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Title: Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a “sweet” crop with “bitter” genomes

Author
item YANG, XIPING - University Of Florida
item SONG, JIAN - University Of Florida
item Todd, James
item PENG, ZE - University Of Florida
item PAUDEL, DEV - University Of Florida
item LUO, ZILIANG - University Of Florida
item MA, XIAOKAI - Fujian Agricultural & Forestry University
item YOU, QIAN - University Of Florida
item HANSON, ERIK - University Of Florida
item ZHAO, ZIFAN - University Of Florida
item ZHANG, JISEN - University Of Florida
item MING, RAY - University Of Florida
item WANG, JIANPING - University Of Florida

Submitted to: Plant Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/21/2018
Publication Date: 7/26/2018
Publication URL: http://handle.nal.usda.gov/10113/6279276
Citation: Yang, X., Song, J., Todd, J.R., Peng, Z., Paudel, D., Luo, Z., Ma, X., You, Q., Hanson, E., Zhao, Z., Zhang, J., Ming, R., Wang, J. 2018. Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a “sweet” crop with “bitter” genomes. Plant Biotechnology. 17(2):488-498. https://doi.org/10.1111/pbi.12992.
DOI: https://doi.org/10.1111/pbi.12992

Interpretive Summary: Sugarcane is an important cash crop for sugar production, and new sugarcane varieties are necessary for continued high yields. Sugarcane breeding would benefit from genetic and genomic research, but is hindered by complex genomes. To increase the number of gentic tools and understand deversity of the world collection of sugarcane and related species better, target enrichment sequencing of 307 accessions from the world collection was made. Candiate genes involved in the domestication of sugarcane and sequence variations in the natural population were identified. These are useful tools that could be used by breeding programs for sugarcane cultivar improvement.

Technical Abstract: Sugarcane (Saccharum spp.) is an important cash crop for sugar and bio-ethanol production. However, research in sugarcane genetics, genomics, and cultivar improvement has been challenging largely due to its complex genomes with high polyploidy level. In this study, we applied target enrichment sequencing of 307 sugarcane accessions selected from the world collection of sugarcane and related grasses to represent the diversity of the sugarcane germplasm with a focus on two major contributing species of modern sugarcane cultivars, S. spontaneum and S. officinarum, in addition to their hybrids. We identified large amounts of sequence variations among the accessions including 4.65 million single-nucleotide polymorphisms (SNPs), 858.1 thousand insertions and deletions, 7,916 presence/absence variants, and 18,991 simple sequence repeats. With the genome-wide SNPs, we evaluated the genetic relationships of this diversity panel, and assigned miss-classified accessions and unknown accessions into their correct groups. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2,739.2 Kbp, and 3,573.6 Kbp for S. spontaneum, S. officinarum, and modern S. hybrids, respectively. We identified 75 candidate selective sweeps and 1,723 candidate genes in the domestication and historical selection. This study cataloged the DNA sequence variations of the natural germplasm population and provided valuable genomic resources for sugarcane research community and breeding programs to strategically utilize the germplasm for sugarcane cultivar improvement.