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Title: Natural Allelic Variations in Highly Polyploidy Saccharum Complex

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. BWAmem 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 ploidymore » 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. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.« less
Authors:
 [1] ;  [2] ;  [3] ;  [3] ;  [4] ;  [5] ;  [6] ;  [7]
  1. Univ. of Florida, Gainesville, FL (United States); Dezhou Univ., Dezhou (China)
  2. Univ. of Florida, Gainesville, FL (United States)
  3. RAPiD Genomics LLC, Gainesville, FL (United States)
  4. United States Dept. of Agriculture-Agricultural Research Service, Houma, LA (United States); United States Dept. of Agriculture-Agricultural Research Service, Canal Point, FL (United States)
  5. Fujian Agriculture and Forestry Univ., Fuzhou (China)
  6. United States Dept. of Agriculture-Agricultural Research Service, Canal Point, FL (United States)
  7. Univ. of Florida, Gainesville, FL (United States); Fujian Agriculture and Forestry Univ., Fuzhou (China)
Publication Date:
Type:
Accepted Manuscript
Journal Name:
Frontiers in Plant Science
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 1664-462X
Publisher:
Frontiers Research Foundation
Research Org:
Univ. of Florida, Gainesville, FL (United States)
Sponsoring Org:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; Saccharum complex; sugarcane; target enrichment sequencing; polyploid; allelic variations; SNP(s)
OSTI Identifier:
1379186

Song, Jian, Yang, Xiping, Resende, Jr., Marcio F. R., Neves, Leandro G., Todd, James, Zhang, Jisen, Comstock, Jack C., and Wang, Jianping. Natural Allelic Variations in Highly Polyploidy Saccharum Complex. United States: N. p., Web. doi:10.3389/fpls.2016.00804.
Song, Jian, Yang, Xiping, Resende, Jr., Marcio F. R., Neves, Leandro G., Todd, James, Zhang, Jisen, Comstock, Jack C., & Wang, Jianping. Natural Allelic Variations in Highly Polyploidy Saccharum Complex. United States. doi:10.3389/fpls.2016.00804.
Song, Jian, Yang, Xiping, Resende, Jr., Marcio F. R., Neves, Leandro G., Todd, James, Zhang, Jisen, Comstock, Jack C., and Wang, Jianping. 2016. "Natural Allelic Variations in Highly Polyploidy Saccharum Complex". United States. doi:10.3389/fpls.2016.00804. https://www.osti.gov/servlets/purl/1379186.
@article{osti_1379186,
title = {Natural Allelic Variations in Highly Polyploidy Saccharum Complex},
author = {Song, Jian and Yang, Xiping and Resende, Jr., Marcio F. R. and Neves, Leandro G. and Todd, James and Zhang, Jisen and Comstock, Jack C. and Wang, Jianping},
abstractNote = {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. BWAmem 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. Furthermore, the target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.},
doi = {10.3389/fpls.2016.00804},
journal = {Frontiers in Plant Science},
number = ,
volume = 7,
place = {United States},
year = {2016},
month = {6}
}