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.

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  • Additional Information
    • Author-Supplied Keywords:
      domestication
      environmental association analysis
      germplasm
      linkage disequilibrium
      Saccharum spp.
      selection
      selective sweeps
      sugarcane
      target enrichment sequencing
    • NAICS/Industry Codes:
      111930 Sugarcane Farming
    • Abstract:
      Summary: Sugarcane (Saccharum spp.) is a highly energy‐efficient crop primarily for sugar and bio‐ethanol production. Sugarcane genetics and cultivar improvement have been extremely challenging largely due to its complex genomes with high polyploidy levels. In this study, we deeply sequenced the coding regions of 307 sugarcane germplasm accessions. Nearly five million sequence variations were catalogued. The average of 98× sequence depth enabled different allele dosages of sequence variation to be differentiated in this polyploid collection. With selected high‐quality genome‐wide SNPs, we performed population genomic studies and environmental association analysis. Results illustrated that the ancient sugarcane hybrids, S. barberi and S. sinense, and modern sugarcane hybrids are significantly different in terms of genomic compositions, hybridization processes and their potential ancestry contributors. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2739.2 Kbp and 3573.6 Kbp for S. spontaneum, S. officinarum and modern S. hybrids respectively. Candidate selective sweep regions and genes were identified during domestication and historical selection processes of sugarcane in addition to genes associated with environmental variables at the original locations of the collection. This research provided an extensive amount of genomic resources for sugarcane community and the in‐depth population genomic analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species. [ABSTRACT FROM AUTHOR]
    • Abstract:
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    • Author Affiliations:
      1Agronomy Department, University of Florida, Gainesville FL, USA
      2Sugarcane Research Unit, USDA‐ARS, Houma LA, USA
      3Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou Fujian, China
      4Department of Plant Biology, University of Illinois at Urbana‐Champaign, Urbana IL, USA
    • Full Text Word Count:
      8808
    • ISSN:
      1467-7644
    • Accession Number:
      10.1111/pbi.12992
    • Accession Number:
      134149400
  • Citations
    • ABNT:
      YANG, X. et al. 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 Journal, [s. l.], v. 17, n. 2, p. 488–498, 2019. Disponível em: . Acesso em: 19 set. 2019.
    • AMA:
      Yang X, Song J, Todd J, et al. 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 Journal. 2019;17(2):488-498. doi:10.1111/pbi.12992.
    • APA:
      Yang, X., Song, J., Todd, J., Peng, Z., Paudel, D., Luo, Z., … Wang, J. (2019). 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 Journal, 17(2), 488–498. https://doi.org/10.1111/pbi.12992
    • Chicago/Turabian: Author-Date:
      Yang, Xiping, Jian Song, James Todd, Ze Peng, Dev Paudel, Ziliang Luo, Xiaokai Ma, et al. 2019. “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 Journal 17 (2): 488–98. doi:10.1111/pbi.12992.
    • Harvard:
      Yang, X. et al. (2019) ‘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 Journal, 17(2), pp. 488–498. doi: 10.1111/pbi.12992.
    • Harvard: Australian:
      Yang, X, Song, J, Todd, J, Peng, Z, Paudel, D, Luo, Z, Ma, X, You, Q, Hanson, E, Zhao, Z, Zhao, Y, Zhang, J, Ming, R & Wang, J 2019, ‘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 Journal, vol. 17, no. 2, pp. 488–498, viewed 19 September 2019, .
    • MLA:
      Yang, Xiping, et al. “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 Journal, vol. 17, no. 2, Feb. 2019, pp. 488–498. EBSCOhost, doi:10.1111/pbi.12992.
    • Chicago/Turabian: Humanities:
      Yang, Xiping, Jian Song, James Todd, Ze Peng, Dev Paudel, Ziliang Luo, Xiaokai Ma, et al. “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 Journal 17, no. 2 (February 2019): 488–98. doi:10.1111/pbi.12992.
    • Vancouver/ICMJE:
      Yang X, Song J, Todd J, Peng Z, Paudel D, Luo Z, et al. 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 Journal [Internet]. 2019 Feb [cited 2019 Sep 19];17(2):488–98. Available from: http://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=asn&AN=134149400&custid=s8280428