Abstract
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.
Highlights
Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring
De novo assembly, and functional annotation Illumina sequencing of eleven libraries for seed, leaf, and stem tissues generated an average of 48,945,309 raw reads and 46,614,613 clean reads, and high-quality clean reads were used for subsequent analyses (Table 1)
A total of 193,082 (74.90%) of the unigenes were annotated against public protein databases, with 160,662 (62.32%), 155,087 (60.16%), 119,080 (46.19%), 113,501 (44.03%), 60,321 (23.4%), 44,775 (17.36%), and 121,098 (46.97%) unigenes having at least one hit from the National Center for Biotechnology Information (NCBI) non-redundant protein database (Nr), nucleotide database (Nt), PFAM, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), KOG, and Gene Ontology (GO) databases, respectively (Fig. 1a)
Summary
Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. 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. Due to high biomass yield, fast growth rate during winter and spring, strong adaptability, and the ability to remain green after seed maturation, B. catharticus has become more and more popular as a cool-season forage grass in the mountainous and hilly areas of Southwest China [3, 4]. As cultivated varieties of B. catharticus were mostly developed through hybrid selection and domestication from wild germplasms, its genomic resources are considerably limited, resulting in slow progress on molecular breeding and taxonomy research. It is still necessary to provide an original reference transcriptome profile for B. catharticus and its relatives
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