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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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Haplotype networks forAsr1 and Asr2. Haplotype networks for Asr1 and Asr2 (subfigures a-f and g-h, respectively). Each node represents a haplotype, its size being proportional to its frequency. A segment corresponds to a subset of substitutions. Hollow nodes are hypothetical" (aka add "a subset" and "nodes"), "shown in subfigures a, c, e, g" (without "b"), "subfigure b, d, f, h" (with "b"). The left or upper figure of each couple contains the drought tolerance states of susceptibility, moderate tolerance and tolerance with intermediate levels (shown in subfigures a, b, c, e, g). The right or lower picture of each couple shows the populations and races identified for wild (subfigures d, f, h) and cultivated (subfigures b, h) common bean. For Asr1, the analysis was carried for the cultivated and the wild collections independently (subfigures a-b and c-f, respectively), and considered the exon and intron regions separately (subfigures c-d and e-f, respectively). For Asr2, the analysis is considered globally. Abbreviations are: Mesoamerican (M1 and M2), Durango (D1 and D2), Guatemala (G), Nueva Granada (NG1 and NG2) and Peru races (P1), and Mesoamerican (M_w), Guatemala (G_w), Colombian (C_w), Ecuador-Northern Peru (ENP_w) and Andean wild populations (A_w).
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Figure 3: Haplotype networks forAsr1 and Asr2. Haplotype networks for Asr1 and Asr2 (subfigures a-f and g-h, respectively). Each node represents a haplotype, its size being proportional to its frequency. A segment corresponds to a subset of substitutions. Hollow nodes are hypothetical" (aka add "a subset" and "nodes"), "shown in subfigures a, c, e, g" (without "b"), "subfigure b, d, f, h" (with "b"). The left or upper figure of each couple contains the drought tolerance states of susceptibility, moderate tolerance and tolerance with intermediate levels (shown in subfigures a, b, c, e, g). The right or lower picture of each couple shows the populations and races identified for wild (subfigures d, f, h) and cultivated (subfigures b, h) common bean. For Asr1, the analysis was carried for the cultivated and the wild collections independently (subfigures a-b and c-f, respectively), and considered the exon and intron regions separately (subfigures c-d and e-f, respectively). For Asr2, the analysis is considered globally. Abbreviations are: Mesoamerican (M1 and M2), Durango (D1 and D2), Guatemala (G), Nueva Granada (NG1 and NG2) and Peru races (P1), and Mesoamerican (M_w), Guatemala (G_w), Colombian (C_w), Ecuador-Northern Peru (ENP_w) and Andean wild populations (A_w).

Mentions: Globally, Asr2 presented more haplotypes than Asr1. Moreover, haplotypes with low frequency were more common at Asr2 than at Asr1 (Table4). A hypothetical haplotype was required to analyze variation in the exon region of Asr1. Furthermore, some patterns suggested by the previous section were revealed by total haplotype frequency for each gene pool division was clearer for Asr1, as well as for each sub-population (Figure3). In particular, Northern Peru population had a unique fixed haplotype of Asr1. The haplotypes with the highest frequency were shared by accessions from Mesoamerican, Guatemala, Colombia and Andean populations for Asr1 and Asr2 genes. A pair of equally high-frequency haplotypes shared by more than two populations was found for Asr2. Interestingly, Ecuador-Northern Peru population did not have any of these haplotypes. A Mesoamerican-Andean gene pool division was clear for both genes, especially for Asr1, as was stated in the previous section.


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)

Haplotype networks forAsr1 and Asr2. Haplotype networks for Asr1 and Asr2 (subfigures a-f and g-h, respectively). Each node represents a haplotype, its size being proportional to its frequency. A segment corresponds to a subset of substitutions. Hollow nodes are hypothetical" (aka add "a subset" and "nodes"), "shown in subfigures a, c, e, g" (without "b"), "subfigure b, d, f, h" (with "b"). The left or upper figure of each couple contains the drought tolerance states of susceptibility, moderate tolerance and tolerance with intermediate levels (shown in subfigures a, b, c, e, g). The right or lower picture of each couple shows the populations and races identified for wild (subfigures d, f, h) and cultivated (subfigures b, h) common bean. For Asr1, the analysis was carried for the cultivated and the wild collections independently (subfigures a-b and c-f, respectively), and considered the exon and intron regions separately (subfigures c-d and e-f, respectively). For Asr2, the analysis is considered globally. Abbreviations are: Mesoamerican (M1 and M2), Durango (D1 and D2), Guatemala (G), Nueva Granada (NG1 and NG2) and Peru races (P1), and Mesoamerican (M_w), Guatemala (G_w), Colombian (C_w), Ecuador-Northern Peru (ENP_w) and Andean wild populations (A_w).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Haplotype networks forAsr1 and Asr2. Haplotype networks for Asr1 and Asr2 (subfigures a-f and g-h, respectively). Each node represents a haplotype, its size being proportional to its frequency. A segment corresponds to a subset of substitutions. Hollow nodes are hypothetical" (aka add "a subset" and "nodes"), "shown in subfigures a, c, e, g" (without "b"), "subfigure b, d, f, h" (with "b"). The left or upper figure of each couple contains the drought tolerance states of susceptibility, moderate tolerance and tolerance with intermediate levels (shown in subfigures a, b, c, e, g). The right or lower picture of each couple shows the populations and races identified for wild (subfigures d, f, h) and cultivated (subfigures b, h) common bean. For Asr1, the analysis was carried for the cultivated and the wild collections independently (subfigures a-b and c-f, respectively), and considered the exon and intron regions separately (subfigures c-d and e-f, respectively). For Asr2, the analysis is considered globally. Abbreviations are: Mesoamerican (M1 and M2), Durango (D1 and D2), Guatemala (G), Nueva Granada (NG1 and NG2) and Peru races (P1), and Mesoamerican (M_w), Guatemala (G_w), Colombian (C_w), Ecuador-Northern Peru (ENP_w) and Andean wild populations (A_w).
Mentions: Globally, Asr2 presented more haplotypes than Asr1. Moreover, haplotypes with low frequency were more common at Asr2 than at Asr1 (Table4). A hypothetical haplotype was required to analyze variation in the exon region of Asr1. Furthermore, some patterns suggested by the previous section were revealed by total haplotype frequency for each gene pool division was clearer for Asr1, as well as for each sub-population (Figure3). In particular, Northern Peru population had a unique fixed haplotype of Asr1. The haplotypes with the highest frequency were shared by accessions from Mesoamerican, Guatemala, Colombia and Andean populations for Asr1 and Asr2 genes. A pair of equally high-frequency haplotypes shared by more than two populations was found for Asr2. Interestingly, Ecuador-Northern Peru population did not have any of these haplotypes. A Mesoamerican-Andean gene pool division was clear for both genes, especially for Asr1, as was stated in the previous section.

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