Identification of quantitative trait loci (QTLs) regulating leaf SPAD value and trichome density in mungbean (Vigna radiata L.) using genotyping-by-sequencing (GBS) approach

Nikki Kumari; Gyan Prakash Mishra; Harsh Kumar Dikshit; Soma Gupta; Anirban Roy; Subodh Kumar Sinha; Dwijesh C Mishra; Shouvik Das; Ranjeet R Kumar; Ramakrishnan Madhavan Nair; Muraleedhar Aski

doi:10.7717/peerj.16722

Identification of quantitative trait loci (QTLs) regulating leaf SPAD value and trichome density in mungbean (Vigna radiata L.) using genotyping-by-sequencing (GBS) approach

PeerJ. 2024 Feb 21:12:e16722. doi: 10.7717/peerj.16722. eCollection 2024.

Affiliations

¹ Genetics, Indian Agricultural Research Institute, New Delhi, Delhi, India.
² Plant Pathology, Indian Agricultural Research Institute, New Delhi, Delhi, India.
³ Biotechnology, National Institute of Plant Biotechnology, New Delhi, Delhi, India.
⁴ Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi, Delhi, India.
⁵ Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, Delhi, India.
⁶ ICRISAT, World Vegetable Center, South Asia, ICRISAT Campus, Patancheru, Hyderabad, India.

^# Contributed equally.

Abstract

Quantitative trait loci (QTL) mapping is used for the precise localization of genomic regions regulating various traits in plants. Two major QTLs regulating Soil Plant Analysis Development (SPAD) value (qSPAD-7-1) and trichome density (qTric-7-2) in mungbean were identified using recombinant inbred line (RIL) populations (PMR-1×Pusa Baisakhi) on chromosome 7. Functional analysis of QTL region identified 35 candidate genes for SPAD value (16 No) and trichome (19 No) traits. The candidate genes regulating trichome density on the dorsal leaf surface of the mungbean include VRADI07G24840, VRADI07G17780, and VRADI07G15650, which encodes for ZFP6, TFs bHLH DNA-binding superfamily protein, and MYB102, respectively. Also, candidate genes having vital roles in chlorophyll biosynthesis are VRADIO7G29860, VRADIO7G29450, and VRADIO7G28520, which encodes for s-adenosyl-L-methionine, FTSHI1 protein, and CRS2-associated factor, respectively. The findings unfolded the opportunity for the development of customized genotypes having high SPAD value and high trichome density having a possible role in yield and mungbean yellow vein mosaic India virus (MYMIV) resistance in mungbean.

Keywords: Candidate genes; Chlorophyll content; Green gram; Marker assisted selection; Trichomes.

MeSH terms

Chromosome Mapping
Genotype
Plant Leaves / genetics
Quantitative Trait Loci* / genetics
Soil
Trichomes / genetics
Vigna* / genetics

Substances

Soil

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 received funding from the long-term strategic donors of 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.