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

Abstract

Background: 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.

Results: 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.

Conclusions: 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.

Keywords: Genetic diversity; Indian dwarf wheat; SNP Triticum sphaerococcum; haplotypes; linkage disequilibrium; population structure.

Fig. 1

Distribution of the filtered 11,680 SNP markers in 1 Mb window size intervals. The chromosome-wise distribution of the markers illustrates dense coverage across the entire genome

Fig. 2

Gene diversity and polymorphism information content of the T. sphaerococcum accessions. The chromosome-wise SNP count of the three different subgenomes is represented as bars in three different colors on the primary axis. GD and PIC values are depicted by red and yellow line graphs on the secondary axis, respectively

Fig. 3

Population structure of the 116 T. sphaerococcum accessions: a Evanno’s method was used to determine the most likely number of clusters in the population, identifying K = 4 based on the highest ad-hoc statistic, ΔK, at K = 4. b A bar plot representing the four subpopulations based on the Q-matrix, where columns on the x-axis represent individuals of the population

Fig. 4

Clustering of the 116 T. sphaerococcum accessions into four subpopulations: a Principal Coordinate Analysis (PCoA) separated the subpopulations, indicated by different colors, by plotting the eigenvalues of PCo1 (26.76%) against PCo2 (13.67%). b Neighbor-Joining (NJ) phylogenetic tree constructed based on the genetic distance among individuals, visualized with different colors (Blue: SP1, Red: SP2, Green: SP3, Purple: SP4). Based on the PCoA and NJ tree construction, SP4 was observed to be the most diverse and exhibited the highest amount of subpopulation variation

Fig. 5

Phylogenetic analysis of T. sphaerococcum and T. aestivum accessions. The clade with branches and individuals labeled in red includes the accessions from T. sphaerococcum while those labeled in green comprises of T. aestivum. This partition underscores the genetic differentiation and evolutionary relationship between the two hexaploid wheat species

Fig. 6

Estimation of Linkage Disequilibrium (LD) decay rate for the a A subgenome, b B subgenome, c D subgenome, and d whole genome. The LD decay rate was observed to be the fastest for the D subgenome in the panel of 116 T. sphaerococcum accessions, based on 11,680 markers

Fig. 7

Haplotype block analysis across the genome revealed the highest number of haplotype blocks on chromosome 2D. The average number of SNPs per block, illustrated by a red line graph on the secondary axis, showed that most blocks were defined by only 2 SNPs. The size of the blocks (kb) was determined by the number of SNPs defining them and the physical distance between the SNPs