Genetic analysis and ecological association of Hina genes based on single nucleotide polymorphisms (SNPs) in wild barley, Hordeum spontaneum
Article first published online: 12 JAN 2010
© 2009 The Authors
Volume 147, Issue 1, pages 18–26, February 2010
How to Cite
Li, W.-T., Huang, X., Wang, J.-R., Chen, G.-Y., Nevo, E., Zheng, Y.-L. and Wei, Y.-M. (2010), Genetic analysis and ecological association of Hina genes based on single nucleotide polymorphisms (SNPs) in wild barley, Hordeum spontaneum. Hereditas, 147: 18–26. doi: 10.1111/j.1601-5223.2009.2151.x
- Issue published online: 29 MAR 2010
- Article first published online: 12 JAN 2010
- Paper received 22 September 2009. manuscript accepted 27 October 2009.
Specific primers were designed to amplify the sequences of Hina genes from 121 wild barley (Hordeum spontaneum) accessions belonging to 18 populations from Iran, Israel and Turkey. Forty-nine single nucleotide polymorphisms (SNPs), nine indels, and 26 haplotypes were determined by sequence analysis. The genetic polymorphism (P), genetic diversity (He), and Shannon's information index (I) in the 18 populations were 0.486, 0.181 and 0.269, respectively. Approximately 2/3 genetic variations of Hina genes were presented within populations, while approximately 1/3 genetic variations were observed between populations. Broad gene flow (Nm= 3.31) and low genetic variation (Gst= 0.0702) were detected. However, the genetic differentiation between populations was independent of geographical distances according to the Mantel test (p = 0.478). The result of Spearman rank correlations (rs) showed that the genetic indices (P, He and I) of Hina were not significantly correlated with ecological factors. Only eight SNP positions correlated significantly with ecological factors. Of the eight SNP positions that positively correlated with ecological factors, only one SNP (769, T-C) was located in the coding region; however, it was not responsible for the amino acid change.