Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

Abstract

Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseq^TM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs.

Fig. 1. Diversity analysis of domesticated hexaploid accessions.

a Multidimensional scaling plot visualized in Curlywhirly of 56,342 domesticated hexaploid accession with 66,067 SNP markers differentiated by biological status based on passport information (elite, landraces, cultivar, synthetic, etc.); b ADMIXTURE ancestry coefficients (k = 6, 12) for a subset of 45,000 samples and dendogram of k = 12; c the 56,342 hexaploids distributed in 12 clusters based on MRD and clustering analysis. The axes X, Y, and Z correspond to first, second, and third dimensions in MDS.

Fig. 2. Diversity analysis of domesticated tetraploid accessions.

a Multidimensional scaling plot visualized in Curlywhirly of 18,946 domesticated tetraploid accessions with 30,806 SNP markers differentiated by biological status based on passport information; b ADMIXTURE ancestry coefficients (k = 7) and its dendrogram; c tetraploids distributed in seven clusters based on MRD.

Fig. 3. Diversity analysis of CWR accessions.

a Multidimensional scaling plot visualized in Curlywhirly of 3903 CWR accessions based on Jaccard distance using 61,505 SilicoDArT markers, including the 27 wild relative species; b CWR distributed in 30 clusters; c Representation of the distribution of 30 groups based on cluster analysis. The graph should be interpreted from left to right. The size of the boxes is proportional to the number of accessions. On the right edge are the numbers of the clusters, species name, and the genome constitution (bold) for each species.

Fig. 4. Analysis of F_ST values on a variant per variant basis across the genome highlights areas of positive selection.

a F_ST analysis of the complete chromosome 3A in cluster 2 (upper half) and 4 (lower half of figures); b zoom in of chromosome 3A positioning of the preharvest sprouting gene TaMFT.

Fig. 5. Genome-wide association analysis for wheat quality characters was performed using an iterative usage of fixed and random model circulating probability implemented by R software with correction of kinship, including the first three PCA values as fixed effects.

The test was adjusted for multiple comparison in terms of P-value cutoff determination and FDR calculation. a The 18 genomic regions were associated with GPC on 12 chromosomes, with the highest peaks on 4A and 4B, followed by 5A, 5B, 7A, and 7B. b The 19 genomic regions associated with SDS on four chromosomes, 1A, 1B, and 1D, previously reported, and a QTL on 2A.