Abstract
Starch is an important nutrient component of maize kernels, and starch granule size largely determines kernel waxiness, viscosity, and other physiochemical and processing properties. To explore the genetic basis of maize starch granule size, 266 tropical, subtropical, and temperate inbred lines were subjected to genome-wide association analyses with an array of 56,110 random single nucleotide polymorphisms (SNPs). In the present panel, the kernel starch granule size ranged from 7–15.8 µm long and 6.8–14.3 µm wide. Fourteen significant SNPs were identified as being associated with the length of starch granules and 9 with their width. One linkage disequilibrium block flanking both sides of a significant SNP was defined as a quantitative trait locus (QTL) interval, and seven QTLs were mapped for both granule length and width. A total of 79 and 88 candidate genes associated with starch length and width, respectively, were identified as being distributed on QTL genomic regions. Among these candidate genes, six with high scores were predicted to be associated with maize starch granule size. A candidate gene association analysis identified significant SNPs within genes GRMZM2G419655 and GRMZM2G511067, which could be used as functional markers in screening starch granule size for different commercial uses.
Highlights
The size of the starch granules, which depends on the plant species, is an important factors affecting starch characteristics[16] and determines the industrial application[17]
Genome-wide association studies (GWASs) have been proven to be useful tools for the identification of candidate loci associated with traits in animal and plant species[29]
An analysis of maize oil biosynthesis identified 74 loci significantly associated with kernel oil concentration and fatty acid composition in a genome-wide association studies (GWASs) using 1 million single nucleotide polymorphisms (SNPs) characterised in 368 inbred maize lines[30]
Summary
The size of the starch granules, which depends on the plant species, is an important factors affecting starch characteristics[16] and determines the industrial application[17]. The starch granule size may influence gelatinisation temperature[20], viscosity[19], and enzymatic susceptibility[21,22,23]. It determines the grain milling yield in hard wheat[24]. Quantitative trait loci (QTLs) of starch granule sizes in Triticeae crops have been identified, including a major QTL related to the A:B ratio of wheat starch granules on chromosome 4S27 and a QTL on barley chromosome 228. We used a set of associated populations to identify significant SNP markers for starch granule size with the aim of predicting associated candidate genes
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