Population structure and genetic diversity characterization of soybean for seed longevity

Abstract

Seed longevity is an important trait in the context of germplasm conservation and economics of seed production. The identification of populations with high level of genetic variability for seed longevity and associated traits will become a valuable resource for superior alleles for seed longevity. In this study, Genotyping-by-sequencing (GBS)-single nucleotide polymorphism (SNP) approach, simple sequence repeats (SSR) markers and agro-morphological traits have been explored to investigate the diversity and population structure of assembled 96 genotypes. The GBS technique performed on 96 genotypes of soybean (Glycine max (L.) Merrill) resulted in 37,897 SNPs on sequences aligned to the reference genome sequence. The average genome coverage was 6.81X with a mapping rate of 99.56% covering the entire genome. Totally, 29,955 high quality SNPs were identified after stringent filtering and most of them were detected in non-coding regions. The 96 genotypes were phenotyped for eight quantitative and ten qualitative traits by growing in field by following augmented design. The STRUCTURE (Bayesian-model based algorithm), UPGMA (Un-weighed Pair Group Method with Arithmetic mean) and principal component analysis (PCA) approaches using SSR, SNP as well as quantitative and qualitative traits revealed population structure and diversity in assembled population. The Bayesian-model based STRUCTURE using SNP markers could effectively identify clusters with higher seed longevity associated with seed coat colour and size which were subsequently validated by UPGMA and PCA based on SSR and agro-morphological traits. The results of STRUCTURE, PCA and UPGMA cluster analysis showed high degree of similarity and provided complementary data that helped to identify genotypes with higher longevity. Six black colour genotypes, viz., Local black soybean, Kalitur, ACC Nos. 39, 109, 101 and 37 showed higher seed longevity during accelerated ageing. Higher coefficient of variability observed for plant height, number of pods per plant, seed yield per plant, 100 seed weight and seed longevity confirms the diversity in assembled population and its suitability for quantitative trait loci (QTL) mapping.

Insights into mechanisms of seed longevity in soybean: a review

“…The molecular and morphological distance-based grouping and model-based structuring of 96 soybean genotypes grouped six black seed coat colour genotypes viz., local black soybean, Kalitur, ACC Nos. 39, 109, 101 and 37 with high seed longevity and seed size into one cluster (Naflath et al, 2022).…”

Population Structure and Genetic Diversity of the 175 Soybean Breeding Lines and Varieties Cultivated in West Siberia and Other Regions of Russia

“…[2][3][4]. Varieties of this species have already been studied [5][6][7][8], while comparative population information about the Russian cultivars has remained unexplored. Russian cultivars widely vary in origin and genetic diversity due to geographical and climatic conditions in different parts of the country from the Far East, Western Siberia, and Ural to the Volga, Southern, and Central (Chernozem) regions [9].…”

“…There are many examples of studies on soybean population genetics [5,[10][11][12][13][14][15][16][17], wholegenome SNP arrays [7][8][9][10], or whole genomic data [11]. These studies uncover comprehensive information about the origin, relatedness between different varieties, genetic differentiation, diversity, and evolutionary forces acting on their genomes.…”

Aluminium Application and Rhizobia Inoculation Effects on Growth, Yield and Nutrients Uptake of Three Kenyan Soy Bean Genotypes

“…In particular areas where soy bean has not been grown before (Aftab et al, 2010), there is no success in nodulation therefore low seed yield especially if not inoculated. The bacteria is able to fix up to 300 kg/ha atmospheric nitrogen that lead to increased grain and biomass yield [9]. It can therefore alleviate low biomass and low grain production of soy bean plants in acidic soils caused by Al.…”