Validating a Major Quantitative Trait Locus and Predicting Candidate Genes Associated With Kernel Width Through QTL Mapping and RNA-Sequencing Technology Using Near-Isogenic Lines in Maize.

Kernel size is an important agronomic trait for grain yield in maize. The purpose of this study was to validate a major quantitative trait locus (QTL), , which was identified in the F and F populations from a cross between the maize inbred lines SG5/SG7 and to predict candidate genes for kernel width (KW) in maize. A major QTL, , was mapped in multiple environments in our previous study. To validate and fine map , near-isogenic lines (NILs) with 469 individuals were developed by continuous backcrossing between SG5 as the donor parent and SG7 as the recurrent parent. Marker-assisted selection was conducted from the BCF generation with simple sequence repeat (SSR) markers near . A secondary linkage map with four markers, PLK12, PLK13, PLK15, and PLK17, was developed and used for mapping the locus. Finally, was mapped between the PLK12 and PLK13 intervals, with a distance of 2.23 cM to PLK12 and 0.04 cM to PLK13, a confidence interval of 5.3 cM and a phenotypic contribution rate of 23.8%. The QTL mapping result obtained was further validated by using selected overlapping recombinant chromosomes on the target segment of maize chromosome 3. Transcriptome analysis showed that a total of 12 out of 45 protein-coding genes differentially expressed between the two parents were detected in the identified physical interval by blasting with the Zea_Mays_B73 v4 genome. GRMZM2G083176 encodes the Niemann-Pick disease type C, and GRMZM2G081719 encodes the nitrate transporter 1 (NRT1) protein. The two genes GRMZM2G083176 and GRMZM2G081719 were predicted to be candidate genes of Reverse transcription-polymerase chain reaction (RT-qPCR) validation was conducted, and the results provide further proof of the two candidate genes most likely responsible for . The work will not only help to understand the genetic mechanisms of KW in maize but also lay a foundation for further cloning of promising loci.