Zhang Hao, Zeng Chunyan, Li Liangxi, Zhu Wei, Xu Lili, Wang Yi, Zeng Jian, Fan Xing, Sha Lina, Wu Dandan, Cheng Yiran, Zhang Haiqin, Chen Guoyue, Zhou Yonghong, Kang Houyang
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China.
Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
Front Plant Sci. 2023 Mar 30;14:1166710. doi: 10.3389/fpls.2023.1166710. eCollection 2023.
, 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 of as a genetic resource for enhancing wheat germplasm. In this study, we sequenced the transcriptome, 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 of , Triticeae species, and Poaceae species was conducted using 68 putative orthologous gene clusters. The data revealed the distant evolutionary relationship between and common wheat as well as the substantial diversity between the genome and the wheat D genome. By comparing the transcriptomes of and Chinese Spring, 750,759 candidate SNPs between Ns 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 between and the other wheat-related species. In addition, five markers are unique to , , and species, which carry the Ns genome. The Ns genome-specific markers in a wheat background were also validated regarding their specificity and stability for detecting chromosomes in four wheat- addition lines. Four and eight SNP markers were detected in wheat- 2Ns and 7Ns addition lines, respectively, and one marker was specific to both wheat- 3Ns, 4Ns, and 7Ns addition lines. These markers developed using transcriptome data may be used to elucidate the genetic relationships among , , and other closely-related species. They may also facilitate precise introgressions and the high-throughput monitoring of exogenous chromosomes or segments in future crop breeding programs.
仅生长于中国华山的[物种名称未给出]是普通小麦重要的野生近缘种，具有许多与小麦育种相关的优良性状。然而，种间系统发育和基因组变异特征描述不完善，以及相对缺乏物种特异性分子标记，限制了[物种名称未给出]作为增强小麦种质遗传资源的利用。在本研究中，我们对[物种名称未给出]的转录组进行了测序，得到50337570条clean reads，组装成65617个单基因，其中38428个（58.56%）至少与公共数据库中的一个序列匹配。使用68个假定的直系同源基因簇对[物种名称未给出]、小麦族物种和禾本科物种进行了系统发育分析。数据揭示了[物种名称未给出]与普通小麦之间遥远的进化关系，以及[物种名称未给出]基因组与小麦D基因组之间的显著差异。通过比较[物种名称未给出]和中国春的转录组，在[物种名称未给出]Ns基因与其普通小麦直系同源基因之间鉴定出750759个候选SNP。在具有不同功能注释的外显子区域的90个SNP中，58个（64.4%）通过KASP基因分型检测在普通小麦背景中被验证为Ns基因组特异性SNP。标记验证分析表明，六个特异性标记可以区分[物种名称未给出]和其他小麦相关物种。此外，五个标记是携带Ns基因组的[物种名称未给出]、[物种名称未给出]和[物种名称未给出]物种所特有的。还验证了小麦背景下Ns基因组特异性标记在检测四个小麦附加系中[物种名称未给出]染色体时的特异性和稳定性。在小麦-2Ns和7Ns附加系中分别检测到四个和八个SNP标记，一个标记对小麦-3Ns、4Ns和7Ns附加系均为特异性。利用转录组数据开发的这些标记可用于阐明[物种名称未给出]、[物种名称未给出]和其他近缘物种之间的遗传关系。它们还可能有助于在未来的作物育种计划中精确导入和高通量监测[物种名称未给出]外源染色体或片段。
