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Background  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.    Results  No statistically significant selection signatures were detected in both  Wx  and  OsC1 gene 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 (π tot  = 0.0053) than nonglutinous type varieties (π tot  = 0.0043). The  OsC1  gene revealed low levels of selection among the colorless apiculus varieties with lower nucleotide diversity (π tot  = 0.0010) than in the colored apiculus varieties (π tot  = 0.0023).    Conclusions  The results revealed that functional mutations at  Wx  and  OsC1 genes 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.

Patterns of nucleotide diversity and phenotypes of two domestication related genes (OsC1 and Wx) in indigenous rice varieties in Northeast India