CP: Genomics; CP: Plants; I. polycarpa; IpSTP5; evolution; fatty acids; genome; oil biosynthesis; Phylogeny; Plant Breeding; Base Sequence; Genome-Wide Association Study; Salicaceae/genetics; Salicaceae; Biochemistry, Genetics and Molecular Biology (all)
Abstract :
[en] The deciduous tree Idesia polycarpa can provide premium edible oil with high polyunsaturated fatty acid contents. Here, we generate its high-quality reference genome, which is ∼1.21 Gb, comprising 21 pseudochromosomes and 42,086 protein-coding genes. Phylogenetic and genomic synteny analyses show that it diverged with Populus trichocarpa about 16.28 million years ago. Notably, most fatty acid biosynthesis genes are not only increased in number in its genome but are also highly expressed in the fruits. Moreover, we identify, through genome-wide association analysis and RNA sequencing, the I. polycarpa SUGAR TRANSPORTER 5 (IpSTP5) gene as a positive regulator of high oil accumulation in the fruits. Silencing of IpSTP5 by virus-induced gene silencing causes a significant reduction of oil content in the fruits, suggesting it has the potential to be used as a molecular marker to breed the high-oil-content cultivars. Our results collectively lay the foundation for breeding the elite cultivars of I. polycarpa.
Disciplines :
Agriculture & agronomy
Author, co-author :
Zuo, Yi ✱; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China, China National Botanical Garden, Beijing 100093, China
Liu, Hongbing ✱; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
Li, Bin ✱; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China, China National Botanical Garden, Beijing 100093, China
Zhao, Hang ; Université de Liège - ULiège > TERRA Research Centre ; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
Li, Xiuli; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
Chen, Jiating; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China, University of Chinese Academy of Sciences, Beijing 100049, China
Wang, Lu; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
Zheng, Qingbo; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China, China National Botanical Garden, Beijing 100093, China
He, Yuqing; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China, Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257300, China
Zhang, Jiashuo; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China, University of Chinese Academy of Sciences, Beijing 100049, China
Wang, Minxian; CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
Liang, Chengzhi; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
Wang, Lei ✱; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China, Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257300, China, China National Botanical Garden, Beijing 100093, China, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: wanglei@ibcas.ac.cn
We thank Dr. Suhua Yang and Dr. Bin Han from the Public Technology Center of the Institute of Botany, Chinese Academy of Sciences, for excellent technical assistance on flow cytometry determination, respectively. We also thank Dr. Chenxu Liu from China Agriculture University for his excellent technical assistance on oil content by low-field nuclear magnetic resonance. This work was supported by Science & Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta (2022SZX13), the Rural Revitalization Projects of the CAS (KFJ-XCZX-202301), and the National Natural Science Foundation of China (nos. 32002066 and 32370307). Y.Z. and H.L. analyzed the data and wrote the article. B.L. performed material collection and RNA sequencing. H.Z. and X.L. analyzed the data. J.C. performed VIGS assay. Lu Wang performed fatty acid determination. Q.Z. Y.H. and J.Z. performed DNA extraction. M.W. C.L. and Lei Wang revised the manuscript. Lei Wang agrees to serve as the author responsible for contact and ensures communication. The authors declare no competing interests.We thank Dr. Suhua Yang and Dr. Bin Han from the Public Technology Center of the Institute of Botany, Chinese Academy of Sciences, for excellent technical assistance on flow cytometry determination, respectively. We also thank Dr. Chenxu Liu from China Agriculture University for his excellent technical assistance on oil content by low-field nuclear magnetic resonance. This work was supported by Science & Technology Specific Projects in Agricultural High-tech Industrial Demonstration Area of the Yellow River Delta ( 2022SZX13 ), the Rural Revitalization Projects of the CAS ( KFJ-XCZX-202301 ), and the National Natural Science Foundation of China (nos. 32002066 and 32370307 ).
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