Tracking Selection Signatures Based on Variation in OsLEA27 within Myanmar Landraces of Upland and Dryland Rice

  Wunna¹, Syed Abdullah Gilani², Makoto Kawase³, Ryo Ohsawa¹, Kazuo N. Watanabe^1*

¹Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.
²Department of Biological Sciences and Chemistry, University of Nizwa, Nizwa, Sultanate of Oman.
³Gene Bank, National Institute of Agrobiological Sciences, Tsukuba, Japan.

DOI: 10.4236/ajps.2015.612195                

Abstract

To track the selection evident along the genome segment of OsLEA27 gene, a member of dehydrin gene family, 2.9-kbp nucleotide sequence containing the promoter 5’ upstream and transcribed region of OsLEA27 was determined for 35 upland and dryland Myanmar landraces from drought-prone areas. Nucleotide diversity, neutrality tests, haplotype network analysis, and linkage disequilibrium (LD) analysis were performed to infer the impact of selection and to investigate nonrandom associations of SNPs within all or part of the entire OsLEA27 region. The evidence for LD, the presence of two distinct haplotype groups across four different geographical regions, and the significant values obtained in a sliding-window analysis of mutation-drift tests all suggest the effects of selection on OsLEA27 in a set of 30 landraces. The neutrality test values for 5’ upstream region of OsLEA27 were significantly negative (p < 0.05) within the set of 30 accessions. The entire OsLEA27 region was significantly negative in accessions of the northern group, indicating a recent increase in population size or selection pressure. This evidence for selection signatures at OsLEA27 in this study sample provides insight into the roles of selection, crop adaptation, and genetic diversity in establishing present-day variation at the OsLEA27 locus.

Keywords

Dehydrine, Linkage Disequilibrium (LD), Nucleotide Diversity, Haplotype, Selection Signature, Upland Rice, Dryland Rice

Conflicts of Interest

The authors declare no conflicts of interest.

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