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Genetic diversity analysis of abiotic stress response gene TaSnRK2.7-A in common wheat

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Abstract

Sucrose non-fermenting1-related protein kinase 2 (SnRK2) plays a key role in plant stress signaling transduction pathways. In this study, one copy of TaSnRK2.7, a SnRK2 member of common wheat, was isolated and characterized for nucleotide diversity among 45 wheat accessions with different stress-response features. Most of the accessions were elite wheat cultivars, which had been subject to population bottlenecks and intensive selection during breeding. Nucleotide and haplotype diversity across the entire TaSnRK2.7-A region was 0.00076 and 0.590, respectively, and diversity in non-coding regions was higher than that in coding regions. Sliding-window analysis showed variable levels of nucleotide variation along the entire TaSnRK2.7-A region; the sixth intron and ninth exon represented variation-enriched regions. As predicted, neutrality tests revealed that population bottlenecks or purifying selection had acted on the TaSnRK2.7-A gene, a relatively conserved gene. Furthermore, strong linkage disequilibrium between SNP loci extends across the entire TaSnRK2.7-A region. These findings demonstrate that the TaSnRK2.7-A genomic region has evolved under extensive selection pressure during crop breeding.

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Abbreviations

bp:

Base pair

cSNP:

Coding single nucleotide polymorphism

InDel:

Insertion/deletion

LD:

Linkage disequilibrium

ORF:

Open reading frame

PCR:

Polymerase chain reaction

QTLs:

Quantitative trait loci

SNP:

Single-nucleotide polymorphism

UTR:

Untranslated region

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Acknowledgments

The authors thank Prof. Robert A. McIntosh (Plant Breeding Institute, University of Sydney, NSW, Australia) for critical reading and comments on the manuscript. This work was supported by the National Basic Research Program of China (973 Program, 2010CB951501) and the National Key Technologies R&D Program (2009ZX08002-012B).

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Authors and Affiliations

  1. The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Hongying Zhang, Xinguo Mao, Jianan Zhang, Xiaoping Chang & Ruilian Jing

  2. College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China

    Hongying Zhang & Chengshe Wang

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  1. Hongying Zhang
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  2. Xinguo Mao
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Correspondence to Ruilian Jing.

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Zhang, H., Mao, X., Zhang, J. et al. Genetic diversity analysis of abiotic stress response gene TaSnRK2.7-A in common wheat. Genetica 139, 743–753 (2011). https://doi.org/10.1007/s10709-011-9579-8

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