柑橘CCD基因家族鉴定及CcCCD4a对果肉颜色的影响

doi:10.3864/j.issn.0578-1752.2020.09.014

Abstract

Abstract:

【Objective】To reveal the distribution, structure and evolution of carotenoid cleavage dioxygenas gene family in the citrus genome (CcCCD), this study were performed to develope marker-assisted selection of flesh color in citrus breeding program, bioinformatics predication, expression analysis and genotype of CcCCD4a in flesh color development and different germplasm accessions. 【Method】The CCD gene family of Citrus clementina genome were identified by homologous search according to previously reported CCD in other plant species. Phylogenetic analysis, subcellular localization prediction, relative molecular weight, theoretical isoelectric point (PI), conserved motif prediction, and scaffold location were studied by bioinformatics methods. Real-time fluorescence quantitative PCR (qRT-PCR) was used to study the expression of CcCCD4a in 10 citrus accessions during the flesh color development period. Haplotype analysis was performed by Tassel software after sequencing of CcCCD4a in 30 citrus varieties. 【Result】Fourteen CCD family genes were found in the Citrus clementina genome, and these genes could be divided into five subfamily, namely, CcCCD1, CcCCD4, CcCCD7, CcCCD8 and CcNCED. Its theoretical isoelectric point were 6.05 to 8.53 and these CCD family genes encoded 412-611 amino acids. The subcellular localization prediction indicated that CcCCD genes mainly were located in chloroplast and cytoplasm. Phylogenetic analysis showed that CCD genes in citrus were also found in other plant species. Obviously, CCD8 subfamily had farther genetic distance with other CCD. Scaffold localization analysis showed that 14 CcCCD members were unevenly distributed in all scaffolds except scaffold 5. The phenotyping of flesh color in 10 citrus varieties demonstrated that the hue angle of flesh color was decreased along with fruit maturing. The relative expression of CcCCD4a in different citrus varieties was significantly different. The expression of CcCCD4a in the flesh color of orange red was significantly lower than that in the flesh color of orange or light orange yellow (P<0.05). There was a significant positive correlation between the relative expression of CcCCD4a and the hue angle during fruit ripening. Genotyping of CcCCD4a in 30 citrus varieties revealed that hap-1, hap-4 and hap-5 were dominant haplotype at orange red flesh varieties. 【Conclusion】The whole genome of Citrus clementina contained 14 members of CCD gene family. All these CCD gene family members contained RPE65 conserved domain, but they were located in different cell components and unevenly distributed at different scaffolds. CcCCD4a was involved in the development of citrus flesh color, and there was a significant positive correlation between its relative expression and the hue angle. Therefore, CcCCD4a could be used as potential marker for citrus fruit color breeding. Especially, hap-1, hap-4 and hap-5 had a high correlation with the phenotypes of orange red flesh, which might be helpful for selecting candidate hybrids in early stage of citrus breeding program.

Key words: citrus, CCD gene family, CcCCD4a, flesh color, gene expression, haplotype

YaFei ZHANG,Jie PENG,YanSong ZHU,ShengNan YANG,Xu WANG,WanTong ZHAO,Dong JIANG. Genome Wide Identification of CCD Gene Family in Citrus and Effect of CcCCD4a on the Color of Citrus Flesh[J].Scientia Agricultura Sinica, 2020, 53(9): 1874-1889.

Figures/Tables 11

Table 1

30 accessions of mandarin germplasms used in this study"

编号 Code	材料名称 Name	种名 Specific name	果实成熟期 Ripen time	果皮颜色 Peel color	果肉颜色 Flesh color
1	丽红 Reikou	Citrus reticulata Blanco	11月下旬 Late Nov.	橙红色 Orange red	橙红色 Orange red
2	红橘 Hong ju	Citrus reticulata Blanco	11月中旬 Middle Nov.	红色 Red	橙红色 Orange red
3	美国糖橘 America tang ju	Citrus reticulata Blanco	11月上旬 Early Nov.	深红色 Deep red	橙红色 Orange red
4	椪柑 Ponkan	Citrus reticulata Blanco	11月下旬 Late Nov.	橙黄色 Orange yellow	橙红色 Orange red
5	茂谷柑 Murcott	Citrus reticulate Blanco × Citrus sinensis (L.) Osbeck	1月上旬 Early Jan.	橙红色 Orange red	橙红色 Orange red
6	沃柑 Orah	Citrus reticulata Blanco	1月上旬 Early Jan.	橙红色 Orange red	橙色 Orange
7	青橘 Qing Ju	Citrus reticulata Blanco	12月上旬 Early Dec.	橙黄色 Orange yellow	橙色 Orange
8	春见 Harumi	Citrus reticulata Blanco	12月上旬 Early Dec.	橙色 Orange	橙色 Orange
9	猴橙 Monkey Orange	Citrus sinensis (L.) Osbeck	11月下旬 Late Nov.	橙色 Orange	橙色 Orange
10	春香 Haruka	Citrus tamurana hort.ex Tanaka Spp.	12月中旬 Middle Dec.	浅橙黄色 Light orange yellow	浅橙黄色 Light orange yellow
11	朱红 Zhu hong ju	Citrus erythrosa Hort.ex Tan.	11月下旬 Late Nov.	红色 Red	橙红色 Orange red
12	汕头酸橘 Shan tou suan ju	Citrus sunki (Hayata) hort.ex Tanaka	12月上旬 Early Dec.	橙色 Orange	橙色 Orange
13	满头红 Man tou hong ju	Citrus reticulata Blanco	12月中旬 Middle Dec.	红色 Red	橙红色 Orange red
14	大红袍 Da hong pao ju	Citrus reticulata Blanco	11月中旬 Middle Nov.	红色 Red	橙红色 Orange red
15	宫本温州蜜柑 Miyamoto wase unshiu	Citrus unshiu Macf.	9月下旬 Late Sep.	橙黄色 Orange yellow	橙红色 Orange red
16	无核红橘 Seedless hong ju	Citrus reticulata Blanco	12月下旬 Late Dec	红色 Red	橙红色 Orange red
17	永春芦柑 Yong chun lu gan	Citrus reticulata Blanco	11月下旬 Late Nov.	橙黄色 Orange yellow	橙红色 Orange red
18	濑户佳实生 Seedling setoka	Citrus tangor	3月上旬 Early Mar.	橙黄色 Orange yellow	橙色 Orange
19	辉优 Hybrid fagllo 4-3	Citrus reticulata Blanco	11月中旬 Middle Nov.	红色 Red	橙红色 Orange red
20	立山椪柑 Li shan ponkan	Citrus reticulata Blanco	11月下旬 Late Nov.	橙色 Orange	橙红色 Orange red
21	肥之曙 Hinoakebono wase	Citrus unshiu Macf.	9月中旬 Middle Sep	橙色 Orange	橙红色 Orange red
22	红晕香柑 Hong yun xiang gan	Citrus tangor	3月上旬 Early Mar.	红色 Red	橙红色 Orange red
23	橘湘早 Ju xiang zao	Citrus unshiu Macf.	10月上旬 Early Oct.	橙黄色 Orange yellow	橙色 Orange
24	爱媛30号杂种3 Ehime No.30 new line	Citrus reticulata Blanco	11月下旬 Late Nov.	橙红色 Orange red	橙红色 Orange red
25	爱妃 Princess fairy	Citrus reticulata Blanco	10月中旬 Middle Oct.	橙红色 Orange red	橙红色 Orange red
26	牛肉红橘 Niu rou hong ju	Citrus reticulata Blanco	11月下旬 Late Nov.	深红色 Orange red	橙红色 Orange red
27	金秋砂糖橘 Gold autum sha tang ju	Citrus reticulata Blanco	10月下旬 Late Oct.	橙红色 Orange red	橙色 Orange
28	华美20号 Hua mei No.20	Citrus reticulata Blanco	10月中旬 Middle Oct.	红色 Red	橙色 Orange
29	华美4号 Hua mei No.4	Citrus reticulata Blanco	10月下旬 Late Oct.	红色 Red	橙红色 Orange red
30	华美41号 Hua mei No.41	Citrus reticulata Blanco	11月中旬 Middle Oct.	橙色 Orange	橙红色 Orange red

Table 1

Table 2

Table 3

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Table 4

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引物名称 Primer name	用途 Usage	引物序列 Primer sequence	片段大小 Length (bp)	循环数/退火温度 Cycles/Annealing temperature (℃)
CcCCD4a	扩增CcCCD4a Amplify CcCCD4a	F：ACTTGCCAGCCTTAAGCCGT	2465	35/56℃
CcCCD4a	扩增CcCCD4a Amplify CcCCD4a	R：CAATATTGTGTGTGGTGGCC	2465	35/56℃
CcCCD4aq	CcCCD4a荧光定量 qRT-PCR primers of CcCCD4a	F：TCTCTCAGCCTCAACCCAAG	220	40/60℃
CcCCD4aq	CcCCD4a荧光定量 qRT-PCR primers of CcCCD4a	R：ACTACCTCACACTCCGTTGG	220	40/60℃
β-Actin	内参基因 Reference gene	F：CCCCATCGTTACCGTCCAG	150	40/60℃
β-Actin	内参基因 Reference gene	F：CGCCTTGCCAGTTGAATATCC	150	40/60℃

基因名称 Gene name	基因组登录号 Gene accession No.	蛋白质大小 Protein length (aa)	RPE65位置 RPE65 domain location	分子量 Molecular mass (KD)	等电点 Isoelectric point (pI)	亚细胞定位 Subcellular localization
CcCCD1a	CICLEv10031014m	597	106—587	67.2	6.33	细胞质 Cytoplasm
CcCCD1b	CICLEv10031039m	589	100—579	66.67	6.05	细胞质 Cytoplasm
CcCCD4a	CICLEv10031003m	603	124—595	66.45	6.87	叶绿体 Chloroplast
CcCCD4b1	CICLEv10028113m	563	87—553	63.06	8.34	叶绿体 Chloroplast
CcCCD4b2	CICLE_v10030384m	508	38—504	56.91	6.56	细胞质 Cytoplasm
CcCCD4c	CICLEv10011335m	597	115—590	66.35	8.53	叶绿体 Chloroplast
CcCCD4d	CICLEv10013726m	412	93—403	45.86	7.25	叶绿体 Chloroplast
CcCCD7	CICLEv10027500m	590	43—580	66.51	6.07	叶绿体 Chloroplast
CcCCD8a	CICLEv10008050m	510	29—508	56.8	5.93	细胞质 Cytoplasm
CcCCD8b	CICLEv10010609m	556	76—554	61.965	5.98	叶绿体 Chloroplast
CcCCD_like	CICLEv10010551m	611	89—598	69.18	6.53	细胞质 Cytoplasm
CcNCED3	CICLEv10019364m	606	134—598	67.01	6.37	叶绿体 Chloroplast
CcNCED5	CICLEv10014639m	609	136—601	67.79	6.3	叶绿体 Chloroplast
CcNCED6	CICLEv10006710m	592	113—583	65.29	7.32	细胞质 Cytoplasm

单倍型 Haplotype	序列 Sequence	材料份数 Number of accession	涉及材料 Related variety
hap-1	ATCGGTTACTCTCTATGTAGTCCGGTGTCTA	12	华美41号 Hua mei No.41、红橘 Hong ju、无核红橘Seedless hong ju、大红袍 Da hong pao、爱媛30杂种3 Ehime No.30 new line、牛肉红橘 Niu rou hong ju、永春芦柑 Yong chun lu gan、立山椪柑 Li shan ponkan、华美4号 Hua mei No.4、朱红 Zhu hong ju、满头红Man tou hong ju、美国糖橘 America tang ju
hap-2	ACCGGTTCCTCTCCAAGTATTCCGGCGTCTA	9	丽红 Reikou、春见 Harumi、爱妃 Princess fairy、红晕香柑 Hong yun xiang gan、华美20号 Hua mei No.20、金秋砂糖橘 Jin qiu sha tang ju、橘湘早Ju xiang zao、肥之曙 Hinoakebono wase、宫本温州Miyamoto wase unshiu
hap-3	ATCGGTTACTCTCCAAGTAGTCCGGCGTCTA	1	华美41号 Hua mei No.41
hap-4	ATCGGTTACTCTCCATGTAGTCCGGTGTCTA	6	红橘 Hong ju、无核红橘 Seedless hong、辉优 Hybrid fagllo 4-3、汕头酸橘 Shan tou suan ju、大红袍 Da hong pao ju、爱媛30杂种3 Ehime No.30 new line
hap-5	ATCGGTTCCTCTCCATGTAGTCCGGTGTCTA	1	牛肉红橘 Niu rou hong ju
hap-6	TTTACTTCCTCTCCATGTAGTCCGCCGCGAG	5	美国糖橘 America tang ju、椪柑 Ponkan、沃柑Orah、濑户佳实生 Seedling setoka、克里曼丁 Clementina
hap-7	TTCACACCCCATACGTGCAGCTAACCGCCTA	1	春香 Haruka、猴橙 Monkey orange
hap-8	ATCGGTTCCTCTCCATGTAGTCCGGCGTCTA	1	青橘 Qing ju
hap-9	TTCACACCTCAAACGTACGGCTAACCATCTA	1	茂谷柑 Murcott

Genome Wide Identification of CCD Gene Family in Citrus and Effect of CcCCD4a on the Color of Citrus Flesh

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