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. 2025 Jul 1;15(1):20795.
doi: 10.1038/s41598-025-99687-1.

QTL mapping for yield contributing traits in mungbean (Vigna radiata L.) using a RIL population

Shashidhar B Reddappa #  1 , Muralidhar S Aski #  1 , Gyan P Mishra  2 , Soma Gupta  1 , Kumbarahally M Shivaprasad  1 , Subodh K Sinha  3 , Ranjeet R Kumar  4 , Anirban Roy  5 , Dwijesh C Mishra  6 , Shouvik Das  7 , Prashant Anupama Mohan Pawar  7 , Ramakrishnan Madhavan Nair  8 , Harsh K Dikshit  9
Affiliations

QTL mapping for yield contributing traits in mungbean (Vigna radiata L.) using a RIL population

Shashidhar B Reddappa et al. Sci Rep. .

Abstract

Mungbean (Vigna radiata L.) is one of the most important yet genomically under-researched leguminous food crop. Its productivity is low due to the complex nature of yield realization, which is regulated by various yield-contributing traits. Thus, understanding the genetic basis of these traits is essential for developing an ideal genotype with high yield. In this study, mapping of quantitative trait loci (QTLs) was conducted for six yield-contributing traits using a recombinant inbred line (RIL) population (166 number), developed by crossing two contrasting genotypes (Pusa Baisakhi × PMR-1). The genotyping-by-sequencing (GBS) of RILs was used to construct the genetic map using 1347 single nucleotide polymorphism (SNPs). The QTL mapping using multiple interval mapping (MIM) and composite interval mapping (CIM) has identified 17 yield contributing QTLs of which, 4 for number of leaves/plant (NL), 3 for plant height (PH), 2 for SPAD value, 3 for 100 seed weight (SW), 2 for number of pods/plant (NP), and 3 for total grain yield (GY). The Logarithm of Odds (LOD) scores for these QTLs ranged from ~ 3-9, while phenotypic variance explained (PVE) ranged from ~ 9-24%. Several candidate genes with mRNA expression and protein-altering mutations were identified as having a direct role in key processes like growth (LOC106756212, LOC106776425, LOC106777991), flowering (LOC106777903, LOC106768860), metabolism (LOC106757749, LOC106758189), etc. The candidate genes are validated through digital gene expression analysis. In addition, Insertion-Deletion (InDel) markers were also developed for the identified QTLs which hold broad applications for the improvement of yield-related traits in mungbean.

Keywords: Candidate genes; Composite interval mapping; Genotyping by sequencing; Multiple interval mapping; Yield traits.

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Conflict of interest statement

Declarations. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Distribution of yield-related traits in the RIL population. (a) Number of leaves; (b) Plant height in cm; (c) SPAD value measured after 25 days of sowing; (d) 100 seed weight in mg; (e) Number of pods; (f) Total yield of three plants in g. Where blue line indicates mean.
Fig. 2
Fig. 2
Composite interval mapping of Yield-related traits in Mungbean. (a) Number of leaves; (b) Plant height; (c) SPAD value; (d) Seed weight; (e) Number of pods; (f) Total grain yield.
Fig. 3
Fig. 3
Effect Plot of important QTLs identified for Yield-related traits in mungbean. Where AA represents PMR-1 and BB represents Pusa Basakhi genotypes.
Fig. 4
Fig. 4
Distribution of QTLs for yield-related traits on chromosomes of mungbean identified using composite interval mapping (CIM).
Fig. 5
Fig. 5
Digital gene expression of plant height candidate genes (a) Inositol-tetrakisphosphate 1-kinase 1-like (LOC106777318) and (b) Abscisic acid receptor PYR1 (LOC106776425).
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