High‐density genotyping of the A.E. Watkins Collection of hexaploid landraces identifies a large molecular diversity compared to elite bread wheat

Abstract

SummaryThe importance of wheat as a food crop makes it a major target for agricultural improvements. As one of the most widely grown cereal grains, together with maize and rice, wheat is the leading provider of calories in the global diet, constituting 29% of global cereal production in 2015. In the last few decades, however, yields have plateaued, suggesting that the green revolution, at least for wheat, might have run its course and that new sources of genetic variation are urgently required. The overall aim of our work was to identify novel variation that may then be used to enable the breeding process. As landraces are a potential source of such diversity, here we have characterized the A.E. Watkins Collection alongside a collection of elite accessions using two complementary high‐density and high‐throughput genotyping platforms. While our results show the importance of using the appropriate SNP collection to compare diverse accessions, they also show that the Watkins Collection contains a substantial amount of novel genetic diversity which has either not been captured in current breeding programmes or which has been lost through previous selection pressures. As a consequence of our analysis, we have identified a number of accessions which carry an array of novel alleles along with a number of interesting chromosome rearrangements which confirm the variable nature of the wheat genome.

Hidden variation in polyploid wheat drives local adaptation

“…The Watkins collection clusters into two main ancestral groups; cluster 1 with 80 accessions (73.8% derived from Europe, Middle Eastern and South Mediterranean/African regions) while cluster 2 has 24 samples (87.5% mainly Asian) (Supplementary Table 4). This genotype-based population structure resembles that from previous analyses of the Watkins collection using array SNP data 15,19 (see Supplementary note 2).…”

“…Table 4). This genotype-based population structure resembles that from previous analyses of the Watkins collection using array SNP data 15,19 (see Supplementary note 2). Table 7).…”

Ancient wheat varieties have a higher ability to interact with plant growth‐promoting rhizobacteria

“…Our results suggest that the search for high‐yield wheat cultivars under agronomically optimized conditions, which caused genetic diversity loss (Bonnin, Bonneuil, Goffaux, Montalent, & Goldringer, ; Roussel, Leisova, Exbrayat, Stehno, & Balfourier, ; Winfield et al, ), did not favor the maintenance of plant genes promoting PGPR interactions. Modern genotypes are mostly dwarf or semidwarf varieties because of the introduction of dwarfism Rht‐B1b and Rht‐D1b alleles in the 1960s, by International Maize and Wheat Improvement Center in Mexico and thereafter during wheat breeding programs in other parts of the world (Borlaug, ; Lumpkin, ; Subira et al, ).…”

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

“…This is because inter‐breeding can occur between wild tetraploid emmer (AABB) and hexaploid wheat, whereas diploid goat grass (DD) and species of higher ploidy levels (such as tetraploid and hexaploid wheat) are reproductively isolated (Dvorak et al ., ; Sutherland and Galloway, ; Figure ). This reduced diversity in modern wheat argues strongly for the use of induced and natural variation to provide novel genetic variation, which has been hitherto unexplored in modern breeding programmes (Winfield et al ., ).…”