Premium
High‐throughput mining of E‐genome‐specific SNP s for characterizing Thinopyrum elongatum introgressions in common wheat
Author(s) -
Lou Haijuan,
Dong Lingli,
Zhang Kunpu,
Wang DaWei,
Zhao Maolin,
Li Yiwen,
Rong Chaowu,
Qin Huanju,
Zhang Aimin,
Dong Zhenying,
Wang Daowen
Publication year - 2017
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12659
Subject(s) - biology , genome , single nucleotide polymorphism , genetics , common wheat , polyploid , ploidy , snp array , triticeae , chromosome , snp genotyping , gene , genotype
Diploid Thinopyrum elongatum ( EE , 2 n = 2 x = 14) and related polyploid species constitute an important gene pool for improving Triticeae grain and forage crops. However, the genomic and molecular marker resources are generally poor for these species. To aid the genetic, molecular, breeding and ecological studies involving Thinopyrum species, we developed a strategy for mining and validating E‐genome‐specific SNP s using Th. elongatum and common wheat ( Triticum aestivum , AABBDD , 2 n = 6 x = 42) as experimental materials. By comparing the transcriptomes between Chinese Spring ( CS , a common wheat variety) and the CS ‐ Th. elongatum octoploid, 35,193 candidate SNP s between E genome genes and their common wheat orthologs were computed. Through comparative genomic analysis, these SNP s were putatively assigned to the seven individual E genome chromosomes. Among 420 randomly selected SNP s, 373 could be validated. Thus, approximately 89% of the mined SNP s may be authentic with respect to their polymorphism and chromosomal location. Using 14 such SNP s as molecular markers, complex E genome introgressions were reliably identified in 78 common wheat‐ Th. elongatum hybrids, and the structural feature of a novel recombinant chromosome formed by 6E and 7E was revealed. Finally, based on testing 33 SNP s assigned to chromosome 3E in multiple genotypes of Th. elongatum , Pseudoroegneria stipifolia (carrying the St genome related to E) and common wheat, we suggest that some of the SNP markers may also be applicable for genetic studies within and among the Thinopyrum species (populations) carrying E and/or St genomes in the future.