菜豆花色全基因组关联分析

doi:10.16420/j.issn.0513-353x.2021-0056

摘要/Abstract

摘要：

以124份菜豆为试验材料,分别在2019年和2020年调查花色表型,利用全基因组关联分析（GWAS）的方法对调控花色的基因进行挖掘。结果表明：2年间供试菜豆花色表型基本一致,仅有1份材料存在差异。对124份菜豆材料进行重测序共获得517.58 Gb的数据量（10×）,通过与菜豆参考基因组比对,获得5 130 030个SNP,过滤后得到3 701 584个SNP。利用这些高质量的SNP基于压缩混合线性模型（compress mixed linear model,cMLM）将菜豆花色调控基因定位在6号染色体322.67 kb的区域内;在候选区域内共鉴定到8个基因,其中,Phvul.006G020200为参与花青素调控的MYB转录因子基因,且在不同花色材料中差异性表达,为调控菜豆花色的关键候选基因。

关键词: 菜豆, 全基因组关联分析, 花色, 表达

Abstract:

Flower color of 124 common beans investigated in 2019 and 2020 was used to identify its controlling genes by Genome-wide association study（GWAS）. The phenotypic data showed that the flower color between the two years had a relatively high similarity besides one individual. We obtained 517.58 Gb（~10×）of raw data by resequencing 124 common bean individuals. A total of 5 130 030 SNP were generated against the common bean reference genome,and 3 701 584 SNP were retained by filtering. GWAS analysis based on these high-quality SNPs with compress mixed linear model（cMLM）located flower color regulatory gene in the 322.67 kb region on chromosome 6. Within the region,eight genes were annotated based on the common bean reference genome. Particularly,Phvul.006G020200 was the MYB transcription factor of anthocyanin regulation and had differential expression in flower color. Thus,we assume that Phvul.006G020200 is a key candidate gene for regulating bean flower color.

Key words: common bean, GWAS, flower color, expressions

中图分类号:

S643.1

卢甜甜, 刘志远, 徐兆生, 张合龙, 李国亮, 折红兵, 钱伟. 菜豆花色全基因组关联分析[J]. 园艺学报, 2022, 49(2): 332-340.

LU Tiantian, LIU Zhiyuan, XU Zhaosheng, ZHANG Helong, LI Guoliang, SHE Hongbing, QIAN Wei. Genome-wide Association Studies for Flower Color in Common Bean[J]. Acta Horticulturae Sinica, 2022, 49(2): 332-340.

图/表 8

参考文献 30

[1]	Ates D, Asciogul T K, Nemli S, Erdogmus S, Esiyok D, Tanyolac M B. 2018. Association mapping of days to flowering in common bean(Phaseolus vulgaris L.)revealed by DArT markers. Mol Breeding, 38:113. doi: 10.1007/s11032-018-0868-0 URL
[2]	Bassett M J, McClean P. 2000. A brief review of the genetics of partly colored seed coats in common bean. Annu Rep Bean Improve Coop, 43:99-101.
[3]	Beninger C W, Hosfield G L, Nair M G. 1998. Flavonol glycosides from the seed coat of a new manteca-type dry bean(Phaseolus vulgaris L.). Agric Food Chem, 46 (8):2906-2910. doi: 10.1021/jf9801522 URL
[4]	Chen Jibao, Jing Ruilian, Mao Xinguo, Chang Xiaoping, Wang Shumin. 2008. A response of PvP5CS2 Gene to abiotic stresses in common bean. Acta Agronomica Sinica,(7):1121-1127. (in Chinese)
	陈吉宝, 景蕊莲, 毛新国, 昌小平, 王述民. 2008. 普通菜豆PvP5CS2基因对逆境胁迫的应答. 作物学报,(7):1121-1127.
[5]	Cong Juan, Li Xiaoling, Gong Li, Li Liangui. 2007. Study on the method and conditions for spinach genomic DNA extraction. Journal of Changchun University of Technology, 28:467-472. (in Chinese)
	丛娟, 李晓玲, 宫莉, 李连贵. 2007. 菠菜基因组DNA提取方法与条件的研究. 长春工业大学学报, 28:467-472.
[6]	Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L. 2010. MYB transcription factors in Arabidopsis. Trends in Plant Science, 15 (10):573-581. doi: 10.1016/j.tplants.2010.06.005 URL
[7]	Emerson R A. 1909. Factors for mottling in beans. Journal of Heredity, 5 (1):368-375. doi: 10.1093/oxfordjournals.jhered.a107897 URL
[8]	Geng Qinghe. 2017. QTL mapping for seed size and shape in common bean[M. D. Dissertation]. Beijing: Chinese Academy of Agricultural Sciences. (in Chinese)
	耿庆河. 2017. 普通菜豆籽粒大小和形状的QTL定位[硕士论文]. 北京: 中国农业科学院.
[9]	Hong Y, Yang L W, Li M L, Dai S L. 2016. Comparative analyses of light-induced anthocyanin accumulation and gene expression between the ray florets and leaves in chrysanthemum. Plant Physiol and Biochem, 103:120-132. doi: 10.1016/j.plaphy.2016.03.006 URL
[10]	Koes R, Verweij W, Quattrochio F. 2005. Flavonoids:a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci, 10:236-242. doi: 10.1016/j.tplants.2005.03.002 URL
[11]	Lamprecht H. 1935. Zur Genetik von Phaseolus vulgaris. XII. Über die vererbung der blüten- und stammfarbe. Hereditas, 21:129-166. doi: 10.1111/j.1601-5223.1936.tb03196.x URL
[12]	Li Y M, Liang J, Zeng X Z, Guo H, Luo Y W, Kear P, Zhang S M, Zhu G T. 2021. Genome-wide analysis of MYB gene family in potato provides insights into tissue-specific regulation of anthocyanin biosynthesis. Horticultural Plant Journal, 7 (2):129-141. doi: 10.1016/j.hpj.2020.12.001 URL
[13]	Lin Qifang, Liu Tingting, Liu Jieru, Cai Ming, Cheng Tangren, Wang Jia, Zhang Qixiang, Pan Huitang. 2021. Flavonoids composition and content in petals of Lagerstroemia and Heimia species and cultivars. Acta Horticulturae Sinica, 48 (10):1956-1968. (in Chinese)
	林启芳, 刘婷婷, 刘洁茹, 蔡明, 程堂仁, 王佳, 张启翔, 潘会堂. 2021. 紫薇属与黄薇属植物花瓣类黄酮组成及含量分析. 园艺学报, 48 (10):1956-1968.
[14]	Lou Qian, Liu Bing, Hu Bichun, Hou Ting, Liu Yali. 2021. Research progress on the color development of blue flowers of monocots. Acta Horticulturae Sinica, 48 (10):2018-2030. (in Chinese)
	娄倩, 刘冰, 胡碧春, 侯婷, 刘雅莉. 2021. 单子叶植物蓝色花呈色机理研究进展. 园艺学报, 48 (10):2018-2030.
[15]	Lu Suwen, Zheng Xuanang, Wang Jiayang, Fang Jinggui. 2021. Research progress on the metabolism of flavonoids in grape. Acta Horticulturae Sinica, 48 (12):2506-2524. (in Chinese)
	卢素文, 郑暄昂, 王佳洋, 房经贵. 2021. 葡萄类黄酮代谢研究进展. 园艺学报, 48 (12):2506-2524.
[16]	Mekapogu M, Vasamsetti B M K, Kwon O K, Ahn M S, Lim S H, Jung 1 J A. 2020. Anthocyanins in floral colors:biosynthesis and regulation in chrysanthemum flowers. International Journal of Molecular Sciences, 21 (18):6537. doi: 10.3390/ijms21186537 URL
[17]	Marrs K A, Alfenito M R, Lloyd A M, Walbot V. 1995. A glutathione S-transferase involved in vacuolar transfer encoded by the maize gene bronze-2. Nature, 375:397-400. doi: 10.1038/375397a0 URL
[18]	McClean P E, Bett K E, Stonehouse R, Lee R, Pflieger S, Moghaddam S M, Geffroy V, Miklas P, Mamidi S. 2018. White seed color in common bean(Phaseolus vulgaris)results from convergent evolution in the P(pigment)gene. New Phytologist, 219 (3):1112-1123. doi: 10.1111/nph.2018.219.issue-3 URL
[19]	Prakken R. 1972. Inheritance of colours in Phaseolus vulgaris L. III. On genes for red seed coat colour and a general synthesis. Meded Landbouwhoge school Wageningen, 29:1-82.
[20]	Schmutz J, McClean P E, Mamidi S, Wu G A, Cannon S B, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C, Torres-Torres M, Geffroy V, Moghaddam S M, Gao D, Abernathy B, Barry K, Blair M, Brick M A, Chovatia M, Gepts P, Goodstein D M, Gonzales M, Hellsten U, Hyten D L, Jia G, Kelly J D, Kudrna D, Lee R, Richard M M S, Miklas P N, Osorno J M, Rodrigues J, Thareau V, Urrea C A, Wang M, Yu Y, Zhang M, Wing R A, Cregan P B, Rokhsar D S, Jackson S A. 2014. A reference genome for common bean and genome-wide analysis of dual domestications. Nat Genet, 46:707-713. doi: 10.1038/ng.3008 pmid: 24908249
[21]	Sundaramoorthy J, Park G T, Chang J H, Lee J D, Kim J H, Seo H S, Chung G, Song J T. 2016. Identification and molecular analysis of four new alleles at the W1 locus associated with flower color in soybean. PLoS ONE, 11 (7):e0159865. doi: 10.1371/journal.pone.0159865 URL
[22]	Tang Xiaoxin, Huang Shuangquan. 2012. Research progress on diversity and variation in flower color. Plant Diversity and Resource, 34 (3):239-247. (in Chinese) doi: 10.3724/SP.J.1143.2012.12030 URL
	汤晓辛, 黄双全. 2012. 花色多样性与变异的研究进展. 植物分类与资源学报, 34 (3):239-247.
[23]	Xi H C, He Y J, Chen H Y. 2021. Functional characterization of SmbHLH13in anthocyanin biosynthesis and flowering in eggplant. Horticultural Plant Journal, 7 (1):73-80. doi: 10.1016/j.hpj.2020.08.006 URL
[24]	Yang Y, Li B, Feng C Y, Wu Q, Wang Q Y, Li S S, Yu X N, Wang L S. 2020. Chemical mechanism of flower color microvariation in Paeonia with yellow flowers. Horticultural Plant Journal, 6 (3):179-190. doi: 10.1016/j.hpj.2020.04.002 URL
[25]	Ying Zhen, Zhou Zhuang. 2019. The research advance of the plant metabolic regulation mechanism. Chinese Wild Plant Resources, 38 (3):75-79,85. (in Chinese)
	应震, 周庄. 2019. 植物花青苷代谢调控机理研究进展. 中国野生植物资源, 38 (3):75-79,85.
[26]	Zeng Meijuan, Liu Jianting, Zhuo Lingling, Chen Mindong, Ye Xinru, Wang Bin, Zhu Haisheng, Wen Qingfang. 2021. Application of genome-wide association study in vegetable breeding. China Vegetables,(4):41-47. (in Chinese)
	曾美娟, 刘建汀, 卓玲玲, 陈敏氡, 叶新如, 王彬, 朱海生, 温庆放. 2021. 全基因组关联分析在蔬菜育种研究中的应用. 中国蔬菜,(4):41-47.
[27]	Zhang C, Dong S, Xu J, He W, Yang T. 2018. PopLDdecay:a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics, 35 (10):1786-1788. doi: 10.1093/bioinformatics/bty875 URL
[28]	Zhang Y, Butelli E, Martin C. 2014. Engineering anthocyanin biosynthesis in plants. Current Opinion in Plant Biology, 19:81-90. doi: 10.1016/j.pbi.2014.05.011 pmid: 24907528
[29]	Zhang Yanming, Xing Guofang, Liu Meitao, Liu Xiaodong, Han Yuanhuai. 2013. Genome wide association study:opportunities and challenges in genomic research. Biotechnology Bulletin,(6):1-6. (in Chinese)
	张雁明, 邢国芳, 刘美桃, 刘晓东, 韩渊怀. 2013. 全基因组关联分析:基因组学研究的机遇与挑战. 生物技术通报,(6):1-6.
[30]	Zheng Qingdong, Wang Yi, Ou Yue, Ke Yujie, Yao Yahe, Wang Mengjie, Chen Jiayi, Ai Ye. 2021. Research advances of genes responsible for flower colors in Orchidaceae. Acta Horticulturae Sinica, 48 (10):2057-2072. (in Chinese)
	郑清冬, 王艺, 欧悦, 柯玉洁, 姚亚合, 王梦洁, 陈嘉忆, 艾叶. 2021. 兰科植物花色相关基因研究进展. 园艺学报, 48 (10):2057-2072.

引物名称Primer name	正向引物（5′-3′）Forward primer	反向引物（5′-3′）Reverse primer
Actin	GAAGTTCTCTTCCAACCATCC	TTCCTTGCTCATTCTGTCCG
Pl-006G020200	ATAAGCTCGAAGCACTCACC	CAGTGTTACTTCCAAACCAAGC
Pl-006G020300	CGACAGTTCGAAATGCTTTCTT	CGACAGTTCGAAATGCTTTCTT
Pl-006G020400	GACTGTGGTCACTAGGAAACTC	GACTGTGGTCACTAGGAAACTC
Pl-006G020500	ATGAAGGTAATCTGAAACTTGCTG	ATGAAGGTAATCTGAAACTTGCTG
Pl-006G020700	ACACATATGGTCCCACAAGAC	ACACATATGGTCCCACAAGAC
Pl-006G020800	CCTTGCTGATCTTAGCCATCTC	CCTTGCTGATCTTAGCCATCTC
Pl-006G020900	AGCGTCGAGTGGGTAAATATG	AGCGTCGAGTGGGTAAATATG
Pl-006G021000	GGTTGAAGTTAATCAATCAGGTCTTC	GGTTGAAGTTAATCAATCAGGTCTTC

引物名称Primer name	正向引物（5′-3′）Forward primer	反向引物（5′-3′）Reverse primer
Actin	GAAGTTCTCTTCCAACCATCC	TTCCTTGCTCATTCTGTCCG
Pl-006G020200	ATAAGCTCGAAGCACTCACC	CAGTGTTACTTCCAAACCAAGC
Pl-006G020300	CGACAGTTCGAAATGCTTTCTT	CGACAGTTCGAAATGCTTTCTT
Pl-006G020400	GACTGTGGTCACTAGGAAACTC	GACTGTGGTCACTAGGAAACTC
Pl-006G020500	ATGAAGGTAATCTGAAACTTGCTG	ATGAAGGTAATCTGAAACTTGCTG
Pl-006G020700	ACACATATGGTCCCACAAGAC	ACACATATGGTCCCACAAGAC
Pl-006G020800	CCTTGCTGATCTTAGCCATCTC	CCTTGCTGATCTTAGCCATCTC
Pl-006G020900	AGCGTCGAGTGGGTAAATATG	AGCGTCGAGTGGGTAAATATG
Pl-006G021000	GGTTGAAGTTAATCAATCAGGTCTTC	GGTTGAAGTTAATCAATCAGGTCTTC

基因名称 Gene ID	基因位置/bp Position	拟南芥基因座 Locus on Arabidopsis	功能注释 Functional annotation
Phvul.006G020200	8 414 030	AT5G06100	编码MYB家族转录因子 Encodes MYB family of transcription factors
Phvul.006G020300	8 364 678	AT1G08400	RINT-1/TIP-1家族,参与内质网对高尔基小泡介导的转运、逆行小泡介导的转运、高尔基到内质网的调节 RINT-1/TIP-1 family,involved in regulation of ER to Golgi vesicle-mediated transport,retrograde vesicle-mediated transport,Golgi to endoplasmic reticulum
Phvul.006G020400	8 544 660	AT5G35732	未见相关注释信息 No annotation information
Phvul.006G020500	8 568 891	AT5G10270	编码CDKC;1,是花椰菜花叶病毒（CaMV）针对病毒基因转录激活的CDKC激酶复合物的一部分,调节植物的生长发育 Encodes CDKC;1,part of a CDKC kinase complex that is targeted by cauliflower mosaic virus（CaMV）for transcriptional activation of viral genes. Also regulates plant growth and development
Phvul.006G020700	8 610 369	AT1G14370	编码蛋白激酶APK2a,参与细菌防御反应的正调控 Encodes protein kinase APK2a,involved in positive regulation of defense response to bacterium
Phvul.006G020800	8 626 154	AT2G30860	编码属于GST phi类的谷胱甘肽转移酶 Encodes glutathione transferase belonging to the phi class of GSTs
Phvul.006G020900	8 642 248	AT2G26980	编码一种丝氨酸-苏氨酸蛋白激酶,主要关于脱落酸激活信号通路,蛋白质磷酸化,脱落酸应答,细胞分裂素应答,信号转导 Encodes a serine-threonine protein kinase,involved in abscisic acid-activated signaling pathway,protein phosphorylation,response to abscisic acid,response to cytokinin,signal transduction
Phvul.006G021000	8 654 928	AT3G20320	编码ABC转运体的通透性样成分,参与从内质网到叶绿体的脂质转移 Encodes a permease-like component of an ABC transporter involved in lipid transfer from ER to chloroplast

基因名称 Gene ID	基因位置/bp Position	拟南芥基因座 Locus on Arabidopsis	功能注释 Functional annotation
Phvul.006G020200	8 414 030	AT5G06100	编码MYB家族转录因子 Encodes MYB family of transcription factors
Phvul.006G020300	8 364 678	AT1G08400	RINT-1/TIP-1家族,参与内质网对高尔基小泡介导的转运、逆行小泡介导的转运、高尔基到内质网的调节 RINT-1/TIP-1 family,involved in regulation of ER to Golgi vesicle-mediated transport,retrograde vesicle-mediated transport,Golgi to endoplasmic reticulum
Phvul.006G020400	8 544 660	AT5G35732	未见相关注释信息 No annotation information
Phvul.006G020500	8 568 891	AT5G10270	编码CDKC;1,是花椰菜花叶病毒（CaMV）针对病毒基因转录激活的CDKC激酶复合物的一部分,调节植物的生长发育 Encodes CDKC;1,part of a CDKC kinase complex that is targeted by cauliflower mosaic virus（CaMV）for transcriptional activation of viral genes. Also regulates plant growth and development
Phvul.006G020700	8 610 369	AT1G14370	编码蛋白激酶APK2a,参与细菌防御反应的正调控 Encodes protein kinase APK2a,involved in positive regulation of defense response to bacterium
Phvul.006G020800	8 626 154	AT2G30860	编码属于GST phi类的谷胱甘肽转移酶 Encodes glutathione transferase belonging to the phi class of GSTs
Phvul.006G020900	8 642 248	AT2G26980	编码一种丝氨酸-苏氨酸蛋白激酶,主要关于脱落酸激活信号通路,蛋白质磷酸化,脱落酸应答,细胞分裂素应答,信号转导 Encodes a serine-threonine protein kinase,involved in abscisic acid-activated signaling pathway,protein phosphorylation,response to abscisic acid,response to cytokinin,signal transduction
Phvul.006G021000	8 654 928	AT3G20320	编码ABC转运体的通透性样成分,参与从内质网到叶绿体的脂质转移 Encodes a permease-like component of an ABC transporter involved in lipid transfer from ER to chloroplast

基因组位置/bp Position in the genome	基因上游 Upstream	B16（紫花） B16（Purple flower）	B12（白花） B12（White flower）
8 413 354	-676	C	T
8 413 372	-658	C	T
8 413 381	-649	A	G
8 413 404	-626	C	T
8 413 418	-612	C	T
8 413 422	-608	AC	-