Zinc Finger Protein 30 Is a Novel Candidate Gene for Kernel Row Number in Maize

TL;DR

This study identifies a new gene, Zm00001eb205550, that influences kernel row number in maize, which is important for increasing crop yield.

Contribution

The study discovers Zm00001eb205550 as a novel candidate gene for kernel row number in maize through QTL mapping and transcriptome analysis.

Findings

A major-effect QTL (qKRN4.09-1) was consistently identified across three environments and BLUP.

The gene Zm00001eb205550 is significantly downregulated in qKRN4.09-1BMY and shows missense variants between BMY and B73.

Pyramiding favorable alleles from five stable QTLs significantly increased kernel row number in maize.

Abstract

Kernel row number (KRN) is a pivotal determinant for yield in maize breeding programs. However, the genetic basis underlying KRN remains largely elusive. To identify candidate genes regulating KRN, a population of 318 BC4F4 chromosomal segment substitution lines (CSSLs) was developed via backcrossing, with Baimaya (BMY) as the donor parent and B73 as the recurrent parent. Furthermore, a high-density genetic linkage map containing 2859 high-quality single-nucleotide polymorphism (SNP) markers was constructed for quantitative trait locus (QTL) mapping of KRN. Notably, 19 QTLs controlling KRN were detected across three environments and in the Best Linear Unbiased Prediction (BLUP) values; among these, a major-effect QTL (qKRN4.09-1) was consistently identified across all three environments and BLUP. Then, the integration of linkage mapping and transcriptome analysis of 5 mm immature ears from near-isogenic lines (NILs) uncovered a candidate gene, Zm00001eb205550. This gene exhibited significant downregulation in qKRN4.09-1BMY, and two missense variants were detected between qKRN4.09-1BMY and qKRN4.09-1B73. Zm00001eb205550 exhibited preferential expression in developing ears. Moreover, the pyramiding of favorable alleles from the five stable QTLs significantly increased KRN in maize. These findings advance our genetic understanding of maize ear development and provide valuable genetic targets for improving KRN in maize breeding.

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