College of Bioscience & Biotechnology, Hunan Agricultural University, Changsha, 410128, PR China.
Hunan Engineering Laboratory of Miscanthus Ecological Applications, Hunan Agricultural University, Changsha, 410128, PR China.
BMC Genomics. 2022 Jan 10;23(1):43. doi: 10.1186/s12864-021-08277-8.
Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.
We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264-364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.
As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.
芒属植物是欧洲和亚洲部分地区主要的专用能源草，预计将在未来生物经济的发展中发挥关键作用。然而，由于其复杂的遗传背景，很难调查该属的系统发育关系。在这里，我们研究了 50 份芒属植物种质资源：1 个母本（荻），30 个候选父本（荻、荻和荻）和 19 个后代。我们使用高通量特异位点扩增片段测序（SLAF-seq）技术在所有种质资源中鉴定出有信息的单核苷酸多态性（SNP）。
我们共鉴定出 257889 个 SLAF 标签，其中 87162 个为多态性。每个标签长 264-364bp。获得的 724773 个群体 SNP 用于研究芒属 3 个种内的遗传关系。我们利用获得的 SNP 构建了 50 个种质资源的系统发育树，并将它们分为两个分支：一个分支仅包含荻，另一个分支包含后代、荻和荻。遗传聚类分析表明，后代的最可能的父本是荻种质资源 C3。
作为一种高通量测序方法，SLAF-seq 可用于鉴定芒属种质资源中的信息 SNP，并快速表征该属内的遗传关系。我们的研究结果将支持利用具有优质生物量或纤维生产潜力的芒属品种的育种计划，以满足发展生物经济的需求。
