Validating a Major Quantitative Trait Locus and Predicting Candidate Genes Associated With Kernel Width Through QTL...

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), qKW-1, which was identified in the F₂ and F_2:3 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, qKW-1, was mapped in multiple environments in our previous study. To validate and fine map qKW-1, 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 BC₂F₁ generation with simple sequence repeat (SSR) markers near qKW-1. A secondary linkage map with four markers, PLK12, PLK13, PLK15, and PLK17, was developed and used for mapping the qKW-1 locus. Finally, qKW-1 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 qKW-1 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 qKW-1. 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 qKW-1. 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.