RNA-seq analysis revealed considerable genetic diversity and enabled the development of specific KASP markers for Psathyrostachys huashanica.
RNA-seq analysis revealed considerable genetic diversity and enabled the development of specific KASP markers for Psathyrostachys huashanica.
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DOI：
10.3389/fpls.2023.1166710
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发表时间：
2023
影响因子：
5.6
通讯作者：
中科院分区：
文献类型：
--
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华山拟小麦（Psathyrostachys huashanica）是中国华山地区特有的普通小麦的重要野生近缘种质，具有许多小麦育种所需的优良性状。然而，由于其种间系统发育和基因组变异特征不明显，且相对缺乏种特异性分子标记，限制了其作为小麦种质资源改良的利用。在本研究中，我们对花楸树的转录组进行了测序，得到50,337,570个干净的reads，组装成65,617个unigenes，其中38,428个（58.56%）至少与公共数据库中的一个序列匹配。利用68个推定的同源基因簇对花山小麦、小麦科和禾科植物进行了系统发育分析。这些数据揭示了花山小麦与普通小麦之间的遥远进化关系，以及花山小麦基因组与小麦D基因组之间的巨大多样性。通过比较花山小麦和中国春小麦的转录组，鉴定出750,759个候选单核苷酸多态性（snp）。在90个不同功能注释外显子区域的snp中，58个（64.4%）通过KASP基因分型验证为普通小麦背景下的Ns基因组特异性snp。标记验证分析表明，6个特异的标记可以区分花山小麦和其他小麦近缘种。此外，有5个标记是携带Ns基因组的花山草、芥菜和羊草所特有的。在小麦背景下，利用Ns基因组特异性标记对4种小麦的花山假单胞菌染色体进行特异性和稳定性检测。花山加线。小麦- p中分别检测到4个和8个SNP标记。华山加2Ns和7Ns附加系，一个标记对两种小麦磷都有特异性。华山卡3Ns， 4Ns和7Ns附加线。利用转录组数据开发的这些标记可用于阐明拟草属、羊草属和其他近缘种之间的遗传关系。在今后的作物育种计划中，它们也可以为花山沙外源染色体或片段的精确渗入和高通量监测提供便利。
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 of P. huashanica as a genetic resource for enhancing wheat germplasm. In this study, we sequenced the P. huashanica 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 P. huashanica, Triticeae species, and Poaceae species was conducted using 68 putative orthologous gene clusters. The data revealed the distant evolutionary relationship between P. huashanica and common wheat as well as the substantial diversity between the P. huashanica genome and the wheat D genome. By comparing the transcriptomes of P. huashanica and Chinese Spring, 750,759 candidate SNPs between P. huashanica 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 P. huashanica and the other wheat-related species. In addition, five markers are unique to P. huashanica, P. juncea, and Leymus 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 P. huashanica chromosomes in four wheat–P. huashanica addition lines. Four and eight SNP markers were detected in wheat–P. huashanica 2Ns and 7Ns addition lines, respectively, and one marker was specific to both wheat–P. huashanica 3Ns, 4Ns, and 7Ns addition lines. These markers developed using transcriptome data may be used to elucidate the genetic relationships among Psathyrostachys, Leymus, and other closely-related species. They may also facilitate precise introgressions and the high-throughput monitoring of P. huashanica exogenous chromosomes or segments in future crop breeding programs.
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