Sequence Variations Of Maize GBSS Genes And Their Associations With Starch Quality Traits

Maize is a staple crop for more than 900 million people. Maize starch accounts for 80 percent of the production of starch of the world market, and is of important economic value for food and industry application. The content and composition of starch are complex quantitative traits controlled by a lot of genes, offering multiple potential targets for intervention. Researches on relationships between genes related to starch synthesis and starch quality traits in maize kernels can provide guidance for maize breeding and genetic improvement of starch quality. Granule bound starch synthase gene GBSSI and GBSSIIa are members of Granule bound starch synthase （GBSS） gene family, which are involved in the synthesis of amylose in maize kernel. In this study, we re-sequenced the genomic sequences of these two genes in 91 elite inbred lines （80 normal maize inbred lines and 11 waxy maize inbred lines）, and detected sequence variations as well as their associations with starch pasting properties:Peak viscosity （PV）, Trough viscosity （TV）, Final viscosity （FV）, Breakdown （BD）, Setback （SB）, Peak time （PT）, Pasting temperature （PTP）, and with thermal properties:Onset temperature （To）, Peak temperature （Tp）, Conclusion temperature （Tc）, enthalpy （ΔH） and amylose content（AC）. The major results were listed as follows:（1） Sequence polymorphism analysis showed that 100 SNPs （Single nucleotide polymorphisms） and 70 InDels （insertion and deletions） in GBSSI gene were identified among 91 maize inbred lines. Averagely, a SNP variation occurred every 43.68bp and an Indel occurred every 62.4bp, respectively.199 SNPs and 54 InDels in GBSSIIa gene were found among 91 maize inbred lines. On average, a SNP variation occurred every 34.6bp and an Indel occurred every 127.4bp, respectively.（2） The variance analysis results exhibited that significant differences of the starch quality traits have been found among 80 normal maize inbred lines or 11 waxy maize inbred lines. Correlation analysis revealed some correlations between starch thermal properties and pasting properties, and between starch thermal properties and AC. Specifically, ΔH was significantly positively related to TV, FV and SB; PTP was significantly correlated to Tp and Tc; AC was significantly correlated to AH. Additionally, there was no significant correlation between AC and pasting properties whether in normal maize or waxy maize.（3） Based on the results of candidate gene association analysis, two SNPs and two InDels of gene GBSSI were detected to be significantly associated with six starch quality traits, including AC, TV, FV, SB, PTP and ΔH, which explained 8.14%～22.34% of total phenotypic variations. Among them, InDel₃ was significantly associated with AC, FV, SB, PTP and AH, with contribution of 19.71%,17.26%,21.97%,8.14% and 9.69% to phenotypic variations, respectively; InDel₂ was significantly associated with AC with a contribution of 17.49% to phenotypic variations. Besides, four SNPs of gene GBSSIIa were found to be significantly associated with three traits, namely Tc, TV and SB, explaining 4.62%～8.09% of total phenotypic variation. Among them, one nonsynonymous site SNP₉ resulting in amino acid variation （L/M） was significantly associated with Tc with a contribution of 8.09%.