or haplotypes. Mexico and Ecuador-Northern Peru regions are detailed in each case.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Geographic distribution of wild common bean accessions. Geographic distribution of wild common bean accessions considering genetic polymorphism and precipitation of driest period for a) Asr1_161 (in significant linkage disequilibrium with Asr1_233) and b) for the two major haplotypes of Asr2. Different circle sizes correspond to different allele or haplotypes. Mexico and Ecuador-Northern Peru regions are detailed in each case.
Mentions: A qualitative evaluation of the possible association between population structure, drought tolerance, and haplotype and nucleotide diversity of candidate genes was made by comparing the allelic diversity with ecological variation for drought tolerance (Figure4). Median Joining Networks aided in this inspection in this way, it was possible to identify genetic variation correlated with estimated habitat drought index and drought severity index for the wild and cultivated genotypes, respectively. In particular, the combination of estimated habitat drought stress, drought severity index, population structure, and candidate gene haplotypes in a qualitative analysis revealed four main categories of relationships, as described below.

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
Related in: MedlinePlus