PMID- 31587087 OWN - NLM STAT- MEDLINE DCOM- 20200915 LR - 20220412 IS - 1432-2242 (Electronic) IS - 0040-5752 (Linking) VI - 133 IP - 1 DP - 2020 Jan TI - Characterization of a Saccharum spontaneum with a basic chromosome number of x = 10 provides new insights on genome evolution in genus Saccharum. PG - 187-199 LID - 10.1007/s00122-019-03450-w [doi] AB - A novel tetraploid S. spontaneum with basic chromosome x = 10 was discovered, providing us insights in the origin and evolution in Saccharum species. Sugarcane (Saccharum spp., Poaceae) is a leading crop for sugar production providing 80% of the world's sugar. However, the genetic and genomic complexities of this crop such as its high polyploidy level and highly variable chromosome numbers have significantly hindered the studies in deciphering the genomic structure and evolution of sugarcane. Here, we developed the first set of oligonucleotide (oligo)-based probes based on the S. spontaneum genome (x = 8), which can be used to simultaneously distinguish each of the 64 chromosomes of octaploid S. spontaneum SES208 (2n = 8x = 64) through fluorescence in situ hybridization (FISH). By comparative FISH assay, we confirmed the chromosomal rearrangements of S. spontaneum (x = 8) and S. officinarum (2n = 8x = 80), the main contributors of modern sugarcane cultivars. In addition, we examined a S. spontaneum accession, Np-X, with 2n = 40 chromosomes, and we found that it was a tetraploid with the unusual basic chromosome number of x = 10. Assays at the cytological and DNA levels demonstrated its close relationship with S. spontaneum with basic chromosome number x = 8 (the most common accessions in S. spontaneum), confirming its S. spontaneum identity. Population genetic structure and phylogenetic relationship analyses between Np-X and 64 S. spontaneum accessions revealed that Np-X belongs to the ancient Pan-Malaysia group, indicating a close relationship to S. spontaneum with basic chromosome number of x = 8. This finding of a tetraploid S. spontaneum with basic chromosome number of x = 10 suggested a parallel evolution path of genomes and polyploid series in S. spontaneum with different basic chromosome numbers. FAU - Meng, Zhuang AU - Meng Z AD - 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. FAU - Han, Jinlei AU - Han J AD - 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. FAU - Lin, Yujing AU - Lin Y AD - 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. FAU - Zhao, Yiyong AU - Zhao Y AD - State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China. FAU - Lin, Qingfang AU - Lin Q AD - 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. FAU - Ma, Xiaokai AU - Ma X AD - 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. FAU - Wang, Jianping AU - Wang J AD - 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. AD - Department of Agronomy, University of Florida, Gainesville, FL, 32611, USA. FAU - Zhang, Muqing AU - Zhang M AD - State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, Guangxi, China. FAU - Zhang, Liangsheng AU - Zhang L AD - 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. FAU - Yang, Qinghui AU - Yang Q AD - Sugarcane Research Institution, Yunnan Agricultural University, Kunming, Yunnan, China. yangqinghui@163.com. FAU - Wang, Kai AU - Wang K AUID- ORCID: 0000-0002-1074-0438 AD - 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. kwang@fafu.edu.cn. AD - State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, Guangxi, China. kwang@fafu.edu.cn. LA - eng GR - 31771862/National Natural Science Foundation of China/ GR - 2017.1.5/National Engineering Research Center of Sugarcane Open Fund/ GR - NER2018.1.5/National Engineering Research Center of Sugarcane Open Fund/ GR - SKLCUSA-b201808/State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/ PT - Journal Article DEP - 20191005 PL - Germany TA - Theor Appl Genet JT - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik JID - 0145600 SB - IM MH - Chromosomes, Plant/*genetics MH - Ecotype MH - *Evolution, Molecular MH - Gene Rearrangement/genetics MH - Genetics, Population MH - *Genome, Plant MH - In Situ Hybridization, Fluorescence MH - Karyotyping MH - Metaphase/genetics MH - Phylogeny MH - Saccharum/*genetics MH - Sequence Analysis, DNA MH - Time Factors EDAT- 2019/10/07 06:00 MHDA- 2020/09/17 06:00 CRDT- 2019/10/07 06:00 PHST- 2019/05/09 00:00 [received] PHST- 2019/09/24 00:00 [accepted] PHST- 2019/10/07 06:00 [pubmed] PHST- 2020/09/17 06:00 [medline] PHST- 2019/10/07 06:00 [entrez] AID - 10.1007/s00122-019-03450-w [pii] AID - 10.1007/s00122-019-03450-w [doi] PST - ppublish SO - Theor Appl Genet. 2020 Jan;133(1):187-199. doi: 10.1007/s00122-019-03450-w. Epub 2019 Oct 5.