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

Abstract

\n Background: 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.Results: 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 expressed in the 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 0.358, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, but Asian accessions demonstrated mixed relationships, which indicated a different probability of gene flow among the two regions. Phylogenetic analysis clustered the studied accessions into four clades. Finally, phenotypic clustering and Mantel analysis suggested the total phenotypic variation was mostly contributed by the genetic component. Stem diameter, plant height, leaf width, and biomass yield significantly correlated with genetic data (r > 0.6, P < 0.001), and might be genetically stable in the future selection and breeding.Conclusion: A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and it relatives in the future.