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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
Genetic regions considered for the diversity analysis of Asr1 and Asr2. Genetic regions considered for the diversity analysis of a. Asr1 and b. Asr2 in the wild and cultivated collections (Core). Silver boxes are introns. Gray markers are transitions and pink markers are transversions.
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Figure 1: Genetic regions considered for the diversity analysis of Asr1 and Asr2. Genetic regions considered for the diversity analysis of a. Asr1 and b. Asr2 in the wild and cultivated collections (Core). Silver boxes are introns. Gray markers are transitions and pink markers are transversions.

Mentions: There are two members of the ASR gene (PF02496) in common bean that could be distinguished by the primers we used here. Both of them have two exons and one intron. The Asr2 gene is smaller than the Asr1 gene. Asr2 includes 100 bp upstream of the ABA domain whilst Asr1 includes 550 bp. In addition, the intron in Asr2 (179 bp) is smaller than the intron in Asr1 (565 bp) (Figure1). This structure was confirmed with the alignment between common bean ESTs (TC2798 and CA910244) and our sequenced region.


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)

Genetic regions considered for the diversity analysis of Asr1 and Asr2. Genetic regions considered for the diversity analysis of a. Asr1 and b. Asr2 in the wild and cultivated collections (Core). Silver boxes are introns. Gray markers are transitions and pink markers are transversions.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Genetic regions considered for the diversity analysis of Asr1 and Asr2. Genetic regions considered for the diversity analysis of a. Asr1 and b. Asr2 in the wild and cultivated collections (Core). Silver boxes are introns. Gray markers are transitions and pink markers are transversions.
Mentions: There are two members of the ASR gene (PF02496) in common bean that could be distinguished by the primers we used here. Both of them have two exons and one intron. The Asr2 gene is smaller than the Asr1 gene. Asr2 includes 100 bp upstream of the ABA domain whilst Asr1 includes 550 bp. In addition, the intron in Asr2 (179 bp) is smaller than the intron in Asr1 (565 bp) (Figure1). This structure was confirmed with the alignment between common bean ESTs (TC2798 and CA910244) and our sequenced region.

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