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Fine mapping qKRN5.04 provides a functional gene negatively regulating maize kernel row number.

Yixin An1, Lin Chen1, Yong-Xiang Li1

  • 1Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik
|April 7, 2022
PubMed
Summary

Researchers identified Zm00001d016075 as a key gene regulating maize kernel row number (KRN). A promoter insertion, InDel308, can serve as a molecular marker for KRN in maize breeding.

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Area of Science:

  • Plant Genetics
  • Maize Breeding
  • Quantitative Trait Loci (QTL) Analysis

Background:

  • Kernel row number (KRN) is a crucial trait in maize (Zea Mays L.) production and domestication, influenced by multiple quantitative trait loci (QTLs).
  • Understanding the genetic basis of KRN variation is essential for improving maize yield and crop development.

Purpose of the Study:

  • To fine-map and identify the gene responsible for the major QTL qKRN5.04 controlling kernel row number in maize.
  • To elucidate the function of the identified gene in regulating KRN and other yield-related traits.

Main Methods:

  • Fine mapping of the qKRN5.04 QTL to a 65-kb region using an advanced backcross population.
  • Regional association mapping in a diverse panel of 236 maize inbred lines.
  • CRISPR-Cas9 gene editing to verify gene function and sequence analysis of promoter variations.

Main Results:

  • The gene Zm00001d016075 was fine-mapped to the qKRN5.04 region and identified as the sole candidate gene.
  • Association mapping revealed significant single nucleotide polymorphisms (SNPs) within Zm00001d016075, correlating with KRN variation.
  • Zm00001d016075 expression was higher in lines with more kernel rows, linked to promoter activity differences.
  • The promoter insertion InDel308 was associated with KRN variation across different maize lines.
  • CRISPR-Cas9 confirmed Zm00001d016075 negatively regulates KRN and moderately affects other yield components.

Conclusions:

  • Zm00001d016075 is a key gene negatively regulating maize kernel row number (KRN).
  • The promoter insertion InDel308 is a potential molecular marker for identifying KRN in maize breeding programs.
  • These findings provide critical insights into the genetic basis of KRN variation and offer targets for maize improvement.