Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
BMC Plant Biol. 2021 Jun 7;21(1):264. doi: 10.1186/s12870-021-03037-y.
Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus.
Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically and highly expressed in seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.364, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, while Asian accessions demonstrated mixed internal relationships, which indicated a different probability of gene flow. Phylogenetic analysis clustered the studied accessions into four clades, being consistent with phenotypic clustering results. Finally, Mantel analysis suggested the total phenotypic variation was mostly contributed by genetic component. Stem diameter, plant height, leaf width, and biomass yield were significantly correlated with genetic data (r > 0.6, P < 0.001), and might be used in the future selection and breeding.
A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and its relatives in the future.
雀麦（Bromus catharticus）是一种典型的冷季饲用作物，具有较高的生物量产量和冬春季节快速生长的特点。然而，由于可用基因组资源有限，其遗传研究和育种一直停滞不前。本研究旨在利用高通量转录组测序生成大规模基因组数据，并对雀麦的 EST-SSR 标记进行初步验证。
从新育成的雀麦高产品种 BCS1103 中收集了 11 个组织样本，包括种子、叶片和茎。共获得 257773 条 unigene，其中 193082 条（74.90%）得到注释。组织间比较分析发现，种子、叶片和茎中分别有 1803、3030 和 1570 个基因特异性高表达。从 unigene 序列中共鉴定出 37288 个 EST-SSR，设计出超过 80000 对引物。我们合成了 420 对引物，从中选择了 52 对多态性高的引物，用于估计全球 24 个雀麦品种的遗传多样性和群体结构。尽管平均遗传距离为 0.364 表明遗传多样性较低，但来自南美洲和亚洲的品种和野生品种表现出较高的遗传多样性。此外，南美洲品种表现出纯正的血统，而亚洲品种表现出混合的内部关系，这表明基因流的可能性不同。系统发育分析将研究的品种聚类为四个分支，与表型聚类结果一致。最后，Mantel 分析表明，总表型变异主要由遗传组成贡献。茎直径、株高、叶宽和生物量产量与遗传数据显著相关（r>0.6，P<0.001），可用于未来的选择和育种。
生成了雀麦基因组资源，有助于未来对雀麦及其近缘种进行遗传和分类学研究以及分子育种。
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