Genomic analysis of Spanish wheat landraces reveals their variability and potential for breeding

Abstract

Background: One of the main goals of the plant breeding in the twenty-first century is the development of crop cultivars that can maintain current yields in unfavorable environments. Landraces that have been grown under varying local conditions include genetic diversity that will be essential to achieve this objective. The Center of Plant Genetic Resources of the Spanish Institute for Agriculture Research maintains a broad collection of wheat landraces. These accessions, which are locally adapted to diverse eco-climatic conditions, represent highly valuable materials for breeding. However, their efficient use requires an exhaustive genetic characterization. The overall aim of this study was to assess the diversity and population structure of a selected set of 380 Spanish landraces and 52 reference varieties of bread and durum wheat by high-throughput genotyping.

Results: The DArTseq GBS approach generated 10 K SNPs and 40 K high-quality DArT markers, which were located against the currently available bread and durum wheat reference genomes. The markers with known locations were distributed across all chromosomes with relatively well-balanced genome-wide coverage. The genetic analysis showed that the Spanish wheat landraces were clustered in different groups, thus representing genetic pools providing a range of allelic variation. The subspecies had a major impact on the population structure of the durum wheat landraces, with three distinct clusters that corresponded to subsp. durum, turgidum and dicoccon being identified. The population structure of bread wheat landraces was mainly biased by geographic origin.

Conclusions: The results showed broader genetic diversity in the landraces compared to a reference set that included commercial varieties, and higher divergence between the landraces and the reference set in durum wheat than in bread wheat. The analyses revealed genomic regions whose patterns of variation were markedly different in the landraces and reference varieties, indicating loci that have been under selection during crop improvement, which could help to target breeding efforts. The results obtained from this work will provide a basis for future genome-wide association studies.

Keywords: DArTseq markers; GBS; Genetic diversity; Local germplasm; Population structure; SNP; Wheat improvement.

Fig. 1

Marker density along chromosome 2A. a T. turgidum raw (blue) and filtered (red) SNP markers. b T. turgidum raw (blue) and filtered (red) DArT markers. c Filtered SNPs in T. turgidum (purple) and T. aestivum (yellow)

Fig. 2

Average PIC distribution in filtered markers. a T. turgidum DArTs. b T. aestivum DArTs. c T. turgidum SNPs. d T. aestivum SNPs

Fig. 3

a T. turgidum STRUCTURE plot based on DArT markers. The number below the Pop indicates the number of accessions clustered in each population. b Collection sites of the different T. turgidum accessions, colored according to their STRUCTURE population assignment. When GPS coordinate data were not available, the coordinates of the capital of the province of origin were used. T. turgidum subsp. durum landraces are shown with circles, subsp. dicoccon with squares and subsp. turgidum with triangles

Fig. 4

Cluster analysis of T. turgidum accessions using PCoA. Accessions from subsp. durum are shown with circles, subsp. dicoccon with squares, subsp. turgidum with triangles and the reference varieties with asterisks. a Graphical representation of PCo1 and PCo2 for the whole collection of durum wheat. Accessions are colored according to their Vrn-A1 alleles. b Graphical representation of PCo1 and PCo2 for subsp. durum accessions, which are colored according to their STRUCTURE population assignment

Fig. 5

a T. aestivum STRUCTURE plot based on DArT markers. The number below the Pop indicates the number of accessions clustered in each population. b Collection sites of the different T. aestivum accessions, colored by their STRUCTURE population assignment. When GPS coordinate data were not available, the coordinate of the capital of the province of origin were used

Fig. 6

Cluster analysis of T. aestivum accessions using PCoA. Accessions from STRUCTURE Pop1 are shown with circles, Pop2 with triangles, Pop3 with squares, Pop 4 with rhombi, and the reference varieties with asterisks. a Graphical representation of PCo1 and PCo2 for the whole collection of bread wheat. Accessions are colored according to their Vrn-A1 allele. b Accessions are colored according to their Glu-B1 allele

Fig. 7

Genetic diversity (Hs) distribution across the genome in the reference varieties and landraces. a T. durum. b T. aestivum. Fixed regions in the reference materials are indicated by red bars. The position of ten key genes in the genome is indicated