SNP Analysis and Haplotype Identification in Chymotrypsin Inhibitor-2 (CI-2) Gene of Barley

Barley chymotrypsin inhibitor-2 (CI-2) was considered to be a promising candidate for enhancing the nutritional value of other cereals by increasing its concentration as it is rich in lysine than any other storage protein. Also, it was proposed that CI-2 might play an important role in the inhibition of proteolytic enzymes from pests or pathogens as CI-2 can strongly inhibit chymotrypsin and subtilisin. In this study, a total of 93 CI-2 gene sequences were isolated from wild and cultivated barley. 48 SNPs and 4 indels were detected across the entire sequences. The frequency of SNPs in the non- coding region (1 out of 9 bases) was slightly higher than that in the coding region (1 out of 10.7 bases). In all, 33.3% of the candidate cSNPs resulted in amino acid changes. As a total, the 24 cSNPs resulted in 15 amino acid changes. Ten distinguishable haplotypes were detected, among which 3 haplotypes were shared in the most barley accessions, whereas the rest of the haplotypes appeared at a lower frequency. In addition, three haplotypes (haplotype 4, 8, and 9) were unique for single accessions. These results suggested that low diversity at the CI-2 locus was detected among the cultivated and wild barley.