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Genetics and Genomics of Polyploid Plants

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Front. Plant Sci. | doi: 10.3389/fpls.2018.00604

Genome Sequencing and Analysis of the Peanut B-genome Progenitor (Arachis ipaensis)

 Qing Lu1, Haifen Li1, Yanbin Hong1, Guoqiang Zhang2, Shijie Wen1, Xingyu Li1, Guiyuan Zhou1, Shaoxiong Li1, Hai Liu1, Haiyan Liu1,  Zhong-Jian Liu2,  Rajeev K. Varshney3, Xiaoping Chen1* and Xuanqiang Liang1*
  • 1South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, China
  • 2Shenzhen Key Laboratory for Orchid Conservation and Utilization, China
  • 3International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), India

Peanut (Arachis hypogaea L.), an important leguminous crop, is widely cultivated in tropical and subtropical regions. Peanut is an allotetraploid, havingA and B subgenomes that maybe have originated in its diploid progenitors Arachis duranensis (A-genome) and Arachis ipaensis (B-genome), respectively. We previously sequenced the former and here present the draft genome of the latter, expanding our knowledge of the unique biology of Arachis. The assembled genome of A. ipaensis is ~1.39 Gb with 39,704 predicted protein-encoding genes. A gene family analysis revealed that the FAR1 family may be involved in regulating peanut special fruit development. Genomic evolutionary analyses estimated that the two progenitors diverged ~3.3 million years ago and suggested that A. ipaensis experienced a whole-genome duplication event after the divergence of Glycine max. We identified a set of disease resistance-related genes and candidate genes for biological nitrogen fixation. In particular, two and four homologous genes that may be involved in the regulation of nodule development were obtained from A.ipaensis and A.duranensis, respectively. We outline a comprehensive network involved in drought adaptation. Additionally, we analyzed the metabolic pathways involved in oil biosynthesis and found genes related to fatty acid and triacylglycerol synthesis. Importantly, three new FAD2 homologous genes were identified from A. ipaensis and one was completely homologous at the amino acid level with FAD2 from A.hypogaea. The availability of the A. ipaensis and A. duranensis genomic assemblies will advance our knowledge of the peanut genome.

Keywords: Arachis ipaensis, genome sequence, genome evolution, polyploidizations, Whole genome duplication

Received: 06 Feb 2018; Accepted: 16 Apr 2018.

Edited by:

Jun Yang, Shanghai Chenshan Plant Science Research Center (CAS), China

Reviewed by:

Junjie Fu, Institute of Crop Sciences (CAAS), China
Xuehui Huang, Shanghai Normal University, China  

Copyright: © 2018 Lu, Li, Hong, Zhang, Wen, Li, Zhou, Li, Liu, Liu, Liu, Varshney, Chen and Liang. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Xiaoping Chen, Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou, China, chenxiaoping@gdaas.cn
Prof. Xuanqiang Liang, Crops Research Institute, Guangdong Academy of Agricultural Sciences, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou, China, liangxuanqiang@gdaas.cn