基于55K SNP芯片揭示小麦育种亲本遗传多样性

doi:10.3724/SP.J.1006.2023.21047

Abstract

Abstract:

The objective of this study is to identify the genetic diversity among wheat parental materials from different provinces. To reveal the genetic diversity and population structure by using wheat 55K SNP chip, 150 wheat accessions from Anhui, Jiangsu, Henan, Sichuan, and Shandong provinces were analyzed. A total of 52,537 SNP loci were detected in the 150 wheat accessions. 39,422 high quality markers were obtained, of which 38,135 were polymorphic, accounting for 96.74%. The distribution of 38,135 polymorphic markers among the genomes showed the least in D subgenome (10,450), the most in B subgenome (15,290). The average polymorphic information content (PIC) was 0.315, with a variation of 0.068-0.375. The averaged genetic distance of accessions differed based on the origin: Henan > Sichuan > Shandong > Jiangsu > Anhui. The results of cluster analysis, principal component analysis, and population structure analysis were highly consistent, and the clustering results were consistent with the pedigree, regional origin, and breeding group. The study revealed that the average polymorphism information content in each province was at a moderate PIC level, but the average genetic distance of the materials was close. This indicated that the high-quality germplasm resources should still be introduced to alleviate the material homogeneity, so as to increase the ability of wheat to cope with stress and reduce the vulnerability and risk in actual wheat production.

Key words: wheat, 55K SNP chip, breeding parents, genetic diversity, cluster analysis

LU Mao-Ang, PENG Xiao-Ai, ZHANG Ling, WANG Jian-Lai, HE Xian-Fang, ZHU Yu-Lei. Genetic diversity of wheat breeding parents revealed by 55K SNP-based microarray[J].Acta Agronomica Sinica, 2023, 49(6): 1708-1714.

Figures/Tables 5

Table S1

Lineage and source of test material"

编号No.	名称Name	系谱Parentage	来源Source
y1	济麦22 Jimai 22	935024/935106	中国山东 Shandong, China
y2	安科1302 Anke 1302	—	中国安徽 Anhui, China
y3	安科157 Anke 157	泰山241/西农1718 Taishan241/Xinong1718	中国安徽 Anhui, China
y4	安农0711 Annong 0711	烟农19/安农0016 Yannong 19/Annong 0016	中国安徽 Anhui, China
y5	百农207 Bainong 207	周16/百农64 Zhou 16/ Bainong 64	中国河南 Henan, China
y6	泛麦5号 Fanmai 5	冀5418/京泛30//周麦13 Jin 5418/Jingfan 30//Zhoumai 13	中国河南 Henan, China
y7	恒进麦8号 Hengjinmai 8	周16/淮麦28 Zhou 16/Huaimai 28	中国安徽 Anhui, China
y8	华成1688 Huacheng 1688	淮麦0566/洛麦13 Huaimai 0566/Luomai 13	中国安徽 Anhui, China
y9	华成2019 Huacheng 2019	(烟农19/宿266)F5/宿02003 (Yannong 19/Su 266)F5/Su 02003	中国安徽 Anhui, China
y10	华成3366 Huacheng 3366	烟农361/宿266 Yannong 361/Su 266	中国安徽 Anhui, China
y11	华成859 Huacheng 859	丰华8829/T59 Fenghua 8829/T59	中国安徽 Anhui, China
y12	华成863 Huacheng 863	新9408/丰华8829/烟农19 Xin 9408/Fenghua 8829/Yan 19	中国安徽 Anhui, China
y13	淮麦22 Huaimai 22	淮麦18/扬麦158 Huaimai 18/Yangmai 158	中国江苏 Jiangsu, China
y14	淮麦29 Huaimai 29	淮麦20/绵阳04254 Huaimai 20/Mianyang 04254	中国江苏 Jiangsu, China
y15	淮麦30 Huaimai 30	郑麦9023/淮86175 Zhengmai 9023/Huai 86175	中国江苏 Jiangsu, China
y16	淮麦33 Huaimai 33	烟农19/郑麦991 Yannong 19/Zhengmai 991	中国江苏 Jiangsu, China
y17	淮麦35 Huaimai 35	周麦13/新麦9号 Zhoumai 13/Xinmai 9	中国江苏 Jiangsu, China
y18	淮麦40 Huaimai 40	—	中国江苏 Jiangsu, China
y19	淮麦44 Huaimai 44	(百农9711/淮麦95079)/淮麦9701 (Bainong 9711/Huaimai 95079)/Huaimai 9701	中国江苏 Jiangsu, China
y20	徽研66 Huiyan 66	鲁原502/9024 Luyuan 502/9024	中国安徽 Anhui, China
y21	徽研912 Huiyan 912	周麦16/烟农19 Zhoumai 16/Yannong 19	中国安徽 Anhui, China
y22	济麦44 Jimai 44	954072/济南17 954072/Jinan 17	中国山东 Shandong, China
y23	乐麦207 Lemai 2	C420/豫同M023 C420/Yutong M023	中国安徽 Anhui, China
y24	连麦2号 Lianmai 2	鉴94(73)/鲁麦21 Jian 94(73)/ Lumai 21	中国江苏 Jiangsu, China
y25	龙科0901 Longke 0901	煤生0308/淮核0308 Meisheng 0308/Huaihe 0308	中国安徽 Anhui, China
y26	龙科1109 Longke 1109	皖麦50/矮抗58 Wanmai 50/Aikang 58	中国安徽 Anhui, China
y27	龙科1221 Longke 1221	良星99/淮0208 Liangxing 99/Huai 0208	中国安徽 Anhui, China
y28	鲁原502 Luyuan 502	9940168/济麦19 9940168/Jimai 19	中国山东 Shandong, China
y29	明麦1号 Mingmai 1	淮麦18号/扬麦158//淮麦20 Huaimai 18/Yangmai 158// Huaimai 20	中国江苏 Jiangsu, China
y30	农麦152 Nongmai 152	新麦18/莱州817 Xinmai 18/Laizhou 817	中国江苏 Jiangsu, China
y31	青农3号 Qingnong 3	永920/蒙花1号 Yong 920/Menghua 1	中国山东 Shandong, China
y32	荃麦725 Quanmai 725	皖麦19/徐麦25//皖麦44///宿043 Wanmai 19/Xumai 25//Wanmai 44///Su 043	中国安徽 Anhui, China
y33	瑞华麦516 Ruihuamai 516	洛麦21/淮麦17 Luomai 21/Huaimai 17	中国江苏 Jiangsu, China
y34	瑞华麦520 Ruihuamai 520	郑州891/黔丰1号 Zhengzhou 891/Qianfeng 1	中国江苏 Jiangsu, China
y35	瑞华麦618 Ruihuamai 618	烟农19/连麦2号 Yannong 19/Lianmai 2	中国江苏 Jiangsu, China
y36	山农17 Shannong 17	L156/莱州137 L156/Laizhou 137	中国山东 Shandong, China
y37	山农20 Shannong 20	PH82-2-2/954072	中国山东 Shandong, China
y38	濉1216 Sui 1216	泛麦5号//泛麦5号/烟1604 Fanmai 5//Fanmai 5/Yan1604	中国山东 Shandong, China
y39	泰农19 Tainong 19	莱州137/济南17 Laizhou 137/Jinan 17	中国山东 Shandong, China
y40	天益科麦5号 Tianyikemai 5	淮0566/洛麦23 Huai 0566/Luomai 23	中国安徽 Anhui, China
y41	皖垦麦0622 Wankenmai 0622	连麦2号/汴123 Lianmai 2/Bian 123	中国安徽 Anhui, China
y42	皖垦麦1号Wankenmai 1	皖麦19/豫麦47 Wanmai 19/Yumai 47	中国安徽 Anhui, China
y43	皖垦麦869 Wankenmai 869	烟优361/T39 Yanyou 361/T39	中国安徽 Anhui, China
y44	皖麦52 Wanmai 52	郑州8329/皖麦19 Zhengzhou 8329/Wanmai 19	中国安徽 Anhui, China
y45	未来0818 Weilai 0818	淮麦18/宿9908 Huaimai 18/Su 9908	中国安徽 Anhui, China
y46	涡麦99 Guomai 99	百农3217/淮9628//鲁麦21 Bainong 3217/Huai 9628//Lumai 21	中国安徽 Anhui, China
y47	涡麦9号Guomai 9	莱州953/百农AK58 Laizhou 953/Bainong AK58	中国安徽 Anhui, China
y48	新麦26 Xinmai 26	新9408E1/济南17 Xin 9408E1/Jinan 17	中国河南 Henan, China
y49	宿553 Su 553	烟农19/宿1264 Yannong 19/Su 1264	中国安徽 Anhui, China
y50	徐农029 Xunong 029	淮麦20/矮抗58 Huaimai 20/Aikang 58	中国江苏 Jiangsu, China
y51	烟农19 Yannong 19	烟1933/陕82-29 Yan 1933/Shaan 82-29	中国山东 Shandong, China
y52	烟农5158 Yannong 5158	烟航2号/烟农15 Yanhang 2/Yannong 15	中国山东 Shandong, China
y53	烟农999 Yannong 999	烟航选2号/临9511//烟BLU14-15 Yanhagnxuan 2/Lin 9511//Yan BLU14-15	中国山东 Shandong, China
y54	郑7698 Zheng 7698	郑麦9405/4B269//周麦16 Zhengmai 9405/4B269//Zhoumai 16	中国河南 Henan, China
y55	中麦578 Zhongmai 578	中麦255/济麦22 Zhongmai 255/Jimai 22	中国河南 Henan, China
y56	中麦895 Zhongmai 895	周麦16/荔垦4号 Zhoumai 16/Liken 4	中国河南 Henan, China
y57	淮麦45 Huaimai 45	淮麦28/淮麦25 Huaimai 28/Huaimai 25	中国江苏 Jiangsu, China
y58	周麦27 Zhoumai 27	周麦16/矮抗58 Zhouamai 16/Aikang 58	中国河南 Henan, China
y59	周麦36 Zhoumai 36	矮抗58/周麦19//周麦22 Aikang 58/Zhou 19//Zhoumai 22	中国河南 Henan, China
y60	紫麦19 Zimai 19	烟农19/潍麦8号 Yanong 19/Weimai 8	中国安徽 Anhui, China
y61	国红6号 Guohong 6	扬麦11/扬麦18 Yangmai 11/Yangmai 18	中国安徽 Anhui, China
y62	浩麦1号 Haomai 1	W4062/郑农11号 W4062/Zhengnong 1	中国福建 Fujian, China
y63	华麦1028 Huamai 1028	扬麦11/华麦0722 Yangmai 11/Huaimai 0722	中国江苏 Jiangsu, China
y64	华麦7号 Huamai 7	扬麦158/小偃8788 Yangmai 158/Xiaoyan 8788	中国江苏 Jiangsu, China
y65	隆垦麦1号 Longkenmai 1	矮败小麦/扬麦158//宁麦13 Aibaixiaomai/Yangmai 158//Ningmai 13	中国安徽 Anhui, China
y66	轮选22 Lunxuan 22	—	中国安徽 Anhui, China
y67	轮选27 Lunxuan 27	矮败小麦/(扬87—158//郑麦9023) Aibaixiaomai/(Yang 87—158//Zhengmai 9023)	中国安徽 Anhui, China
y68	罗麦10号 Luomai 10	557/罗麦8号 577/Luomai 8	中国安徽 Anhui, China
y69	明麦133 Mingmai 133	郑麦9023/扬麦11 Zhengmai 9023/Yangmai 11	中国江苏 Jiangsu, China
y70	宁麦13 Ningmai 13	宁麦9号 Ningmai 9	中国江苏 Jiangsu, China
y71	宁麦21 Ningmai 21	宁9312/扬麦158//宁9312 Ning 9312/Yangmai 158//Ning 9312	中国江苏 Jiangsu, China
y72	宁麦26 Ningmai 26	宁9531/宁麦9号 Ning 9531/Ningmai 9	中国江苏 Jiangsu, China
y73	农麦126 Nongmai 126	扬麦16/宁麦9号 Yangmai 16/Ningmai 9	中国江苏 Jiangsu, China
y74	安农1012 Nuo 1012	扬麦12/安农糯01032 Yangmai 12/Annongnuo 01032	中国安徽 Anhui, China
y75	安农1019 Nuo 1019	安农0419/安农糯01032 Annong 0419/Annongnuo 01032	中国安徽 Anhui, China
y76	苏隆128 Sulong 128	5E007/宁麦9号 5E007/Ningmai 9	中国浙江 Zhejiang, China
y77	苏麦11 Sumai 11	宁麦9/扬麦11 Ningmai 9/Yangmai 11	中国江苏 Jiangsu, China
y78	苏麦10号 Sumai 10	宁麦9/扬麦11 Ningmai 9/Yangmai 11	中国江苏 Jiangsu, China
y79	苏麦188 Sumai 188	扬辐麦2号 Yangfumai 2	中国江苏 Jiangsu, China
y80	皖麦606 Wanmai 606	—	中国安徽 Anhui, China
y81	皖西麦0638 Wanximai 0638	扬麦9号/Y18 Yangmai 9/Y 18	中国安徽 Anhui, China
y82	扬辐麦6号 Yangfumai 6	扬辐麦4号/扬麦14M1 Yangfumai 4/Yangmai 14M1	中国江苏 Jiangsu, China
y83	扬辐麦7号 Yangfumai 7	扬麦11//(扬麦11/扬辐麦9311) Yangmai 11//(Yangmai 11/Yangfumai 9311)	中国江苏 Jiangsu, China
y84	扬辐麦8号 Yangfumai 8	扬辐麦4号1-1274/扬麦11 Yangfumai 4 1-1274/Yangmai 11	中国江苏 Jiangsu, China
y85	扬麦13 Yangmai 13	扬84-84//Maristorve/扬麦3号 Yang 84-84//Maristorve/Yangmai 3	中国江苏 Jiangsu, China
y86	扬麦15 Yangmai 15	扬89-40/川育21526 Yang 89-40/Chuanyu 21526	中国江苏 Jiangsu, China
y87	扬麦16 Yangmai 16	扬91F138/扬90-30 Yang 91F138/Yang 90-30	中国江苏 Jiangsu, China
y88	扬麦20 Yangmai 20	扬麦9/扬10 Yangmai 9/Yang 10	中国江苏 Jiangsu, China
y89	扬麦22 Yangmai 22	扬麦9号3/97033-2 Yangmai 9 3/97033-2	中国江苏 Jiangsu, China
y90	扬麦24 Yangmai 24	扬麦17//扬11/豫麦18 Yangmai 17//Yang 11/Yumai 18	中国江苏 Jiangsu, China
y91	扬麦25 Yangmai 25	扬172//扬11/豫麦18 Yang 172//Yang 11/Yumai 18	中国江苏 Jiangsu, China
y92	扬麦27 Yangmai 27	扬麦19/扬07纹5418 Yangmai 19/Yang 07 Wen 5418	中国江苏 Jiangsu, China
y93	扬麦28 Yangmai 28	(山红麦/扬麦162)/扬麦18//扬麦162 (Shanhongmai/Yangmai 162)/Yangmai 18//Yangmai 162	中国江苏 Jiangsu, China
y94	亿麦9号 Yimai 9	郑麦9023/亿6325 Zhengmai 9023/Yi 6325	中国河南 Henan, China
y95	镇麦11 Zhenmai 11	扬麦15号/镇麦5号 Yangmai 15/Zhenmai 5	中国江苏 Jiangsu, China
y96	镇麦12 Zhenmai 11	镇麦168 Zhengmai 168	中国江苏 Jiangsu, China
y97	镇麦168 Zhenmai 168	苏麦6号/97G59 Sumai 6/97G59	中国江苏 Jiangsu, China
y98	镇麦9号 Zhenmai 9	苏麦6号/97G59 Sumai 6/97G59	中国江苏 Jiangsu, China
y99	18A101	C420/豫同M023 C420/Yutong M023	中国安徽 Anhui, China
y100	18A104	(宿9908/皖北848)//新麦19 (Su 9908/Wanbei 848)//Xinmai 19	中国安徽 Anhui, China
y101	18A105	百农矮抗58/周麦18 Bainongaikang 58/Zhoumai 18	中国安徽 Anhui, China
y102	18A107	皖麦38/淮麦18 Wanmai 38/Huaimai 18	中国安徽 Anhui, China
y103	18A108	700/F240	中国安徽 Anhui, China
y104	18A111	—	中国安徽 Anhui, China
y105	18A126	淮麦25/泛麦5号 Huaimai 25/Fanmai 5	中国安徽 Anhui, China
y106	18A130	安农0628/泛麦5号 Annong 0628/Fanmai 5	中国安徽 Anhui, China
y107	18B130	辐照06725 Fuzhao 06725	中国安徽 Anhui, China
y108	18B128	宿544/淮麦18 Su 544/Huaimai 18	中国安徽 Anhui, China
y109	18B132	—	中国安徽 Anhui, China
y110	18B141	明天0408/C511 Mingtian 0408/C511	中国安徽 Anhui, China
y111	18B151	济麦22 Jimai 22	中国安徽 Anhui, China
y112	18B177	13B286/鲁麦14 13B286/Lumai 14	中国安徽 Anhui, China
y113	18B186	F300/良星66 F300/Liangxing 66	中国安徽 Anhui, China
y114	18B187	豫农88/郑麦112 Yunong 88/Zhengmai 112	中国安徽 Anhui, China
y115	18B189	皖科2058 Wanke 2058	中国安徽 Anhui, China
y116	18B190	乐麦185 Lemai 185	中国安徽 Anhui, China
y117	18B191	皖科421 Wanke 421	中国安徽 Anhui, China
y118	18B194	中洛3号/百农64 Zhongluo 3/Bainong 64	中国安徽 Anhui, China
y119	18B210	11A148/扬麦158 11A148/Yangmai 158	中国安徽 Anhui, China
y120	18B223	连麦2号/山农20 Lianmai 2/Shannong 20	中国安徽 Anhui, China
y121	18B233	连麦2号/泛麦5号 Lianmai 2/Fanmai 5	中国安徽 Anhui, China
y122	18B248	14B52/连麦2号 14B52/Lianmai 2	中国安徽 Anhui, China
y123	18B257	衡09636/皖科09636 Heng 09636/Wanke 09636	中国安徽 Anhui, China
y124	18B259	周麦23/济麦22 Zhoumai 23/Jimai 22	中国安徽 Anhui, China
y125	18B369	烟5158/皖麦44 Yan 5158/Wanmai 44	中国安徽 Anhui, China
y126	18B375	淮麦25/泛麦5号 Huaimai 25/Fanmai 5	中国安徽 Anhui, China
y127	CP03-28-1	—	中国北京 Beijing, China
y128	川42 Chuan 42	—	中国四川 Sichuan, China
y129	扬麦158 Yangmai 158	扬麦4号//St1472/506 Yangmai 4//St1472/506	中国江苏 Jiangsu, China
y130	安科1604 Anke 1604	—	中国安徽 Anhui, China
y131	CP01-27-3	—	中国北京 Beijing, China
y132	扬糯麦1号 Yangnuomai 1	—	中国江苏 Jiangsu, China
y133	950218-54	—	中国安徽 Anhui, China
y134	百农64 Bainong 64	(百农8717/ (偃大72-629-52/石82-5594) F2)/百农84-4046-1 (Bainong 8717/(Yanda 72-629-52/Shi 82-5594)F2)/Bainong 84-5594	中国河南 Henan, China
y135	外引材料 External citation material	—	以色列 Israel
y136	华安麦825 Huaanmai 825	—	中国安徽 Anhui, China
y137	川麦42 Chuanmai 42	SynCD768/SW3243//川6415 SynCD768/SW3243//Chuan 6415	中国四川 Sichuan, China
y138	新原958 Xinyuan 958	豫麦34/新麦9号 Yumai 34/Xinmai 9	中国河南 Henan, China
y139	中科麦138 Zhongkemai 138	川麦42/川育16 Chuanmai 42/Chuanyu 16	中国四川 Sichuan, China
y140	川农16 Chuannong 16	川育12/87-429 Chuanyu 12/87-429	中国四川 Sichuan, China
y141	西科麦8号 Xikemai 8	97-392/云22574-5 97-392/Yun 225747-5	中国四川 Sichuan, China
y142	绵麦367 Mianmai 267	1275-1/99-1522	中国四川 Sichuan, China
y143	21946	—	中国四川 Sichuan, China
y144	西农916 Xinong 916	—	中国陕西 Shaanxi, China
y145	B12-6-1	—	中国四川 Sichuan, China
y146	绵麦37 Mianmai 37	96EW37/90-100	中国四川 Sichuan, China
y147	川麦82 Chuanmai 82	Singh6/3*1231	中国四川 Sichuan, China
y148	F06-4198	—	中国四川 Sichuan, China
y149	2011	—	中国四川 Sichuan, China
y150	206A	—	中国安徽 Anhui, China

Table S1

Fig. 1

Fig. 2

Fig. 3

Fig. 4

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