Scientia Agricultura Sinica ›› 2013, Vol. 46 ›› Issue (4): 668-677.doi: 10.3864/j.issn.0578-1752.2013.04.002

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

Analysis on the Genetic Diversity in Chinese Barley Landrace and Genomic Wide Association of α-amylase Activity Genes

 JIANG  Xiao-Dong, GUO  Gang-Gang, ZHANG  Jing   

  1. 1.中国农业科学院作物科学研究所，北京 100081
    2.山西农业大学农学院，山西太谷 030801
  • Received:2012-12-03 Online:2013-02-15 Published:2013-01-23

PDF

743

Abstract: 【Objective】The objective of this study is to understand genetic diversity in Chinese barley landraces and screen valuable molecular marker for α-amylase activity.【Method】 A total 257 Chinese barley landraces were genotyped with 41 SSR markers distributing on seven chromosomes of barley. Nei’s genetic distance and neighbour-joining were adoped in cluster analysis.【Result】A total of 709 alleles were identified at 41 SSR loci in 257 Chinese barley landraces. The number of alleles per locus ranged from 5 to 44, with an average of 17. The polymorphism information content value for SSRs ranged from 0.23 (Bmag 0385) to 0.94(Bmac0032) with a mean of 0.6385. Cluster analysis detected that nine clusters were identified based on Nei’s genetic distance in 257 accessions. Association analysis showed that five SSR markers significantly associated with α–amylase activity. 【Conclusion】 Chinese barley landraces have rich genetic diversity and could be clustered into nine different groups based on morphological characteristics, geographic origin and genetic relationships. Among the five SSR markers associated with α–amylase activity, Bmag0385 on chromosome-7H carrying allele A215 possessed the highest α-amylase activity, and Bmac0273 on 7H carrying with allele A141 had relatively high positive effect on α-amylase activity. All of them could be used in marker-assisted selection for malting barley breeding.

Key words: Chinese barley , genetic diversity , allele effect , α-amylase activity , association mapping

[1]Russell J R, Fuller J D, Macaulay M, Hatz B G, Jahoor A, Powell W, Waugh R. Direct comparison of levels of genetic variation amongbarley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theoretical and Applied Genetics, 1997, 95: 714-722.

[2]Yang G, Zhang Q F. Polymorphism of α-amylase activity in barley landraces and cultivars from China. Euphytica, 1990, 48: 245-251.

[3]Fox G P, Panozzo J F, Li C D, Lance R C M, Inkerman P A, Henry R J. Molecular basis of barley quality. Australian Journal of Agricutulral Research, 2003, 54: 1081-1101.

[4]Struss D, Plieske J. The use of microsatellite markers for detection of genetic diversity in barley populations. Theoretical and Applied Genetics, 1998, 97: 308-315.

[5]Strelchenko P, kovalyova O, Okuno K. Genetic differentiation and geographical distribution of barley germplasm based on RAPD markers. Genetic Resources and Crop Evolution, 1999, 46(2): 193-205.

[6]Chabane K , Ablett G A, Cordeiro G M, Valkoun J, Henry R J. EST versus genomic derived microsatellite markers for genotyping wild and cultivated barley. Genetic Resources and Crop Evolution, 2005, 52(7): 903-909.

[7]Malysheva-Otto L V, Ganal M W, Röder M S. Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genetics, 2006, 7: 6.

[8]张赤红, 张京, 赵会英, 张云霞, 李珍, Michael B. 应用SSR标记对61个国家大麦遗传多样性的研究. 植物遗传资源学报, 2008, 9(1): 15-19.

Zhang C H, Zhang J, Zhao H Y, Zhang Y X, Li Z, Michael B. Study on genetic diversity of barley from 61 countries using SSR makers. Journal of Plant Genetic Resources, 2008, 9(1): 15-19. (in Chinese)

[9]姜晓东, 张京, 郭刚刚. 大麦Amy32b的遗传多样性及其对α-淀粉酶活性的影响. 中国农业科学, 2012, 45(5): 823-831.

Jiang X D, Zhang J, Guo G G. Polymorphism of the Amy32b gene and its effect on the α-amylase activity in barley. Scientia Agricultura Sinica, 2012, 45(5): 823-831. (in Chinese)

[10]Marquez-Cedillo L A, Hayes P M, Jones B L, Kleinhofs A, Legge W G, Rossnagel B G, Sato K, Ullrich E, Wesenberg D M. QTL analysis of malting quality in barley based on the doubled-haploid progeny of two elite North American varieties representing different germplasm groups. Theoretical and Applied Genetics, 2000, 101: 173-184.

[11]Emebiri L C, Moody D B, Panozzo J F, Read B J. Mapping of QTL for malting quality attributes in barley based on a cross of parents with low grain protein concentration. Field Crops Research, 2004, 87: 195-205.

[12]Schmalenbach I, Pillen K. Detection and verification of malting quality QTLs using wild barley introgression lines. Theoretical and Applied Genetics, 2009, 118(8): 1411-1427.

[13]Karakousis A, Barr A R, Kretschmer J M, Manning S, Logue S J, Roumeliotis S, Collins H M, Chalmers K J, Li C D, Lance R C M. Mapping and QTL analysis of the barley population Galleon×Haruna Nijo. Australian Journal of Agricultural Research, 2003, 54(12): 1131-1135.

[14]Stein N, Prasad M, Scholz U, Thile T, Zhang H, Wolf M, Kota R, Varshney R K, Perovic D, Grosse I, Graner A. A 1000-loci transcript map of the barley genome: New anchoring points for integrative grass genomic. Theoretical and Applied Genetics, 2007, 114(5): 823-889.

[15]Varshney R K, Marcel T C, Ramsay L, Russell J, Roder M S, Stein N, Waugh R, Langridge P, Niks R E, Graner A. A high density barley microsatellite consensus map with 775 SSR loci. Theoretical and Applied Genetic, 2007, 114(6): 1091-1103.

[16]Pritchard J K, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics, 2000, 155: 945-959.

[17]Breseghello F, Mark E S. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics, 2006, 172: 1165-1177.

[18]文自翔, 赵团结, 郑永战, 刘顺湖, 王春娥, 王芳, 盖钧镒. 中国栽培和野生大豆农艺及品质性状与SSR标记的关联分析II. 优异等位变异的发掘. 作物学报, 2008, 34(8): 1339-1349.

Wen Z X, Zhao T J, Zheng Y Z, Liu S H, Wang C E, Wang F, Gai J Y. Association analysis of agronomic and quality traits with SSR Markers in Glycine max and Glycine soja in China: II. Exploration of elite alleles. Acta Agronomica Sinica, 2008, 34(8): 1339-1349. (in Chinese)

[19]Udupa S, Baum M. High mutation rate and mutational bias at (TAA)n microsatellite loci in chickpea (Cicer arietinum L.). Molecular Genetic and Genomic, 2001, 265(6): 1097-1103.

[20]Senior M L, Murphy J P, Goodman M M, Stuber C W. Utility of SSRs for determining genetic similarities and relationships in maize using an agarose gel system. Crop Science, 1998, 38(4): 1088-1098.

[21]Henderson S T, Petes T D. Instability of simple sequence DNA in Saccharomyces cerevisiae. Molecular and Celluar Biology, 1992, 12(6): 2749-2757.

[22]Liu S, Cantrell R G, McCarty J C, Stewart J M D. Simple sequence repeat-based assessment of genetic diversity in cotton race stock accessions. Crop Science, 2000, 40(5): 1459-1469.

[23]Erkkila M J, Leah R, Ahokas H, Cameron M V. Allele-dependent barley grain β-amylase activity. Plant Physiology, 1998, 117: 679-685.

[24]Garvin D F, Brown A H D, Burdon J J. Inheritance and chromosome locations of scald-resistance genes derived from Iranian and Turkish wild barleys. Theoretical and Applied Genetics, 1997, 94(8): 1086-1091.

[25]Matus I A, Hayes P M. Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats. Genome, 2002, 45(6): 1095-1106.

[26]Barr A R, Karakousis A, Lance R C M, Logue S J, Manning S, Chalmers K J, Kretschmer J M, Boyd W J R, Collins H M, Roumeliotis S. Mapping and QTL analysis of the barley population Chebec×Harrington. Australian journal of Agricultural Research, 2003, 54(12): 1125-1130.

[27]Li C D, Tarr A, Lance R C M, Harasymow S, Uhlmann J, Westcot S, Young K J, Grime C R, Cakir M, Broughton S, Appels R. A major QTL controlling seed dormancy and pre-harvest sprouting/grain α-amylase in two-rowed barley (Hordeum vulgare L.). Australian Journal of Agricultural Research, 2003, 54(12): 1303-1313.

[28]Collins H M, Panozzo J F, Logue S J, Jefferies S P, Barr A R. Mapping and validation of chromosome regions associated with high malt extract in barley (Hordeum vulgare L.). Australian Journal of Agricultural Research, 2003, 54(12): 1223-1240.

[29]Emebiri L, Michael P, Moody D B, Ogbonnaya F C, Black C. Pyramiding QTLs to improve malting quality in barley: Gains in phenotype and genetic diversity. Molecular Breeding, 2009, 23(2): 219-228.

[30]Zhang X Q, Li C D, Panozzo J, Westcott S, Zhang G P, Tay A, Appels R, Jones M, Lance R. Dissecting the telomere region of barley chromosome 5HL using rice genomic sequences as references: New markers for tracking a complex region in breeding. Molecular Breeding, 2011, 27(1): 1-9.

[31]Hayes P M, Liu B H, Knapp J, Chen F, Jones B, Blake T, Franckwiak J, Rasmusson D, Sorrells M, Ullrich S E. Quantitative trait locus effects and environmental interaction in a sample of North American barley germ plasm. Theoretical and Applied Genetics, 1993, 87: 392-401.
[1] ZHANG YiZhong, ZHANG XiaoJuan, LIANG Du, GUO Qi, FAN XinQi, NIE MengEn, WANG HuiYan, ZHAO WenBo, DU WeiJun, LIU QingShan. Genetic Diversity Analysis and Comprehensive Evaluation of Sorghum Breeding Materials Based on Phenotypic Traits [J]. Scientia Agricultura Sinica, 2023, 56(15): 2837-2853.
[2] LI Huan, YAN XiaoQing, YANG ZhanLie, TAN JinYu, LI XiaoBing, CHEN NengGang, WU RongJu, CHEN HuiCha, RUAN RenChao. Analysis and Comprehensive Evaluation of Phenotype Genetic Diversity in Kam Sweet Rice Germplasm Resources in Guizhou [J]. Scientia Agricultura Sinica, 2023, 56(11): 2035-2046.
[3] JIANG Peng, ZHANG Peng, YAO JinBao, WU Lei, HE Yi, LI Chang, MA HongXiang, ZHANG Xu. Phenotypic Characteristics and Related Gene Analysis of Ningmai Series Wheat Varieties [J]. Scientia Agricultura Sinica, 2022, 55(2): 233-247.
[4] 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.
[5] YingLing WAN,MengTing ZHU,AiQing LIU,YiJia JIN,Yan LIU. Phenotypic Diversity Analysis of Chinese Ornamental Herbaceous Peonies and Its Germplasm Resource Evaluation [J]. Scientia Agricultura Sinica, 2022, 55(18): 3629-3639.
[6] HU GuangMing,ZHANG Qiong,HAN Fei,LI DaWei,LI ZuoZhou,WANG Zhi,ZHAO TingTing,TIAN Hua,LIU XiaoLi,ZHONG CaiHong. Screening and Application of Universal SSR Molecular Marker Primers in Actinidia [J]. Scientia Agricultura Sinica, 2022, 55(17): 3411-3425.
[7] CHEN Xu,HAO YaQiong,NIE XingHua,YANG HaiYing,LIU Song,WANG XueFeng,CAO QingQin,QIN Ling,XING Yu. Association Analysis of Main Characteristics of Bur and Nut with SSR Markers in Chinese Chestnut [J]. Scientia Agricultura Sinica, 2022, 55(13): 2613-2628.
[8] XU Xiao,REN GenZeng,ZHAO XinRui,CHANG JinHua,CUI JiangHui. Accurate Identification and Comprehensive Evaluation of Panicle Phenotypic Traits of Landraces and Cultivars of Sorghum bicolor (L.) Moench in China [J]. Scientia Agricultura Sinica, 2022, 55(11): 2092-2108.
[9] TANG XiuJun,FAN YanFeng,JIA XiaoXu,GE QingLian,LU JunXian,TANG MengJun,HAN Wei,GAO YuShi. Genetic Diversity and Origin Characteristics of Chicken Species Based on Mitochondrial DNA D-loop Region [J]. Scientia Agricultura Sinica, 2021, 54(24): 5302-5315.
[10] LI XinYuan, LOU JinXiu, LIU QingYuan, HU Jian, ZHANG YingJun. Genetic Diversity Analysis of Rhizobia Associated with Medicago sativa Cultivated in Northeast and North China [J]. Scientia Agricultura Sinica, 2021, 54(16): 3393-3405.
[11] WANG FuQiang,ZHANG Jian,WEN ChangLong,FAN XiuCai,ZHANG Ying,SUN Lei,LIU ChongHuai,JIANG JianFu. Identification of Grape Cultivars Based on KASP Markers [J]. Scientia Agricultura Sinica, 2021, 54(13): 2830-2842.
[12] ZHANG MaoNing,HUANG BingYan,MIAO LiJuan,XU Jing,SHI Lei,ZHANG ZhongXin,SUN ZiQi,LIU Hua,QI FeiYan,DONG WenZhao,ZHENG Zheng,ZHANG XinYou. Genetic Analysis of Peanut Kernel Traits in a Nested-crossing Population by Major Gene Plus Polygenes Mixed Model [J]. Scientia Agricultura Sinica, 2021, 54(13): 2916-2930.
[13] YANG Tao,HUANG YaJie,LI ShengMei,REN Dan,CUI JinXin,PANG Bo,YU Shuang,GAO WenWei. Genetic Diversity and Comprehensive Evaluation of Phenotypic Traits in Sea-Island Cotton Germplasm Resources [J]. Scientia Agricultura Sinica, 2021, 54(12): 2499-2509.
[14] ShuGuang LI,YongCe CAO,JianBo HE,WuBin WANG,GuangNan XING,JiaYin YANG,TuanJie ZHAO,JunYi GAI. Genetic Dissection of Protein Content in a Nested Association Mapping Population of Soybean [J]. Scientia Agricultura Sinica, 2020, 53(9): 1743-1755.
[15] ZaiDong LIU,Shan MENG,JianBo HE,GuangNan XING,WuBin WANG,TuanJie ZHAO,JunYi GAI. A Comparative Study on Linkage and Association QTL Mapping for Seed Isoflavone Contents in a Recombinant Inbred Line Population of Soybean [J]. Scientia Agricultura Sinica, 2020, 53(9): 1756-1772.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备09089781号-30
Copyright 2018 © Editorial office of Scientia Agricultura Sinica
Tel: 86-010-82106279    E-mail: zgnykx@mail.caas.net.cn
Supported by Beijing Magtech Co.Ltd