https://www.frontiersin.org/articles/10.3389/fpls.2023.1166710/full
Frontiers in Plant Science，30 March 2023，Volume 14 - 2023
Hao Zhang, Chunyan Zeng,Liangxi Li, Wei Zhu, Lili Xu,Yi Wang,Jian Zeng,Xing Fan, Lina Sha,Dandan Wu,Yiran Cheng,Haiqin Zhang, Guoyue Chen,Yonghong Zhou and Houyang Kang
Abstract
Psathyrostachys huashanica, which grows exclusively in Huashan, China, is an important wild relative of common wheat that has many desirable traits relevant for wheat breeding. However, the poorly characterized interspecific phylogeny and genomic variations and the relative lack of species-specific molecular markers have limited the utility ofP. huashanicaas a genetic resource for enhancing wheat germplasm. In this study, we sequenced theP. huashanicatranscriptome, resulting in 50,337,570 clean reads that were assembled into 65,617 unigenes, of which 38,428 (58.56%) matched at least one sequence in public databases. The phylogenetic analysis ofP. huashanica, Triticeae species, and Poaceae species was conducted using 68 putative orthologous gene clusters. The data revealed the distant evolutionary relationship betweenP. huashanicaand common wheat as well as the substantial diversity between theP. huashanicagenome and the wheat D genome. By comparing the transcriptomes ofP. huashanicaand Chinese Spring, 750,759 candidate SNPs betweenP. huashanicaNs genes and their common wheat orthologs were identified. Among the 90 SNPs in the exon regions with different functional annotations, 58 (64.4%) were validated as Ns genome-specific SNPs in the common wheat background by KASP genotyping assays. Marker validation analyses indicated that six specific markers can discriminate betweenP. huashanicaand the other wheat-related species. In addition, five markers are unique toP. huashanica,P. juncea, andLeymusspecies, which carry the Ns genome. The Ns genome-specific markers in a wheat background were also validated regarding their specificity and stability for detectingP. huashanicachromosomes in four wheat–P. huashanicaaddition lines. Four and eight SNP markers were detected in wheat–P. huashanica2Ns and 7Ns addition lines, respectively, and one marker was specific to both wheat–P. huashanica3Ns, 4Ns, and 7Ns addition lines. These markers developed using transcriptome data may be used to elucidate the genetic relationships amongPsathyrostachys,Leymus, and other closely-related species. They may also facilitate precise introgressions and the high-throughput monitoring ofP. huashanicaexogenous chromosomes or segments in future crop breeding programs.
