|SONG, JIAN - University Of Florida|
|YANG, XIPING - University Of Florida|
|RESENDE, MARCIO - Collaborator|
|NEVES, LEANDRO - Collaborator|
|ZHANG, JISEN - Fujian Agricultural & Forestry University|
|WANG, JIANPING - Fujian Agricultural & Forestry University|
Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/23/2016
Publication Date: 6/8/2016
Publication URL: https://handle.nal.usda.gov/10113/63019
Citation: Song, J., Yang, X., Resende, M., Neves, L.G., Todd, J.R., Zhang, J., Comstock, J.C., Wang, J. 2016. Natural allelic variations in highly polyploidy Saccharum complex. Frontiers in Plant Science. 7:804. DOI: 10.3389/fpls.2016.00804.
Interpretive Summary: Sugarcane and its relatives are genetically complex with multiple sets of chromosomes and genes. Getting a better understanding of natural variation within the different forms of genes or allelic variation would help in the research of genes that affect species adaptation and important agronomic traits. To characterize this diversity, probes developed from sugarcane genes and the sorghum genome was used to make a library of sugarcane fragments that were sequenced. The sequence information was used to find 1,112,915 markers representing individual changes within the genome which was used to find the divergence between the related species and could be used in maps and associations in the future. The hybridization based target enrichment method proved to be an efficient way find gene variation in sugarcane. A high amount of diversity and genetic variations was found within Sugarcane and its relatives. This information will be useful to plant breeders as they predict the genetic potential of different clones for crossing to improve the yield of the next generation.
Technical Abstract: Sugarcane (Saccharum spp.) as important sugar and biofuel crop are highly polypoid with complex genomes. A large amount of natural phenotypic variation exists in sugarcane germplasm. Understanding its allelic variance has been challenging but is a critical foundation for discovery of the genomic sequence variations and dissecting alleles and allele variant recombination controlling species adaptation and important agronomical traits. To characterize natural allelic variance in the “Saccharum complex”, a target enrichment approach followed by deep sequencing was applied on 12 representative germplasm accessions. In total, 55,946 probes were designed from sorghum genome and sugarcane unigene set targeting 6.7 Mb corresponding sequence regions of the 12 accessions. A pipeline for polyploidy sequence variance and genotype calling was established. A total of 1,112,915 non-redundant single nucleotide polymorphisms (SNPs), 19,354 InDels, 1,021 gene copy number variations, and 3,086 gene presence/absence variants were detected among the 12 accessions. The majority of SNPs were bi-allelic and widely dispersed across the entire genome. The genotypes based on the SNP loci of each accession and their ploidy levels were estimated as largely homozygote. A total of 13,584 haplotype blocks were inferred according to 406 candidate genes. The synonymous and non-synonymous substitution rates analysis revealed that the highest divergence time among the Saccharum spp. was 1.2 million years ago (MYA), Saccharum spp. diverged from Erianthus and Sorghum, two close genera of Saccharum, approximately 5 and 6 MYA respectively. The results demonstrated that hybridization based target enrichment sequencing approach provided an effective way to discover natural allelic variation in highly polyploid and heterozygous species. The catalog of sequence variants among different genotypes in “Saccharum complex” will facilitate further gene/trait association studies for polyploidy sugarcane improvement.