Mining of Genetic Locus of Phenylethyl Alcohol Primrose Glycoside Abundance in Tea Plants

doi:10.16420/j.issn.0513-353x.2023-0105

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (1): 77-90.doi: 10.16420/j.issn.0513-353x.2023-0105

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Mining of Genetic Locus of Phenylethyl Alcohol Primrose Glycoside Abundance in Tea Plants

ZHANG Lilan, YANG Jun, WANG Rangjian^*()

Fujian Branch，National Center for Tea Improvement，Tea Research Institute，Fujian Academy of Agricultural Science，Fuzhou 350013，China

Received:2023-08-28 Revised:2023-12-01 Online:2024-01-25 Published:2024-01-16
Contact: * （E-mail：rangjian.wang@163.com）

Abstract

Abstract:

In this study，169 tea germplasms were used as the association population，and 675 245 high-quality SNP markers developed based on the simplified genome sequencing technology were used to perform genome-wide association study（GWAS）on the content of phenylethanol primrose glycosides in tea shoots from 2018 to 2020. The results demonstrated that the variation coefficient of phenylethanol primrose glycoside content among tea germplasms in different years was 61.50%-62.09%，the correlation coefficient was 0.95-0.98（P < 0.01），and the generalized heritability was 67.49%. Three GWAS analysis models detected a total of 24 stable sites（P < 0.001）which significantly associated with phenylethanol primrose glycosides in tea plants，explaining phenotypic variation rates ranging from 0.01% to 10.63%. Thirty-six excellent germplasm with excellent allelic variations at 24 major loci were identified and significantly increased phenylethanol primrose glycoside content by allelic effect analysis. A total of 10 candidate genes related to phenylethanol primrose glycoside content were preliminarily screened，namely TEA020086.1，TEA003248.1，TEA013029.1，TEA021435.1，TEA016196.1，TEA029411.1，TEA014564.1，TEA014567.1，TEA014571.1，and TEA014573.1，mainly involving secondary metabolism and transcrip- tional regulation molecular processes.

Key words: Camellia sinensis, phenylethyl alcohol primrose glycoside, genome-wide association study, candidate gene, elite allele

ZHANG Lilan, YANG Jun, WANG Rangjian. Mining of Genetic Locus of Phenylethyl Alcohol Primrose Glycoside Abundance in Tea Plants[J]. Acta Horticulturae Sinica, 2024, 51(1): 77-90.

Figures/Tables 8

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母本来源（♀） Maternal parent	名称 Name	母本来源（♀） Maternal parent	名称 Name	母本来源（♀） Maternal parent	名称 Name	母本来源（♀） Maternal parent	名称 Name
FT104	04-1	FT104	04-49	FT516	16-16	FT516	16-55
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	04-11		04-50		16-18		16-57
	04-12		04-51		16-19		16-58
	04-13		04-52		16-2		16-59
	04-14		04-53		16-20		16-6
	04-15		04-54		16-21		16-60
	04-16		04-55		16-22		16-61
	04-17		04-56		16-23		16-62
	04-18		04-57		16-24		16-63
	04-19		04-58		16-25		16-64
	04-2		04-59		16-26		16-65
	04-20		04-6		16-27		16-66
	04-21		04-60		16-28		16-67
	04-22		04-61		16-29		16-68
	04-23		04-62		16-3		16-69
	04-24		04-63		16-30		16-7
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	04-3		04-69		16-36		16-75
	04-30		04-7		16-37		16-76
	04-31		04-70		16-38		16-77
	04-32		04-71		16-39		16-78
	04-33		04-72		16-4		16-79
	04-34		04-73		16-40		16-8
	04-35		04-74		16-41		16-80
	04-36		04-75		16-42		16-81
	04-37		04-76		16-43		16-82
	04-38		04-77		16-44		16-83
	04-39		04-78		16-45		16-84
	04-4		04-79		16-46		16-85
	04-40		04-8		16-47		16-86
	04-41		04-9		16-48		16-87
	04-42	FT516	16-1		16-49		16-88
	04-43		16-10		16-5		16-89
	04-44		16-11		16-50		16-9
	04-45		16-12		16-51		16-90
	04-46		16-13		16-52
	04-47		16-14		16-53
	04-48		16-15		16-54

母本来源（♀） Maternal parent	名称 Name	母本来源（♀） Maternal parent	名称 Name	母本来源（♀） Maternal parent	名称 Name	母本来源（♀） Maternal parent	名称 Name
FT104	04-1	FT104	04-49	FT516	16-16	FT516	16-55
	04-10		04-5		16-17		16-56
	04-11		04-50		16-18		16-57
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	04-13		04-52		16-2		16-59
	04-14		04-53		16-20		16-6
	04-15		04-54		16-21		16-60
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	04-42	FT516	16-1		16-49		16-88
	04-43		16-10		16-5		16-89
	04-44		16-11		16-50		16-9
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	04-46		16-13		16-52
	04-47		16-14		16-53
	04-48		16-15		16-54

年份 Year	均值 ± 标准差/ （μg · mL^-1）	变幅/ （μg · mL^-1）	变异系数/% CV	偏度 Skewness	峰度 Kurtosis	相关系数 Correlation coefficient			遗传力/% H²
Year	Mean ± SD	Range	变异系数/% CV	偏度 Skewness	峰度 Kurtosis	2018	2019	2020	遗传力/% H²
2018	0.5030 ± 0.3106	1.9442	61.74	1.20	2.16	1.00			67.49
2019	0.3698 ± 0.2296	1.5171	62.09	1.36	3.19	0.98^**	1.00
2020	0.1964 ± 0.1208	0.8040	61.50	1.28	3.00	0.94^**	0.95^**	1.00

年份 Year	均值 ± 标准差/ （μg · mL^-1）	变幅/ （μg · mL^-1）	变异系数/% CV	偏度 Skewness	峰度 Kurtosis	相关系数 Correlation coefficient			遗传力/% H²
Year	Mean ± SD	Range	变异系数/% CV	偏度 Skewness	峰度 Kurtosis	2018	2019	2020	遗传力/% H²
2018	0.5030 ± 0.3106	1.9442	61.74	1.20	2.16	1.00			67.49
2019	0.3698 ± 0.2296	1.5171	62.09	1.36	3.19	0.98^**	1.00
2020	0.1964 ± 0.1208	0.8040	61.50	1.28	3.00	0.94^**	0.95^**	1.00

标记	染色体	物理位置/bp	P值	等位基因	贡献率/% R²			共同年份
SNP	Chromosome	Position	P-value	Allele	2018	2019	2020	Common year
BYC_238_925613	Scaffold238	925 613	5.30E-08 ~ 9.70E-08	G/A	0.35	-	-	2018
BYC_238_925654	Scaffold238	925 654	3.53E-10 ~ 2.57E-08	C/A	1.08	1.05	0.21	2018、2019、2020
BYC_238_925695	Scaffold238	925 695	5.66E-10 ~ 9.19E-08	G/A	1.14	1.44	1.23	2018、2019、2020
BYC_238_925709	Scaffold238	925 709	3.24E-08 ~ 1.09E-07	T/C	0.59	0.58	-	2018、2019
BYC_238_925863	Scaffold238	925 863	3.02E-08 ~ 1.24E-07	A/G	4.72	5.27	-	2018、2019
BYC_238_925872	Scaffold238	925 872	5.66E-10 ~ 9.19E-08	C/T	7.84	8.21	7.68	2018、2019、2020
BYC_238_925894	Scaffold238	925 894	5.77E-10 ~ 6.23E-08	A/G	6.14	6.83	5.87	2018、2019、2020
BYC_238_925921	Scaffold238	925 921	2.09E-08 ~ 1.51E-07	G/T	6.78	7.22	6.10	2018、2019、2020
BYC_238_925929	Scaffold238	925 929	5.77E-10 ~ 6.23E-08	A/G	6.14	6.83	5.87	2018、2019、2020
BYC_238_947814	Scaffold238	947 814	6.17E-10 ~ 9.83E-08	G/A	0.03	0.07	0.04	2018、2019、2020
BYC_924_453206	Scaffold924	453 206	3.39E-08 ~ 1.02E-07	G/A	8.53	8.02	-	2018、2019
BYC_2437_362928	Scaffold2437	362 928	2.04E-09 ~ 3.27E-08	G/A	6.04	6.03	6.12	2018、2019、2020
BYC_1504_1577565	Scaffold1504	1 577 565	2.26E-08 ~ 9.40E-08	A/T	7.94	7.43	-	2018、2019
BYC_411_3676073	Scaffold411	3 676 073	6.45E-11 ~ 1.14E-07	G/A	4.70	4.87	5.10	2018、2019、2020
BYC_4560_230492	Scaffold4560	230 492	4.90E-09 ~ 6.59E-08	C/T	9.50	-	-	2018
BYC_4560_230673	Scaffold4560	230 673	2.08E-09 ~ 1.34E-07	C/A	4.89	4.67	-	2018、2019
BYC_4560_234100	Scaffold4560	234 100	2.98E-08 ~ 6.03E-08	C/A	3.76	-	-	2018
BYC_4560_234109	Scaffold4560	234 109	2.98E-08 ~ 6.03E-08	C/T	10.63	-	-	2018
BYC_4560_234338	Scaffold4560	234 338	2.98E-08 ~ 6.03E-08	T/C	1.79	-	-	2018
BYC_4560_234397	Scaffold4560	234 397	2.98E-08 ~ 6.03E-08	T/A	1.79	-	-	2018
BYC_933_263351	Scaffold933	263 351	4.08E-09 ~ 1.45E-07	T/C	2.66	2.66	2.78	2018、2019、2020
BYC_933_309886	Scaffold933	309 886	8.16E-10 ~ 7.81E-08	G/A	2.10	1.85	2.23	2018、2019、2020
BYC_933_309918	Scaffold933	309 918	8.16E-10 ~ 7.81E-08	C/T	7.42	7.04	7.69	2018、2019、2020
BYC_933_309931	Scaffold933	309 931	8.16E-10 ~ 7.81E-08	T/C	0.02	0.06	0.01	2018、2019、2020

Mining of Genetic Locus of Phenylethyl Alcohol Primrose Glycoside Abundance in Tea Plants

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序号 Number	候选基因 Candidate gene	基因功能注释 Gene function annotation	SNP显著区域 SNP significant region
1	TEA020086.1	蛋白磷酸酶2C Protein phosphatase 2C	Scaffold238（995 124 ~ 1 051 190）
2	TEA003248.1	MYB相关蛋白MYB-related protein	Scaffold924（387 562 ~ 443 110）
3	TEA013029.1	尿苷二磷酸-葡萄糖6-脱氢酶UDP-glucose 6-dehydrogenase	Scaffold2437（313 377 ~ 460 604）
4	TEA021435.1	赤霉素调控蛋白Gibberellin-regulated protein	Scaffold1504（1 502 834 ~ 1 665 205）
5	TEA016196.1	半乳糖醛酸转移酶Galacturonosyltransferase	Scaffold411（3 592 135 ~ 3 738 121）
6	TEA029411.1	7-脱氧洛根酸葡萄糖基转移酶7-Deoxyloganetic acid glucosyltransferase	Scaffold4560（187 046 ~ 334 711）
7	TEA014564.1	花青素5-芳香酰基转移酶Anthocyanin 5-aromatic acyltransferase	Scaffold933（166 365 ~ 350 362）
8	TEA014567.1	花青素5-芳香酰基转移酶Anthocyanin 5-aromatic acyltransferase
9	TEA014571.1	花青素5-芳香酰基转移酶Anthocyanin 5-aromatic acyltransferase
10	TEA014573.1	转录因子TCP13Transcription factor TCP13

种质 Germplasms	苯乙醇樱草糖苷含量/（μg · mL^-1） Phenylethyl alcohol primrose glycoside abundance			种质 Germplasms	苯乙醇樱草糖苷含量/（μg · mL^-1）Phenylethyl alcohol primrose glycoside abundance			种质 Germplasms	苯乙醇樱草糖苷含量/（μg · mL^-1 ）Phenylethyl alcohol primrose glycoside abundance
种质 Germplasms	2018	2019	2020	种质 Germplasms	2018	2019	2020	种质 Germplasms	2018	2019	2020
04-77	0.6484	0.4844	0.2567	04-40	0.5730	0.4280	0.1954	16-70	0.9566	0.7146	0.3787
04-9	0.5321	0.3975	0.2107	16-2	0.5060	0.3780	0.2003	16-69	1.0295	0.7690	0.4076
04-69	0.9554	0.7137	0.3783	16-4	1.1673	0.8720	0.4622	16-23	0.8887	0.6639	0.3519
04-16	1.1641	0.8696	0.4609	16-87	1.1430	0.8538	0.4525	16-24	0.7237	0.5406	0.2865
04-63	0.7571	0.5655	0.3970	16-85	0.7279	0.5438	0.2882	16-66	1.1658	0.8708	0.4615
04-20	0.7910	0.5909	0.3132	16-79	0.6436	0.4808	0.2548	16-27	0.7963	0.5948	0.3153
04-62	0.6434	0.4806	0.2547	16-78	0.8606	0.6429	0.3407	16-64	0.5261	0.3930	0.2083
04-21	0.4964	0.3708	0.1906	16-76	1.1257	0.8409	0.3151	16-29	0.8263	0.4709	0.2496
04-24	0.9371	0.7000	0.3342	16-75	0.9036	0.6750	0.3882	16-33	0.4859	0.3630	0.1924
04-59	0.7962	0.5947	0.3152	16-73	0.5006	0.3739	0.1982	16-58	1.0580	0.7903	0.4189
04-25	0.6051	0.4520	0.2396	16-19	1.1584	0.8653	0.4586	16-53	0.8429	0.3873	0.2053
04-47	1.3902	1.0385	0.3000	16-20	0.6487	0.4846	0.2568	16-47	0.6333	0.4070	0.2157

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