Population Structure Analysis of Old Germplasms of Chinese Bayberry Based on WGS

doi:10.16420/j.issn.0513-353x.2023-0723

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (10): 2267-2280.doi: 10.16420/j.issn.0513-353x.2023-0723

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

Population Structure Analysis of Old Germplasms of Chinese Bayberry Based on WGS

ZHANG Shuwen¹, LIANG Senmiao¹, YU Zheping¹, SUN Li¹, YE Haiping³, HU Xiaojin⁴, YAN Liju⁶, WU Yuyong⁵, YING Zhengzheng⁵, ZHENG Xiliang¹, QI Xingjiang¹^,²^,^*()

¹ State Key Laboratory for Managing Biotic and Chemical Threats to Quality and Safety of Agro-products，Institute of Horticulture，Zhejiang Academy of Agricultural Sciences，Hangzhou 310021，China
² Xianghu Laboratory，Hangzhou 311231，China
³ Huangyan Fruit Tree Technology Promotion Station，Huangyan，Zhejiang 318026，China
⁴ Bureau of Agriculture and Rural Affairs of Jingzhou County，Jingzhou，Hunan 418400，China
⁵ Xianju Specialty Technology Promotion Center，Xianju，Zhejiang 317300，China
⁶ Linhai Specialty and Technology Extension Station，Linhai，Zhejiang 317000，China

Received:2024-05-28 Revised:2024-08-08 Online:2024-10-25 Published:2024-10-21
Contact: QI Xingjiang

Abstract

Abstract:

Based on whole genome sequencing（WGS）technology，SNPs covering the whole genome of Chinese bayberry were excavated，and the distribution characteristics of SNPs were clarified. A population structure analysis of 36 old germplasm was conducted. A total of 36 germplasm resources obtained high-quality sequencing data of 398.26 Gb，with a sequencing depth of 37.34×，an average GC content of 38.57%，and a Q30 of 97.56%. A total of 5 362 434 SNP loci were detected，and SNP numbers ranging from 655 299 to 897 575 for Chr.1 to Chr.8. A total of 16 regions with low SNP variation frequency with a total length of 9.45 Mb. Population evolution analysis were divided into three groups，with six germplasm from Tengchong，Yunnan clustered into groupⅠ，which has the farthest genetic relationship with other germplasm. Four germplasms from Jingzhou，Hunan were clustered into Group Ⅱ. The the other 26 germplasms are clustered into Group Ⅲ，the closest genetic relationship exists between Huangyan and Xianju germplasm in Zhejiang Province，with‘Dongkui’being the main cultivar. The analysis of population linkage imbalance found that the linkage disequilibrium（LD）decay rate of the Tengchong，Yunnan population was the fastest，followed by the Huangyan，Zhejiang population，and the Cixi，Zhejiang population was the slowest. A F_st analysis was conducted on the populations of Huangyan（‘Dongkui’）and Cixi（‘Biqizhong’）in Zhejiang Province. The genes with significant differences between these two populations were mainly related to stress resistance，secondary metabolites，and plant morphogenesis，resulting in phenotypic differences between these two varieties. Population structure analysis found that the genetic backgrounds of Fujian，Jingzhou，Hunan and Laifeng，Hubei included the genetic backgrounds of more than three populations，including Xianju，Zhejiang. Additionally，hybridization signals were also found in the Jingzhou，Hunan population，indicating that the quality of Xianju，Zhejiang bayberry had a significant impact on the formation of cultivated cultivars in Fujian，Hunan and Hubei over the past century.

Key words: Chinese bayberry, whole genome, SNP, resource, population evolution, population structure

ZHANG Shuwen, LIANG Senmiao, YU Zheping, SUN Li, YE Haiping, HU Xiaojin, YAN Liju, WU Yuyong, YING Zhengzheng, ZHENG Xiliang, QI Xingjiang. Population Structure Analysis of Old Germplasms of Chinese Bayberry Based on WGS[J]. Acta Horticulturae Sinica, 2024, 51(10): 2267-2280.

Figures/Tables 10

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采样地点 Sampling location	经度Longitude	纬度 Latitude	海拔/m Altitude	品种 Cultivar	种质编号 Number	估计树龄/a Tree-age（estimated）
浙江黄岩 Huangyan，Zhejiang	121.17°	28.36°	30 ~ 60	东魁 Dongkui	HY-1，HY-2，HY-4	70
					HY-5	180
					HY-9	40
浙江仙居 Xianju，Zhejiang	120.47°	28.76°	150 ~ 170	水梅 Shuimei	XJ-1，XJ-3，XJ-5， XJ-7，XJ-9	100
浙江慈溪 Cixi，Zhejiang	121.15°	30.56°	30	荸荠种 Biqizhong	CX-1，CX-2，CX-3，CX-4，CX-5	120
湖南靖州 Jingzhou，Hunan	109.63°	26.66°	370	木洞大叶 Mudong Daye	HN-1	120
					HN-2	130
				上冲梅 Shangchongmei	HN-3，HN-7	110
					HN-4	120
湖北来凤 Laifeng，Hubei	109.29°	29.61°	580 ~ 695	红梅 Hongmei	HB-1，HB-2	150
					HB-4，HB-5	100
				乌梅 Wumei	HB-6	100
云南腾冲 Tengchong，Yunnan	98.34°	25.19°	1 550 ~ 1 600	野生种质 Wild germplasm	YN-1，YN-6	190
					YN-2	130
					YN-3，YN-4	200
					YN-5	300
浙江临海（原产地福建） Linhai，Zhejiang（Origin is Fujian Province）	119.28°	26.08°	130	硬丝 Yingsi	FJ-1	30
				软丝 Ruansi	FJ-2
				浮宫一号Fugong 1	FJ-3
				安海王子Anhai Wangzi	FJ-4
				安海早 Anhaizao	FJ-5

采样地点 Sampling location	经度Longitude	纬度 Latitude	海拔/m Altitude	品种 Cultivar	种质编号 Number	估计树龄/a Tree-age（estimated）
浙江黄岩 Huangyan，Zhejiang	121.17°	28.36°	30 ~ 60	东魁 Dongkui	HY-1，HY-2，HY-4	70
					HY-5	180
					HY-9	40
浙江仙居 Xianju，Zhejiang	120.47°	28.76°	150 ~ 170	水梅 Shuimei	XJ-1，XJ-3，XJ-5， XJ-7，XJ-9	100
浙江慈溪 Cixi，Zhejiang	121.15°	30.56°	30	荸荠种 Biqizhong	CX-1，CX-2，CX-3，CX-4，CX-5	120
湖南靖州 Jingzhou，Hunan	109.63°	26.66°	370	木洞大叶 Mudong Daye	HN-1	120
					HN-2	130
				上冲梅 Shangchongmei	HN-3，HN-7	110
					HN-4	120
湖北来凤 Laifeng，Hubei	109.29°	29.61°	580 ~ 695	红梅 Hongmei	HB-1，HB-2	150
					HB-4，HB-5	100
				乌梅 Wumei	HB-6	100
云南腾冲 Tengchong，Yunnan	98.34°	25.19°	1 550 ~ 1 600	野生种质 Wild germplasm	YN-1，YN-6	190
					YN-2	130
					YN-3，YN-4	200
					YN-5	300
浙江临海（原产地福建） Linhai，Zhejiang（Origin is Fujian Province）	119.28°	26.08°	130	硬丝 Yingsi	FJ-1	30
				软丝 Ruansi	FJ-2
				浮宫一号Fugong 1	FJ-3
				安海王子Anhai Wangzi	FJ-4
				安海早 Anhaizao	FJ-5

SNP位置SNP ID	F1	F2	R
Chr1：9855573	TTGTCCACATCAATGCCGCAT	TTGTCCACATCAATGCCGCAC	GTTGGATTAGATACTTATGACATTGCTACG
Chr1：24875516	AGGCACTCAGCCTTGCTGCTC	AGGCACTCAGCCTTGCTGCTG	GCGACTTAACTGTTATTATCACAGC
Chr2：1096506	CTGAGTGTAGATAGAATAGAGCTCC	CTGAGTGTAGATAGAATAGAGCTCT	GGGATATGCACTTACGGATTGC
Chr2：34942573	GCTATGTAAAAATACGTATCGCCAG	GCTATGTAAAAATACGTATCGCCAT	GGCAATCTCTACCAGCATAATG
Chr3：3035320	TACTGCTTTTCTTTTATC	TACTGCTTTTCTTTTATT	TGAGCCCCAAAGATATTGCAAGAACATAAC
Chr3：25557841	TCTAGGATGAGATTTTGTG	TCTAGGATGAGATTTTGTT	TTCAAAGACAAGAATGCAGCATG
Chr4：2150997	GAAGGTGACCAAGTTCATGCTGTACTCAATTTTTGACTT	GAAGGTCGGAGTCAACGGATTGTACTCAATTTTTGACTC	TTCAAAGCCACATCCAACATCA
Chr4：30168356	CTCATCACCAAGAGTCTTCCG	CTCATCACCAAGAGTCTTCCA	CAGTTGACACTGACAGAGCTGG
Chr5：6997703	CAGGATATGATCTAGGAAGTTGTGC	CAGGATATGATCTAGGAAGTTGTGT	TGGCGCAATCACCCCAATTTTAACTGGA
Chr5：19892053	GGTCGATTTGTGGAGGTTTTTCAGT	GGTCGATTTGTGGAGGTTTTTCAGG	AGGCCTCGATGACCACTTTGCCACCCAC
Chr6：4338019	CTCTTTGCAAAGCTCGCTC	CTCTTTGCAAAGCTCGCTT	TTTCTCAATCATAAGAGCGGCCTCTT
Chr6：17174448	TGTTGATGGACCATCCACGGAGTAA	TGTTGATGGACCATCCACGGAGTAC	TTAATTTGTTTTTTATTTATCACC
Chr6：20374169	GTTAAGTCATCCCCTCAAT	GTTAAGTCATCCCCTCAAC	AAGCGACCTCTTCCTCACACAA
Chr6：28747343	TGCTGAAATGAGGCTCAGTGG	TGCTGAAATGAGGCTCAGTGA	AATGATCAGGCTTCATAAGCTC
Chr6：32048517	CCTCCTAGAATTTCAACGCTCTTAA	CCTCCTAGAATTTCAACGCTCTTAT	AACATGACTCGTTTGGTTCAAAT
Chr7：7268907	GCAACAATCTTCCTCGCTTTT	GCAACAATCTTCCTCGCTTTC	GAAAGAGAAGCCCTCCTCAAATTCAGTCAG
Chr7：31486783	CCTCGAAATGTGGAGGTCCCAGC	CCTCGAAATGTGGAGGTCCCAGT	CATGGCGCAATCACCAAATCCCATACTG
Chr8：7003270	CCAACAAATGATAGCGCTTTAG	CCAACAAATGATAGCGCTTTAA	GCTAAAAGTCTTGAGGGTATTA
Chr8：18551161	GGTTGTGAGAGGATTAAAAGTA	GGTTGTGAGAGGATTAAAAGTG	AAATTCCAATTGCATGAGGTTTTCGG
Chr8：28476059	TTCTGCGTTCTCCGACGTTCTTCCC	TTCTGCGTTCTCCGACGTTCTTCCT	TGCATGTGTTATGAACGGATGT

SNP位置SNP ID	F1	F2	R
Chr1：9855573	TTGTCCACATCAATGCCGCAT	TTGTCCACATCAATGCCGCAC	GTTGGATTAGATACTTATGACATTGCTACG
Chr1：24875516	AGGCACTCAGCCTTGCTGCTC	AGGCACTCAGCCTTGCTGCTG	GCGACTTAACTGTTATTATCACAGC
Chr2：1096506	CTGAGTGTAGATAGAATAGAGCTCC	CTGAGTGTAGATAGAATAGAGCTCT	GGGATATGCACTTACGGATTGC
Chr2：34942573	GCTATGTAAAAATACGTATCGCCAG	GCTATGTAAAAATACGTATCGCCAT	GGCAATCTCTACCAGCATAATG
Chr3：3035320	TACTGCTTTTCTTTTATC	TACTGCTTTTCTTTTATT	TGAGCCCCAAAGATATTGCAAGAACATAAC
Chr3：25557841	TCTAGGATGAGATTTTGTG	TCTAGGATGAGATTTTGTT	TTCAAAGACAAGAATGCAGCATG
Chr4：2150997	GAAGGTGACCAAGTTCATGCTGTACTCAATTTTTGACTT	GAAGGTCGGAGTCAACGGATTGTACTCAATTTTTGACTC	TTCAAAGCCACATCCAACATCA
Chr4：30168356	CTCATCACCAAGAGTCTTCCG	CTCATCACCAAGAGTCTTCCA	CAGTTGACACTGACAGAGCTGG
Chr5：6997703	CAGGATATGATCTAGGAAGTTGTGC	CAGGATATGATCTAGGAAGTTGTGT	TGGCGCAATCACCCCAATTTTAACTGGA
Chr5：19892053	GGTCGATTTGTGGAGGTTTTTCAGT	GGTCGATTTGTGGAGGTTTTTCAGG	AGGCCTCGATGACCACTTTGCCACCCAC
Chr6：4338019	CTCTTTGCAAAGCTCGCTC	CTCTTTGCAAAGCTCGCTT	TTTCTCAATCATAAGAGCGGCCTCTT
Chr6：17174448	TGTTGATGGACCATCCACGGAGTAA	TGTTGATGGACCATCCACGGAGTAC	TTAATTTGTTTTTTATTTATCACC
Chr6：20374169	GTTAAGTCATCCCCTCAAT	GTTAAGTCATCCCCTCAAC	AAGCGACCTCTTCCTCACACAA
Chr6：28747343	TGCTGAAATGAGGCTCAGTGG	TGCTGAAATGAGGCTCAGTGA	AATGATCAGGCTTCATAAGCTC
Chr6：32048517	CCTCCTAGAATTTCAACGCTCTTAA	CCTCCTAGAATTTCAACGCTCTTAT	AACATGACTCGTTTGGTTCAAAT
Chr7：7268907	GCAACAATCTTCCTCGCTTTT	GCAACAATCTTCCTCGCTTTC	GAAAGAGAAGCCCTCCTCAAATTCAGTCAG
Chr7：31486783	CCTCGAAATGTGGAGGTCCCAGC	CCTCGAAATGTGGAGGTCCCAGT	CATGGCGCAATCACCAAATCCCATACTG
Chr8：7003270	CCAACAAATGATAGCGCTTTAG	CCAACAAATGATAGCGCTTTAA	GCTAAAAGTCTTGAGGGTATTA
Chr8：18551161	GGTTGTGAGAGGATTAAAAGTA	GGTTGTGAGAGGATTAAAAGTG	AAATTCCAATTGCATGAGGTTTTCGG
Chr8：28476059	TTCTGCGTTCTCCGACGTTCTTCCC	TTCTGCGTTCTCCGACGTTCTTCCT	TGCATGTGTTATGAACGGATGT

种质编号 Sample code	有效数据量/Gb Clean base	GC含量/% GC content	Q20/%	Q30/%	重复率/% Duplication rate	测序深度/× Average depth
HY-1	10.69	38.18	99.96	97.61	35.40	36.09
HY-2	10.36	38.00	99.96	97.63	36.83	34.97
HY-4	10.45	39.43	99.96	97.72	39.03	35.27
HY-5	12.17	39.51	99.96	97.72	35.50	41.09
HY-9	11.58	38.34	99.96	97.72	35.30	39.07
XJ-1	11.38	38.09	99.89	97.53	35.40	38.42
XJ-3	10.52	39.18	99.88	97.66	33.84	35.50
XJ-5	10.75	39.07	99.88	97.63	36.80	36.29
XJ-7	10.40	38.05	99.93	97.69	34.34	35.12
XJ-9	11.72	38.43	99.94	97.57	36.30	39.55
CX-1	10.32	38.16	99.92	97.52	29.90	34.84
CX-2	10.99	38.08	99.93	97.66	36.70	37.11
CX-3	11.11	38.24	99.93	97.51	35.91	37.51
CX-4	10.60	38.00	99.95	97.58	34.70	35.77
CX-5	10.24	39.14	99.95	97.70	30.24	34.57
HN-1	12.86	39.00	99.97	97.62	37.40	43.40
HN-2	11.12	39.13	99.96	97.64	34.70	37.54
HN-3	11.20	39.11	99.96	97.62	38.10	37.81
HN-4	10.06	38.00	99.96	97.66	35.30	33.96
HN-7	10.90	39.24	99.96	97.62	36.27	36.80
HB-1	10.22	40.04	99.93	97.68	35.20	34.48
HB-2	11.88	39.00	99.94	97.56	38.44	40.11
HB-4	11.14	40.30	99.94	97.64	36.80	37.62
HB-5	10.75	38.00	99.96	97.79	36.24	36.30
HB-6	11.42	38.27	99.96	97.59	35.15	38.54
FJ-1	10.01	38.14	99.99	97.00	27.05	33.80
FJ-2	16.08	38.42	99.99	97.62	27.70	54.28
FJ-3	10.35	38.00	99.99	96.94	25.20	34.93
FJ-4	11.59	38.28	99.99	97.06	25.33	39.13
FJ-5	11.75	38.12	99.99	97.63	25.42	39.68
YN-1	10.63	38.51	99.93	97.72	30.77	35.88
YN-2	10.81	38.34	99.93	97.44	31.30	36.51
YN-3	10.78	38.07	99.93	97.46	31.04	36.40
YN-4	10.54	38.16	99.93	97.48	29.22	35.57
YN-5	10.50	38.31	99.93	97.36	30.62	35.46
YN-6	10.37	38.16	99.93	97.49	28.15	35.01
平均Average	11.06	38.57	99.95	97.56	33.38	37.34

Population Structure Analysis of Old Germplasms of Chinese Bayberry Based on WGS

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样本 Sample	SNP数量 Number of SNPs	转换位点 Number of transition	颠换位点 Number of transversion	转换/颠换 Transition/ transversion	杂合变异位点 Number of heterozygosity	纯合变异位点 Number of homozygosity	杂合率/% Heterozygosity rate
HY-1	2 050 938	1 411 884	639 054	2.21	1 724 369	326 569	84.08
HY-2	2 048 642	1 410 307	638 335	2.21	1 721 860	326 782	84.05
HY-4	2 052 202	1 412 718	639 484	2.21	1 724 844	327 358	84.05
HY-5	2 052 967	1 413 221	639 746	2.21	1 723 585	329 382	83.96
HY-9	2 052 974	1 413 453	639 521	2.21	1 725 777	327 197	84.06
XJ-1	2 020 543	1 392 832	627 711	2.22	1 794 440	226 103	88.81
XJ-3	2 015 957	1 389 488	626 469	2.22	1 788 704	227 253	88.73
XJ-5	2 014 444	1 388 425	626 019	2.22	1 785 481	228 963	88.63
XJ-7	2 019 041	1 391 447	627 594	2.22	1 792 393	226 648	88.77
XJ-9	2 053 334	1 413 369	639 965	2.21	1 726 162	327 172	84.07
CX-1	1 726 871	1 187 340	539 531	2.20	1 563 406	163 465	90.53
CX-2	2 355 419	1 621 539	733 880	2.21	2 094 979	260 440	88.94
CX-3	1 726 465	1 187 243	539 222	2.20	1 562 720	163 745	90.52
CX-4	1 730 185	1 189 641	540 544	2.20	1 565 862	164 323	90.50
CX-5	1 726 906	1 187 304	539 602	2.20	1 561 793	165 113	90.44
HN-1	2 001 119	1 380 042	621 077	2.22	1 513 540	487 579	75.63
HN-2	2 159 194	1 494 361	664 833	2.25	1 779 964	379 230	82.44
HN-3	2 063 061	1 423 165	639 896	2.22	1 570 871	492 190	76.14
HN-4	2 063 833	1 423 804	640 029	2.22	1 574 460	489 373	76.29
HN-7	2 062 759	1 422 958	639 801	2.22	1 571 669	491 090	76.19
HB-1	2 023 343	1 399 019	624 324	2.24	1 519 121	504 222	75.08
HB-2	2 022 311	1 394 607	627 704	2.22	1 476 575	545 736	73.01
HB-4	2 014 613	1 389 561	625 052	2.22	1 466 369	548 244	72.79
HB-5	2 058 455	1 421 689	636 766	2.23	1 566 655	491 800	76.11
HB-6	1 893 434	1 305 944	587 490	2.22	1 222 637	670 797	64.57
FJ-1	2 049 201	1 417 215	631 986	2.24	1 636 785	412 416	79.87
FJ-2	2 135 600	1 477 909	657 691	2.25	1 751 915	383 685	82.03
FJ-3	2 059 344	1 422 225	637 119	2.23	1 645 218	414 126	79.89
FJ-4	2 144 618	1 486 049	658 569	2.26	1 738 952	405 666	81.08
FJ-5	2 109 931	1 460 493	649 438	2.25	1 725 461	384 470	81.78
YN-1	3 517 942	2 430 232	1 087 710	2.23	966 536	2 551 406	27.47
YN-2	3 508 535	2 422 505	1 086 030	2.23	913 854	2 594 681	26.05
YN-3	3 512 213	2 426 292	1 085 921	2.23	952 693	2 559 520	27.13
YN-4	3 505 810	2 421 699	1 084 111	2.23	943 055	2 562 755	26.90
YN-5	3 499 575	2 416 870	1 082 705	2.23	884 303	2 615 272	25.27
YN-6	3 504 092	2 418 865	1 085 227	2.23	857 631	2 646 461	24.48

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