Format

Send to

Choose Destination
Nat Genet. 2018 Nov;50(11):1565-1573. doi: 10.1038/s41588-018-0237-2. Epub 2018 Oct 8.

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

Author information

1
Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China. zjisen@fafu.edu.cn.
2
Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China.
3
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
4
Hawaii Agriculture Research Center, Kunia, HI, USA.
5
Institute for Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
6
Department of Plant Biology, University of Georgia, Athens, GA, USA.
7
Department of Horticulture, Michigan State University, East Lansing, MI, USA.
8
Department of Mathematics and Statistics, University of Ottawa, Ottawa, Ontario, Canada.
9
Department of Microbiology, Immunology and Biochemistry, University of Tennessee HSC, Memphis, TN, USA.
10
Chinese Academy of Sciences-Max-Planck-Gesellschaft Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China.
11
China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, China.
12
Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
13
Department of Agronomy, University of Florida, Gainesville, FL, USA.
14
Texas A&M AgriLife Research, Texas A&M University System, Dallas, TX, USA.
15
Centro de Investigación de la Caña de Azúcar de Colombia (Cenicaña), Cali, Colombia.
16
Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
17
Departments of Computer Science and Biology, Johns Hopkins University, Baltimore, MD, USA.
18
Microsoft Research, Redmond, WA, USA.
19
Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil.
20
Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
21
Hawaii Agriculture Research Center, Kunia, HI, USA. cnagai@harc-hspa.com.
22
Fujian Agriculture and Forestry University and University of Illinois at Urbana-Champaign School of Integrative Biology Joint Center for Genomics and Biotechnology, National Sugarcane Engineering Technology Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China. rayming@illinois.edu.
23
Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA. rayming@illinois.edu.

Abstract

Modern sugarcanes are polyploid interspecific hybrids, combining high sugar content from Saccharum officinarum with hardiness, disease resistance and ratooning of Saccharum spontaneum. Sequencing of a haploid S. spontaneum, AP85-441, facilitated the assembly of 32 pseudo-chromosomes comprising 8 homologous groups of 4 members each, bearing 35,525 genes with alleles defined. The reduction of basic chromosome number from 10 to 8 in S. spontaneum was caused by fissions of 2 ancestral chromosomes followed by translocations to 4 chromosomes. Surprisingly, 80% of nucleotide binding site-encoding genes associated with disease resistance are located in 4 rearranged chromosomes and 51% of those in rearranged regions. Resequencing of 64 S. spontaneum genomes identified balancing selection in rearranged regions, maintaining their diversity. Introgressed S. spontaneum chromosomes in modern sugarcanes are randomly distributed in AP85-441 genome, indicating random recombination among homologs in different S. spontaneum accessions. The allele-defined Saccharum genome offers new knowledge and resources to accelerate sugarcane improvement.

PMID:
30297971
DOI:
10.1038/s41588-018-0237-2

Supplemental Content

Full text links

Icon for Nature Publishing Group
Loading ...
Support Center