Abstract
Tef is a cereal crop of cultural and economic importance in Ethiopia. It is grown primarily for its grain though it is also an important source of fodder. Tef suffers from lodging that reduces both grain yield and quality. As a first step toward executing a marker-assisted breeding program for lodging resistance and grain yield improvement, a linkage map was constructed using 151 F9 recombinant inbred lines obtained by single-seed-descent from a cross between Eragrostis tef and its wild relative Eragrostis pilosa. The map was primarily based on microsatellite (SSR) markers that were developed from SSR-enriched genomic libraries. The map consisted of 30 linkage groups and spanned a total length of 1,277.4 cM (78.7% of the genome) with an average distance of 5.7 cM between markers. This is the most saturated map for tef to date, and for the first time, all of the markers are PCR-based. Using agronomic data from 11 environments and marker data, it was possible to map quantitative trait loci (QTL) controlling lodging, grain yield and 15 other related traits. The positive effects of the QTL identified from the wild parent were mainly for earliness, reduced culm length and lodging resistance. In this population, it is now possible to combine lodging resistance and grain yield using a marker-assisted selection program targeting the QTL identified for both traits. The newly developed SSR markers will play a key role in germplasm organization, fingerprinting and monitoring the success of the hybridization process in intra-specific crosses lacking distinctive morphological markers.
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References
Ahmad M, Sorrells ME (2002) Distribution of microsatellite alleles linked to Rht8 dwarfing gene in wheat. Euphytica 123:235–240
Assefa K, Ketema S, Tefera H, Kefyalew T, Chundera F (2000) Trait diversity, heritability and genetic advance in selected germplasm lines of tef [Eragrostis tef (Zucc.) Trotter]. Hereditas 133:29–37
Assefa K, Tefera H, Merker A, Kefyalew T, Hundera F (2001) Quantitative trait diversity in tef [Eragrostis tef (Zucc.) Trotter] germplasm from central and northern Ethiopia. Genet Resour Crop Evol 48:53–61
Assefa K, Merker A, Tefera H (2002) Qualitative trait variation in tef [Eragrostis tef (Zucc.) Trotter] germplasm from western and southern Ethiopia. Euphytica 127:399–410
Ayele M, Nguyen HT (2000) Evaluation of amplified fragment length polymorphism markers in tef, Eragrostis tef (Zucc.) Trotter, and related species. Plant Breed 119:403–409
Bai G, Tefera H, Ayele M, Nguyen HT (1999a) A genetic linkage map of tef [Eragrostis tef (Zucc.) Trotter] based on amplified fragment length polymorphism. Theor Appl Genet 99:599–604
Bai GH, Ayele M, Tefera H, Nguyen HT (1999b) Amplified fragment length polymorphism analysis of tef [Eragrostis tef (Zucc.) Trotter]. Crop Sci 39:819–824
Bai G, Ayele M, Tefera H, Nguyen HT (2000) Genetic diversity in tef [Eragrostis tef (Zucc) Trotter] and its relatives as revealed by Random Amplified Polymorphic DNAs. Euphytica 112:15–22
Bassam B, Caetano-Anollés G, Gresshoff P (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83
Bertin I, Zhu JH, Gale MD (2005) SSCP-SNP in pearl millet—a new marker system for comparative genetics. Theor Appl Genet 110:1467–1472
Börner A, Schumann E, Fürste A, Cöster H, Leithold B, Röder M, Weber W (2002) Mapping of quantitative trait loci determining agronomic important characters in hexaploid wheat (Triticum aestivum L.). Theor Appl Genet 105:921–936
Brown SM, Hopkins MS, Mitchell SE, Senior ML, Wang TY, Duncan RR, Gonzalez-Candelas F, Kresovich S (1996) Multiple methods for the identification of polymorphic simple sequence repeats (SSRs) in sorghum [Sorghum bicolor (L.) Moench]. Theor Appl Genet 93:190–198
Bryan GJ, Collins AJ, Stephenson P, Orry A, Smith JB, Gale MD (1997) Isolation and characterisation of microsatellites from hexaploid bread wheat. Theor Appl Genet 94:557–563
Cai H, Morishima H (2002) QTL clusters reflect character associations in wild and cultivated rice. Theor Appl Genet 104:1217–1228
Caldicott JJB, Nuttall AM (1979) A method for the assessment of lodging in cereal crops. J Natl Inst Agric Bot 15:88–91
Chanyalew S, Singh H, Tefera H, Sorrels M (2005) Molecular genetic map and QTL analysis of agronomic traits based on a Eragrostis tef × E-pilosa recombinant inbred population. J Genet Breed 59:53–66
Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567
DeVicente MC, Tanksley SD (1993) QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics 134:585–596
Dida MM, Ramakrishnan S, Bennetzen JL, Gale MD, Devos KM (2007) The genetic map of finger millet, Eleusine coracana. Theor Appl Genet 114:321–332
Ellis M, Spielmeyer W, Gale K, Rebetzke G, Richards R (2002) “Perfect” markers for the Rht-B1b and Rht-D1b dwarfing genes in wheat. Theor Appl Genet 105:1038–1042
Fishman L, Kelly AJ, Morgan E, Willis JH (2001) A genetic map in the Mimulus guttatus species complex reveals transmission ratio distortion due to heterospecific interactions. Genetics 159:1701
Flint-Garcia SA, Jampatong C, Darrah LL, McMullen MD (2003) Quantitative trait locus analysis of stalk strength in four maize populations. Crop Sci 43:13
Gilmour AR, Gogel BJ, Cullis BR, Thompson R (2006) ASReml user guide release 2.0. VSN International Ltd, Hemel Hempstead, UK
Hai L, Guo H, Xiao S, Jiang G, Zhang X, Yan C, Xin Z, Jia J (2005) Quantitative trait loci (QTL) of stem strength and related traits in a doubled-haploid population of wheat (Triticum aestivum L.). Euphytica 141:1–9
Hedden P (2003) The genes of the Green Revolution. Trends Genet 19:5–9
Holland JB, Nyquist WE, Cervantes-Martinez CT (2003) Estimating and interpreting heritability for plant breeding: an update. Plant Breed Rev 22:9–112
Hopman GD (2008) Gluten intake and gluten-free diet in the Netherlands. Department Pediatry, Leiden University Medical Center (LUMC), Leiden University, Leiden
Huang HR, Zhou G, Ge XJ, Wei X, Jiang YS, Tang H (2009) Eight polymorphic microsatellite loci for the Chinese medicinal plant Artemisia annua L. (Asteraceae). Conserv Genet 10:593–595
Hundera F, Nelson LA, Baenziger PS, Bechere E, Tefera H (2000) Association of lodging and some morpho-agronomic traits in tef [Eragrostis tef (Zucc.) Trotter]. Trop Agric 77:169–173
Ingram AL, Doyle JJ (2003) The origin and evolution of Eragrostis tef (Poaceae) and related polyploids: evidence from nuclear waxy and plastid rps16. Am J Bot 90:116–122
Inoue M, Gao Z, Cai H (2004) QTL analysis of lodging resistance and related traits in Italian ryegrass (Lolium multiflorum Lam.). Theor Appl Genet 109:1576–1585
Ishimaru K, Togawa E, Ookawa T, Kashiwagi T, Madoka Y, Hirotsu N (2008) New target for rice lodging resistance and its effect in a typhoon. Planta 227:601–609
Jenczewski E, Gherardi M, Bonnin I, Prosperi JM, Olivieri I, Huguet T (1997) Insight on segregation distortions in two intraspecific crosses between annual species of Medicago (Leguminosae). Theor Appl Genet 94:682–691
Jiang GM, Sun JZ, Liu HQ, Qu CM, Wang KJ, Guo RJ, Bai KZ, Gao LM, Kuang TY (2003) Changes in the rate of photosynthesis accompanying the yield increase in wheat cultivars released in the past 50 years. J Plant Res 116:347–354
Jones ES, Dupal MP, Kölliker R, Drayton MC, Forster JW (2001) Development and characterisation of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.). Theor Appl Genet 102:405–415
Kantety RV, Graznak E, Hailu T, Sorrells ME (2001) Comparative mapping in tef. In: Tefera H, Belay G, Sorrells M (eds) Narrowing the rift: tef research and development. Ethiopian Agricultural Research Organization, Addis Ababa, pp 99–107
Kashiwagi T, Sasaki H, Ishimaru K (2005) Factors responsible for decreasing sturdiness of the lower part in lodging of rice (Oryza sativa L.). Plant Prod Sci 8:166–172
Kashiwagi T, Togawa E, Hirotsu N, Ishimaru K (2008) Improvement of lodging resistance with QTLs for stem diameter in rice (Oryza sativa L.). Theor Appl Genet 117:749–757
Kelbert AJ, Spaner D, Briggs KG, King JR (2004) The association of culm anatomy with lodging susceptibility in modern spring wheat genotypes. Euphytica 136:211–221
Keller M, Karutz C, Schmid JE, Stamp P, Winzeler M, Keller B, Messmer MM (1999) Quantitative trait loci for lodging resistance in a segregating wheat × spelt population. Theor Appl Genet 98:1171–1182
Ketema S (1997) Tef, Eragrostis tef (Zucc.) Trotter. Promoting the conservation and use of under-utilised and neglected crops, vol 18. Institute of Plant Genetics and Crop Plant Research, Gatersleben/International Plant Genetics Resources Institute, Rome
Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175
Ky CL, Barre P, Lorieux M, Trouslot P, Akaffou S, Louarn J, Charrier A, Hamon S, Noirot M (2000) Interspecific genetic linkage map, segregation distortion and genetic conversion in coffee (Coffea sp.). Theor Appl Genet 101:669–676
Li JZ, Huang XQ, Heinrichs F, Ganal MW, Röder MS (2006) Analysis of QTLs for yield components, agronomic traits, and disease resistance in an advanced backcross population of spring barley. Genome 49:454–466
Milach SCK, Rines HW, Phillips RL (2002) Plant height components and gibberellic acid response of oat dwarf lines. Crop Sci 42:1147
Moncada P, Martinez CP, Borrero J, Chatel M, Gauch H Jr, 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
Pamidimarri D, Sinha R, Kothari P, Reddy MP (2009) Isolation of novel microsatellites from Jatropha curcas L. and their cross-species amplification. Mol Ecol Resour 9:431–433
Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607
Peng J, Richards DE, Hartley NM, Murphy GP, Devos KM, Flintham JE, Beales J, Fish LJ, Worland AJ, Pelica F (1999) ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400:256–261
Rafalski JA, Vogel JM, Morgante M, Powell W, Andre C, Tingey SV (1996) Generating and using DNA markers in plants. In: Birren B, Lai E (eds) Analysis of non-mammalian genomes–a practical guide. Academic Press, New York, pp 75–134
Rao HS, Basha OP, Singh NK, Sato K, Dhaliwal HS (2007) Frequency distributions and composite interval mapping for QTL analysis in ‘Steptoe’ × ‘Morex’ barley mapping population. Barley Genet Newslett 37:5–20
Rosell S, Holmer B (2007) Rainfall change and its implications for belg harvest in south Wollo, Ethiopia. Geogr Ann 89:287–299
Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386
Saha MC, Cooper JD, Mian MAR, Chekhovskiy K, May GD (2006) Tall fescue genomic SSR markers: development and transferability across multiple grass species. Theor Appl Genet 113:1449–1458
Septiningsih EM, Prasetiyono J, Lubis E, Tai TH, Tjubaryat T, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for yield and yield components in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1419–1432
Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–481
Sim SC, Yu JK, Jo Y, Sorrells ME, Jung G (2009) Transferability of cereal EST-SSR markers to ryegrass. Genome 52:431–437
Song QJ, Shi JR, Singh S, Fickus EW, Costa JM, Lewis J, Gill BS, Ward R, Cregan PB (2005) Development and mapping of microsatellite (SSR) markers in wheat. Theor Appl Genet 110:550–560
Sorrells ME (1992) Development and application of RFLPs in polyploids. Crop Sci 32:1086
Spaenij-Dekking L, Kooy-Winkelaar Y, Koning F (2005) The Ethiopian cereal tef in celiac disease. N Engl J Med 353:1748–1749
Tai TH, Tanksley SD (1990) A rapid and inexpensive method for isolation of total DNA from dehydrated plant tissue. Plant Mol Biol Rep 8:297–303
Tavassoli A (1986) The cytology of Eragrostis with special reference to E. tef and its relatives. Ph.D. thesis, Royal Holloway College, University of London, UK
Tefera H, Assefa K, Belay G (2003) Evaluation of interspecific recombinant inbred lines of Eragrostis tef × E pilosa. J Genet Breed 57:21–30
Tefera H, Belay G, Assefa K (2008) Genetic variation in F2 populations and their potential in the improvement of grain yield in tef (Eragrostis tef). Euphytica 164:105–111
Teklu Y, Tefera H (2005) Genetic improvement in grain yield potential and associated agronomic traits of tef (Eragrostis tef). Euphytica 141:247–254
Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452
Thomson MJ, Tai TH, McClung AM, Lai XH, Hinga ME, Lobos KB, Xu Y, Martinez CP, McCouch SR (2003) Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet 107:479–493
Tinker NA, Mather DE, Rossnagel BG, Kasha KJ, Kleinhofs A, Hayes PM, Falk DE, Ferguson T, Shugar LP, Legge WG (1996) Regions of the genome that affect agronomic performance in two-row barley. Crop Sci 36:1053–1062
Van Ooijen JW, Voorrips RE (2001) JoinMap® 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The Netherlands
Wang S, Basten CJ, Zeng ZB (2007) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm
Xu Y, Zhu L, Xiao J, Huang N, McCouch SR (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Gen Genet 253:535–545
Yu J, Sun Q, La Rota M, Edwards H, Tefera H, Sorrells ME (2006a) Expressed sequence tag analysis in tef (Eragrostis tef (Zucc) Trotter). Genome 49:365
Yu JK, Kantety RV, Graznak E, Benscher D, Tefera H, Sorrells ME (2006b) A genetic linkage map for tef [Eragrostis tef (Zucc.) Trotter]. Theor Appl Genet 113:1093–1102
Yu JK, Graznak E, Breseghello F, Tefera H, Sorrells ME (2007) QTL mapping of agronomic traits in tef [Eragrostis tef (Zucc) Trotter]. BMC Plant Biol 7:13
Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16
Zeid M, Mitchell S, Link W, Carter M, Nawar A, Fulton T, Kresovich S (2009) Simple sequence repeats (SSRs) in faba bean: new loci from Orobanche-resistant cultivar ‘Giza 402’. Plant Breed 128:149–155
Zeid M, Yu J, Goldowitz I, Denton ME, Costich DE, Jayasuriya CT, Saha M, Elshire R, Benscher D, Breseghello F, Munkvold J, Varshney RK, Belay G, Sorrells ME (2010) Cross-amplification of EST-derived markers among sixteen grass species. Field Crops Res. doi:10.1016/j.fcr.2010.03.014
Zhang D, Ayele M, Tefera H, Nguyen HT (2001) RFLP linkage map of the Ethiopian cereal tef [Eragrostis tef (Zucc) Trotter]. Theor Appl Genet 102:957–964
Zhang Y, He J, Zhao PX, Bouton JH, Monteros MJ (2008) Genome-wide identification of microsatellites in white clover (Trifolium repens L.) using FIASCO and phpSSRMiner. Plant Methods 4:19
Zuber U, Winzeler H, Messmer MM, Keller M, Keller B, Schmid JE, Stamp P (1999) Morphological traits associated with lodging resistance of spring wheat (Triticum aestivum L.). J Agron Crop Sci 182:17–24
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The McKnight Foundation’s Collaborative Crop Research Program financed this work through the African Chloridoid Cereals project (Grant No. 06-448).
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Communicated by H. H. Geiger.
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Zeid, M., Belay, G., Mulkey, S. et al. QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef. Theor Appl Genet 122, 77–93 (2011). https://doi.org/10.1007/s00122-010-1424-4
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DOI: https://doi.org/10.1007/s00122-010-1424-4