Genome-wide Association Studies for Flower Color in Common Bean

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

Acta Horticulturae Sinica ›› 2022, Vol. 49 ›› Issue (2): 332-340.doi: 10.16420/j.issn.0513-353x.2021-0056

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Genome-wide Association Studies for Flower Color in Common Bean

LU Tiantian, LIU Zhiyuan, XU Zhaosheng, ZHANG Helong, LI Guoliang, SHE Hongbing, QIAN Wei()

Institute of Vegetables and Flowers,Chinese Academy of Agricultural Sciences,Beijing 100081,China

Received:2021-04-16 Revised:2021-11-18 Online:2022-02-25 Published:2022-02-28

Abstract

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

CLC Number:

S643.1

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.

Figures/Tables 8

References 30

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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	-

Genome-wide Association Studies for Flower Color in Common Bean

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