Identification of QTLs controlling some morphological traits in barley under salinity stress by association mapping

Document Type : Research Paper


1 PhD Graduate, Department of Plant Breeding and Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran

2 Department of Plant Breeding and Biotechnology, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran

3 Seed and Plant Improvement Research Department, Khorasan Razavi Agricultural and Natural Resources Research and Education Center, AREEO, Mashhad, Iran

4 Seed and Plant Improvement Research Department, Yazd Agricultural and Natural Resources Research and Education Center, AREEO, Yazd, Iran

5 PhD Student, Department of Water Engineering, Islamic Azad University, Kerman Branch, Iran


The present study used the association mapping method to identify molecular markers associated with morphological traits using 407 SSR and AFLP markers for 148 barley genotypes. This experiment was carried out as an alpha-lattice design with five incomplete blocks in two replications under normal and salinity stress conditions (EC = 12 ds m-1) at the Agriculture and Natural Resources Research Station, Yazd, Iran. The genetic structure of the population was divided into two subpopulations (K = 2) using the Bayesian method and Structure 2.3.4 software. Association mapping was performed based on a mixed linear model using TASSEL4.3.15 software. Association mapping under normal and salinity stress conditions identified 38 and 43 significant marker-trait associations. Also, several common QTLs for the studied traits were identified. Common markers among traits can be due to pleiotropic effects or linkage between genomic regions involved in these traits. Several QTLs were stable for plant height and flag leaf area in different environmental conditions and can be regarded as stable QTLs. Markers HVM40-144, HVM40-147, HVM40-152, and HVM40-162 for plant height and marker Bmag0606-147 for flag leaf area showed a significant association with these traits in both normal and salinity-stress experiments. So, these QTLs can be suggested as stable gene loci. Identifying major gene loci influencing salinity tolerance in barley can assist in the breeding of salinity tolerance in this crop.


Article Title [Persian]

شناسایی مکان‌های ژنی کنترل کننده برخی صفات مورفولوژیک جو تحت تنش شوری با نقشه‌یابی ارتباطی

Authors [Persian]

  • مهدیه زارع کهن 1
  • نادعلی بابائیان جلودار 2
  • رضا اقنوم 3
  • سید علی طباطبایی 4
  • محمدرضا قاسمی نژاد رائینی 5
1 دانش آموخته دکتری گروه اصلاح نباتات و بیوتکنولوژی، دانشگاه علوم کشاورزی و منابع طبیعی، ساری
2 گگروه اصلاح نباتات و بیوتکنولوژی، دانشگاه علوم کشاورزی و منابع طبیعی، ساری
3 بخش تحقیقات اصلاح و تهیه نهال و بذر، مرکز تحقیقات و آموزش کشاورزی و منابع طبیعی استان خراسان رضوی، سازمان تحقیقات، آموزش و ترویج کشاورزی، مشهد
4 بخش تحقیقات اصلاح و تهیه نهال و بذر، مرکز تحقیقات و آموزش کشاورزی و منابع طبیعی استان یزد، سازمان تحقیقات، آموزش و ترویج کشاورزی، یزد
5 دانشجوی دکتری گروه مهندسی آب، دانشگاه آزاد اسلامی، واحد کرمان
Abstract [Persian]

پژوهش حاضر در راستای شناسایی نشانگرهای مولکولی مرتبط با صفات مورفولوژیک و با استفاده از 407 نشانگر SSR و AFLP روی 148 ژنوتیپ جو به روش نقشه یابی ارتباطی انجام شد. این آزمایش در قالب طرح آلفا لاتیس با پنج بلوک ناقص در دو تکرار تحت شرایط بدون تنش و تنش شوری (EC= 12 dsm-1) در مزرعه مرکز تحقیقات و آموزش کشاورزی و منابع طبیعی یزد صورت گرفت. ساختار ژنتیکی جمعیت با روش بیزی و نرم افزار Structure 2.3.4 به دو زیرجمعیت فرعی (2=K) تقسیم شد. نقشه‌یابی ارتباطی بر اساس مدل خطی مخلوط با استفاده از نرم‌افزار TASSEL4.3.15 انجام شد. به کمک نقشه‌یابی ارتباطی در شرایط نرمال و تنش شوری به ترتیب 38 و 43 ارتباط معنی ­دار نشانگر-صفت مشاهده شد. در این مطالعه چندین  QTL مشترک برای صفات مورد مطالعه شناسایی شد. وجود نشانگرهای مشترک در میان صفات می‌تواند ناشی از اثرات پلیوتروپی و یا پیوستگی نواحی ژنومی دخیل در کنترل این صفات باشد. تعدادی از QTLها برای صفات ارتفاع بوته و مساحت برگ پرچم در شرایط محیطی متفاوت پایدار بودند که به عنوان QTLهای پایدار معرفی شدند. نشانگرهای HVM40-144، HVM40-147، HVM40-152 و HVM40-162 با ارتفاع بوته و نشانگر Bmag0606-147 با مساحت برگ پرچم در هر دو آزمایش نرمال و تنش شوری ارتباط معنی­ داری نشان دادند. پس، این QTLها را می‌توان به‌عنوان مکان‌های ژنی پایدار معرفی کرد. شناسایی مکان‌های ژنی اصلی مؤثر در تحمل به شوری در جو می‌تواند به اصلاح تحمل به شوری در این گیاه کمک کند.

Keywords [Persian]

  • تنش شوری
  • جو
  • مدل خطی مخلوط
  • نقشه‌یابی ارتباطی
Aghnoum R, Marcel TC, Johrde A, Pecchioni N, Schweizer P, and Niks RE, 2010. Basal host resistance of barley to powdery mildew: connecting quantitative trait loci and candidate genes. Molecular Plant-Microbe Interactions 23(1): 91-102.
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, and Buckler ES, 2007. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23(19): 2633-2635.
Breseghello F and Sorrells ME, 2006. Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172(2): 1165-1177.
Caldwell KS, Russell J, Langridge P, and Powell W, 2006. Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172(1): 557-567.
Colmer TD, Munns R, and Flowers TJ, 2005. Improving salt tolerance of wheat and barley: future prospects. Australian Journal of Experimental Agriculture 45(11): 1425-1443.
Elakhdar A, EL-Sattar MA, Amer K, and Kumamaru T, 2016a. Genetic diversity and association analysis among Egyptian barley (Hordeum vulgare L.) genotypes with different adaptations to saline conditions analyzed by SSR markers. Australian Journal of Crop Science 10(5): 637-645.
Elakhdar A, EL-Sattar MA, Amer K, Rady A, and Kumamaru T, 2016b. Population structure and marker-trait association of salt tolerance in barley (Hordeum vulgare L.). Comptes Rendus Biologies 339(11-12): 454-461.
EL-Denary ME, Noaman MN, Abdelkhalek AF, and Mariey SA, 2012. Marker traits association of some barley genotypes under soil salinity conditions using SSR markers. Egyptian Journal of Genetics and Cytology 41(2): 229-252.
Eleuch L, Jilal A, Grando S, Ceccarelli S, Schmising MK, Hajer A, Daaloul A, and Baum M, 2008. Genetic diversity and association analysis for salinity tolerance, heading date and plant height of barley germplasm using SSR markers. Journal of Integrative Plant Biology 50(8): 1004-1014.
Falush D, Stephens M, and Pritchard JK, 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164(4): 1567-1587.
Fan Y, Zhou G, Shabala S, Chen ZH, Cai S, Li C, and Zhou M, 2016. Genome-wide association study reveals a new QTL for salinity tolerance in barley (Hordeum vulgare L.). Frontiers in Plant Science 7: 946.
Gupta PK, Rustgi S, and Kulwal PL, 2005. Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Molecular Biology 57(4): 461-485.
Gyenis L, Yun SJ, Smith KP, Steffenson BJ, Bossolini E, Sanguineti MC, and Muehlbauer GJ, 2007. Genetic architecture of quantitative trait loci associated with morphological and agronomic trait differences in a wild by cultivated barley cross. Genome 50(8): 714-723.
Inostroza L, del Pozo A, Matus I, Castillo D, Hayes P, Machado S, and Corey A, 2009. Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines  (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background. Molecular Breeding 23: 365-376.
Jabbari M, Fakheri BA, Aghnoum R, Mahdi Nezhad N, and Ataei R, 2018. GWAS analysis in spring barley (Hordeum vulgare L.) for morphological traits exposed to drought. PLoS One 13(9): e0204952.
Jun TH, Van K, Kim MY, Lee SH, and Walker DR, 2008. Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 162: 179-191.
Khalili M and Mohammadian R, 2016. Identifying QTLs associated with salinity tolerance in early stages of barley germination. Journal of Crop Biotechnology 5(13): 41 -55 (In Persian with English Abstract).
Koochakpour Z, Solouki M, Fakheri B, Aghnoum R, Mahdi Nezhadand N, and Jabbari M, 2021. Identification of genomic loci controlling phenologic and morphologic traits in barley (Hordeum vulgare L.) genotypes using association analysis. Iranian Journal of Crop Sciences 22(4): 291-304 (In Persian with English Abstract).
Kraakman ATW, Martıinez F, Mussiraliev B, van Eeuwijk FA, and Niks RE, 2006. Linkage disequilibrium mapping of morphological, resistance, and other agronomically relevant traits in modern spring barley cultivars. Molecular Breeding 17: 41-58.
Kraakman ATW, Niks RE, Van den berg PMMM, Stam P, and Van Eeuwijk FA, 2004. Linkage disequilibrium mapping of yield and yield stability in modern spring barley cultivars. Genetics 168(1): 435-446.
Liu L, Sun G, Ren X, Li C, and Sun D, 2015. Identification of QTL underlying physiological and morphological traits of flag leaf in barley. BMC Genetics 16: 29.
Long NV, Dolstra O, Malosetti M, Kilian B, Graner A, Visser RGF, and van der Linden CG, 2013. Association mapping of salt tolerance in barley (Hordeum vulgare L.). Theoretical and Applied Genetics 126(9): 2335-2351.
Munns R, 2005. Genes and salt tolerance: bringing them together. New Phytologist 167(3): 645-663.
Pasam RK, Sharma R, Malosetti M, Eeuwijk FAV, Haseneyer G, Kilian B, and Graner A, 2012. Genome-wide association studies for agronomical traits in a worldwide spring barley collection. BMC Plant Biology 12: 16.
Pritchard JK and Donnelly P, 2001. Case-control studies of association in structured or admixed populations. Theoretical Population Biology 60(3): 227-237.
Pritchard JK, Stephens M, and Donnelly P, 2000. Inference of population structure using multilocus genotype data. Genetics 155(2): 945-959.
Ramsay L, Comadran J, Druka A, Marshall DF, Thomas WTB, Macaulay M, MacKenzie K, Simpson C, Fuller J, Bonar N, Hayes PM, Lundqvist U, Franckowiak JD, Close TJ, Muehlbauer GJ, and Waugh R, 2011. INTERMEDIUM-C, a modifier of lateral spikelet fertility in barley, is an ortholog of the maize domestication gene TEOSINTE BRANCHED 1. Nature Genetics 43(2): 169-172.
Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ, and Waugh R, 2006. Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. The Proceedings of the National Academy of Sciences of the United States of America 103(49): 18656-18661.
Sallam A, Alqudah AM, Dawood MFA, Baenziger PS, and Börner A, 2019. Drought stress tolerance in wheat and barley: advances in physiology, breeding and genetics research. International Journal of Molecular Sciences 20(13): 3137.
Sayed MA, Nassar SM, Moustafa ES, Said MT, Börner A, and Hamada A, 2021. Genetic mapping reveals novel exotic and elite QTL alleles for salinity tolerance in barley. Agronomy 11(9): 1774.
Sbei H, Sato K, Shehzad T, Harrabi M, and Okuno K, 2014. Detection of QTLs for salt tolerance in Asian barley (Hordeum vulgare L.) by association analysis with SNP markers. Breeding Science 64(4): 378-388.
Shahraki H and Fakheri BA, 2016. QTLs mapping of morphophysiological traits of flag leaf in Steptoe × Morex doubled haploid lines of barley in normal and salinity stress conditions. International Journal of Farming and Allied Sciences 5(5): 356-362.
Spataro G, Tiranti B, Arcaleni P, Bellucci E, Attene G, Papa R, Spagnoletti Zeuli P, and Negri V, 2011. Genetic diversity and structure of a worldwide collection of Phaseolus coccineus L. Theoretical and Applied Genetics 122(7): 1281-1291.
Wang J, Yang J, Jia Q, Zhu J, Shang Y, Hua W, and Zhou M, 2014. A new QTL for plant height in barley (Hordeum vulgare L.) showing no negative effects on grain yield. PLoS One 9(2): e90144.
Xu R, Wang J, Li C, Johnson P, Lu C, and Zhou M, 2012. A single locus is responsible for salinity tolerance in a Chinese landrace barley (Hordeum vulgare L.). PLoS One 7(8): e43079.
Xue D, Chen M, Zhou M, Chen S, Mao Y, and Zhang G, 2008. QTL analysis of flag leaf in barley (Hordeum vulgare L.) for morphological traits and chlorophyll content. Journal of Zhejiang University Science B 9(12): 938-943.
Xue D, Huang Y, Zhang X, Wei K, Westcott S, Li C, Chen M, Zhang G, and Lance R, 2009. Identification of QTLs associated with salinity tolerance at late growth stage in barley. Euphytica 169(2): 187-196.
Yu J and Buckler ES, 2006. Genetic association mapping and genome organization of maize. Current Opinion in Biotechnology 17(2): 155-160.
Yu J, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB Kresovich S, and Buckler ES, 2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genetics 38: 203-208.
Zaare M and Jafari H, 2013. Quantitative trait loci diversity for salt tolerance at the early growth stage of barley (Hordeum vulgare L.). Crop Breeding Journal 3(2): 69-77.
Zhang Q, Wu C, Ren F, Li Y, and Zhang C, 2012. Association analysis of important agronomical traits of maize inbred lines with SSRs. Australian Journal of Crop Science 6(6): 1131-1138.