Unraveling the genetic diversity, population structure, and stability for yield-related traits of rice genotypes in mid-hills of northeastern India

Riya Raj; Amit Kumar; Balakrishnan C; Simardeep Kaur; Veerendra Kumar Verma; Mayank Rai; S P Das; Vinay Kumar Mishra

doi:10.1007/s13353-024-00925-5

Unraveling the genetic diversity, population structure, and stability for yield-related traits of rice genotypes in mid-hills of northeastern India

J Appl Genet. 2024 Nov 29. doi: 10.1007/s13353-024-00925-5. Online ahead of print.

Authors

Riya Raj¹, Amit Kumar², Balakrishnan C¹, Simardeep Kaur³, Veerendra Kumar Verma³, Mayank Rai¹, S P Das⁴, Vinay Kumar Mishra³

Affiliations

¹ School of Crop Improvement, College of Post Graduate Studies -Agricultural Sciences, Central Agricultural University, Umiam, Meghalaya, India.
² ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, India. amit4118@gmail.com.
³ ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, India.
⁴ ICAR-National Research Centre for Orchids, Pakyong, Sikkim, India.

PMID: 39609356
DOI: 10.1007/s13353-024-00925-5

Abstract

The cultivation of nearly 10,000 indigenous rice landraces in the North-Eastern Hill (NEH) region by various ethnic groups creates opportunities for the utilization of unique landraces through systematic evaluation of genetic variability. In the present study, a set of 102 rice landraces were assessed based on morphological and SSR markers, and five checks in augmented design vis-à-vis high-yielding rice genotypes with stable performance were identified. The presence of high estimates of heritability, genotypic coefficient of variation, and genetic advance over mean indicated the predominance of additive gene action, which necessitated the effectiveness of selection in augmenting productivity. A total of 83.73% of the total variation was accounted by the first five principal components. A total of 132 alleles were detected, with an average of 3 alleles per locus. The PIC values ranged from 0.01 to 0.70, with an average of 0.40. Based on F_ST value (5.1%), significant differences between the genotypes of Arunachal Pradesh and Sikkim were observed. The percentage of variation among the population, among individuals within the population, and within individuals was 5.14, 75.66, and 19.2%, respectively. Both Nei's genetic distance and model-based clustering have differentiated the genotypes into five distinct clusters. Principal coordinate analysis illustrated that the genotypes of Manipur were scattered in all quadrants, showing that they are highly diverse, while the genotypes of Nagaland, Sikkim, and Meghalaya were found together, which represent the chance of mixing of the population at a certain point in time. Markers, namely RM 474, OSR 13, RM 413, and RM 259, were found to be associated with key traits for increasing yielding ability of plant. In a stability evaluation based on AMMI analysis and multi-trait genotype-ideoptype distance matrix (MGIDI), genotypes, namely Jyotrirmayie, RCPL 1-411, Tsamum firri, Ching Phouren, Rato Bhan Joha, MN-47, and Tara bali, were selected with higher yield potential.

Keywords: Diversity; GGE biplot; MGIDI; Population structure; Rice; SSR markers.