Combined linkage mapping and association analysis reveal the genetic control of starch content in maize kernel

Starch is a major component of kernel weight that strongly affects maize yield, yet the genetic regulation of starch content in maize kernel is not fully elucidated. Here, we carried out a linkage mapping for starch content using an IBM Syn10 DH population derived from B73 and Mo17, which comprises 222 inbred lines with 6618 bin markers, evaluated across four environments. A total of 13 quantitative trait loci were detected, among which five were simultaneously identified across multiple environments. By integrating the gene-based association analyses, we identified the candidate gene Zm00001d039265 that encodes β-amylase 4, a potential modulator underlying leaf starch degradation. Gene-based association analysis was performed using a natural panel including 285 germplasms collected from the breeding program of Southwest China. The variant SNP-3-826178 residing in 3'-UTR of Zm00001d039265 was significantly associated with kernel starch content, which categorized these germplasms into two genotypes (high starch content: allele C; low starch content: allele T). We further validated this allelic effect in an independent recombinant inbred line population containing 248 inbred lines derived from A188 and B73, confirming that lines carrying the C allele possessed significantly higher kernel starch accumulation than those harboring the T allele. Finally, we developed a derived cleaved amplified polymorphic sequence marker targeting SNP-3-826178, which was able to distinguish T allele and C allele among the inbred lines with different backgrounds. Our findings deepen the understanding of the genetic basis governing maize kernel starch formation and provide an available molecular marker for identifying germplasms with high starch content in maize breeding.Key Message Gene Zm00001d039265 underlying starch content was excavated by linkage mapping and gene-based association analysis. According to the SNP-3-826178 within Zm00001d039265, a dCAPS marker was successfully developed.