Genetic diversity analysis of 64 white-fruited pepper germplasm resources

doi:10.16178/j.issn.0528-9017.20240153

Abstract

Abstract:

White-fruited pepper is the most regionally characteristic type of pepper (capsicum) in Zhejiang Province, understanding its genetic diversity serves as an essential foundation for promoting the breeding of new varieties of white-fruited pepper. In this study, 64 white-fruited pepper inbred lines collected from China and abroad were sequenced by Hyper-seq. Principal component analysis, cluster analysis and population structure analysis were also performed. The results showed that a total of 3 511 122 single nucleotide polymorphism (SNP) variation and 922 513 insertion-deletion (InDel) were identified from 12 chromosomes of pepper. The average number of SNPs and InDels per chromosome was 292 593.5 and 76 876.0, respectively. The annotation results revealed that InDel and SNP variation predominantly manifested in the intergenic regions, reaching a quantity of 4 000 310.The next significant occurrence was within intronic regions, totaling 226 301. Cluster analysis and population structure analysis, based on SNP diversity, classified the 64 white pepper materials into two main groups: one comprised 36 fresh white-fruited pepper and 1 ornamental white-fruited pepper, while the other consisted of 27 ornamental white-fruited pepper. The principal component analysis results indicated that two groups clustered distinctly in the PC1 and PC2 regions. This study unveils the genetic structure and genetic diversity of white-fruited pepper germplasm resources, providing a foundational understanding for the future development and application of white-fruited pepper germplasm.

Key words: white-fruited pepper, Hyper-seq, SNP variation, genetic diversity, population structure

CLC Number:

S641.3

FANG Pingping, ZHANG Ting, WEI Jing, WANG Xueyan, LI Chaosen, LIU Huiqin, WAN Hongjian, GUO Qinwei. Genetic diversity analysis of 64 white-fruited pepper germplasm resources[J]. Journal of Zhejiang Agricultural Sciences, 2024, 65(5): 1056-1063.

Figures/Tables 8

References 18

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编号	资源名称	资源类型	原始数据	有效数据	Q20/%	Q30/%	GC含量/%	比对率/%
1	D40-2	鲜食	5 383 126	5 041 630	94.793	87.260	39.444	99.15
2	B1901	鲜食	5 439 770	5 300 980	95.894	89.055	38.639	99.44
3	BJB-2	鲜食	5 482 822	5 261 980	95.504	88.479	39.857	99.46
4	05B03	鲜食	5 270 356	5 109 864	95.932	89.351	40.450	99.72
5	B1-2	鲜食	5 696 008	5 457 042	95.532	88.498	39.092	99.32
6	HZB	鲜食	5 408 052	5 195 202	95.386	88.258	39.271	99.56
7	B15	鲜食	5 283 366	5 130 098	95.805	88.981	39.333	99.36
8	78-4	鲜食	5 708 012	5 562 356	95.808	88.973	39.332	99.42
9	79-3	鲜食	6 022 764	5 828 310	95.614	88.682	39.696	99.58
10	BDR6-73	鲜食	6 076 500	5 891 180	95.615	88.574	39.154	99.42
11	19366	鲜食	6 478 984	6 259 214	95.600	88.594	39.101	99.19
12	D38	鲜食	6 261 442	5 606 574	93.967	85.986	40.171	98.76
13	82-16	鲜食	6 794 910	6 539 454	95.491	88.454	39.758	99.54
14	B7	鲜食	6 123 734	5 924 996	95.623	88.614	39.807	99.68
15	J5-8	鲜食	5 939 370	5 690 576	95.333	88.193	39.860	99.47
16	77-14	鲜食	6 377 144	6 124 990	95.396	88.303	40.298	99.60
17	G4	观赏	7 997 982	7 749 450	95.605	88.636	39.422	98.98
18	L19	鲜食	7 497 060	7 286 784	95.806	88.940	39.193	99.61
19	77-3	鲜食	7 145 158	6 906 132	95.662	88.723	39.956	99.50
20	85-2	鲜食	7 271 872	7 139 356	96.207	89.613	39.732	99.44
21	Y801	鲜食	6 572 104	6 407 592	96.037	89.482	41.476	99.74
22	92-20	鲜食	7 079732	6 883 616	95.791	88.948	38.948	99.35
23	G2	观赏	6 898 254	6 697 662	95.889	89.141	40.419	98.92
24	G15	观赏	7 501 626	7 311 380	95.966	89.257	38.308	98.57
25	1961-7	鲜食	8 352 668	8 192 506	96.612	90.811	39.004	99.08
26	BE	鲜食	7 901 140	7 728 712	96.144	89.728	40.631	99.79
27	19364	鲜食	7 600 394	7 386 584	95.907	89.228	39.540	98.64
28	G27	观赏	8 758216	8 542 260	95.981	89.351	40.206	98.82
29	Y802	鲜食	7 671 398	7 474 346	95.950	89.359	40.476	99.67
30	92-11	鲜食	7 645 046	7 472 758	95.812	88.937	39.395	98.81
31	D36	鲜食	7 477 866	7 267 264	95.839	89.067	38.936	99.32
32	qu-1	鲜食	7 170 338	6 978 328	95.956	89.357	43.274	87.04
33	05B11	鲜食	7 405 520	7 251 454	96.175	89.647	39.780	99.75
34	HDL	观赏	9 241 860	9 069 152	96.615	90.782	39.001	98.83
35	0917	鲜食	9 589 742	9 392 372	96.633	90.882	38.791	98.90
36	93-4	鲜食	10 135 900	9 946 782	96.621	90.823	39.410	98.88
37	G10	观赏	5 445 160	5 224 420	95.464	88.438	39.865	99.29
38	G14	观赏	5 439 674	5 258 568	95.693	88.789	39.884	99.30
39	G13	观赏	6 241 872	6 079 850	95.748	88.871	39.061	97.95
40	G19	观赏	5 648 976	5 454 952	95.721	88.899	39.553	99.05
41	G25	观赏	5 954 426	5 757 390	95.590	88.620	40.307	99.14
42	G8	观赏	5 772 566	5 612 894	95.733	88.850	39.415	99.31
43	G12	观赏	7 762 274	7 602 638	95.866	88.993	38.482	99.02
44	G3	观赏	5 610 018	5 466 564	95.737	88.838	37.832	99.38
45	baiyu	鲜食	6 042 306	5 875 348	95.889	89.164	41.007	99.70
46	qu-3	鲜食	6 558 170	6 394 914	95.942	89.221	38.999	98.17
47	qu-5	鲜食	6 645 886	6 522 008	96.312	89.845	39.199	98.51
48	G1	观赏	6 234 006	5 990 522	95.511	88.504	39.975	98.99
49	G24	观赏	7 061 848	6 780 320	95.173	87.878	39.642	99.46
50	G28	观赏	6 820 046	6 639 342	95.817	89.099	39.723	93.06
51	G7	观赏	7 433 492	7 305 984	95.997	89.238	39.424	99.22
52	G5	观赏	6 563 982	6 382 772	95.690	88.734	39.725	98.52
53	G18	观赏	7 009 938	6 799 832	95.769	88.945	39.325	97.52
54	G20	观赏	7 253 538	7 084 588	95.872	89.076	39.546	97.69
55	G22	观赏	6 981 804	6 816 276	96.014	89.386	41.273	99.54
56	G26	观赏	6568718	6 382 498	95.744	88.857	40.243	98.29
57	G6	观赏	7 516 956	7 284 710	95.614	88.663	39.821	97.41
58	D40-1	鲜食	14 368 730	14 181 536	97.094	91.885	37.781	99.16
59	G16	观赏	9 235 496	8 987 892	96.566	90.763	40.178	99.15
60	YZJ	观赏	8 001 034	7 764 936	95.781	89.004	40.785	90.09
61	G9	观赏	12 964 146	12 638 556	96.812	91.410	39.251	96.12
62	G23	观赏	9 698 788	9 515 068	96.601	90.847	39.276	99.28
63	G21	观赏	9 705 118	9 533 304	96.670	90.939	39.728	99.19
64	G17	观赏	11 084 048	10 889 934	96.770	91.146	39.490	98.11

编号	资源名称	资源类型	原始数据	有效数据	Q20/%	Q30/%	GC含量/%	比对率/%
1	D40-2	鲜食	5 383 126	5 041 630	94.793	87.260	39.444	99.15
2	B1901	鲜食	5 439 770	5 300 980	95.894	89.055	38.639	99.44
3	BJB-2	鲜食	5 482 822	5 261 980	95.504	88.479	39.857	99.46
4	05B03	鲜食	5 270 356	5 109 864	95.932	89.351	40.450	99.72
5	B1-2	鲜食	5 696 008	5 457 042	95.532	88.498	39.092	99.32
6	HZB	鲜食	5 408 052	5 195 202	95.386	88.258	39.271	99.56
7	B15	鲜食	5 283 366	5 130 098	95.805	88.981	39.333	99.36
8	78-4	鲜食	5 708 012	5 562 356	95.808	88.973	39.332	99.42
9	79-3	鲜食	6 022 764	5 828 310	95.614	88.682	39.696	99.58
10	BDR6-73	鲜食	6 076 500	5 891 180	95.615	88.574	39.154	99.42
11	19366	鲜食	6 478 984	6 259 214	95.600	88.594	39.101	99.19
12	D38	鲜食	6 261 442	5 606 574	93.967	85.986	40.171	98.76
13	82-16	鲜食	6 794 910	6 539 454	95.491	88.454	39.758	99.54
14	B7	鲜食	6 123 734	5 924 996	95.623	88.614	39.807	99.68
15	J5-8	鲜食	5 939 370	5 690 576	95.333	88.193	39.860	99.47
16	77-14	鲜食	6 377 144	6 124 990	95.396	88.303	40.298	99.60
17	G4	观赏	7 997 982	7 749 450	95.605	88.636	39.422	98.98
18	L19	鲜食	7 497 060	7 286 784	95.806	88.940	39.193	99.61
19	77-3	鲜食	7 145 158	6 906 132	95.662	88.723	39.956	99.50
20	85-2	鲜食	7 271 872	7 139 356	96.207	89.613	39.732	99.44
21	Y801	鲜食	6 572 104	6 407 592	96.037	89.482	41.476	99.74
22	92-20	鲜食	7 079732	6 883 616	95.791	88.948	38.948	99.35
23	G2	观赏	6 898 254	6 697 662	95.889	89.141	40.419	98.92
24	G15	观赏	7 501 626	7 311 380	95.966	89.257	38.308	98.57
25	1961-7	鲜食	8 352 668	8 192 506	96.612	90.811	39.004	99.08
26	BE	鲜食	7 901 140	7 728 712	96.144	89.728	40.631	99.79
27	19364	鲜食	7 600 394	7 386 584	95.907	89.228	39.540	98.64
28	G27	观赏	8 758216	8 542 260	95.981	89.351	40.206	98.82
29	Y802	鲜食	7 671 398	7 474 346	95.950	89.359	40.476	99.67
30	92-11	鲜食	7 645 046	7 472 758	95.812	88.937	39.395	98.81
31	D36	鲜食	7 477 866	7 267 264	95.839	89.067	38.936	99.32
32	qu-1	鲜食	7 170 338	6 978 328	95.956	89.357	43.274	87.04
33	05B11	鲜食	7 405 520	7 251 454	96.175	89.647	39.780	99.75
34	HDL	观赏	9 241 860	9 069 152	96.615	90.782	39.001	98.83
35	0917	鲜食	9 589 742	9 392 372	96.633	90.882	38.791	98.90
36	93-4	鲜食	10 135 900	9 946 782	96.621	90.823	39.410	98.88
37	G10	观赏	5 445 160	5 224 420	95.464	88.438	39.865	99.29
38	G14	观赏	5 439 674	5 258 568	95.693	88.789	39.884	99.30
39	G13	观赏	6 241 872	6 079 850	95.748	88.871	39.061	97.95
40	G19	观赏	5 648 976	5 454 952	95.721	88.899	39.553	99.05
41	G25	观赏	5 954 426	5 757 390	95.590	88.620	40.307	99.14
42	G8	观赏	5 772 566	5 612 894	95.733	88.850	39.415	99.31
43	G12	观赏	7 762 274	7 602 638	95.866	88.993	38.482	99.02
44	G3	观赏	5 610 018	5 466 564	95.737	88.838	37.832	99.38
45	baiyu	鲜食	6 042 306	5 875 348	95.889	89.164	41.007	99.70
46	qu-3	鲜食	6 558 170	6 394 914	95.942	89.221	38.999	98.17
47	qu-5	鲜食	6 645 886	6 522 008	96.312	89.845	39.199	98.51
48	G1	观赏	6 234 006	5 990 522	95.511	88.504	39.975	98.99
49	G24	观赏	7 061 848	6 780 320	95.173	87.878	39.642	99.46
50	G28	观赏	6 820 046	6 639 342	95.817	89.099	39.723	93.06
51	G7	观赏	7 433 492	7 305 984	95.997	89.238	39.424	99.22
52	G5	观赏	6 563 982	6 382 772	95.690	88.734	39.725	98.52
53	G18	观赏	7 009 938	6 799 832	95.769	88.945	39.325	97.52
54	G20	观赏	7 253 538	7 084 588	95.872	89.076	39.546	97.69
55	G22	观赏	6 981 804	6 816 276	96.014	89.386	41.273	99.54
56	G26	观赏	6568718	6 382 498	95.744	88.857	40.243	98.29
57	G6	观赏	7 516 956	7 284 710	95.614	88.663	39.821	97.41
58	D40-1	鲜食	14 368 730	14 181 536	97.094	91.885	37.781	99.16
59	G16	观赏	9 235 496	8 987 892	96.566	90.763	40.178	99.15
60	YZJ	观赏	8 001 034	7 764 936	95.781	89.004	40.785	90.09
61	G9	观赏	12 964 146	12 638 556	96.812	91.410	39.251	96.12
62	G23	观赏	9 698 788	9 515 068	96.601	90.847	39.276	99.28
63	G21	观赏	9 705 118	9 533 304	96.670	90.939	39.728	99.19
64	G17	观赏	11 084 048	10 889 934	96.770	91.146	39.490	98.11

排序	注释的位置	变异数量
1	基因间隔区	4 000 310
2	内含子	226 301
3	外显子	74 516
4	下游	43 624
5	上游	41 576
6	3'端UTR区	8 672
7	5'端UTR区	6 180
8	上游;下游	1 350
9	剪切区	1 234
10	外显子;剪切区	7

排序	注释的位置	变异数量
1	基因间隔区	4 000 310
2	内含子	226 301
3	外显子	74 516
4	下游	43 624
5	上游	41 576
6	3'端UTR区	8 672
7	5'端UTR区	6 180
8	上游;下游	1 350
9	剪切区	1 234
10	外显子;剪切区	7