The maize starch synthesis ZmSSIIa elongates amylopectin chains from degree of polymerization 6-10 to degree of polymerization 12-25 in the pathway of starch biosynthesis, and plays important roles in kernel yield and quality. The analysis of sequence polymorphism of maize ZmSSIIa gene will provide information for further detection of beneficial mutants associated with yield and quality. In order to reveal the sequence polymorphism of the maize ZmSSIIa gene, a total of 4836 bp sequence of this locus is captured in 86 elite maize inbred lines through a NimbleGensequence capture array. Analysis of the sequence polymorphism reveals that there are 78 SNPs and 19 Indels in this locus. The coding sequences of the maize ZmSSIIa gene contain 24 SNPs, which divide the coding regions into 9 haploytpes, and 7 different ZmSSIIa proteins are encoded by the tested inbred lines. At least 8 recombination events are found to contribute to the haplotype diversity and linkage disequilibrium between polymorphic sites in the maize ZmSSIIa gene. According to the results of the test of neutral evolution, there is no evidence of artificial selection for this gene in the tested inbred lines.

maize  /  ZmSSIIa gene  /  sequence polymorphism  /  haplotype  /  linkage disequilibrium