Recent polyploidization events in three Saccharum founding species

Zhang, Jisen; Zhang, Qing; Li, Leiting; Tang, Haibao; Zhang, Qiong; Chen, Yang; Arrow, Jie; Zhang, Xingtan; Wang, Aiqin; Miao, Chenyong; Ming, Ray

doi:10.1111/pbi.12962

Title: Recent polyploidization events in three Saccharum founding species

Journal Article · 24 July 2018 · Plant Biotechnology Journal

DOI: https://doi.org/10.1111/pbi.12962 · OSTI ID:1461564

Zhang, Jisen ^[1]; Zhang, Qing ^[2];

^[3]; Tang, Haibao ^[4]; Zhang, Qiong ^[5]; Chen, Yang ^[6]; Arrow, Jie ^[7]; Zhang, Xingtan ^[4]; Wang, Aiqin ^[8]; Miao, Chenyong ^[4];

^[9]

FAFU and UIUC Joint Center for Genomics and Biotechnology Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture Fujian Agriculture and Forestry University Fuzhou Fujian China, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of Genetics Breeding and Multiple Utilization of Corps Ministry of Education Fujian Agriculture and Forestry University Fuzhou Fujian China, College of Life Sciences Fujian Normal University Fuzhou China
FAFU and UIUC Joint Center for Genomics and Biotechnology Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture Fujian Agriculture and Forestry University Fuzhou Fujian China, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of Genetics Breeding and Multiple Utilization of Corps Ministry of Education Fujian Agriculture and Forestry University Fuzhou Fujian China, College of Life Sciences Fujian Agriculture and Forestry University Fuzhou Fujian China
College of Horticulture Nanjing Agricultural University Nanjing China
FAFU and UIUC Joint Center for Genomics and Biotechnology Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture Fujian Agriculture and Forestry University Fuzhou Fujian China, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of Genetics Breeding and Multiple Utilization of Corps Ministry of Education Fujian Agriculture and Forestry University Fuzhou Fujian China
Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical Garden Chinese Academy of Sciences Wuhan China
College of Life Sciences Fujian Normal University Fuzhou China
Department of Plant Biology University of Illinois at Urbana‐Champaign Urbana IL USA
State Key Lab for Conservation and Utilization of Subtropical Agro‐biological Resources Guangxi University Nanning China
FAFU and UIUC Joint Center for Genomics and Biotechnology Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture Fujian Agriculture and Forestry University Fuzhou Fujian China, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of Genetics Breeding and Multiple Utilization of Corps Ministry of Education Fujian Agriculture and Forestry University Fuzhou Fujian China, Department of Plant Biology University of Illinois at Urbana‐Champaign Urbana IL USA

Summary The complexity of polyploid Saccharum genomes hindered progress of genome research and crop improvement in sugarcane. To understand their genome structure, transcriptomes of 59 F ₁ individuals derived from S. officinarum LA Purple and S. robustum Molokai 5829 (2 n = 80, x = 10 for both) were sequenced, yielding 11 157 and 8998 SNP s and 83 and 105 linkage groups, respectively. Most markers in each linkage group aligned to single sorghum chromosome. However, 71 interchromosomal rearrangements were detected between sorghum and S. officinarum or S. robustum , and 24 (33.8%) of them were shared between S. officinarum and S. robustum , indicating their occurrence before the speciation event that separated these two species. More than 2000 gene pairs from S. spontaneum , S. officinarum and S. robustum were analysed to estimate their divergence time. Saccharum officinarum and S. robustum diverged about 385 thousand years ago, and the whole‐genome duplication events occurred after the speciation event because of shared interchromosomal rearrangements. The ancestor of these two species diverged from S. spontaneum about 769 thousand years ago, and the reduction in basic chromosome number from 10 to 8 in S. spontaneum occurred after the speciation event but before the two rounds of whole‐genome duplication. Our results proved that S. officinarum is a legitimate species in its own right and not a selection from S. robustum during the domestication process in the past 10 000 years. Our findings rejected a long‐standing hypothesis and clarified the timing of speciation and whole‐genome duplication events in Saccharum .

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Sponsoring Organization:: USDOE

Grant/Contract Number:: DE‐SC0010686

OSTI ID:: 1461564

Alternate ID(s):: OSTI ID: 1461565

Journal Information:: Plant Biotechnology Journal, Journal Name: Plant Biotechnology Journal Vol. 17 Journal Issue: 1; ISSN 1467-7644

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Cited by: 28 works

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