Meta-QTL Analysis and Identification of Candidate Genes Associated with Stalk Lodging in Maize (Zea mays L.)

TL;DR

This study identifies key genetic regions and candidate genes in maize associated with stalk lodging, which can help improve breeding for stronger, more stable crops.

Contribution

The study introduces a meta-QTL analysis approach to identify stable and conserved candidate genes for stalk lodging in maize.

Findings

67 meta-QTLs were identified, with 32 classified as core MQTLs and 67% validated by GWAS.

802 candidate genes were found in core MQTL regions, enriched in cell wall reinforcement pathways.

Transcriptomic evidence supports the role of these genes in lignin biosynthesis and mechanical strength.

Abstract

Stalk lodging constitutes a primary constraint on achieving consistently high yields in maize. Genetic improvement of lodging resistance requires the identification of stable quantitative trait loci (QTL) to facilitate the application of genomics-assisted breeding for improving selection efficiency in breeding programs. In this study, we performed a meta-analysis to identify consensus loci and functionally characterized candidate genes associated with stalk lodging-related traits. Through meta-analysis integrating 889 reported lodging-related QTLs using the IBM2 2008 Neighbors high-density genetic map, we identified 67 meta-QTLs (MQTLs), of which 32 were determined as core MQTLs. Among them, 67% were validated by co-localized marker–trait associations from genome-wide association studies (GWAS). Comparative genomics further revealed 40 evolutionarily conserved orthologs via protein alignment with rice lodging genes, while screening of core MQTL regions detected 802 candidate genes with KEGG enrichment implicating galactose degradation II in cell wall reinforcement, supported by transcriptomic evidence of their roles in lignin biosynthesis pathways modulating mechanical strength. In conclusion, the MQTL identified and validated in our study have significant scope in marker-assisted selection (MAS) breeding and map-based cloning programs for improving maize stalk lodging.

Figures