QTL Analysis and Fine Mapping of a Major QTL Conferring Kernel Size in Maize (Zea mays)

Kernel size is an important agronomic trait for grain yield in maize. The purpose of this study is to map QTLs and predict candidate genes for kernel size in maize. A total of 199 F2 and its F2:3 lines from the cross between SG5/SG7 were developed. A composite interval mapping (CIM) method was used to detect QTLs in three environments of F2 and F2:3 populations. The result showed that a total of 10 QTLs for kernel size were detected, among which were five QTLs for kernel length (KL) and five QTLs for kernel width (KW). Two stable QTLs, qKW-1, and qKL-2, were mapped in all three environments. Three QTLs, qKL-1, qKW-1, and qKW-2, were overlapped with the QTLs identified from previous studies. In order to validate and fine map qKL-2, near-isogenic lines (NILs) were developed by continuous backcrossing between SG5 as the donor parent and SG7 as the recurrent parent. Marker-assisted selection was conducted from BC2F1 generation with molecular markers near qKL-2. A secondary linkage map with six markers around the qKL-2 region was developed and used for fine mapping of qKL-2. Finally, qKL-2 was confirmed in a 1.95 Mb physical interval with selected overlapping recombinant chromosomes on maize chromosome 9 by blasting with the Zea_Mays_B73 v4 genome. Transcriptome analysis showed that a total of 11 out of 40 protein-coding genes differently expressed between the two parents were detected in the identified qKL-2 interval. GRMZM2G006080 encoding a receptor-like protein kinase FERONIA, was predicted as a candidate gene to control kernel size. The work will not only help to understand the genetic mechanisms of kernel size of maize but also lay a foundation for further fine mapping and even cloning of the promising loci.