Abstract
Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.
Highlights
Sugarcane (Saccharum spp.) is grown in over 100 countries, mainly in tropical and subtropical areas of the world
S. barberi and S. sinense have been considered as interspecific hybrids between S. officinarum and S. spontaneum following by a series of mutations in India and China, respectively (Grivet et al, 2006)
A hybridization-based target enrichment sequencing approach was used to investigate the allelic variation of 12 accessions representing variety of different species in Saccharum complex
Summary
Sugarcane (Saccharum spp.) is grown in over 100 countries, mainly in tropical and subtropical areas of the world. The genus Saccharum is considered to include six species, namely S. officinarum, S. spontaneum, S. sinense, S. robustum, Natural Allelic Variations in Saccharum Complex. Saccharum officinarum (2n = 8x = 80) is the primary sugar producing species, which has been domesticated from wild species S. robustum (2n = 6x–8x = 60–80) (Grivet et al, 2006). S. barberi and S. sinense have been considered as interspecific hybrids between S. officinarum and S. spontaneum following by a series of mutations in India and China, respectively (Grivet et al, 2006). (2n = 2x–6x = 20–60) in the Saccharum complex were used as breeding materials to broaden the genetic base and increase the stress tolerance of modern sugarcane cultivars (Tsuruta et al, 2012; Moore et al, 2014)
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