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Acta Agronomica Sinica ›› 2023, Vol. 49 ›› Issue (6): 1708-1714.doi: 10.3724/SP.J.1006.2023.21047

• RESEARCH NOTES • Previous Articles     Next Articles

Genetic diversity of wheat breeding parents revealed by 55K SNP-based microarray

LU Mao-Ang2(), PENG Xiao-Ai2, ZHANG Ling2, WANG Jian-Lai1, HE Xian-Fang1,2,*(), ZHU Yu-Lei2,*()   

  1. 1Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230001, Anhui, China
    2College of Agronomy, Anhui Agricultural University, Hefei 230036, Anhui, China
  • Received:2022-07-03 Accepted:2022-10-10 Online:2023-06-12 Published:2022-11-10
  • Contact: *E-mail: xianfanghe@126.com;E-mail: zhuyulei2011@126.com
  • Supported by:
    Anhui Wheat Seed Joint Research Project(2021-);National Natural Science Youth Science Foundation of China(31901540)

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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

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17*2//扬11/豫麦18 Yang 17*2//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

Fig. 1

Distribution of polymorphic SNP markers on chromosome (A), homoeologous group (B), and subgenome (C)"

Fig. 2

Boxplots of polymorphic SNP minimum allele (A), gene diversity (B), polymorphic information content (C), and genetic distance (D) box line map"

Fig. 3

Clustering plot of the test materials"

Fig. 4

PCA analysis (A) and population genetic structure analysis (B and C) of the wheat accessions used in this study"

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