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Acta Agron Sin ›› 2015, Vol. 41 ›› Issue (02): 197-206.doi: 10.3724/SP.J.1006.2015.00197

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genetic Diversity of Registered Wheat Varieties in Henan Province Based on Pedigree and Single-Nucleotide Polymorphism

CAO Ting-Jie1,2,XIE Jing-Zhong1,WU Qiu-Hong1,CHEN Yong-Xing1,WANG Zhen-Zhong1,ZHAO Hong2,WANG Xi-Cheng2,ZHAN Ke-Hui3,XU Ru-Qiang4,WANG Ji-Rui5,LUO Ming-Cheng6,LIU Zhi-Yong1,*   

  1. 1 Department of Plant Genetics & Breeding, China Agricultural University, Beijing 100193, China; 2 Wheat Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; 3 Henan Agricultural University, Zhengzhou 450002, China; 4 School of Life Science, Zhengzhou University, Zhengzhou 450001, China; 5 Wheat Research Institute, Sichuan Agricultural University, Chengdu 611130, China; 6 University of California at Davis, Davis, CA 95616, USA
  • Received:2014-06-30 Revised:2014-12-19 Online:2015-02-12 Published:2014-12-29
  • Contact: 刘志勇, E-mail: zhiyongliu@cau.edu.cn E-mail:caotingjie893@163.com

Abstract:

To understand the genetic diversity of wheat varieties in Henan Province at whole genome level, we selected 96 registered wheat varieties in the past decade for SNP genotyping using the Illumina 90k iSelect SNP chip. The results showed that 47.39% of the SNPs (38 661 out of 81 587) were polymorphism between varieties. The genome distribution of polymorphic SNPs showed a tendency of B > A > D. The genetic similarity of the 96 varieties ranged from 0.552 to 0.998 with an average value of 0.719. However, genetic similarity of 0.652 to 0.812 was found for 94.3% of the tested varieties, indicating highly similarity for most of the varieties in Henan province. The 96 wheat varieties could be classified as seven groups by UPGMA analyses. Based on pedigree and SNP analyses, very narrow genetic background was observed for the registered varieties in the past decade in Henan province. It is an urgent task for wheat breeders to explore and introduce diversified germplasm resources into wheat breeding program to increase the yield potential and stress tolerance in the future.

Key words: Henan province, Wheat varieties, Genetic Diversity, SNPs

[1]郝晨阳, 王兰芬, 张学勇, 游光霞, 董玉琛, 贾继增, 刘旭, 尚勋武, 刘三才, 曹永生. 我国五十年来育成小麦品种的遗传多样性演变. 中国科学: C辑, 2005, 35: 408–415

Hao C Y, Wang L F, Zhang X Y, You G X, Dong Y S, Jia J Z, Liu X, Shang X W, Liu S C, Cao Y S. Genetic diversity changes of Chinese cultivars in the past 50 years. Sci China (Ser C), 2005, 35:408–415 (in Chinese)

[2]Tanksley S D, Mccouch S R. Seed banks and molecular maps: unlocking genetic potential from the wild. Science, 1997, 277: 1063–1066

[3]Sun Q X, Ni Z F, Liu Z Y, Gao J W, Huang T C. Genetic relationships and diversity among Tibetan wheat, common wheat and European spelt wheat revealed by RAPD markers. Euphytica, 1998, 99: 205–211

[4]Wang H Y, Wang X, Chen P D, Liu D J. Assessment of genetic diversity of Yunnan, Tibetan, and Xinjiang wheat using SSR markers. J Genet Genomics, 2007, 34: 623–633

[5]Talebi R, Fayyaz F. Quantitative evaluation of genetic diversity in Iranian modern cultivars of wheat (Triticum aestivum L.) using morphological and amplified fragment length polymorphism (AFLP) markers. Biharean Biol, 2012, 6: 14–18

[6]Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y. Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res, 2002, 9: 163–171

[7]邹喻苹, 葛颂. 新一代分子标记-SNPs及其应用, 生物多样性, 2003, 11: 370–382

Zhou Y P, Ge S. A novel molecular marker: SNPs and its application. Biodiversity Sci, 2003, 11: 370–382 (in Chinese with English abstract)

[8]Nishida N, Koike A, Tajima A, Ogasawara Y, Ishibashi Y, Uehara Y, Inoue I, Tokunaga K. Evaluating the performance of Afrymetrix SNP array 6.0 platform with 400 Japanese individuals. BMC Genomics, 2008, 9: 431

[9]Karlsson E K, Baranowska I, Wade C M, Salmon Hillbertz N H, Zody M C, Anderson N, Biagi T M, Patterson N, Pielberg G R, Kulbokas E J, Comstock K E, Keller E T, Mesirov J P, von Euler H, K?mpe O, Hedhammar A, Lander E S, Andersson G, Andersson L, Lindblad-Toh K. Efficient mapping of Mendelian traits in dogs through genome-wide association. Nat Genet, 2007, 39: 1321–1328

[10]Anderson L. Genome-wide association analysis in domestic animals: a powerful approach for genetic dissection of trait loci. Genetica, 2009, 136: 341–349

[11]Clark R M, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu T T, Fu G, Hinds D A, Chen H, Frazer K A, Huson D H, Sch?lkopf B, Nordborg M, R?tsch G, Ecker J R, Weigel D. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science, 2007, 317: 338–342

[12]Rafalski A: Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol, 2002, 5: 94–100

[13]Cavanagh C R, Chao S, Wang S, Huang B E, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira G L, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Reynolds M, da Silva M L, Bockelman H, Talbert L, Anderson J A, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell P L, Dubcovsky J, Morell M K, Sorrells M E, Hayden M J, Akhunov E. Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci USA, 2013, 110: 8057–8062

[14]Wang S, Wong D, Forrest K, Allen A, Chao S, Huang B E, Maccaferri M, Salvi S, Milner S G, Cattivelli L, Mastrangelo A M, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova A R, Feuillet C, Salse J, Morgante M, Pozniak C, Luo M C, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards K J, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J, 2014, 12: 787–796

[15]Ren J, Chen L, Sun D, You F M, Wang J, Peng Y, Nevo E, Beiles A, Sun D, Luo M C, Peng J. SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors. BMC Evol Biol, 2013, 13: 169

[16]Chao S, Dubcovsky J, Dvorak J, Luo M C, Baenziger S P, Matnyazov R, Clark D R, Talbert L E, Anderson J A, Dreisigacker S, Glover K, Chen J, Campbell K, Bruckner P L, Rudd J C, Haley S, Carver B F, Perry S, Sorrells M E, Akhunov E D. Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.). BMC Genomics, 2010, 11: 727

[17]Wurschum T, Langer S M, Longin C F, Korzun V, Akhunov E, Ebmeyer E, Schachschneider R, Schacht J, Kazman E, Reif J C. Population structure, genetic diversity and linkage disequilibrium in elite winter wheat assessed with SNP and SSR markers. Theor Appl Genet, 2013, 126: 1477–1486

[18]Saghai-Maroof M A, Soliman K M, Jorgensen R A, Allard R W. Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA, 1984, 81: 8014–8018

[19]贾继增, 张正斌, Devos K, Gale M D. 小麦21条染色体RFLP作图位点遗传多样性分析. 中国科学: C 辑, 2001, 31: 13–21

Jia J Z, Zhang Z B, Devos K, Gale M D. Genetic diversity of 21 chromosomes in wheat revealed by RFLP mapping. Sci China (Ser C), 2001, 31: 13–21 (in Chinese)

[20]倪中福, 张义荣, 梁荣奇, 刘广田, 孙其信. 普通小麦D染色体组微卫星分子标记遗传差异研究. 作物学报, 2003, 29: 145–151

Ni Z F, Zhang Y R, Liang R Q, Liu G T, Sun Q X. Genetic diversity of D-genome revealed by SSR markers in wheat (Triticum aestivum L.). Acta Agron Sin, 2003, 29: 145–151 (in Chinese with English abstract)

[21]蒲艳艳, 程凯, 李斯深. 山东省近期育成小麦品种遗传多样性的SSR分析. 分子植物育种, 2011, 9: 443–449

Pu Y Y, Cheng K, Li S S. Genetic diversity of recent wheat cultivars in Shandong Province using SSR markers. Mol Plant Breed, 2011, 9: 443–449 (in Chinese with English abstract)

[22]李志波, 王睿辉, 张茶, 梁虹, 马峙英, 赵玉欣, 王静华. 河北省小麦品种基于农艺性状的遗传多样性分析. 植物遗传资源学报, 2009, 10: 436–442

Li Z B, Wang R H, Zhang C, Liang H, Ma Z Y, Zhao Y X, Wang J H. Genetic diversity analysis of bread wheat (Triticum aestivum L.) cultivars in Hebei Province based on agronomic traits. J Plant Genet Resour, 2009, 10: 436–442 (in Chinese with English abstract)

[23]傅体华, 王春梅, 任正隆.四川育成小麦品种的SSR遗传多态性及系谱关系.四川农业大学学报, 2007, 25: 1–7

Fu T H, Wang C M, Ren Z L. SSR genetic diversity among modern advanced wheat cultivars (Triticum aestivum L.) in Sichuan and its relationships with their pedigree. J Sichuan Agric Univ, 2007, 25: 1–7 (in Chinese with English abstract)

[24]李学军, 潘玉朋, 王小利, 李立群, 王培, 冯毅, 王辉. 陕西育成小麦品种的遗传多样性演变. 西北农林科技大学学报(自然科学版), 2011, 39: 48–54

Li X J, Pan Y P, Wang X L, Li L Q, Wang P, Feng Y, Wang H. Evolution of genetic diversity of the winter varieties grown at Shaanxi. J Northwest A&F Univ (Nat Sci Edn), 2011, 39: 48–54 (in Chinese with English abstract)

[25]潘玉朋, 李立群, 郑锦娟, 王培, 冯毅, 李学军. 黄淮麦区近年大面积推广小麦品种的遗传多样性分析. 西北农业学报, 2011, 20: 47–52

Pang Y P, Li L Q, Zheng J J, Wang P, Feng Y, Li X J. Analysis of genetic diversity of the large-scale promoted wheat varieties grown at Huang-Huai area in recent years. Acta Agric Boreali-Occid Sin, 2011, 20: 47–52 (in Chinese with English abstract)

[26]耿惠敏, 刘红彦, 宋玉立, 王俊美, 李锁平. 40个河南省审定小麦品种遗传多样性的SSR标记分析. 西北农业学报, 2005, 14: 27–32

Geng H M, Liu H Y, Song Y L, Wang J M, Li S P. SSR analysis of genetic diversity among forty released wheat cultivars in Henan Province. Acta Agric Boreali-Occident Sin, 2005, 14: 27–32 (in Chinese with English abstract)

[27]徐晓丹, 冯晶, 蔺瑞明, 赵蕾, 林风, 徐世昌. 河南小麦主栽品种亲缘系数的分析. 麦类作物学报, 2011, 31: 653–659

Xu X D, Feng J, Lin R M, Zhao L, Lin F, Xu S C. Coefficient of parentage analysis for leading wheat cultivars in Henan Province. J Triticeae Crops, 2011, 31: 653–659 (in Chinese with English abstract)

[28]王冬梅, 冯晶, 王凤涛, 蔺瑞明,徐世昌. 2010–2011年度四省小麦区试品种遗传多样性和抗条锈性分析. 植物保护, 2013, 39: 21–28

Wang D M, Feng J, Wang F T, Lin R M, Xu S C. Genetic diversity and stripe rust resistance of regional trial wheat cultivars in four provinces in 2010–2011. Plant Prot, 2013, 39: 21–28 (in Chinese with English abstract)

[29]张清海, 王志和, 刘华山, 李铁庄, 周新宝, 李汉中, 韩秀云, 张智伟, 闵保锋, 张宏涛. 河南主要推广小麦品种系谱追溯及其亲本组配技术分析. 中国农学通报, 2000, 16: 3–6

Zhang QH, Wang Z H, Liu H S, Li T Z, Zhou X B, Li HZ, Han XY, Zhang Z W, Wen B F, Zhang H T. The pedigree analysis and techniques for parent combination of the major wheat extension varieties in Henan Province. Chin Agric Sci Bull, 2000, 16: 3–6 (in Chinese with English abstract)

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