Work

Integrating genome-wide association study and RNA-seq to identify rhizobium inoculation- responsive genes in mung bean (Vigna radiata)

Year: 2026

Type: preprint

Abstract: Background Mung bean ( Vigna radiata ) is an important leguminous crop capable of establishing nitrogen-fixing symbioses with rhizobia. However, nodulation responses vary significantly among mung bean genotypes, and the genetic determinants underlying this variation remain poorly understood. To address this gap, we integrated phenotypic profiling, genome-wide association study (GWAS), and transcriptome analysis (RNA-seq) to investigate the genetic basis of nodulation and growth-related responses to rhizobial inoculation and identify candidate genes associated with these traits. Results A panel of 218 genetically diverse mung bean genotypes was evaluated under field conditions following rhizobial inoculation across two consecutive growing seasons (2024–2025). Responses of nodulation and major agronomic traits were systematically evaluated at multiple developmental stages. Across the 20 surveyed traits, the number of genotypes exhibiting negative responses to rhizobial inoculation ranged from 39 to 155, while mean response values ranged from − 0.93 to 5.37, indicating substantial genotypic variation in rhizobial responsiveness. GWAS identified 357 significantly associated SNP loci, and 901 candidate genes were annotated within the 50-kb flanking regions of these loci. Transcriptome analysis of the contrasting genotypes LD164 and LD55 identified 561 differentially expressed genes (DEGs). Integration of GWAS and RNA-seq data prioritized 24 candidate genes encoding proteins including pectate lyase, superoxide dismutase, NRT1/PTR family transporters, and MYB transcription factors. Quantitative real-time PCR (qPCR) validation of six selected genes confirmed expression patterns consistent with the RNA-seq results. Conclusion These findings demonstrate substantial phenotypic variation and a complex genetic basis underlying rhizobial responses in mung bean. The identified candidate genes and associated SNP loci provide valuable resources for further functional characterization and may facilitate marker-assisted selection of mung bean varieties with improved symbiotic performance and reduced dependence on synthetic nitrogen fertilizer.

Source: Research Square

DOI: 10.21203/rs.3.rs-10837774/v1

Authors: Mengjiao Li, Qing Yu, Jiawang Wei, Fei Liu, Baolong Xing

Institution: Shanxi Agricultural University

Language: English

Topic: Legume Nitrogen Fixing Symbiosis

Subfield: Plant Science

Field: Agricultural and Biological Sciences

Domain: Life Sciences

SDG: Zero hunger

Open Access status: green

Funder: National Key Research and Development Program of China