Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers

BMC Plant Biology

Shangang Jia¹  Xiao Ma²  Chenglin Zhang²  Wendan Wu²  Yi Xiong²  Junming Zhao²  Zhixiao Dong²  Jian Yang²  Ming Sun³  Jianbo Zhang⁴ 

[1] College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China;Key Laboratory of Pratacultural Science, Beijing Municipality, China Agricultural University, 100193, Beijing, China;Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China;Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, 611130, Chengdu, Sichuan, China;College of Grassland Science and Technology, China Agricultural University, 100193, Beijing, China;Sichuan Academy of Grassland Science, 611731, Chengdu, Sichuan, China;

关键词: Bromus catharticus;    Transcriptome sequencing;    Differentially expressed genes;    Marker development;    Diversity analysis;   

DOI  :  10.1186/s12870-021-03037-y

来源: Springer

【 摘 要 】

BackgroundPrairie 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.ResultsEleven 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.ConclusionA 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.

【 授权许可】

CC BY