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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 F 2  and its F 2  :  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 F 2  and F 2  :  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 BC 2 F 1  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.

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