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

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 SNP s, 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 genomicmore » analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species.« less

Authors:

Yang, Xiping ^[1]; Song, Jian ^[1]; Todd, James ^[2]; Peng, Ze ^[1]; Paudel, Dev ^[1]; Luo, Ziliang ^[1]; Ma, Xiaokai ^[3]; You, Qian ^[4]; Hanson, Erik ^[1]; Zhao, Zifan ^[1]; Zhao, Yang ^[1]; Zhang, Jisen ^[3]; Ming, Ray ^[5]; Wang, Jianping  ^[4]

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+ Show Author Affiliations

1. Agronomy Department University of Florida Gainesville FL USA
2. Sugarcane Research Unit USDA‐ARS Houma LA USA
3. Center 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
4. Agronomy Department University of Florida Gainesville FL USA, Center 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
5. Center 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, Department of Plant Biology University of Illinois at Urbana‐Champaign Urbana IL USA

Publication Date:

Wed Aug 29 00:00:00 EDT 2018

Sponsoring Org.:

USDOE

OSTI Identifier:

1467750

Alternate Identifier(s):

OSTI ID: 1467751

Grant/Contract Number:  

DE‐SC0006995

Resource Type:

Published Article

Journal Name:

Plant Biotechnology Journal

Additional Journal Information:

Journal Name: Plant Biotechnology Journal Journal Volume: 17 Journal Issue: 2; Journal ID: ISSN 1467-7644

Publisher:

Wiley-Blackwell

Country of Publication:

United Kingdom

Language:

English