College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China.
Sichuan Academy of Grassland Science, Chengdu 611731, China.
Genes (Basel). 2023 Jan 23;14(2):302. doi: 10.3390/genes14020302.
L. is the largest genus in the Triticeae tribe. Most species in this genus are highly stress resistant, with excellent forage value. a rare species endemic to the Qinghai-Tibet Plateau (QTP), is declining due to habitat fragmentation. However, genetic data for are limited, with expressed sequence tag (EST) markers being particularly rare, hampering genetic studies and protection measures.
We obtained 9.06 Gb clean sequences from the transcriptome of , generating 171,522 unigenes, which were assembled and functionally annotated against five public databases. We identified 30,668 SSRs in the transcriptome, from which 103 EST-SSR primer pairs were randomly selected. Of these, 58 pairs of amplified products of the expected size, and 18 of the amplified products were polymorphic. Model-based Bayesian clustering, the unweighted pair group method with arithmetic average (UPGMA), and principal coordinate analysis (PCoA) of 179 wild in 12 populations using these EST-SSRs were generally consistent, grouping the 12 populations into two major clades. Analysis of molecular variance (AMOVA) found 70% of the genetic variation among the 12 populations and 30% within the populations, indicating a high level of genetic differentiation (or low gene exchange) among the 12 populations. The transferability of the 58 successful EST-SSR primers to 22 related hexaploid species was 86.2-98.3%. UPGMA analysis generally grouped species with similar genome types together.
Here, we developed EST-SSR markers from the transcriptome of The transferability of these markers was evaluated, and the genetic structure and diversity of were explored. Our results provide a basis for the conservation and management of this endangered species, and the obtained molecular markers represent valuable resources for the exploration of genetic relationships among species in the genus.
L. 是小麦族中最大的属。该属的大多数物种具有很强的抗逆性，饲用价值极高。 是青藏高原特有的珍稀物种，由于生境破碎化而数量减少。然而， 的遗传数据有限，表达序列标签 (EST) 标记尤其罕见，这阻碍了遗传研究和保护措施的开展。
我们从 的转录组中获得了 9.06 Gb 的清洁序列，生成了 171522 条非冗余基因，这些基因被组装并针对五个公共数据库进行了功能注释。我们在 转录本中鉴定了 30668 个 SSR，从中随机选择了 103 对 EST-SSR 引物。其中，58 对扩增产物的大小与预期相符，18 对扩增产物具有多态性。使用这些 EST-SSR 对 12 个群体的 179 个野生 进行基于模型的贝叶斯聚类、非加权对组平均法 (UPGMA) 和主坐标分析 (PCoA)，结果基本一致，将 12 个群体分为两个主要分支。基于分子方差 (AMOVA) 的分析表明，12 个群体间的遗传变异占 70%，群体内的遗传变异占 30%，表明 12 个群体间存在较高水平的遗传分化（或基因交流较少）。58 对成功的 EST-SSR 引物在 22 种相关六倍体物种中的可转移性为 86.2-98.3%。UPGMA 分析通常将基因组类型相似的物种聚在一起。
本研究从 的转录组中开发了 EST-SSR 标记，评估了这些标记的转移能力，并探讨了 的遗传结构和多样性。我们的研究结果为该濒危物种的保护和管理提供了依据，获得的分子标记为探索该属物种间的遗传关系提供了有价值的资源。
