A combination of QTL mapping and genome‑wide association study revealed the key gene for husk number in maize

https://doi.org/10.1007/s00122-024-04617-w

Abstract

Key messageTwo key genesZm00001d021232andZm00001d048138were identifed by QTL mapping and GWAS. Additionally, they were verifed to be signifcantly associated with maize husk number (HN) using gene-based association study.

Abstract   As a by-product of maize production, maize husk is an important industrial raw material. Husk layer number (HN) is an important trait that afects the yield of maize husk. However, the genetic mechanism underlying HN remains unclear. Herein, a total of 13 quantitative trait loci (QTL) controlling HN were identifed in an IBM Syn 10 DH population across diferent locations. Among these, three QTL were individually repeatedly detected in at least two environments. Meanwhile, 26 unique single nucleotide polymorphisms (SNPs) were detected to be signifcantly (p< 2.15 × 1 0–6) associated with HN in an association pool. Of these SNPs, three were simultaneously detected across multiple environments or environments and best linear unbiased prediction (BLUP). We focused on these environment-stable and population-common genetic loci for excavating the candidate genes responsible for maize HN. Finally, 173 initial candidate genes were identifed, of which 22 were involved in both multicellular organism development and single-multicellular organism process and thus confrmed as the candidate genes for HN. Gene-based association analyses revealed that the variants in four genes were signifcantly (p< 0.01/N) correlated with HN, of whichZm00001d021232andZm00001d048138were highly expressed in husks and early developing ears among diferent maize tissues. Our study contributes to the understanding of genetic and molecular mechanisms of maize husk yield and industrial development in the future.