Exploring the genetic diversity and population structure of an ancient hexaploid wheat species Triticum sphaerococcum using SNP markers

• Published in: BMC plant biology 2024-12, Vol.24 (1), p.1188-13
• Main Authors: Mazumder, Amit Kumar, Budhlakoti, Neeraj, Kumar, Manjeet, Pradhan, Anjan Kumar, Kumar, Sundeep, Babu, Prashanth, Yadav, Rajbir, Gaikwad, Kiran B
• Format: Article
• Language: English
• Subjects: Alleles; Biological diversity; Genes; Genetic diversity; Genetic Variation; Genetics, Population; Genomics; Genotype; haplotypes; Indian dwarf wheat; linkage disequilibrium; Plant Breeding; Polymorphism, Single Nucleotide; Polyploidy; population structure; SNP Triticum sphaerococcum; Triticum - genetics
• ISSN: 1471-2229; 1471-2229
• DOI: 10.1186/s12870-024-05968-8

Understanding genetic diversity and population structure is crucial for strategizing and enhancing breeding efficiency. Wheat, a globally cultivated crop, is a significant source of daily calories for humans. To overcome challenges such as extreme climatic fluctuations, stagnant yields, and diminishing genetic variation, it is essential to develop diverse germplasms with new alleles. Triticum sphaerococcum, an underutilized ancient hexaploid wheat species, shows promise for contributing beneficial alleles. However, the genetic diversity of its germplasms remains unstudied. This is the first report where we have examined the genetic diversity and population structure of 116 T. sphaerococcum accessions using a 35 K SNP Array. The objective of this study is to apply these findings to improve wheat breeding programs. Analysis of the population's genetic structure identified four potential subpopulations, which was supported by principal coordinate analysis. Allele neutrality tests showed an abundance of intermediate genotypes, suggesting that many beneficial alleles are maintained through balancing selection. Among the three subgenomes, subgenome B exhibited the highest genetic diversity. AMOVA (Analysis of Molecular Variance) revealed significant variation both among (35%) and within (65%) the four subpopulations. The high genetic differentiation between subpopulations was corroborated by a moderate level of haploid migrant numbers (Nm = 1.286), indicating sufficient gene flow. SP4 emerged as the most diverse subpopulation, showing the highest values for allelic pattern indices due to its larger size and higher percentage of polymorphic loci. The D subgenome displayed a faster linkage disequilibrium (LD) decay rate compared to the A and B subgenomes. Haplotype block analysis identified 260 haplotype blocks of varying sizes distributed across the genome. This research demonstrates that Indian dwarf wheat accessions, sourced from three distinct gene banks and local collections, possess considerable genetic diversity. These germplasm collections offer valuable opportunities to investigate their unexplored genetic potential. They can be utilized in wheat improvement initiatives to tackle both present and future breeding challenges. Furthermore, these accessions can introduce new alleles to broaden the genetic base of modern wheat varieties, enhancing their overall diversity.