马铃薯品种（系）田间晚疫病抗性评价和全基因组遗传多样性分析

doi:10.3864/j.issn.0578-1752.2022.18.002

Abstract

Abstract:

【Objective】To evaluate the late blight resistance in field. To use SNP markers to analyze the genetic diversity of late blight resistance of potato germplasm and discern the genetic segments that may affect the phenotype of potato late blight resistance, and to provide a theoretical basis for the innovation and utilization of potato late blight resistant germplasm.【Method】Field resistance to late blight was evaluated in potato germplasm at multiple locations and over the course of several years. SNP markers were detected using a dd-RAD simplified genome sequencing strategy. The population genetic structure was analyzed using Admixture, principal component analysis was conducted using GCTA, a phylogenetic tree was constructed using fastTree, population genetic diversity parameters were calculated using the populations command in the Stacks package, selective sweep parameters were calculated using vcftools, protein sequences were aligned using Clustal Omega, and a proteins phylogenetic tree was drawn using MEGA6. Genome-wide association analysis was constructed using GEMMA 0.98.1 and QQ and manhattan plots were drawn using CMplot.【Result】Through years of evaluation of late blight field resistance in multiple locations, potato germplasm of 101 late blight resistant varieties (lines) and 21 susceptible varieties were obtained. A total of 8 697 602 relatively evenly distributed SNPs were obtained using dd-RAD simplified genome sequencing on these germplasms. This germplasm can be further divided into 6 populations through structural analysis, principal component analysis and phylogenetic analysis. The average nucleotide diversity (π) within the 6 populations ranged from 0.2055 to 0.2572 and the fixation index (Fst) among the six populations ranged from 0.156909 to 0.187336, revealing a relatively large genetic diversity for these germplasms. The expected heterozygosity (He) within the 6 populations ranged from 0.187 to 0.2297 and the observed heterozygosity (Ho) ranged from 0.0829 to 0.1186. The values of Ho were less than those of He in all six populations. Meanwhile, the inbreeding coefficient (Fis) for the six populations ranged from 0.2412 to 0.3554, indicating inbreeding events during the breeding process. To identify the genetic segments that may affect the phenotype of potato late blight resistance, π ratios and Fst among different late blight resistance germplasms in the whole potato genome were calculated using 20 kb as the window length and 5 kb as the step length. The 745 genetic segments which had a π ratio value in the lowest 5% and a Fst value in highest 10% were further analyzed by performing a selective sweep analysis. These selected segments contain a total of 507 genes, including 4 NBS-LRR genes. A genome-wide association analysis was also conducted, yielding 9 SNP highly associated with late blight resistance. Of the 69 genes located in the genome within 50 kb around the 9 SNPs, 15 genes were predicted to be involved in stress response, and 12 genes were predicted to be involved in removing peroxide radicals.【Conclusion】Large amount of SNPs, which are relatively evenly distributed in the potato genome, can be genotyped by dd-RAD simplified genome sequencing. Potato late blight field resistance germplasm has a large genetic diversity, but had inbreeding events in the process of breeding. Population structure analysis can reveal the genetic relationship between potato germplasms, which can further provide a theoretical basis for parental selection in breeding. Selective sweep and genome-wide association analyses help to isolate genetic segments that may affect late blight resistance traits.

Key words: potato (Solanum tuberosum L.), late blight (Phytophthora infestans), single nucleotide polymorphism (SNP), genetic diversity, selective sweep, association mapping

XiaoChuan LI,ChaoHai WANG,Ping ZHOU,Wei MA,Rui WU,ZhiHao SONG,Yan MEI. Deciphering of the Genetic Diversity After Field Late Blight Resistance Evaluation of Potato Breeds[J].Scientia Agricultura Sinica, 2022, 55(18): 3484-3500.

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Figures/Tables 8

Table 1

The 122 potato germplasm and 2d-RAD simplified genome sequencing results"

序号 Serial	品种（系） Varieties (lines)	数据量 Total bases (bp)	高质量序列数 HQ reads	序列比对数 Mapped reads	序列比对比 Mapping rate (%)	覆盖度 Coverage (%)	代号* Code
1	云薯801 YunShu801	1389519882	9887037	9820720	99.33	15.86	X14
2	L0277-17	1479741228	10573903	10516208	99.45	17.45	X67
3	云薯105 YunShu105	1430954730	10217553	10151185	99.35	17.33	X65
4	会薯14号HuiShu14	1475603937	10491378	10412675	99.25	17.69	X16
5	会薯8号HuiShu8	1724226138	12327810	12244428	99.32	17.89	X59
6	毕薯2号BiShu2	1630027647	11604162	11524406	99.31	17.50	X56
7	13-10-34	1457291493	10464271	10391818	99.31	18.53	X19
8	37-47	1381932198	9859731	9801329	99.41	17.06	X20
9	Nicola	1517566095	10836793	10759790	99.29	17.89	V11
10	Katahdin	2005973730	14308809	14210061	99.31	18.08	V13
11	会薯13号HuiShu13	1513824426	10822275	10750664	99.34	16.87	X53
12	丽薯10号LiShu10	2074351050	14945235	14855932	99.40	18.44	X79
13	云薯107 YunShu107	1808600760	12934108	12849969	99.35	18.82	X62
14	86-4	1773098289	12852561	12769137	99.35	19.27	X78
15	S04-109	1553937930	11214590	11132884	99.27	17.59	X101
16	宣薯5号XuanShu5	1522850355	10889989	10826007	99.41	18.03	X70
17	11-48	1544878800	11048219	10967798	99.27	17.90	X7
18	定薯5号DingShu5	1235218653	8850250	8781613	99.22	16.64	X33
19	毕薯8号BiShu8	1849000239	13074100	12968752	99.19	17.76	X36
20	288-39	2031266196	14592056	14486152	99.27	18.60	X41
21	92-101	1427750136	10224526	10132842	99.10	16.06	X31
22	167-327	1233568926	8833599	8752753	99.08	15.32	X24
23	77-29	1607038884	11485513	11406544	99.31	18.07	X8
24	Agria	1873257894	13391597	13304811	99.35	18.36	V4
25	定薯3号DingShu3	1939569498	14050420	13959591	99.35	21.62	X95
26	鄂薯18号EShu18	1748400651	12591486	12507551	99.33	19.14	X94
27	A153	1546019631	11036891	10967645	99.37	17.67	X58
28	77-21	2340564876	16498728	16352763	99.12	27.14	X4
29	43-36	1785437622	12769189	12689774	99.38	18.40	X38
30	104-376	2081927016	15013206	14909294	99.31	19.49	X75
31	198-151	1506050649	10766415	10707633	99.45	18.30	X69
32	225-177	1428782715	10123094	10060117	99.38	17.33	X12
33	43-20	1217961666	8719306	8665729	99.39	16.04	X32
34	中薯17号ZhongShu17	1636463898	11773432	11589241	98.44	20.53	V21
35	Favorita	1749736224	12528593	12449651	99.37	19.32	V3
36	Russet Burbank	1915560153	13773752	13690282	99.39	22.08	V20
37	Norchip	1232854965	8755118	8690255	99.26	16.97	V16
38	Spunta	1701510795	12281997	12189765	99.25	17.37	V1
39	S10-557	1800904824	12904151	12826113	99.40	16.87	X74
40	S10-676	1875586428	13457582	13376099	99.39	17.68	X71
41	S04-921	1369934361	9804477	9747198	99.42	17.17	X66
42	云薯902 YunShu902	2269214694	16348796	16240617	99.34	18.44	X89
43	LZ111	1701482616	12279442	12210831	99.44	18.88	X77
44	S06-277	1976278086	14233248	14130408	99.28	18.36	X100
45	A89	1705085901	12127056	12058833	99.44	19.33	X68
46	Kennebec	1894451013	13515960	13429500	99.36	18.93	V2
47	12-9	1642531869	11661138	11584044	99.34	16.91	X55
48	云薯1号YunShu1	1932156747	13982565	13887872	99.32	20.44	X96
49	云薯505 YunShu505	2278091020	16058092	15921163	99.15	25.27	X3
50	丽薯13号LiShu13	1792673208	12943700	12860661	99.36	18.37	X90
51	宣薯6号XuanShu6	1743643143	12416240	12333510	99.33	18.19	X57
52	16-811-92	2571656553	18433648	18323584	99.40	18.79	X81
53	16-81-19 C5	1566249921	11152065	11073521	99.30	18.36	X44
54	105-148	1830419676	13169922	13060177	99.17	18.40	X72
55	YS481	2176126065	15681885	15582664	99.37	18.08	X92
56	Superior	1795602987	12872912	12799481	99.43	19.35	V12
57	毕薯10号BiShu10	1946519667	13906796	13820590	99.38	18.21	X40
58	10-61	1881900756	13451123	13366356	99.37	18.91	X64
59	32-80	1839399849	13188933	13101780	99.34	19.30	X35
60	19-182	1542493908	10949872	10868390	99.26	18.30	X9
61	19-75-22	1418241816	10277631	10215203	99.39	20.37	X48
62	33-46	1433188962	10193577	10125468	99.33	16.44	X15
63	C149	1663146900	11887115	11796792	99.24	18.77	X6
64	6-25	1966347081	14091871	13993199	99.30	19.31	X39
65	Desiree	1741237884	12436565	12357551	99.36	18.31	V5
66	Hertha	1184096367	8370420	8327303	99.48	16.57	V15
67	4-151	1457695764	10419341	10333207	99.17	17.23	X5
68	25-2	1341393498	9611717	9544222	99.30	16.70	X34
69	24-37-55	1976929830	14344412	14259611	99.41	21.19	X86
70	Chieftain	1999068759	14306469	14194123	99.21	19.47	V6
71	Shepody	1696532877	12146034	12060607	99.30	18.70	V9
72	Ranger Russet	1745461386	12518041	12422160	99.23	19.28	V18
73	Snowden	2128781160	15119156	15004489	99.24	19.65	V7
74	Felsina	2037316590	14511003	14421521	99.38	21.57	V19
75	Atlantic	1752787368	12542637	12455169	99.30	19.79	V8
76	Lenape	1054845711	7540802	7470305	99.07	17.88	V17
77	丽薯18号LiShu18	1983366639	14258000	14169149	99.38	19.30	X73
78	BP0806-30	1665025128	11779252	11694069	99.28	18.13	X60
79	BP0806-21	1712587932	12322410	12234910	99.29	17.99	X106
80	鄂薯14号EShu14	957120660	6750190	6701577	99.28	16.68	X2
81	Belchip	994979286	7074600	6985059	98.73	16.27	V14
82	Innovator	2129532228	15201441	15094352	99.30	20.18	V10
83	24-2-74	1512989658	10836722	10732355	99.04	17.65	X47
84	丽薯6号LiShu6	1335983409	9559009	9479823	99.17	18.40	X29
85	NSN8	1707356961	12237252	12148835	99.28	17.14	X98
86	YSN3	1918037115	13780834	13684547	99.30	18.49	X93
87	合作88 HeZuo88	1241992494	8892503	8826214	99.25	17.50	X49
88	cip88	1592733159	11381458	11294212	99.23	18.37	X50
89	c88	1114612254	7962710	7903628	99.26	16.30	X51
90	威芋6号WeiYu6	1698505965	12078111	11949277	98.93	17.52	X17
91	威芋7号WeiYu7	1089760050	7749041	7680101	99.11	15.71	X1
92	V2011-2	1350470763	9632054	9534464	98.99	17.40	X11
93	Z59	1266584391	9067253	9018186	99.46	18.61	X63
94	12-1-4	1493397441	10657657	10595044	99.41	18.36	X61
95	WY08002	1340769375	9582631	9512250	99.27	16.92	X52
96	11-86-90	2101533741	15105304	15001569	99.31	18.42	X83
97	青薯9号QingShu9	1995336018	14349098	14254442	99.34	18.41	X76
98	云薯401 YunShu401	1565585901	11348147	11277951	99.38	20.10	X42
99	会薯15号HuiShu15	1314918630	9407429	9347588	99.36	16.58	X30
100	0401-11	1672961841	12084421	11968695	99.04	19.40	X99
101	威薯9号WeiShu9	1728903294	12517795	12432832	99.32	19.66	X97
102	H3	1367316783	9812205	9723683	99.10	17.92	X54
103	2005-1	1671491790	12050460	11974544	99.37	17.86	X104
104	23-61-259	1225347075	8768959	8702442	99.24	15.53	X25
105	19-61-96	2114742438	15292497	15184121	99.29	20.07	X87
106	27-81-72	1291962231	9201567	9126131	99.18	17.03	X28
107	会薯16号HuiShu16	1872061542	13363101	13282357	99.40	19.22	X37
108	川芋A50 ChuanYuA50	1426170996	10109290	10017617	99.09	17.12	X13
109	23-13-5	1264771449	9051622	8975710	99.16	16.74	X27
110	23-57-63	1244052630	8919865	8861964	99.35	16.49	X26
111	黔芋7号QianYu7	1345688424	9563048	9495424	99.29	18.20	X10
112	22-91-24	1732358151	12397229	12322974	99.40	18.39	X85
113	18-81-325	1247259735	8913644	8805094	98.78	16.25	X21
114	22-92-256	1175470803	8422225	8337731	99.00	16.58	X22
115	18-91-127	1660783212	11832737	11752580	99.32	18.56	X45
116	27-3-52	2069760663	14913871	14796774	99.21	18.70	X82
117	200-10-50	1721414934	12260394	12144291	99.05	19.31	X18
118	225-10-21	1145114208	8192235	8107691	98.97	15.94	X23
119	22-83-38	1928771919	13864980	13742071	99.11	18.21	X88
120	278-10-74	2072509092	14889774	14797496	99.38	18.15	X80
121	24-79-59	1460479347	10417428	10343662	99.29	17.79	X46
122	22-69-90	1375713009	9810708	9739261	99.27	17.58	X43

Table 1

Table 2

Fig. 1

Fig. 2

Table 3

Table 4

Fig. 3

Fig. 4

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SNP类型SNP type		数目Number	占比Percentage (%)
外显子区域Exotic total	同义突变Synonymous SNP	182507	2.10
	非同义突变Nonsynonymous SNP	209566	2.41
	获得终止密码子的 SNP Stopgain	4602	0.05
	丢失终止密码子的 SNP Stoploss	569	0.01
	总计Total	397244	4.57
拼接接头区域Splicing		1762	0.02
内含子区域Intronic		970743	11.16
基因间区域Intergenic		6650230	76.46
5′UTR区域5′UTR		46263	0.53
3′UTR区域3′UTR		98348	1.13
UTR5; UTR3		29	0.00
转录起始位点上游1 kb的区域Upstream 1 kb		247351	2.84
转录终止位点下游1 kb的区域Downstream 1 kb		251705	2.89
其他Others		33956	0.39
总计Total		8697602	100

群体 Population	核苷酸多样性 Pi (π)	观测杂合度 Obs Het (Ho)	期望杂合度 Exp Het (He)	近交系数 Fis
Ⅰ	0.2055	0.0829	0.187	0.2858
Ⅱ	0.2572	0.1186	0.2297	0.3319
Ⅲ	0.2137	0.091	0.1913	0.2716
Ⅳ	0.2188	0.1051	0.1942	0.2412
Ⅴ	0.2098	0.0918	0.1898	0.2692
Ⅵ	0.2319	0.0838	0.2124	0.3554

群体 Population	II	III	IV	V	VI
I	0.159407	0.172889	0.172479	0.174660	0.165741
II		0.163408	0.156909	0.176573	0.170987
III			0.170947	0.183461	0.158484
IV				0.187336	0.159748
V					0.160706

Deciphering of the Genetic Diversity After Field Late Blight Resistance Evaluation of Potato Breeds

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