High-throughput mining of E-genome-specific SNPs for characterizing Thinopyrum elongatum introgressions in common wheat.
Diploid Thinopyrum elongatum (EE, 2n = 2x = 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 SNPs using Th. elongatum and common wheat (Triticum aestivum, AABBDD, 2n = 6x = 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 SNPs between E genome genes and their common wheat orthologs were computed. Through comparative genomic analysis, these SNPs were putatively assigned to the seven individual E genome chromosomes. Among 420 randomly selected SNPs, 373 could be validated. Thus, approximately 89% of the mined SNPs may be authentic with respect to their polymorphism and chromosomal location. Using 14 such SNPs 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 SNPs 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.
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
Haijuan
H
Lou
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Lingli
L
Dong
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Kunpu
K
Zhang
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.|University of Chinese Academy of Sciences, Beijing 100049, China.
Da-Wei
DW
Wang
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Maolin
M
Zhao
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Yiwen
Y
Li
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Chaowu
C
Rong
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Huanju
H
Qin
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Aimin
A
Zhang
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Zhenying
http://orcid.org/0000-0002-1418-5638
Z
Dong
The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.|The Collaborative Innovation Center for Grain Crops, Henan Agricultural University, Zhengzhou, 450002, China.
Daowen
D
Wang
D002678:Chimera; D019143:Evolution, Molecular; D018745:Genome, Plant; D006109:Poaceae / Q000145:classification* / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D059467:Transcriptome

Thinopyrum elongatum
; SNPs; transcriptome sequencing; wheat; wide hybridization