Abstract
Sudangrass, Sorghum sudanense, is an important forage in warm regions. But little is known about its genome. In this study, the transcriptomes of sudangrass S722 and sorghum Tx623B were sequenced by Illumina sequencing. More than 4Gb bases were sequenced for each library. For Tx623B and S722, 88.79% and 83.88% reads, respectively were matched to the Sorghum bicolor genome. A total of 2,397 differentially expressed genes (DEGs) were detected by RNA-Seq between the two libraries, including 849 up-regulated genes and 1,548 down-regulated genes. These DEGs could be divided into three groups by annotation analysis. A total of 44,495 single nucleotide polymorphisms (SNPs) were discovered by aligning S722 reads to the sorghum reference genome. Of these SNPs, 61.37% were transition, and this value did not differ much between different chromosomes. In addition, 16,928 insertion and deletion (indel) loci were identified between the two genomes. A total of 5,344 indel markers were designed, 15 of which were selected to construct the genetic map derived from the cross of Tx623A and Sa. It was indicated that the indel markers were useful and versatile between sorghum and sudangrass. Comparison of synonymous base substitutions (Ks) and non-synonymous base substitutions (Ka) between the two libraries showed that 95% orthologous pairs exhibited Ka/Ks<1.0, indicating that these genes were influenced by purifying selection. The results from this study provide important information for molecular genetic research and a rich resource for marker development in sudangrass and other Sorghum species.
Highlights
Sorghum is a diverse genus consisting of cultivated and wild species, many of which are diploid, possessing considerable genetic and morphological diversity [1]
The results showed that most reads of the two libraries (88.79% and 83.88% for Tx623B and S722, respectively) matched to the S. bicolor genes (Table 1)
16,928 indel loci were identified by aligning S722 reads to the sorghum reference genome (S5 Table)
Summary
Sorghum is a diverse genus consisting of cultivated and wild species, many of which are diploid, possessing considerable genetic and morphological diversity [1]. Sorghum bicolor (S. bicolor), commonly called sorghum, is an important cultivated species in the Sorghum genus and is used as food, forage and biofuel [2]. Sorghum sudanense (S. sudanense), commonly called sudangrass, is used as forage for ruminants. It was introduced into the United States in 1909 and PLOS ONE | DOI:10.1371/journal.pone.0154947. It was introduced into the United States in 1909 and PLOS ONE | DOI:10.1371/journal.pone.0154947 May 6, 2016
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