Studies on Genetic Variation of‘Tieguanyin’Tea Trees Asexual Reproduction Based on High-depth Genome Resequencing

doi:10.16420/j.issn.0513-353x.2022-0521

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (7): 1505-1517.doi: 10.16420/j.issn.0513-353x.2022-0521

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

Studies on Genetic Variation of‘Tieguanyin’Tea Trees Asexual Reproduction Based on High-depth Genome Resequencing

HOU Binghao¹, GAO Ting¹, WEI Yuede², GAO Shuilian¹, CAI Yinbi³, CHEN Zhiming⁴, JIN Shan¹, ZHANG Xingtan⁵, WANG Pengjie¹^,⁵^,^*(), YE Naixing¹^,^*()

¹ Key Laboratory of Tea Science at Universities in Fujian，College of Horticulture，Fujian Agriculture and Forestry University，Fuzhou 350002，China
² Fujian Anxi Qishan Weiyin Famous Tea Co.，Ltd.，Quanzhou，Fujian 362431，China
³ Fujian Bama Tea Industry Co.，Ltd.，Anxi，Fujian 362442，China
⁴ Anxi Tea Industry Development Center，Anxi，Fujian 362400，China
⁵ Agricultural Genomics Institute，Chinese Academy of Agricultural Sciences，Shenzhen，Guangdong 518120，China

Received:2022-12-05 Revised:2023-04-28 Online:2023-07-25 Published:2023-07-26
Contact: WANG Pengjie, YE Naixing

Abstract

Abstract:

The genome of Camellia sinensis（L.）O. Kuntze‘Tieguanyin’mother tree and its three consecutive asexual reproductions and three‘Tieguanyin’trees from multi-generation that used for actual production were resequenced with over 50× in this study. Through SNP and InDel detection and annotation，it was found that most of the variants were located in intergenic regions，only 1.09%-1.13% of SNPs and 0.51%-0.61% of InDels were located in gene coding regions. In the whole genome and coding regions，the total number of mutation sites of the three consecutive asexual reproductions had little differences，and the number of genes involved in the mutation was basically the same in each sample. It was speculated that the varietal characteristics of‘Tieguanyin’had been generally stable during asexual reproduction. The KEGG（Kyoto Encyclopedia of Genes and Genomes）enrichment analysis showed that purine and carbohydrate metabolic pathways were significantly enriched in three ‘Tieguanyin’trees used for actual production，and the caffeine metabolic pathway was extremely significant enriched. It was speculated that some of the quality and flavor-related metabolic pathway genes were varied during the long-term asexual reproduction process in‘Tieguanyin’. Compared with the three consecutive asexual reproductions，the sequence of three genes such as FAR1，WAT1，and MYB that related to growth and development and five genes such as PP2A，BTB/POZ，BAT2，RPP13，and Lr10 that related to stress response had been mutated in three‘Tieguanyin’trees used for actual production.

Key words: Camellia sinensis, asexual reproduction, resequencing, genetic variation

HOU Binghao, GAO Ting, WEI Yuede, GAO Shuilian, CAI Yinbi, CHEN Zhiming, JIN Shan, ZHANG Xingtan, WANG Pengjie, YE Naixing. Studies on Genetic Variation of‘Tieguanyin’Tea Trees Asexual Reproduction Based on High-depth Genome Resequencing[J]. Acta Horticulturae Sinica, 2023, 50(7): 1505-1517.

Figures/Tables 11

References 38

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样本 Sample	过滤后读长 Clean data	比对读长 Mapped read	比对率/% Mapped rate	平均深度 Average depth
母树铁观音 Mother tree Tieguanyin	1 661 654 911	1 654 322 653	99.56	58.62
第1代无性繁殖铁观音 First generation clonal Tieguanyin	1 942 084 886	1 926 646 985	99.21	62.38
第2代无性繁殖铁观音 Second generation clonal Tieguanyin	1 554 521 258	1 545 693 484	99.43	55.77
第3代无性繁殖铁观音 Third generation clonal Tieguanyin	1 609 686 577	1 600 019 432	99.40	57.34
西坪铁观音 Xiping Tieguanyin	1 788 588 003	1 782 581 945	99.66	60.24
参内铁观音 Cannei Tieguanyin	1 596 305 309	1 592 821 732	99.78	54.76
龙门铁观音 Longmen Tieguanyin	1 606 148 602	1 599 373 019	99.58	56.50

样本 Sample	过滤后读长 Clean data	比对读长 Mapped read	比对率/% Mapped rate	平均深度 Average depth
母树铁观音 Mother tree Tieguanyin	1 661 654 911	1 654 322 653	99.56	58.62
第1代无性繁殖铁观音 First generation clonal Tieguanyin	1 942 084 886	1 926 646 985	99.21	62.38
第2代无性繁殖铁观音 Second generation clonal Tieguanyin	1 554 521 258	1 545 693 484	99.43	55.77
第3代无性繁殖铁观音 Third generation clonal Tieguanyin	1 609 686 577	1 600 019 432	99.40	57.34
西坪铁观音 Xiping Tieguanyin	1 788 588 003	1 782 581 945	99.66	60.24
参内铁观音 Cannei Tieguanyin	1 596 305 309	1 592 821 732	99.78	54.76
龙门铁观音 Longmen Tieguanyin	1 606 148 602	1 599 373 019	99.58	56.50

样本 Sample	剪切位点 Splicing	基因间 Intergenic	基因上游1K Upstream 1K	基因下游1K Downstream 1K	内含子 Intronic	外显子 Exonic	UTR5	UTR3	总计 Total
母树铁观音 Mother tree Tieguanyin	1 806	30 475 411	529 507	478 199	1 933 210	375 582	35 833	57 981	33 887 529
第1代无性繁殖铁观音 First generation clonal Tieguanyin	1 806	30 121 975	518 716	471 653	1 918 601	374 478	35 554	57 545	33 500 328
第2代无性繁殖铁观音 Second generation clonal Tieguanyin	1 798	29 750 290	488 872	456 722	1 880 822	374 563	35 280	57 208	33 045 555
第3代无性繁殖铁观音 Third generation clonal Tieguanyin	1 816	29 734 927	489 997	456 220	1 881 652	374 475	35 343	57 130	33 031 560
西坪铁观音 Xiping Tieguanyin	1 821	30 932 819	580 244	497 384	1 984 508	377 436	36 279	58 231	34 468 722
参内铁观音 Cannei Tieguanyin	1 834	31 031 666	580 974	498 669	1 986 676	376 733	36 398	58 390	34 571 340
龙门铁观音 Longmen Tieguanyin	1 809	29 719 349	493 033	457 181	1 881 683	373 905	35 303	57 218	33 019 481

样本 Sample	剪切位点 Splicing	基因间 Intergenic	基因上游1K Upstream 1K	基因下游1K Downstream 1K	内含子 Intronic	外显子 Exonic	UTR5	UTR3	总计 Total
母树铁观音 Mother tree Tieguanyin	1 806	30 475 411	529 507	478 199	1 933 210	375 582	35 833	57 981	33 887 529
第1代无性繁殖铁观音 First generation clonal Tieguanyin	1 806	30 121 975	518 716	471 653	1 918 601	374 478	35 554	57 545	33 500 328
第2代无性繁殖铁观音 Second generation clonal Tieguanyin	1 798	29 750 290	488 872	456 722	1 880 822	374 563	35 280	57 208	33 045 555
第3代无性繁殖铁观音 Third generation clonal Tieguanyin	1 816	29 734 927	489 997	456 220	1 881 652	374 475	35 343	57 130	33 031 560
西坪铁观音 Xiping Tieguanyin	1 821	30 932 819	580 244	497 384	1 984 508	377 436	36 279	58 231	34 468 722
参内铁观音 Cannei Tieguanyin	1 834	31 031 666	580 974	498 669	1 986 676	376 733	36 398	58 390	34 571 340
龙门铁观音 Longmen Tieguanyin	1 809	29 719 349	493 033	457 181	1 881 683	373 905	35 303	57 218	33 019 481

样本 Sample	非同义突变 Non-synonymous	同义突变 Synonymous	终止密码子缺失 Stop loss	提前终止 Stop gain	未知 Unknown	总计 Total
母树铁观音 Mother tree Tieguanyin	214 220	147 538	1 002	6 746	5 611	375 117
第1代无性繁殖铁观音 First generation clonal Tieguanyin	213 626	147 006	999	6 769	5 617	374 017
第2代无性繁殖铁观音 Second generation clonal Tieguanyin	213 677	147 053	992	6 767	5 651	374 140
第3代无性繁殖铁观音 Third generation clonal Tieguanyin	213 497	147 210	998	6 753	5 562	374 020
西坪铁观音 Xiping Tieguanyin	215 605	147 805	1 003	6 875	5 688	376 976
参内铁观音 Cannei Tieguanyin	215 234	147 446	1 016	6 857	5 747	376 300
龙门铁观音 Longmen Tieguanyin	213 272	146 862	1 008	6 752	5 550	373 444

Studies on Genetic Variation of‘Tieguanyin’Tea Trees Asexual Reproduction Based on High-depth Genome Resequencing

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样本 Sample	剪切位点 Splicing	基因间 Intergenic	基因上游1K Upstream 1K	基因下游1K Downstream 1K	内含子 Intronic	外显子 Exonic	UTR5	UTR3	总计 Total
母树铁观音 Mother tree Tieguanyin	763	3 284 018	118 826	104 746	378 518	22 430	16 414	14 256	3 939 971
第1代无性繁殖铁观音 First generation clonal Tieguanyin	757	3 224 454	115 638	102 999	374 098	22 433	16 405	14 166	3 870 950
第2代无性繁殖铁观音 Second generation clonal Tieguanyin	751	3 016 071	103 982	95 662	354 251	22 263	16 097	13 910	3 622 987
第3代无性繁殖铁观音 Third generation clonal Tieguanyin	770	3 025 491	105 106	95 894	355 677	22 179	16 123	13 938	3 635 178
西坪铁观音 Xiping Tieguanyin	776	3 658 809	144 595	11 7148	415 208	22 351	16 732	14 615	4 390 234
参内铁观音 Cannei Tieguanyin	776	3 641 989	143 626	11 6725	413 129	22 376	16 688	14 583	4 369 892
龙门铁观音 Longmen Tieguanyin	751	3 030 584	105 222	96 204	355 957	22 190	16 161	13 902	3 640 971

样本 Sample	非移码突变 Non-frameshift	移码突变 Frameshift	终止密码子缺失 Stop loss	提前终止 Stop gain	未知 Unknown	总计 Total
母树铁观音 Mother tree Tieguanyin	8 036	13 152	76	514	518	22 296
第1代无性繁殖铁观音 First generation clonal Tieguanyin	8 013	13 150	84	513	524	22 284
第2代无性繁殖铁观音 Second generation clonal Tieguanyin	8 016	12 991	78	505	530	22 120
第3代无性繁殖铁观音 Third generation clonal Tieguanyin	7 957	13 018	81	485	504	22 045
西坪铁观音 Xiping Tieguanyin	7 971	13 043	81	569	539	22 203
参内铁观音 Cannei Tieguanyin	7 915	13 149	85	557	532	22 238
龙门铁观音 Longmen Tieguanyin	7 913	13 052	80	496	513	22 054

样本 Sample	基因组总突变 Genome mutation	编码区总突变 Coding region mutation	涉及基因总数 Genes involved
母树铁观音 Mother tree Tieguanyin	37 827 500	397 413	29 421
第1代无性繁殖铁观音 First generation clonal Tieguanyin	37 371 278	396 301	29 458
第2代无性繁殖铁观音 Second generation clonal Tieguanyin	36 668 542	396 260	29 454
第3代无性繁殖铁观音 Third generation clonal Tieguanyin	36 666 738	396 065	29 507
西坪铁观音 Xiping Tieguanyin	38 858 956	399 179	29 449
参内铁观音 Cannei Tieguanyin	38 941 232	398 538	29 427
龙门铁观音Longmen Tieguanyin	36 660 452	395 498	29 459

类型Type	ID	注释 Annotation
逆境响应 Stress response	CsTGY02G0001488	PP2A
	CsTGY02G0002579	BTB/POZ
	CsTGY03G0000235	BAT2 domain protein
	CsTGY03G0001953	RPP13
	CsTGY06G0000804	Lr10
生长发育 Growth and development	CsTGY03G0002260	FAR1
	CsTGY07G0002129	WAT1
	CsTGY12G0000888	MYB
酶 Enzyme	CsTGY03G0001145	焦磷酸酶基因 PPase
	CsTGY03G0002361	尿苷核苷酶基因 UPP
	CsTGY05G0000881	DNA甲基转移酶基因 DNMT
	CsTGY05G0001818	醛酮还原酶基因 AKR
	CsTGY06G0000171	酸性磷酸酶基因 ACP
	CsTGY06G0000219	氧类固醇结合蛋白酶基因 OSBP
	CsTGY07G0001696	尿酸氧化酶基因 UO
	CsTGY10G0001326	锌指结构酶基因 ZFN
	CsTGY12G0001281	核酸外切酶基因 EXO
	CsTGY13G0000964	多萜醇激酶基因 DOLK
	CsTGY13G0001265	细胞色素P450酶基因 CYP450
	CsTGY14G0001226	果胶酶抑制蛋白酶基因 PME
未知 Unknown	CsTGY01G0002129	/
	CsTGY01G0003692	/
	CsTGY06G0002804	/
	CsTGY07G0000579	/
	CsTGY07G0001055	/
	CsTGY07G0001417	/
	CsTGY07G0002060	/
	CsTGY08G0001756	/
	CsTGY08G0001967	/
	CsTGY08G0002508	/
	CsTGY12G0000749	/
	CsTGY13G0000037	/
	CsTGY15G0001824	/

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