Novel candidate genes and genetic basis analysis of kernel starch content in tropical maize.

Background: Starch is the most abundant carbohydrate in maize grains, serving as a primary energy source for both humans and animals, and playing a crucial role in various industrial applications. Increasing the starch content of maize grains is beneficial for improving the grain yield and quality. To gain insight into the genetic basis of starch content in maize kernels, a multiparent population (MPP) was constructed and evaluated for starch content in three different environments.

Results: The integration of QTL mapping and genome-wide association analysis (GWAS) identified two SNPs, 8_166371888 and 8_178656036, which overlapped the QTL interval of qSC8-1, identified in the tropical maize line YML46. The phenotypic variance explained (PVE) by the QTL qSC8-1 was12.17%, while the SNPs 8_166371888 and 8_178656036 explained 10.19% and 5.72% of the phenotypic variance. Combined GWAS and QTL analyses led to the identification of two candidate genes, Zm00001d012005 and Zm00001d012687 located on chromosome 8.

Conclusions: The candidate gene Zm00001d012005 encodes histidine kinase, which is known to play a role in starch accumulation in rice spikes. Related histidine kinases, such as AHK1, are involved in endosperm transfer cell development in barley, which affects grain quality. Zm00001d012687 encodes triacylglycerol lipase, which reduces seed oil content. Since oil content in cereal kernels is negatively correlated with starch content, this gene is likely involved in regulating the starch content in maize kernels. These findings provide insights into the genetic mechanisms underlying kernel starch content and establish a theoretical basis for breeding maize varieties with high starch content.