Integrated GWAS and linkage mapping in a multi-parent population prioritizes candidate genes for kernel number per row in maize
Abstract
Background: Kernel number per row (KNPR) is a key component of maize yield. The molecular mechanisms and favorable allelic variants underlying KNPR variation remain poorly characterized in temperate non-Reid germplasm. This study aimed to improve mapping resolution and prioritize candidate loci associated with KNPR using a multi-parent population.
Results: We established a multi-parent population comprising 530 recombinant inbred lines derived from crosses between the Reid inbred Ye107 and four genetically distinct elite lines. An integrated analytical pipeline combining genome-wide association analysis, linkage QTL mapping, haplotype analysis, protein-structure modeling, and spatiotemporal expression profiling was used to identify KNPR-associated regions and prioritize candidate genes. An exploratory GEBV analysis was conducted separately to describe model-derived genomic-value patterns. Four candidate genes were prioritized as testable hypotheses: ZmNMD3 (ribosomal nuclear export), ZmPAPS1 (mRNA processing), ZmNAC70 (NAC transcription factor), and ZmF-box1 (F-box protein).
Conclusions: Multi-parent populations can facilitate the discovery of allelic variation in temperate non-Reid maize germplasm. The candidate genes and haplotypes prioritized here provide testable hypotheses for future functional validation. Favorable effects confirmed in replicated, multi-environment experiments would justify subsequent evaluation of targeted introgression and multi-gene pyramiding for precision maize breeding.
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BibTeX
@article{luo2026integrated,
title = {{Integrated GWAS and linkage mapping in a multi-parent population prioritizes candidate genes for kernel number per row in maize}},
author = {Yuxiang Luo and Fuyan Jiang and Haoran Lyu and Ranjan K. Shaw and Xingfu Yin and Guohong Wang and Xingming Fan},
journal = {BMC Genomics},
year = {2026},
month = oct,
doi = {10.1186/s12864-026-13436-w},
url = {https://link.springer.com/10.1186/s12864-026-13436-w},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Integrated GWAS and linkage mapping in a multi-parent population prioritizes candidate genes for kernel number per row in maize
AU - Yuxiang Luo
AU - Fuyan Jiang
AU - Haoran Lyu
AU - Ranjan K. Shaw
AU - Xingfu Yin
AU - Guohong Wang
AU - Xingming Fan
PY - 2026
DA - 2026/10/08
JO - BMC Genomics
DO - 10.1186/s12864-026-13436-w
UR - https://link.springer.com/10.1186/s12864-026-13436-w
AB - Background: Kernel number per row (KNPR) is a key component of maize yield. The molecular mechanisms and favorable allelic variants underlying KNPR variation remain poorly characterized in temperate non-Reid germplasm. This study aimed to improve mapping resolution and prioritize candidate loci associated with KNPR using a multi-parent population. Results: We established a multi-parent population comprising 530 recombinant inbred lines derived from crosses between the Reid inbred Ye107 and four genetically distinct elite lines. An integrated analytical pipeline combining genome-wide association analysis, linkage QTL mapping, haplotype analysis, protein-structure modeling, and spatiotemporal expression profiling was used to identify KNPR-associated regions and prioritize candidate genes. An exploratory GEBV analysis was conducted separately to describe model-derived genomic-value patterns. Four candidate genes were prioritized as testable hypotheses: ZmNMD3 (ribosomal nuclear export), ZmPAPS1 (mRNA processing), ZmNAC70 (NAC transcription factor), and ZmF-box1 (F-box protein). Conclusions: Multi-parent populations can facilitate the discovery of allelic variation in temperate non-Reid maize germplasm. The candidate genes and haplotypes prioritized here provide testable hypotheses for future functional validation. Favorable effects confirmed in replicated, multi-environment experiments would justify subsequent evaluation of targeted introgression and multi-gene pyramiding for precision maize breeding.
SN - 1471-2164
ER -