Identification of Quantitative Trait Loci and Candidate Genes for Maize Starch Granule Size through Association Mapping

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.

Volatilome–Genome-Wide Association Study on Wholemeal Maize Flour

“…Considering the association panel size and looking at the background noise in the obtained Manhattan plots, this threshold of −log 10 ( P -value) = 4 seemed acceptable to prevent missing potentially interesting regions, at the cost of using a more conservative kind of correction such as Bonferroni. Examples of other maize studies with similar association panel sizes and the number of markers using the same threshold are found in the works reported by Liu et al , For the SNPs significantly associated with the 15 volatiles variation [log 10 ( P -value) > 4], the effect of the minor frequency SNP variant, reported when compared to the most frequent allele reference, was also calculated.…”

Supplemental Information 2: Explanation and formulas for the morphological parameters of the starch granules micro images (https://imagej.nih.gov/ij/).

“…Recently, several genome association studies with starch granules size distribution were published for maize (Liu et al, 2018), wheat (Li et al, 2017;Chia et al, 2020) and Japonica rice (Biselli et al, 2019). In the present study, no noticeable SNPs with p-values higher than Bonferroni or FDR levels were found for average values for the "Area", "Feret's diameter", "Minimal Feret's diameter" and "Solidity" traits.…”

Genetic loci determining potato starch yield and granule morphology revealed by genome-wide association study (GWAS)

“…Recently, several genome association studies with starch granules size distribution were published for maize ( Liu et al, 2018 ), wheat ( Li et al, 2017 ; Chia et al, 2020 ) and Japonica rice ( Biselli et al, 2019 ). In the present study, no noticeable SNPs with p -values higher than Bonferroni or FDR levels were found for average values for the “Area”, “Feret’s diameter”, “Minimal Feret’s diameter” and “Solidity” traits.…”