title: Natural Allelic Variations in Highly Polyploidy Saccharum Complex.
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.
authors.affiliation: Agronomy Department, University of FloridaGainesville, FL, USA; College of Life Sciences, Dezhou UniversityDezhou, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Song
authors.affiliation: Agronomy Department, University of Florida Gainesville, FL, USA.
authors.forename: Xiping
authors.initials: X
authors.lastname: Yang
authors.affiliation: RAPiD Genomics LLC Gainesville, FL, USA.
authors.forename: Marcio F R
authors.initials: MF
authors.lastname: Resende
authors.affiliation: RAPiD Genomics LLC Gainesville, FL, USA.
authors.forename: Leandro G
authors.initials: LG
authors.lastname: Neves
authors.affiliation: Sugarcane Research Unit, United States Department of Agriculture-Agricultural Research ServiceHouma, LA, USA; Sugarcane Field Station, United States Department of Agriculture-Agricultural Research Service, Canal PointFL, USA.
authors.forename: James
authors.initials: J
authors.lastname: Todd
authors.affiliation: Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University Fuzhou, China.
authors.forename: Jisen
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Sugarcane Field Station, United States Department of Agriculture-Agricultural Research Service, Canal Point FL, USA.
authors.forename: Jack C
authors.initials: JC
authors.lastname: Comstock
authors.affiliation: Agronomy Department, University of FloridaGainesville, FL, USA; Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhou, China; Plant Molecular and Biology Program, Genetics Institute, University of FloridaGainesville, FL, USA.
authors.forename: Jianping
authors.initials: J
authors.lastname: Wang
keywords: SNP(s); Saccharum complex; allelic variations; polyploid; sugarcane; target enrichment sequencing