Abstract
A population of 186 recombinant inbred lines of bread wheat (Superhead#2/Roshan) was evaluated to identify quantitative trait loci (QTL) for yield and yield components under normal (2 ds m–1) and salt-stress (10–12 ds m–1) conditions. A genetic map was constructed with 451 markers, including, 23 simple sequences repeats (SSRs) and 428 diversity arrays technology markers (DArTs). The main-effect QTL were identified by composite interval mapping (CIM) analysis using QTL Cartographer v2.5 and Qgene v4.3.2 and a mixed-model-based composite interval mapping (MCIM) method using QTLNetwork v2.1. A total of 98 significant QTL were detected at two testing locations on 20 chromosomes. Of these, only 40 QTL were detected by at least two of these software programs. A total of 24 QTL on ten chromosomes were identified for grain yield, most of which had a minor effect, contributing less than 10 % of the total phenotypic variation. Two grain-yield QTL intervals were detected on 1A1 and 3B, which contributed 11.02 % and 10.3 % to the total phenotypic variation, respectively. Roshan alleles were associated with an increase in grain yield under stress conditions on 1A1, 2B3, 3B, 6B1, 1D, 2D1. Among the 20 chromosomes, chromosome 3B with 27 QTL and two distinctive cluster regions was the most important. SSR markers gwm282, gwm247, gwm566, and gwm33 were tightly linked to QTL for the same or different traits under normal, stress or both conditions, and accounted for about 17 %, 43 %, 43 % and 20 % of the total phenotypic variation, respectively. These markers are suitable for marker-assisted selection to improve grain yield under normal and salt-stress conditions.
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References
Akbari M, Wenzl P, Caig V, Carlig J, Xia L, Yang S, Uszynski G, Mohler V, Ehmensiek A, Howes N, Sharp P, Huttner E, Kilian A (2006) Diversity arrays technology (DArT) for highthroughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420
Börner A, Schumann E, Furste A, Coster H, Leithold B, Röder MS, Weber WE (2002) Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L). Theor Appl Genet 105:921–936
Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971, PMID:7851788
Crossa J, Burgueño J, Dreisigacker S, Vargas M, Herrera-Foessel SA, Lillemo M, Singh RP, Trethowan R, Warburton M, Franco J, Reynolds M, Crouch JH, Ortiz R (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177:1889–1913
Cuthbert JL, Somers DJ, Brûlé-Babel AL, Brown PD, Crow GH (2008) Molecular mapping of quantitative trait loci for yield and yield components in spring wheat (Triticum aestivum L.). Theor Appl Genet 117:595–608
Darvasi A, Weinreb A, Minke V, Weller JI, Soller M (1993) Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. Genetics 134:943–51
Díaz De León JL, Escoppinichi R, Geraldo N, Castellanos T, Mujeeb-Kazi A, Röder MS (2011) Quantitative trait loci associated with salinity tolerance in field grown bread wheat. Euphytica 181:371–383
Dubcovsky J, Maria GS, Epstein E et al (1996) Mapping of the K+/Na+ discrimination locus Kna1 in wheat. Theor Appl Genet 92:448–454
Edwards J, Shavrukov Y, Ramsey C, Tester M, Langridge P, Schnurbusch T (2008) Identification of a QTL on chromosome 7AS for sodium exclusion in bread wheat. In: Appels R, Eastwood R, Lagudah E, Langridge P, Mackay M, McIntyre L, Sharp P (eds) Proc. 11th Int. Wheat Genetics Symposium. Brisbane, vol 3. Sydney University Press, Sydney, pp 891–893
Elangovan M, Rai R, Dholakia BB, Lagu MD, Tiwari R, Gupta RK, Rao VS, Röder MS, Gupta VS (2008) Molecular genetic mapping of quantitative trait loci associated with loaf volume in hexaploid wheat (Triticum aestivum). J Cereal Sci 47:587–598
FAO (2012) Status and New Developments on the Use of Brackish Water for Agricultural Production in the Near East. Iran Country Report
Flowers T, Yeo A (1995) Breeding for salinity resistance in crop plants: where next? Aust J Plant Physiol 22:875–884
Genc Y, Oldach K, Verbyla AP, Lott G, Hassan M, Tester M, Wallwork H, McDonald GK (2010) Sodium exclusion QTL associated with improved seedling growth. in bread wheat under salinity stress. Theor Appl Genet 121:877–894
Gupta PK (2002) Molecular markers and QTL analysis in crop plants. Curr Sci 83:113–114
Gupta PK, Balyan HS, Edwards KJ, Isaac P, Korzun V, Roder M, Gautier MF, Joudrier P, Schlatter AR, Dubcovsky J, De la Pena RC, Khairallah M, Penner G, Hayden MJ, Sharp P, Keller B, Wang RCC, Hardouin JP, Jack P, Leroy P (2002) Genetic mapping of 66 new microsatellite (SSR) loci in bread wheat. Theor Appl Genet 105:413–422
Guyomarc’h H, Sourdille P, Edwards KJ, Bernard M (2002) Studies of the transferability of microsatellites derived from Triticum tauschii to hexaploid wheat and to diploid related species using amplification, hybridization and sequence comparisons. Theor Appl Genet 105:736–744
Hao Y, Chen Z, Wang Y, Bland D, Buck J, Brown-Guedira G, Johnson J (2011) Characterization of a major QTL for adult plant resistance to stripe rust in US soft red winter wheat. Theor Appl Genet 123:1401–1411
Heidari B, Sayed-Tabatabaei BE, Saeidi G, Kearsey M, Suenaga K (2011) Mapping QTL for grain yield, yield components, and spike features in a doubled haploid population of bread wheat. Genome 54:517–527
Huang XQ, Kempf H, Ganal MW, Ro¨der MS (2004) Advanced backcross QTL analysis in progenies derived from a cross between a German elite winter wheat variety and synthetic wheat (Triticum aestivum L.). Theor Appl Genet 109:933–943
Huang XQ, Cloutier S, Lycar L, Radovanovic N, Humphreys DG, Noll JS, Somers DJ, Brown PD (2006) Molecular detection of QTL for agronomic and quality traits in a doubled haploid population derived from two Canadian wheats (Triticum aestivum L.). Theor Appl Genet 113:753–766
SAS Institute (1990) SAS/STAT user’s guide: version 6 (vol 2). SAS Institute, Cary, NC
Jansen RC (1993) Interval mapping of multiple quantitative trait loci. Genetics 135:205–211
Jing HC, Bayon C, Kanyuka K, Berry S, Wenzl P, Huttner E, Kilian A, Hammond-Kosack KE (2009) DArT markers: diversity analyses, genomes comparison, mapping and integration with SSR markers in Triticum monococcum. BMC Genomics 10:458
Joehanes R, Nelson JC (2008) QGene 4.0, an extensible Java QTLanalysis platform. Bioinformatics. i:10.1093/bioinformatics/btn523
Kammholz SJ, Campbell AW, Sutherland MW, Hollamby GJ, Martin PJ, Eastwood RF, Barclay I, Wilson RE, Brennan PS, Sheppard JA (2001) Establishment and characterisation of wheat genetic mapping populations. Aust J Agric Res 52:1079–1088
Kato K, Miura H, Sawada S (2000) Mapping QTL controlling grain yield and its components on chromosome 5A of wheat. Theor Appl Genet 101:1114–1121
Kearsey MJ (1998) The principles of QTL analysis (a minimal mathematics approach). J Exp Bot 49:1619–1623. doi:10.1093/jexbot/49.327.1619
Kearsey MJ, Farquhar AGL (1998) QTL analysis in plants: where are we now? Heredity 80:137–142
Khedikar YP, Gowda MVC, Sarvamangala C, Patgar KV, Upadhyaya HD, Varshney RK (2010) A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.). Theor Appl Genet 121:971–984
Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175
Koyama ML, Levesley A, Koebner RMD, Flowers TJ, Yeo AR (2001) Quantitative trait loci for component physiological trait determining salt tolerance in rice. Plant Physiol 125:406–422
Kuchel H, Williams KJ, Langridge P, Eagles HA, Jefferies SP (2007) Genetic dissection of grain yield in bread wheat. I. QTL analysis. Theor Appl Genet 115:1029–1041
Kumar N, Kulwal PL, Balyan HS, Gupta PK (2007) QTL mapping for yield and yield contributing traits in two mapping population of bread wheat. Mol Breed 19:163–177. doi:10.1007/s11032-006-9056-8
Lin HX, Zhu MZ, Yano M, Gao JP, Liang ZW, Su WA, Hu XH, Ren ZH, Chao DY (2004) QTL for Na and K uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet 108:253–260
Lindsay MP, Lagudah ES, Hare RA, Munns R (2004) A locus for sodium exclusion (Nax1), a trait for salt tolerance, mapped in durum wheat. Funct Plant Biol 31:1105–1114
Ma L, Zhou E, Huo N, Zhou R, Wang G, Jia J (2007) Genetic analysis of salt tolerance in a recombinant inbred population of wheat (Triticum aestivum L.). Euphytica 153:109–117
Manly KF, Cudmore RH, Meer JM (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12:930–932
Manneh B, Stam P, Struik PC, Bruce-Oliver S, Van Eeuwijk FA (2007) QTL-based analysis of genotype-by-environment interaction for grain yield of rice in stress and non-stress environments. Euphytica 156:213–226
Mantovani P, Maccaferri M, Sanguineti MC, Tuberosa R, Catizone I, Wenzl P, Thomson B, Carling J, Huttner E, DeAmbrogio E, Kilian A (2008) An integrated DArT-SSR linkage map of durum wheat. Mol Breed 22:629–648
Marone D, Laidò G, Gadaleta A, Colasuonno P, Ficco DB, Giancaspro A, Giove S, Panio G, Russo MA, De Vita P, Cattivelli L, Papa R, Blanco A, Mastrangelo AM (2012) A high-density consensus map of A and B wheat genomes. Theor Appl Genet 125:1619–38
Marza F, Bai GH, Carver BF, Zhou WC (2006) Quantitative trait loci for yield and related traits in the wheat population Ning7840 × Clark. Theor Appl Genet 112:688–98
McCartney CA, Somers DJ, Humphreys DG, Lukow O, Ames N, Noll J, Cloutier S, McCallum BD (2005) Mapping quantitative trait loci controlling agronomic traits in the spring wheat cross RL4452 · ‘AC Domain’. Genome 48:870–883
Moncada P, Martínez CP, Borrero J, Chatel M, Gauch H, Guimaraes E, Tohme J, McCouch SR (2001) Quantitative trait loci for yield and yield components in an Oryza sativa×Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet 102:41–52
Narasimhamoorthy B, Gill BS, Fritz AK, Nelson JC, Brown-Guedira GL (2006) Advanced backcross QTL analysis of a hard winter wheat x synthetic wheat population. Theor Appl Genet 112:787–96
Ogbonnaya FC, Huang S, Steadman E, Livinus E, Dreccer F, Lagudah ES, Munns R (2008) Mapping quantitative trait loci associated with salinity tolerance in synthetic derived backcrossed bread lines. The 11th International Wheat Genetics Symposium proceedings. Sydney University Press, Sydney
Peleg Z, Saranga Y, Suprunova T, Ronin Y, Röder MS, Kilian A, Korol AB, Fahima TM (2008) High-density genetic map of durum wheat x wild emmer wheat based on SSR and DArT markers. Theor Appl Genet 117:103–115
Pinto RS, Reynolds MP, Mathews KL, McIntyre CL, Olivares-Villegas JJ, Chapman SC (2010) Heat and drought adaptive QTL in a wheat population designed to minimize confounding agronomic effects. Theor Appl Genet 121:1001–1021. doi: 10.1007/s00122-010-1351-4
Qadir M, Qureshi AS, Cheraghi SAM (2008) Extent and charateristion of salt-affected soils in Iran and strategies for their amelioration and management. Land Degrad Dev 19:214–227
Quarrie SA, Steed A, Calestani C, Semikhodskii A, Lebreton C, Chinoy C, Steele N, Pljevljakusic D, Waterman E, Weyen J, Schondelmaier J, Habash DZ, Farmer P, Saker L, Clarkson DT, Abugalieva A, Yessimbekova M, Turuspekov Y, Abugalieva S, Tuberosa R, Sanguineti MC, Hollington PA, Aragues R, Royo A, Dodig D (2005) A high-density genetic map of hexaploid wheat (Triticum aestivum L.) from the cross Chinese Spring × SQ1 and its use to compare QTL for grain yield across a range of environments. Theor Appl Genet 110:865–880
Ravi K, Vadez V, Isobe S, Mir RR, Guo Y, Nigam SN, Gowda MV, Radhakrishnan T, Bertioli DJ, Knapp SJ, Varshney RK (2011) Identification of several small main-effect QTL and a large number of epistatic QTL for drought tolerance related traits in groundnut (Arachis hypogaea L.). Theor Appl Genet 122:1119–1132
Richards RA (1983) Should selection for yield be made on saline or non-saline soils? Euphytica 32:431–438
Röder M, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leory P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023
Semagn K, Bjørnstad Å, Ndjiondjop N (2006a) Principles, requirements and prospects of genetic mapping in plants. Afr J Biotechnol 5:2569–2587
Semagn K, Bjørnstad Å, Skinnes H, Marøy AG, Tarkegne T, William M (2006b) Distribution of DArT, AFLP, and SSR markers in a genetic linkage map of a doubled haploid hexaploid wheat population. Genome 49:545–555
Singh K, Ghai M, Garg M, Chhuneja P, Kaur P, Schnurbusch T, Keller B, Dhaliwal HS (2007) An integrated molecular linkage map of diploid wheat based on a Triticum boeoticum x T. monococcum RIL population. Theor Appl Genet 115:301–12
Song QJ, Fickus EW, Cregan PB (2002) Characterization of trinucleotide SSR motifs in wheat. Theor Appl Genet 104:286–293
Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J et al (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110:550–560. doi:10.1007/s00122-004-1871
Spielmeyer W, Hyles J, Joaquim P, Azanza F, Bonnett D, Ellis ME, Moore C, Richards RA (2007) A QTL on chromosome 6A in bread wheat (Triticum aestivum) is associated with longer coleoptiles, greater seedling vigour and final plant height. Theor Appl Genet 115:59
Srinivasachary, Gosman N, Steed A, Hollins TW, Bayles R, Jennings P, Nicholson P (2009) Semi-dwarfing Rht-B1 and Rht-D1 loci of wheat differ significantly in their influence on resistance to Fusarium head blight. Theor Appl Genet 118:695
Tanksley SD (1993) Mapping polygenes. Annu Rev Genet 27:205–233
Thomson MJ, Ocampo MD, Egdane J, Rahman MA, Sajise AG, Adorada DL, Tumimbang-Raiz E, Blumwald E, Seraj ZI, Singh RK, Gregorio GB, Ismail AM (2010) Characterizing the saltol quantitative trait locus for salinity tolerance in rice. Rice 3:148–160
Villalta I, Bernet GP, Carbonell EA, Asins MJ (2007) Comparative QTL analysis of salinity tolerance in terms of fruit yield using two Solanum populations of F7 lines. Theor Appl Genet 114:1001–1017
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTL. J Hered 93:77–78. doi:10.1093/jhered/93.1.77
Wang Z, Cheng J, Chen Z, Huang J, Bao Y, Wang J, Zhang H (2012a) Identification of QTL with main, epistatic and QTL × environment interaction effects for salt tolerance in rice seedlings under different salinity conditions. Theor Appl Genet 125:807–15
Wang S, Basten CJ, Zeng ZB (2012b) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm
Xu YF, An DG, Liu DC, Zhang AM, Xu HX, Li B (2012) Mapping QTL with epistatic effects and QTL × treatment interactions for salt tolerance at seedling stage of wheat. Euphytica 186:233–245
Xue D, Huang Y, Zhang X, Wei K, Westcott S, Li C, Chen M, Zhang G, Lance R (2009) Identification of QTL associated with salinity tolerance at late growth stage in barley. Euphytica 169:187–196
Yang J, Hu C, Hu H, Yu R, Xia Z, Ye X, Zhu J (2008) QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics 24:721–723
Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136(4):1457–68
Zhang LP, Xu XQ, Zhao CP, Shan FH, Yuan S, Sun H (2011) QTL analysis of plant height in photoperiod-thermo sensitive male sterile wheat. Mol Plant Breed 2:92–97
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This research was supported by the Agricultural Biotechnology Research Institute of Iran (ABRII).
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Azadi, A., Mardi, M., Hervan, E.M. et al. QTL Mapping of Yield and Yield Components under Normal and Salt-stress Conditions in Bread Wheat (Triticum aestivum L.). Plant Mol Biol Rep 33, 102–120 (2015). https://doi.org/10.1007/s11105-014-0726-0
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DOI: https://doi.org/10.1007/s11105-014-0726-0