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As an important component, 1,000 kernel weight (TKW) plays a significant role in the formation of yield traits of wheat. Kernel size is significantly positively correlated to TKW. Although numerous loci for kernel size in wheat have been reported, our knowledge on loci for kernel area (KA) and kernel circumference (KC) remains limited. In the present study, a recombinant inbred lines (RIL) population containing 371 lines genotyped using the Wheat55K SNP array was used to map quantitative trait loci (QTLs) controlling the KA and KC in multiple environments. A total of 54 and 44 QTLs were mapped by using the biparental population or multienvironment trial module of the inclusive composite interval mapping method, respectively. Twenty-two QTLs were considered major QTLs. BLAST analysis showed that major and stable QTLs  QKc.sau-6A.1  (23.12–31.64 cM on 6A) for KC and  QKa.sau-6A.2  (66.00–66.57 cM on 6A) for KA were likely novel QTLs, which explained 22.25 and 20.34% of the phenotypic variation on average in the 3 year experiments, respectively. Two Kompetitive allele-specific PCR (KASP) markers,  KASP-AX-109894590  and  KASP-AX-109380327 , were developed and tightly linked to  QKc.sau-6A.1  and  QKa.sau-6A.2 , respectively, and the genetic effects of the different genotypes in the RIL population were successfully confirmed. Furthermore, in the interval where  QKa.sau-6A.2  was located on Chinese Spring and  T. Turgidum  ssp.  dicoccoides  reference genomes, only 11 genes were found. In addition, digenic epistatic QTLs also showed a significant influence on KC and KA. Altogether, the results revealed the genetic basis of KA and KC and will be useful for the marker-assisted selection of lines with different kernel sizes, laying the foundation for the fine mapping and cloning of the gene(s) underlying the stable QTLs detected in this study.

QTL Mapping and Validation for Kernel Area and Circumference in Common Wheat via High-Density SNP-Based Genotyping