Subgenomic Diversity Patterns Caused by Directional Selection in Bread Wheat Gene Pools

Abstract

Genetic diversity represents the fundamental key to breeding success, providing the basis for breeders to select varieties with constantly improving yield performance. On the other hand, strong selection during domestication and breeding have eliminated considerable genetic diversity in the breeding pools of major crops, causing erosion of genetic potential for adaptation to emerging challenges like climate change. High-throughput genomic technologies can address this dilemma by providing detailed knowledge to characterize and replenish genetic diversity in breeding programs. In hexaploid bread wheat (Triticum aestivum L.), the staple food for 35% of the world's population, bottlenecks during allopolyploidisation followed by strong artificial selection have considerably narrowed diversity to the extent that yields in many regions appear to be unexpectedly stagnating. In this study, we used a 90,000 single nucleotide polymorphism (SNP) wheat genotyping array to assay high-frequency, polymorphic SNP markers in 460 accessions representing different phenological diversity groups from Asian, Australian, European, and North American bread wheat breeding materials. Detailed analysis of subgroup diversity at the chromosome and subgenome scale revealed highly distinct patterns of conserved linkage disequilibrium between different gene pools. The data enable identification of genome regions in most need of rejuvenation with novel diversity and provide a high-resolution molecular basis for genomic-assisted introgression of new variation into chromosome segments surrounding directionally selected metaloci conferring important adaptation and quality traits.

High‐density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool

“…The reasons for this skewed distribution are unclear, for although larger contigs tended to contain more SNPs, this alone is not sufficient to account for the large differences in SNP frequency between the contigs. The complexity of the wheat genome and its large proportion of non-coding sequences is one possible reason for the biased distribution of polymorphic SNPs in the contigs (Gupta et al, 2008;Voss-Fels et al, 2015). Further detailed investigation will be necessary to de-convolute the effects of gene density, polymorphism rate and contig size on SNP density.…”

“…Firstly, we examined the array for SNPs previously identified from a species not used in our original design. For this, we used the SNPs identified by Tiwari et al (2014) from chromosome 5M of Ae. geniculata.…”

“…The high level of sequence polymorphism between hexaploid wheat and its wild relatives makes it difficult to design polymerase chain reaction (PCR) primers for array-based probes. Recently, Tiwari et al (2014) overcame this problem by sequencing flow-sorted wheat chromosomes to identify SNPs on the homoeologous group five chromosomes in a cross between Chinese Spring and Aegilops geniculata. Their work, however, also highlighted the high cost and attrition level of developing large numbers of validated SNP markers.…”

Haplotype hitchhiking promotes trait coselection in Brassica napus

“…New high‐density genome screening tools provide an unprecedented level of insight into local LD patterns in even complex crop genomes (Edwards et al ., ; Voss‐Fels and Snowdon, ). For example, strongly selected haplotype patterns detected in high‐density population genomic studies have been associated with domestication, adaptation and breeding in sorghum (Mace et al ., ), rapeseed (Qian et al ., ) and bread wheat (Voss‐Fels et al ., ), respectively.…”

“…Elucidating the evolutionary relationships among local haplotypes can further improve the detection power of GWAS scans (Buntjer et al ., ). For example, detailed analysis of LD surrounding major QTL revealed strong signatures of artificial selection associated with important traits in different breeding pools of rapeseed and bread wheat (Qian et al ., ; Voss‐Fels and Snowdon, ; Voss‐Fels et al ., ). In such cases, haplotypes reveal the extent to which genetic variation in a given chromosome region is described by clustering markers.…”