黄秋葵嫩果多糖含量性状全基因组关联分析
Genome-Wide Association Analysis of Polysaccharide Content in Young Fruits of Okra
DOI: 10.12677/BR.2021.106094, PDF,    国家自然科学基金支持
作者: 戴志刚, 粟建光：中国农业科学院麻类研究所，湖南 长沙；孙 健：中国农业科学院麻类研究所，湖南 长沙；南通大学生命科学学院，江苏 南通；程玉静：江苏沿江地区农业科学研究所，江苏 南通；陆旭鹏, 李世玉, 谢冬微*：南通大学生命科学学院，江苏 南通
关键词: 黄秋葵；多糖含量；GWAS；SNP；候选基因；Okra； Polysaccharide Content； GWAS； SNP； Candidate Gene
摘要: 植物多糖是具有保健功能的生物活性成分，黄秋葵鲜嫩果具有很高的多糖含量。对黄秋葵多糖含量进行全基因组关联分析(Genome-wide Association Study, GWAS)，挖掘相关基因位点，可以为利用分子育种手段培育高多糖黄秋葵新品种奠定理论和材料基础。对180份黄秋葵种质进行GBS建库测序(Genotyping by sequencing, GBS)，结合多环境下黄秋葵多糖含量的表型数据进行全基因组范围的关联分析，以明确与多糖含量显著关联的SNP位点，挖掘位点附近可能与多糖含量相关的基因。通过4个环境共检测到46个显著关联的SNPs位点，其中Cluster1671-67622和Cluster86-210279位点至少在两个环境下稳定出现。在这2个显著关联的位点附近的100 Mb区域内发掘出黄秋葵多糖含量性状关系密切的候选基因，经过分析筛选确定UGT-糖基转移酶和MYB转录因子为候选基因。UGT-糖基转移酶和MYB转录因子与黄秋葵嫩果中多糖的合成、积累和分解紧密相关。本研究结果为阐明多糖的遗传调控机制提供了新的视角，亦为黄秋葵嫩果多糖含量的遗传改良奠定了一定的理论基础。
Abstract: Plant polysaccharide is a biological active component with health care function. The fresh and tender fruit of okra has a high content of polysaccharide. Genome-wide Association Study (GWAS) on the polysaccharide content of okra and the mining of relevant gene loci can lay a theoretical and material foundation for the cultivation of new varieties of okra with high polysaccharide by molecular breeding methods. Based on the accurate determination of polysaccharide content of 180 okra Germplasms in multi environment, the whole genome sequencing (Genotyping by sequencing, GBS) of the tested materials was carried out, and the genome-wide association analysis was carried out combined with the phenotypic data of polysaccharide content in multi environment, to identify the SNP sites significantly associated with polysaccharide content. Meanwhile, excellent genes which may be related to the content of polysaccharide near the sites were mined. A total of 46 SNPs were detected in four environments, and two of them were selected as candidate sites. In the 100 Mb region near these two significant loci, candidate genes closely related to the polysaccharide content traits of okra were found. UGT-glycosyltransferase and MYB transcription factor were finally identified as candidate genes. UGT-glycosyltransferase and MYB transcription factor are closely related to the synthesis, accumulation, and decomposition of polysaccharides in okra tender fruit. The results of this study provided a new perspective to clarify the genetic regulation mechanism of polysaccharides, and laid a theoretical basis for the genetic improvement of polysaccharide content in okra tender fruit.
文章引用：戴志刚, 孙健, 程玉静, 陆旭鹏, 李世玉, 谢冬微, 粟建光. 黄秋葵嫩果多糖含量性状全基因组关联分析[J]. 植物学研究, 2021, 10(6): 749-760. https://doi.org/10.12677/BR.2021.106094

参考文献

[1] 卢隆杰, 苏浓, 岳森. 菜药花兼用型植物——黄秋葵[J]. 特种经济动植物, 2004(10): 36.
[2] Yoshida, T. (2001) Synthesis of Polysaccharides Having Specific Biological Activities. Progress in Polymer Science, 26, 379-441. [Google Scholar] [CrossRef] 
[3] Adelakun, O.E., Oyelade, O.J., Ade-Omowaye, B.I.O., Adeyemi, I.A. and Van de Venter, M. (2009) Chemical Composition and the Antioxidative Properties of Nigerian Okra Seed (Abelmoschus esculentus Moench) Flour. Food and Chemical Toxicology, 47, 1123-1126. [Google Scholar] [CrossRef] [PubMed]
[4] Ameena, K., Dilip, C., Saraswathi, R., Krishnan, P.N. and Sankar, C. and Simi, S.P. (2010) Isolation of the Mucilages from Hibiscus Rosasinensis Linn. And Okra (Abelmoschus esculentus L.) and Studies of the Binding Effects of the Mucilages. Asian Pacific Journal of Tropical Medicine, 3, 539-543. [Google Scholar] [CrossRef] 
[5] Mehta, N., Asati, B.S. and Mamidwar, S.R. (2007) Heterosis and Gene Action in Okra. Bangladesh Journal of Agricultural Research, 32, 421-432. [Google Scholar] [CrossRef] 
[6] Wammanda, D.T., Kadams, A.M. and Jonah, P.M. (2010) Combining ability Analysis and Heterosis in a Diallel Cross of Okra (Abelmoschus esculentus (L.) Moench). African Journal of Agricultural Research, 5, 2108-2115.
[7] Olayiwola, M.O. and Ariyo, O.J. (2013) Relative Discriminatory Ability of GGE Biplot and YSi in the Analysis of Genotype×Environment Interaction in Okra (Abelmoschus esculentus). International Journal of Plant Breeding and Genetics, 7, 146-158. [Google Scholar] [CrossRef] 
[8] Islam, M., Hossain, N., Alamgir, M. and Kibria, G., (2014) Comparative Effects of Biogas Plant Residues, Poultry Manure and Inorganic Fertilizer on Growth and Yield of Ladies Finger. IOSR Journal of Agriculture and Veterinary Science, 7, 2319-2372.
[9] 黄阿根, 陈学好, 高云中, 车婧. 黄秋葵的成分测定和分析[J]. 食品科学, 2007, 28(10): 451-455.
[10] Mairuae, N., Connor, J.R., Lee, S.Y. and Cheepsunthorn, P. and Tongjaroenbuangam, W. (2015) The Effects of Okra (Abelmoschus esculentus Linn.) on the Cellular Events Associated with Alzheimer’s Disease in a Stably Expressed HFE Neuroblastoma SH-SY5Y Cell Line. Neuroscience Letters, 603, 6-11. [Google Scholar] [CrossRef] [PubMed]
[11] Monte, L.G., Santi-Gadelha, T., Reis, L.B., Braganhol, E., Prietsch, R.F., Dellagostin, O.A., Lacerda, R.R.E., Gadelha, A.A., Concei, F.R.O. and Pinto, L.S. (2014) Lectin of Abelmoschus esculentus (Okra) Promotes Selective Antitumor Effects in Human Breast Cancer Cells. Biotechnology Letters, 36, 461-469. [Google Scholar] [CrossRef] [PubMed]
[12] 王旭, 韩春乐, 周亚楠, 王春国, 宋文芹, 陈成彬. 黄秋葵查尔酮合成酶基因AeCHS的克隆与表达分析[J]. 植物遗传资源学报, 2014, 15(3): 561-567.
[13] 张少平, 邱珊莲, 郑云云, 张帅, 吴松海, 何炎森, 郑开斌. 紫色黄秋葵转录组功能基因测序及分析[J]. 核农学报, 2017, 31(4): 643-653.
[14] 李和平, 姚运法, 练冬梅, 赖正锋, 洪建基. 黄秋葵果实转录组测序及分析[J]. 生物技术通报, 2018, 34(3): 121-127.
[15] 韩文韬. 海带岩藻多糖合成关键基因家族的全基因组鉴定和系统发育研究[D]: [硕士学位论文]. 上海: 上海海洋大学, 2019.
[16] 范华. 盐胁迫下发菜多糖代谢相关差异表达基因的克隆与原核表达[D]: [硕士学位论文]. 西安: 陕西科技大学, 2017.
[17] 耿腊, 黄业昌, 李梦迪, 谢尚耿, 叶玲珍, 张国平. 大麦籽粒β-葡聚糖含量的全基因组关联分析[J]. 作物学报, 2021, 47(7): 1205-1214.
[18] Alexander, D.H., Novembre, J. and Lange, K. (2009) Fast Model-Based Estimation of Ancestry in Unrelated Individual. Genome Research, 19, 1655-1664. [Google Scholar] [CrossRef] [PubMed]
[19] Bradbury, P.J., Zhang, Z., Kroon, D.E., Casstevens, T.M., Ramdoss, Y. and Buckler, E.S. (2007) TASSEL: Software for Association Mapping of Complex Traits in Diverse Samples. Bioinformatics, 23, 2633-2635. [Google Scholar] [CrossRef] [PubMed]
[20] Gu, X.R., Feng, C.G., Ma, L., Song, C., Wang, Y., Da, Y., et al. (2011) Genome-Wide Association Study of Body Weight in Chicken F2 Resource Population. PLoS ONE, 6, Article ID: e21872. [Google Scholar] [CrossRef] [PubMed]
[21] Liu, R.R., Sun, Y.F., Zhao, G.P., Wang, F., Wu, D., Zheng, M., et al. (2013) Genome-Wide Association Study Identifies Loci and Candidate Genes for Body Composition and Meat Quality Traits in Beijing-You Chickens. PLoS ONE, 8, Article ID: e61172. [Google Scholar] [CrossRef] [PubMed]
[22] Zhao, X., Han, Y., Li, Y., Liu, D., Sun, M., Zhao, Y., et al. (2015) Loci and Candidate Gene Identification for Resistance to Sclerotinia sclerotiorum in Soybean (Glycine max L. Merr.) via Association and Linkage Maps. The Plant Journal, 82, 245-255. [Google Scholar] [CrossRef] [PubMed]
[23] Han, Y., Zhao, X., Cao, G., Wang, Y., Li, Y., Liu, D., et al. (2015) Genetic Characteristics of Soybean Resistance to HG Type 0 and HG Type 1.2.3.5.7 of the Cyst Nematode Analyzed by Genome-Wide Association Mapping. BMC Genomics, 16, Article No. 598. [Google Scholar] [CrossRef] [PubMed]
[24] Su, J., Pang, C., Wei, H., Li, L., Liang, B., Wang, C., et al. (2016) Identification of Favorable SNP Alleles and Candidate Genes for Traits Related to Early Maturity via GWAS in Upland Cotton. BMC Genomics, 17, Article No. 687. [Google Scholar] [CrossRef] [PubMed]
[25] Yang, X., Nong, B., Xia, X., Zhang, Z., Zeng, Y., Liu, K., et al. (2016) Rapid Identification of a New Gene Influencing Low Amylose Content in Rice Landraces (Oryza sativa L.) Using Genome-Wide Association Study with Specific-Locus Amplified Fragment Sequencing. Genome, 60, 465-472. [Google Scholar] [CrossRef] [PubMed]
[26] 田鹏, 刘占林. 糖基转移酶超家族[J]. 生命的化学, 2011, 31(5): 732-736.
[27] 陈云, 赵丽婷, 顾正华, 李由然, 石贵阳, 丁重阳. 糖基转移酶GL24971对灵芝多糖合成的影响[J]. 食品与发酵工业, 2021: 1-9. [Google Scholar] [CrossRef] 
[28] 孙浩然. 铝胁迫下大豆三个UDP-糖基转移酶基因的功能分析[D]: [硕士学位论文]. 长春: 吉林大学, 2018.
[29] Stracke, R., Ishihara, H., Huep, G., Barsch, A., Mehrtens, F., Niehaus, K., et al. (2007) Differential Regulation of Closely Related R2R3-MYB Transcription Factors Controls Flavonol Accumulation in Different Parts of the Arabidopsis Thaliana Seedling. The Plant Journal, 50, 660-677. [Google Scholar] [CrossRef] 
[30] Song, S., Qi, T., Huang, H., Ren, Q., Wu, D., Chang, C., et al. (2011) The Jasmonate-ZIM Domain Proteins interact with the R2R3-MYB Transcription Factors MYB21 and MYB24 to Affect Jasmonate-Regulated Stamen Development in Arabidopsis. The Plant Cell, 23, 1000-1013. [Google Scholar] [CrossRef] [PubMed]
[31] Pesch, M. and Huelskamp, M. (2009) One, Two, Three ... Models for Trichome Patterning in Arabidopsis. Current Opinion in Plant Biology, 12, 587-592. [Google Scholar] [CrossRef] [PubMed]
[32] Walford, S.-A., Wu, Y., Llewellyn, D.J. and Dennis, E.S. (2011) GhMYB25-Like: A Key Factor in Early Cotton Fiber Development. The Plant Journal, 65, 785-797. [Google Scholar] [CrossRef] 
[33] Byrne, M.E., Barley, R., Curtis, M., Arroyo, J.M., Dunham, M., Hudson, A. et al. (2000) Asymmetric leaves1 Mediates Leaf Patterning and Stem Cell Function in Arabidopsis. Nature, 408, 967-971. [Google Scholar] [CrossRef] [PubMed]
[34] Shin, R., Burch, A.Y., Huppert, K.A., Tiwari, S.B., Murphy, A.S., Guilfoyle, T.J., et al. (2007) The Arabidopsis Transcription Factor MYB77 Modulates Auxin Signal Transduction. The Plant Cell, 19, 2440-2453. [Google Scholar] [CrossRef] [PubMed]
[35] Mu, R.L., Cao, Y.R., Liu, Y.F., Lei, G., Zou, H.-F., Liao, Y., et al. (2009) An R2R3-Type Transcription Factor Gene AtMYB59 Regulates Root Growth and Cell Cycle Progression in Arabidopsis. Cell Research, 19, 1291-304. [Google Scholar] [CrossRef] [PubMed]
[36] Cominelli, E., Galbiati, M., Vavasseur, A., Conti, L., Sala, T., Vuylsteke, M., et al. (2005) A Guard-Cellspecific MYB Transcription Factor Regulates Stomatal Movements and Plant Drought Tolerance. Current Biology, 15, 1196-1200. [Google Scholar] [CrossRef] [PubMed]
[37] Jung, C., Seo, J.S., Han, S.W., Koo, Y.J., Kim, C.H., Song, S.I., et al. (2008) Overexpression of AtMYB44 Enhances Stomatal Closure to Confer Abiotic Stress Tolerance in Transgenic Arabidopsis. Plant Physiology, 146, 623-635. [Google Scholar] [CrossRef] [PubMed]
[38] Park, M.Y., Kang, J.Y. and Kim, S.Y. (2011) Overexpression of AtMYB52 Confers ABA Hypersensitivity and Drought Tolerance. Molecular Cells, 31, 447-54. [Google Scholar] [CrossRef] [PubMed]