Comparative Population Genomics of Bread Wheat(Triticum aestivum)Reveals Its Cultivation and Breeding History in China

Abstract

22The evolution of bread wheat (Triticum aestivum) is distinctive in that 23 domestication, natural hybridization, and allopolyploid speciation have all had 24 significant effects on the diversification of its genome. Wheat was spread around 25 the world by humans and has been cultivated in China for ~4,600 years. Here, 26we report a comprehensive assessment of the evolution of wheat based on the 27 genome-wide resequencing of 120 representative landraces and elite wheat 28 accessions from China and other representative regions. We found substantially 29 higher genetic diversity in the A and B subgenomes than in the D subgenome. 30 Notably, the A and B subgenomes of the modern Chinese elite cultivars were 31 mainly derived from European landraces, while Chinese landraces had a greater 32 contribution to their D subgenomes. The duplicated copies of homoeologous 33 genes from the A, B, and D subgenomes were commonly found to be under 34 different levels of selection. Our genome-wide assessment of the genetic changes 35 associated with wheat breeding in China provides new strategies and practical 36 targets for future breeding. 37 38 Main 39 Bread wheat (Triticum aestivum) differs from other major grain crops, such as maize 40 (Zea mays), rice (Oryza sativa), and barley (Hordeum vulgare), by having an 41 allohexaploid genome with six sets of chromosomes, two sets each from three closely 42 related ancestral species that formed the A, B, and D subgenomes. Archaeological and 43 genetic evidence indicated that wheat underwent two polyploidization events during 44 its domestication. The first occurred ~0.82 million years ago between two diploid 45 species, T. urartu (AA) and an unknown close relative of Aegilops speltoides (SS), 46 which produced the allotetraploid T. turgidum (AABB). The second polyploidization 47 occurred during cultivation around 8,000-10,000 years ago, when T. turgidum 48 crossed with another diploid grass, Ae. tauschii (DD), to form the ancestral bread 49 wheat (T. aestivum, AABBDD) 1-4 . In addition, a recent genome analysis suggested 50 that Ae. tauschii originated from a more ancient homoploid hybridization event 51 between the A and B lineage ancestors 5 . The A, B, and D subgenomes comprise the 52 ~17-Gb allohexaploid bread wheat genome. Enormous genome sequencing efforts 53 have resulted in the recent publication of a reference genome sequence for wheat 4,6-9 , 54 which has greatly enhanced our understanding of the genome of this vital crop. 55After its evolution in the Middle East and Mediterranean regions, bread wheat 56 gradually spread to the rest of the world and was domesticated for human use 10 . China 57 3 has been cultivating bread wheat for ~4,600 years 11,12 , and has been the largest wheat-58 producing country for more than two decades. Wheat has been under continuous 59 artificial selection in the diverse ecological zones of China for thousands of years 11,13 ; 60 thus, the domestication and breeding of bread wheat in this country provides unique 61 evolutionary insights into h...

High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat

“…tauschii to bread wheat is much more difficult than that from wild and/or cultivated tetraploid T. turgidum (AABB) due to the different crossabilities between Ae. tauschii or tetraploid T. turgidum and common wheat (Chen et al, 2019a). Overall, the LD decay in the D sub-genome was slower than that in the A or B subgenome (Figure 1C), which is consistent with previous studies (Ogbonnaya et al, 2017;Li et al, 2019a;Jamil et al, 2019).…”

Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

“… Cavanagh et al (2013) also reported that the winter wheat from the European population displayed robust genetic differentiation in their study. Chen et al (2019) described that West Asian, European, numerous Central and South Asian landraces, and most East Asian cultivars grouped in the same cluster, whiles most of the East Asian landraces were grouped with South, Central and West Asian landraces. Lee et al (2018) described that most Japanese, Korean and genotypes from Afghanistan were grouped in a cluster, while the Middle Eastern, Chinese, and Caucasus germplasm were in a separate group.…”

Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing

“…Strelchenko et al (2005) analyzed 78 wheat landraces originating from 22 countries and reported that the landraces were separated into European and Asian groups. Chen et al (2019) reported that West Asian landraces, the majority of European landraces, several South and Central Asian landraces, and the majority of East Asian cultivars clustered together, whereas the majority of East Asian landraces were clustered with several West Asian landraces and the majority of South and Central Asian landraces. Lee et al (2018) reported that many accessions from Afghanistan, Japan, and Korea were clustered in the same group, while germplasm from China, the Middle East, and Caucasus clustered in a separate group, and an intermediate group largely consisted mainly of accessions from Afghanistan, Japan, and Korea.…”

“…The area between the Black Sea and the Caspian Sea, and just south of this region (Iraq), is the assumed location of the center of origin of wheat domestication and seems to be a site of population consolidation. Chen et al (2019) showed that Chinese wheat accessions were mainly derived from European landraces. In the present study, the accessions originating from China tended to cluster with European accessions (Figure 9).…”