Choudhury Baharul Islam, Khan Mohammed Latif, Dayanandan Selvadurai
Forest and Evolutionary Genomics Laboratory and Centre for Structural and Functional Genomics, Biology Department, Concordia University Montréal, 7141 Sherbrooke St, West, Montréal, Quebec H4B 1R6, Canada.
BMC Genet. 2014 Jun 16;15:71. doi: 10.1186/1471-2156-15-71.
During the domestication of crops, individual plants with traits desirable for human needs have been selected from their wild progenitors. Consequently, genetic and nucleotide diversity of genes associated with these selected traits in crop plants are expected to be lower than their wild progenitors. In the present study, we surveyed the pattern of nucleotide diversity of two selected trait specific genes, Wx and OsC1, which regulate amylose content and apiculus coloration respectively in cultivated rice varieties. The analyzed samples were collected from a wide geographic area in Northeast (NE) India, and included contrasting phenotypes considered to be associated with selected genes, namely glutinous and nonglutinous grains and colored and colorless apiculus.
No statistically significant selection signatures were detected in both Wx and OsC1gene sequences. However, low level of selection that varied across the length of each gene was evident. The glutinous type varieties showed higher levels of nucleotide diversity at the Wx locus (πtot = 0.0053) than nonglutinous type varieties (πtot = 0.0043). The OsC1 gene revealed low levels of selection among the colorless apiculus varieties with lower nucleotide diversity (πtot = 0.0010) than in the colored apiculus varieties (πtot = 0.0023).
The results revealed that functional mutations at Wx and OsC1genes considered to be associated with specific phenotypes do not necessarily correspond to the phenotypes in indigenous rice varieties in NE India. This suggests that other than previously reported genomic regions may also be involved in determination of these phenotypes.
在作物驯化过程中，具有人类所需性状的个体植株已从其野生祖先中被挑选出来。因此，预计作物中与这些选定性状相关的基因的遗传和核苷酸多样性低于其野生祖先。在本研究中，我们调查了两个选定的性状特异性基因Wx和OsC1的核苷酸多样性模式，这两个基因分别调控栽培水稻品种中的直链淀粉含量和颖尖颜色。分析的样本采集自印度东北部的广泛地理区域，包括被认为与选定基因相关的对比表型，即糯性和非糯性籽粒以及有色和无色颖尖。
在Wx和OsC1基因序列中均未检测到具有统计学意义的选择信号。然而，每个基因长度上不同程度的低水平选择是明显的。糯性品种在Wx位点的核苷酸多样性水平（πtot = 0.0053）高于非糯性品种（πtot = 0.0043）。OsC1基因在无色颖尖品种中的选择水平较低，其核苷酸多样性（πtot = 0.0010）低于有色颖尖品种（πtot = 0.0023）。
结果表明，被认为与特定表型相关的Wx和OsC1基因的功能突变不一定与印度东北部本地水稻品种的表型相对应。这表明除了先前报道的基因组区域外，其他区域也可能参与这些表型的决定。
