大豆种子颜色遗传调控机制研究进展

doi:10.3724/SP.J.1006.2021.14022

Abstract

Abstract:

The color of soybean seeds is an important morphological marker and evolutionary trait. During the process of domestication, seed coat has gradually evolved from black to yellow, green, black, brown, and bicolor, and cotyledons has evolved from green to yellow. The dark seed coat contains anthocyanins, which are natural pigments with medicinal and nutritional values. Therefore, it is of great importance to study the genetic regulation mechanism of seed color for evolutionary theory, variety breeding, and practical application. The pigment content and composition of seeds result in diverse seed coat colors through complex molecular regulatory mechanisms. In this paper, we described the research progress on genetic loci, related genes, regulatory mechanisms, and flavonoid biosynthesis pathways that controlling the color of soybean seeds. Specifically, we introduced the 9 classical genetic loci I, R, T, O, W1, K1, G, D1, D2, and related molecular markers, as well as the interactions between the loci; 22 related genes that controlling seed color, and the regulatory mechanisms of some allelic variants; as well as the physiological functions of the flavonoid biosynthesis pathways and major metabolites involved in the related genes. The progress of researches on genetic regulation of the color of seed coat, seed hilum, and cotyledon in soybean was reviewed, in addition the regulatory network was mapped with genetic loci, genes, allelic regulatory mechanisms, and flavonoid metabolic pathways, in order to provide references for the quality of seed appearance and genetic improvement of anthocyanin components.

Key words: soybean, seed color, genetic regulation, related gene, flavonoid biosynthesis pathway

QIU Hong-Mei, CHEN Liang, HOU Yun-Long, WANG Xin-Feng, CHEN Jian, MA Xiao-Ping, CUI Zheng-Guo, ZHANG Ling, HU Jin-Hai, WANG Yue-Qiang, QIU Li-Juan. Research progress on genetic regulatory mechanism of seed color in soybean (Glycine max)[J].Acta Agronomica Sinica, 2021, 47(12): 2299-2313.

Figures/Tables 6

Table 1

Information of classical genetic loci controlling seed color"

遗传位点 Genetic locus	连锁群 Linkage group	染色体 Chromosome	控制性状 Character	等位基因 Allele	表型 Phenotype	参考文献 Reference
I	A2	8	种皮、种脐是否含有花色素 The seed coat and hilum were controlled to contain anthocyanins.	I	黄种皮黄脐 Fully yellow seed coat and hilum	Terao^[9], Todd et al.^[26]
				iⁱ	黄种皮黑脐 Yellow seed coat with black hilum	Terao^[9], Tuteja et al.^[27]
				i^k	鞍挂Black saddle	Terao^[9], Tuteja et al.^[27]
				i	黑种皮或褐种皮 Black or brown seed coat	Terao^[9], Clough et al.^[28]
R	K	9	种皮为黑色或褐色 The seed coat was black or brown.	R	黑种皮Black seed coat	Owen^[10], Song et al.^[29]
				R*	黑种皮Black seed coat	Zabala et al.^[57]
				r	褐种皮Brown seed coat	Zabala et al.^[57]
				r^m	虎斑Black spots or concentric rings of black pigment superimposed on an otherwise brown seed coat	Zabala et al.^[57]
T	C2	6	种皮的着色程度及茸毛颜色 Control the pigmentation degree of seed coat and the color of trichomes.	T	深褐种皮、棕色茸毛 Dark brown seed coat, tawny trichomes	Owen^[10], Zabala et al.^[29,30]
				t	褐种皮、灰色茸毛 Brown seed coat, gray trichomes	Owen^[10], Zabala et al.^[29,30]
				t^m	深褐和褐色种皮、棕和灰色茸毛 Dark brown and brown seed coat, tawny and gray trichomes	Zabala et al.^[29,30]
O	A2	8	种皮的褐色程度 Control the brown degree of seed coat.	O	褐种皮Brown seed coat	Owen^[10], Yang et al.^[32]
O	A2	8	种皮的褐色程度 Control the brown degree of seed coat.	o	红褐种皮Red-brown seed coat	Owen^[10], Yang et al.^[32]
W1	G	13	种皮着色程度及花的颜色 Control the pigmentation degree of seed coat and the color of flowers.	W1	黑种皮、紫花 Black seed coat and purple flowers	Owen^[10], Zabala et al.^[33]
W1	G	13		w1	浅褐种皮、白花 Buff seed coat and white flowers	Owen^[10], Zabala et al.^[33]
K1	B1	11	控制色素在鞍区的分布 Control the distribution of pigment in saddle region.	K1	黄种皮Yellow seed coat	Cho et al.^[34]
K1	B1	11		k1	鞍挂Black saddle	Cho et al.^[34]
G	D1a	1	种皮、子叶是否含有叶绿素 The seed coat and cotyledon were controlled to contain chlorophyll.	G	绿种皮、绿子叶 Green seed coat and cotyledon	Owen^[10], Song et al.^[21]
G	D1a	1		g	黄种皮、黄子叶 Yellow seed coat and cotyledon	Owen^[10], Song et al.^[21]
D1	D1a	1	种皮、子叶是否含有叶绿素 The seed coat and cotyledon were controlled to contain chlorophyll.	D1	黄种皮、黄子叶 Yellow seed coat and cotyledon	Fang et al.^[35], Song J ^[12]
D1	D1a	1		d1	绿种皮、绿子叶 Green seed coat and cotyledon	Fang et al.^[35], Song J^[12]
D2	B1	11	种皮、子叶是否含有叶绿素 The seed coat and cotyledon were controlled to contain chlorophyll.	D2	黄种皮、黄子叶 Yellow seed coat and cotyledon	Fang et al.^[35], Song J^[12]
D2	B1	11		d2	绿种皮、绿子叶 Green seed coat and cotyledon	Fang et al.^[35], Song J ^[12]
CytG	—	—	种皮、子叶是否含有叶绿素 The seed coat and cotyledon were controlled to contain chlorophyll.	CytG	黄种皮、黄子叶 Yellow seed coat and cotyledon	Guiamét et al.^[39]
CytG	—	—		cytG	绿种皮、绿子叶 Green seed coat and cotyledon	Guiamét et al.^[39]

Table 1

Fig. 1

Fig. 2

Table 2

Genetic information related to seed color regulation"

序号 No.	基因编号(v2.1) Gene ID (v2.1)	基因名称 Gene name	英文缩写 Abbreviation	遗传位点 Genetic locus	编码产物注释 Annotation of coding products	参考文献 Reference
1	Glyma.08G109500	查尔酮合成酶1 Chalcone synthase 1	CHS1	I	类黄酮合成途径酶：合成柚皮苷查尔酮 Flavonoid biosynthesis pathway enzyme: synthesis of naringin chalcone	Akada et al.^[51]
2	Glyma.08G110300	查尔酮合成酶3 Chalcone synthase 3	CHS3	I	类黄酮合成途径酶：合成柚皮苷查尔酮 Flavonoid biosynthesis pathway enzyme: synthesis of naringin chalcone	Senda et al.^[52] Cho et al.^[53]
3	Glyma.08G109200	查尔酮合成酶4 Chalcone synthase 4	CHS4	I	类黄酮合成途径酶：合成柚皮苷查尔酮 Flavonoid biosynthesis pathway enzyme: synthesis of naringin chalcone	Liu et al.^[54] ^Tuteja et al.^[55]
4	Glyma.11G190900	Argonaute 5蛋白 Argonaute 5 protein	AGO5	K1	调控CHS siRNAs在种皮的分布 Regulation of CHS siRNAs distribution in seed coat	Rogers et al.^[58] Song et al.^[59]
5	Glyma.09G025300	内啡肽酶同源物2a Endorphinase homolog 2a	DCL2a	—	切割含长LIR的转录本,生成22nt siRNA LIR-derived transcripts are predominately processed by GmDCL2 into 22-nt siRNAs	Jia et al.^[60]
6	Glyma.09G025400	内啡肽酶同源物2b Endorphinase homolog 2a	DCL2b	—	切割含长LIR的转录本,生成22nt siRNA LIR-derived transcripts are predominately processed by GmDCL2 into 22-nt siRNAs	Jia et al.^[60]
7	Glyma.06G202300	黄烷酮3’-羟化酶 Flavanone 3’-hydroxylase	F3’H	T	类黄酮合成途径酶：催化黄烷酮羟基化 Flavonoid biosynthesis pathway enzymes: catalyzing the hydroxylation of flavanones	Toda et al.^[61] ^Guoet al.^[62]
8	Glyma.13G072100	黄烷酮3’,5’-羟化酶 Flavanone 3’,5’-hydroxylase	F3’5’H	W1	类黄酮合成途径酶：催化黄烷酮羟基化 Flavonoid biosynthesis pathway enzymes: catalyzing the hydroxylation of flavanones	Zabala et al.^[33]
9	Glyma.08G062000	花青素还原酶 Anthocyanidin reductase	ANR1	O	类黄酮合成途径酶：形成原花青素 Flavonoid biosynthesis pathway enzymes: procyanidins production	Yang et al.^[32]
10	Glyma.08G062100	花青素还原酶 Anthocyanidin reductase	ANR2	O	类黄酮合成途径酶：形成原花青素 Flavonoid biosynthesis pathway enzymes: procyanidins production	Yang et al.^[32]
11	Glyma.09G235100	R2R3 MYB转录因子 Transcripion foctor R2R3 MYB	R2R3 MYB	R	转录因子：调控ANS基因的表达 Transcription factors: regulation of ANS gene expression	^Yanet al.^[63] Zabala et al.^[64]
12	Glyma.01G198500	CAAX自身免疫蛋白酶 CAAX protease self-immunity	CPSI	G	防止叶绿素降解使成熟种皮保持绿色 Prevent chlorophyll degradation to keep the mature seed coat green	Xie et al.^[65] Wang et al.^[66]
13	Glyma.01g214600	保持绿色蛋白1 Protein stay-green 1	SGR1	D1	使成熟种子保持绿色 Mature seeds stay-green	Fang et al.^[34] 宋健^[12] Fang et al.^[34] ^{Song J[12]}
14	Glyma.11g027400	保持绿色蛋白2 Protein stay-green 2	SGR2	D2	使成熟种子保持绿色 Mature seeds stay-green	Fang et al.^[34] 宋健^[12] Fang et al.^[34] ^{Song J[12]}
15	Glyma.20G241500	查尔酮异构酶1A Chalcone isomerase 1A	CHI1A	—	类黄酮合成途径酶：催化分子内环化反应 Flavonoid synthesis pathway enzymes: catalyzing intramolecular cyclization	Kovinich et al.^[63]
16	Glyma.20G241700	查尔酮异构酶2 Chalcone isomerase 2	CHI2	—	类黄酮合成途径酶：催化分子内环化反应 Flavonoid synthesis pathway enzymes: catalyzing intramolecular cyclization	Kovinich et al.^[63]
17	Glyma.02G048400	黄烷酮3-羟化酶 Naringenin 3-dioxygenase	F3H	Wp	类黄酮合成途径酶：催化黄烷酮羟基化 Flavonoid biosynthesis pathway enzymes: catalyzing the hydroxylation of flavanones	Zabala et al.^[64]
18	Glyma.14G072700	二氢黄酮醇还原酶1 Dihydroflavonol 4-reductase 1	DFR1	W3	类黄酮合成途径酶：形成无色花青素 Flavonoid synthesis pathway enzymes: formation of colorless anthocyanins	Xu et al.^[65]
19	Glyma.17G252200	二氢黄酮醇还原酶2 Dihydroflavonol 4-reductase 2	DFR2	W4	类黄酮合成途径酶：形成无色花青素 Flavonoid synthesis pathway enzymes: formation of colorless anthocyanins	Xu et al.^[65]
20	Glyma.01G214200	花青素合成酶2 Anthocyanidin synthase 2	ANS2	—	类黄酮合成途径酶：形成花色素 Flavonoid biosynthesis pathway enzymes: anthocyanin formation	Kovinich et al.^[68]
21	Glyma.11G027700	花青素合成酶3 Anthocyanidin synthase 3	ANS3	—	类黄酮合成途径酶：形成花色素 Flavonoid biosynthesis pathway enzymes: anthocyanin formation	Kovinich et al.^[68]
22	Glyma.08G066800	UDP类黄酮葡萄糖基转移酶 UDP-flavonoid 3-O-glucosyltransferase	UF3GT	—	类黄酮合成途径酶：形成花色苷 Flavonoid biosynthesis pathway enzymes: anthocyanin formation	Kovinich et al.^[68]
23	—	光系统Ⅱ反应中心M亚基 Photosystem II reaction center M subunit	Psbm	—	具有叶绿素b降解功能 Degradation of chlorophyll b	Kohzuma et al.^[40]

Table 2

Table 3

Regulation mechanism of alleles controlling seed color"

基因/编号 Gene ID	突变基因型 Mutant genotype	种子颜色 Seed color	变异方式 Variation	检测方法 Detection method	参考文献 Reference
I Glyma.08G109500 Glyma.08G110300 Glyma.08G109200	iⁱ	黄种皮黑脐 Yellow seed coat with black hilum	CHS基因的拷贝数增加 The copy number of CHS gene increased	BAC重测序 BAC resequencing	Cho et al.^[53]
	i^k	鞍挂 Black saddle	基因间序列缺失 Deletion of intergenic sequencesl	BAC重测序 BAC resequencing	Cho et al.^[53]
	i	深色种皮 Dark pigment seed coat	基因及基因间序列大片段缺失 Large deletions of genes and intergenic sequences	BAC重测序 BAC resequencing	Cho et al.^[53]
R Glyma.09G235100	R*	黑种皮 Black seed coat	第2内含子插入CACTA转座子及CACTA序列的甲基化 Insertion of the second intron into the CACTA transposon and methylation of the CACTA sequence	长片段PCR扩增、表达谱分析、甲基化检测 Long fragment PCR amplification, expression profile analysis, methylation detection	Zabala et al.^[64]
	r	褐种皮 Brown seed coat	第2外显子单碱基C缺失 Single base C deletion in exon 2	克隆测序 Cloning and sequencing	Zabala et al.^[64]
	r^m	虎斑 Black spots or concentric rings of black pigment superimposed on an otherwise brown seed coat	第2内含子插入CACTA转座子 Insertion of the second intron into the CACTA transposon	长片段PCR扩增、表达谱分析、甲基化检测 Long fragment PCR amplification, expression profile analysis, methylation detection	Zabala et al.^[64]
T Glyma.06G202300	t	褐种皮 Brown seed coat	第3外显子单碱基A的缺失或非同义突变或单碱基C的缺失 Deletion of single base A or non synonymous mutation or deletion of single base C in exon 3	PCR测序 PCR sequencing	Guo et al.^[62]
T Glyma.06G202300	t^m	深褐和褐色种皮 Dark brown and brown seed coat,	第1内含子插入CACTA转座子 The first intron was inserted into the CACTA transposon	长片段PCR扩增 Long fragment PCR amplification	Zabala et al.^[31]
W1 Glyma.13G072100	w1	淡褐种皮 Buff seed coat	第3外显子插入53 bp The third exon was inserted 53 bp sequence	克隆测序 Cloning and sequencing	Guo et al.^[62]
K1 Glyma.11G190900	k1	鞍挂 Black saddle	第7外显子129 bp的缺失 Deletion of 129 bp sequence in exon 7	转录组与小RNA测序、PCR测序、全基因组深度重测序 Ranscriptome and micro RNA sequencing, PCR sequencing, whole genome deep resequencing	Cho et al.^[34]
G Glyma.01G198500	g	黄种皮 Yellow seed coat	第8内含子末端发生碱基突变 A base mutation occurred at the end of intron 8	克隆测序 Cloning and sequencing	Wang et al.^[66]
D1 Glyma.01g214600	d1	绿种皮、绿子叶 Green seed coat and cotyledon	第2外显子单碱基T缺失 Single base T deletion in exon 2	基因组重测序、克隆测序 Genome resequencing, cloning and sequencing	Fang et al.^[35],Song J^[12]
D2 Glyma.11g027400	d2	绿种皮、绿子叶 Green seed coat and cotyledon	322 bp重复插入 322 bp sequence repeated insertion	基因组重测序、克隆测序 Genome resequencing, cloning and sequencing	Fang et al.^[35],Song J^[12]
CytG	cytG	绿种皮、绿子叶 Green seed coat and cotyledon	5 bp插入 5 bp sequence insertion	对叶绿体基因组广泛的测序 Extensively sequenced the chloroplast genome	Kohzuma et al.^[40]

Table 3

Fig. 3

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Research progress on genetic regulatory mechanism of seed color in soybean (Glycine max)

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