Genome-wide association studies for earliness, MYMIV resistance, and other associated traits in mungbean (Vigna radiata L. Wilczek) using genotyping by sequencing approach

Manju Kohli; Hina Bansal; Gyan Prakash Mishra; Harsh Kumar Dikshit; Shashidhar B Reddappa; Anirban Roy; Subodh Kumar Sinha; K M Shivaprasad; Nikki Kumari; Atul Kumar; Ranjeet R Kumar; Ramakrishnan Madhavan Nair; Muraleedhar Aski

doi:10.7717/peerj.16653

Genome-wide association studies for earliness, MYMIV resistance, and other associated traits in mungbean (Vigna radiata L. Wilczek) using genotyping by sequencing approach

PeerJ. 2024 Jan 26:12:e16653. doi: 10.7717/peerj.16653. eCollection 2024.

Authors

Affiliations

¹ Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India.
² Genetics, Indian Agricultural Research Institute, Delhi, Delhi, India.
³ Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, Delhi, India.
⁴ Biotechnology, National Institute of Plant Biotechnology, New Delhi, Delhi, India.
⁵ Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi, Delhi, India.
⁶ Biochemistry, Indian Agricultural Research Institute, New Delhi, Delhi, India.
⁷ World Vegetable Center, South Asia, ICRISAT Campus, Patancheru, Hyderabad, Andhra Pradesh, India.

^# Contributed equally.

Abstract

Yellow mosaic disease (YMD) remains a major constraint in mungbean (Vigna radiata (L.)) production; while short-duration genotypes offer multiple crop cycles per year and help in escaping terminal heat stress, especially during summer cultivation. A comprehensive genotyping by sequencing (GBS)-based genome-wide association studies (GWAS) analysis was conducted using 132 diverse mungbean genotypes for traits like flowering time, YMD resistance, soil plant analysis development (SPAD) value, trichome density, and leaf area. The frequency distribution revealed a wide range of values for all the traits. GBS studies identified 31,953 high-quality single nucleotide polymorphism (SNPs) across all 11 mungbean chromosomes and were used for GWAS. Structure analysis revealed the presence of two genetically distinct populations based on ΔK. The linkage disequilibrium (LD) varied throughout the chromosomes and at r² = 0.2, the mean LD decay was estimated as 39.59 kb. Two statistical models, mixed linear model (MLM) and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) identified 44 shared SNPs linked with various candidate genes. Notable candidate genes identified include FPA for flowering time (VRADI10G01470; chr. 10), TIR-NBS-LRR for mungbean yellow mosaic India virus (MYMIV) resistance (VRADI09G06940; chr. 9), E3 ubiquitin-protein ligase RIE1 for SPAD value (VRADI07G28100; chr. 11), WRKY family transcription factor for leaf area (VRADI03G06560; chr. 3), and LOB domain-containing protein 21 for trichomes (VRADI06G04290; chr. 6). In-silico validation of candidate genes was done through digital gene expression analysis using Arabidopsis orthologous (compared with Vigna radiata genome). The findings provided valuable insight for marker-assisted breeding aiming for the development of YMD-resistant and early-maturing mungbean varieties.

Keywords: Earliness; Flowering; GWAS; MYMIV; Mungbean; YMD.

MeSH terms

Bayes Theorem
Genome-Wide Association Study
Genotype
Plant Breeding
Vigna* / genetics

Grants and funding

This research was funded by the Indian Council of Agricultural Research (ICAR), New Delhi, and SERB (Science and Engineering Research Board), New Delhi (CRG/2019/002024). Ramakrishnan M. Nair was supported by long-term strategic donors to the World Vegetable Center: Taiwan, the United States Agency for International Development (USAID), the UK Government’s Foreign, Commonwealth & Development Office (FCDO), the Australian Centre for International Agricultural Research (ACIAR), Germany, Thailand, Philippines, Korea, Japan, and funding from the ACIAR Project on International Mungbean Improvement Network (CROP/2019/144). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.