title: The iSelect 9 K SNP analysis revealed polyploidization induced revolutionary changes and intense human selection causing strong haplotype blocks in wheat.
abstract: A Chinese wheat mini core collection was genotyped using the wheat 9 K iSelect SNP array. Total 2420 and 2396 polymorphic SNPs were detected on the A and the B genome chromosomes, which formed 878 haplotype blocks. There were more blocks in the B genome, but the average block size was significantly (P < 0.05) smaller than those in the A genome. Intense selection (domestication and breeding) had a stronger effect on the A than on the B genome chromosomes. Based on the genetic pedigrees, many blocks can be traced back to a well-known Strampelli cross, which was made one century ago. Furthermore, polyploidization of wheat (both tetraploidization and hexaploidization) induced revolutionary changes in both the A and the B genomes, with a greater increase of gene diversity compared to their diploid ancestors. Modern breeding has dramatically increased diversity in the gene coding regions, though obvious blocks were formed on most of the chromosomes in both tetraploid and hexaploid wheats. Tag-SNP markers identified in this study can be used for marker assisted selection using haplotype blocks as a wheat breeding strategy. This strategy can also be employed to facilitate genome selection in other self-pollinating crop species.
authors.affiliation: Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Chenyang
authors.initials: C
authors.lastname: Hao
authors.affiliation: Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Yuquan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: US Department of Agriculture-Agricultural Research Service Biosciences Research Laboratory, Fargo, ND 58102, USA.
authors.forename: Shiaoman
authors.initials: S
authors.lastname: Chao
authors.affiliation: Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Tian
authors.initials: T
authors.lastname: Li
authors.affiliation: Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Hongxia
authors.initials: H
authors.lastname: Liu
authors.affiliation: Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Lanfen
authors.initials: L
authors.lastname: Wang
authors.affiliation: Key Laboratory of Crop Gene Resources and Germplasm Enhancment, Ministry of Agriculture/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
authors.forename: Xueyong
authors.initials: X
authors.lastname: Zhang
mesh_terms: D001947:Breeding; D032461:Chromosomes, Plant / Q000235:genetics; D003433:Crosses, Genetic; D019143:Evolution, Molecular; D005819:Genetic Markers; D018745:Genome, Plant; D006239:Haplotypes / Q000235:genetics*; D006801:Humans; D015810:Linkage Disequilibrium / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D025341:Principal Component Analysis; D011995:Recombination, Genetic / Q000235:genetics; D013045:Species Specificity; D057891:Tetraploidy; D014908:Triticum / Q000235:genetics*
chemical_list: D005819:Genetic Markers