《植物生理学报》 2018, 54(4): 581-593

三倍体香蕉优良品种‘Grand Nain’全基因组变异挖掘

邵秀红^1,2,#, 胡春华^2,#, 盛鸥², 毕方铖², 邓贵明², 杨乔松^2,*, 易干军^2,*

¹湖南农业大学园艺园林学院, 长沙410128; ²广东省农业科学院果树研究所, 农业部南亚热带果树生物学与遗传资源利用重点实验室, 广东省热带亚热带果树研究重点实验室, 广州510640

通信作者：杨乔松；E-mail: yiganjun@vip.163.com, soyang@hotmail.com

摘　要：

为全面揭示香蕉(Musa spp.)优良品种的全基因组变异类型, 本研究采用高通量重测序技术, 对当前香蕉主栽品种‘Grand Nain’ (AAA group, Cavendish subgroup)开展全基因组重测序, 测序深度53.79 X。与野生香蕉‘DH-Pahang’参考基因组比对, 共检测到4 598 633个单核苷酸多态位点(SNP), 484 752个小片段插入缺失位点(Indel), 57 047个结构变异(SV), 共导致36 277个基因变异; 代谢通路分析(KEGG)发现, 植物激素信号转导途径相关基因的变异最多, 存在442个基因变异, 其中乙烯合成和信号转导途径中1-氨基环丙烷-1-羧酸氧化酶基因(ACO)、1-氨基环丙烷-1-羧酸合成酶基因(ACS)、EIN3/EILs、ERS、RAN、EBF、EIN2等基因都存在变异。特别是序列分析发现‘Grand Nain’中的MaACO1基因与参考基因组相比存在2个变异位点并导致氨基酸的突变, 且在A和B基因组中MaACO1基因存在2个相邻的变异位点。本研究为香蕉贮藏保鲜等相关分子标记开发、基因功能研究, 以及基于基因组编辑技术的香蕉遗传改良提供依据。

关键词：香蕉; 全基因组重测序; 单核苷酸多态; 小片段插入缺失; 结构变异; 基因变异

收稿：2017-09-11   修定：2018-03-14

资助：国家自然科学基金(31372018、31772267和31601720)、农业部“948”项目(2011-G16和2016-X22)、国家香蕉产业技术体系项目(CARS-32-01)、公益性行业(农业)科研专项经费(201403036)、广东省省级科技计划项目(2012-A020100007、2014B050502007、2016B020233002和2017A030303044)、“十二五”农村领域国家科技计划项目(2013BAD02B02)和广州市科技计划项目(2017-07010154)。

Genome-wide variations of triploid banana (AAA group) ‘Grand Nain’ by whole-genome resequencing

SHAO Xiu-Hong^1,2,#, HU Chun-Hua^2,#, SHENG Ou², BI Fang-Cheng², DENG Gui-Ming², YANG Qiao-Song^2,*, YI Gan-Jun^2,*

¹Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China; ²Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture; Guangdong Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China

Corresponding author: YANG Qiao-Song; E-mail: yiganjun@vip.163.com, soyang@hotmail.com

Abstract:

For an overall understanding of the whole genome of important banana (Musa sp.) cultivar Grand Nain, high-throughput sequencing technology was used by resequencing with 53.79 X depth to detect its variations. Results revealed 4 598 633 single nucleotide polymorphisms (SNP), 484 752 small insertion-deletions (Indels) and 57 047 structural variations (SV). They confer 36 277 DNA variations. Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of variations showed that 442 genes of plant hormone signal transduction had DNA variations. These variations include two main enzymes, 1-aminocyclopropane-1-carboxylate oxidase (ACO) and 1-aminocyclopropane-1-carboxylate synthase (ACS), in ethylene biosynthesis pathway. In addition, several variations in ethylene signal transduction such as ethylene-insensitive 3-like (EIN3/EILs), ethylene response sensor (ERS), response-to-antagonist (RAN), ethylene-insensitive 3-binding F-box (EBF), and EIN2 were also detected in ‘Grand Nain’, compared to the reference genome. The results of DNA and protein sequencing analyses of MaACO1 showed that, there were two nucleotide variations in DNA sequence, leading to changes in protein sequence, and the two nucleotide variations in MaACO1 were also detected in A and B genomes of banana. These results would improve genetic engineering and forward genetic accomplishments with an aim to molecular breeding in banana.

Key words: banana; whole-genome resequencing; single nucleotide polymorphism; small Indel; structural variation; gene variation