Candidate loci involved in domestication and improvement detected by a published 90K wheat SNP array

Abstract

Selection is one of the most important forces in crop evolution. Common wheat is a major world food crop and a typical allopolyploid with a huge and complex genome. We applied four approaches to detect loci selected in wheat during domestication and improvement. A total of 7,984 candidate loci were detected, accounting for 23.3% of all 34,317 SNPs analysed, a much higher proportion than estimated in previous reports. We constructed a first generation wheat selection map which revealed the following new insights on genome-wide selection: (1) diversifying selection acted by increasing, decreasing or not affecting gene frequencies; (2) the number of loci under selection during domestication was much higher than that during improvement; (3) the contribution to wheat improvement by the D sub-genome was relatively small due to the bottleneck of hexaploidisation and diversity can be expanded by using synthetic wheat and introgression lines; and (4) clustered selection regions occur throughout the wheat genome, including the centromere regions. This study will not only help future wheat breeding and evolutionary studies, but will also accelerate study of other crops, especially polyploids.

A Genome-Wide Association Study of Wheat Spike Related Traits in China

“…In this research, artificial selection signal analysis was conducted in the wheat natural population which contained landraces and cultivars. As the result, a lot of window clusters were detected for the selective sweep candidates that tended to occur in clusters (Gao et al, 2017 ). Fortunately, lots of candidate genes involved in improvement-related agronomic traits such as stress response, seed size, seed number, seed maturation, seed dormancy and flowering time were obtained in the selective sweep regions.…”

“…However, it is blindness, empirical, inefficiency and costs a long time. Fortunately, the hardworking and intelligence of the breeders would have kept signatures in the wheat genome during crop improvement, and this selection signal could be detected using different methods (Gao et al, 2017 ). Identification of selection signal has been reported in many plants, such as soybean (Zhou et al, 2015 ; Wang J. et al, 2016 ), rice (Xu et al, 2012 ), peach (Cao et al, 2016 ), tomato (Lin et al, 2014 ), and wheat (Cao et al, 2016 ).…”

Architecture of parallel adaptation to freshwater in multiple populations of threespine stickleback

“…The high speed of adaptation of threespine stickleback populations to the freshwater environment is made possible by the fact that the freshwater alleles are present at low frequencies in the ancestral marine population (Colosimo et al 2005;Schluter and Conte 2009). Adaptation to such a radically different environment is likely to be genetically complex and to involve many loci, as was shown for other species (Renaut et al 2013;Gao et al 2017). Identifying all loci responsible for a complex adaptation is a difficult task (Hoban et al 2016).…”

Allele mining of TaGRF-2D gene 5’-UTR in Triticum aestivum and Aegilops tauschii genotypes

“…in the wheat polyploid, as a result of the bottleneck effect only a small percentage of the entire variety of genotypes of one or another species participated in the process of wheat polyploidization [21]. The D-subgenome was the last to be included in allohexaploid, thus it is the youngest among all subgenomes, which has the minimum genetic diversity compared to subgenomes A and B due to the bottleneck of polyploidization [22][23][24][25]. It is noted that 1D and 2D chromosomes show the greatest diversity among D-genome chromosomes [26].…”