GWAS to spot candidate genes associated with grain quality traits in diverse rice accessions of North East India

• Published in: Molecular biology reports Vol. 49; no. 6; pp. 5365 - 5377
• Main Authors: Verma, Rahul K., Chetia, S. K., Sharma, Vinay, Baishya, Samindra, Sharma, Himanshu, Modi, M. K.
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01.06.2022; Springer Nature B.V
• Subjects: Animal Anatomy; Animal Biochemistry; Biomedical and Life Sciences; Breeding; Crop improvement; Genetic variability; Genome-wide association studies; Genomes; Genotypes; Histology; Life Sciences; Morphology; Original Article; Phenotypic variations; Progress in genomics; Quantitative trait loci; Rice; Single-nucleotide polymorphism; transcriptomics and breeding of crops; India; Grain quality traits; Marker-trait associations; Candidate genes; Rice
• ISSN: 0301-4851; 1573-4978
• DOI: 10.1007/s11033-021-07113-2

Introduction North East (NE) India is the second centre for the origin of rice and is enriched with a diverse collection of traditional rice accessions. These genotypes possess unique traits of breeding interest and are rich in grain nutritional and cooking qualities. Therefore, quantitative trait loci (QTLs)/genes associated with the various quality traits may be identified through genome-wide association studies (GWAS) and used in crop improvement programmes. Methods and results A pool of 526 unique rice accessions from Assam, North East (NE) India were characterized by using 9 grain-quality traits and grouped into 16 clusters. Among these, the highest number of 156 (29.65%) genotypes belongs to diverse phenotypic classes; Sali, Lahi, and Chokuwa were grouped into cluster 6. The first three principal components showed 54.76% of morphological variability with Eigenvalue >1. Genome-wide association studies (GWAS) was performed in 103 rice accessions using 42,446 SNP markers. A total of 11 significant marker-trait associations were detected for 5 grain-quality traits, explaining 0.22-8.86% of phenotypic variation (PV). In-silico mining of QTLs detected ‘candidate genes’ associated with the quality traits. Conclusions The phenotypic diversity among the 526 rice accessions of NE India was studied using grain quality traits and grouped into 16 significantly different clusters. The QTLs, or candidate genes identified for various grain quality traits, may be used in breeding programmes for the development of improved rice varieties.