Abstract
Genetic mapping of major genes and quantitative traits loci (QTLs) for many important agricultural traits is increasing the integration of biotechnology with the conventional breeding process. Exploitation of the information derived from the map position of traits with agronomical importance and of the linked molecular markers, can be achieved through marker assisted selection (MAS) of the traits during the breeding process. However, empirical applications of this procedure have shown that the success of MAS depends upon several factors, including the genetic base of the trait, the degree of the association between the molecular marker and the target gene, the number of individuals that can be analyzed and the genetic background in which the target gene has to be transferred. MAS for simply inherited traits is gaining increasing importance in breeding programs, allowing an acceleration of the breeding process. Traits related to disease resistance to pathogens and to the quality of some crop products are offering some important examples of a possible routinary application of MAS. For more complex traits, like yield and abiotic stress tolerance, a number of constraints have determined severe limitations on an efficient utilization of MAS in plant breeding, even if there are a few successful applications in improving quantitative traits. Recent advances in genotyping technologies together with comparative and functional genomic approaches are providing useful tools for the selection of genotypes with superior agronomical performancies.
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Abbreviations
- G × E:
-
genotype × environment
- LD:
-
linkage disequilibrium
- MAS:
-
marker assisted selection
- NILs:
-
near isogenic lines
- Q × E:
-
QTL × environment
- RILs:
-
recombinant inbred lines
References
F Abe K Saito K Miura K Toriyama (2002) ArticleTitleA single nucleotide polymorphism in the alternative oxidase gene among rice varieties differing in low temperature tolerance FEBS Lett. 527 IssueID1– 3 181–185 Occurrence Handle10.1016/S0014-5793(02)03218-0 Occurrence Handle12220657
JA Anderson RW Stack S Liu BL Waldron AD Fjeld C Coyne B Moreno-Sevilla J Mitchell Fetch QJ Song PB Cregan RC Frohberg (2001) ArticleTitleDNA markers for Fusarium head blight resistance QTLs in two wheat populations Theor. Appl. Genet. 102 1164–1168 Occurrence Handle10.1007/s001220000509
L Arru N Faccini C Govoni L Cattivelli N Pecchioni G Delogu AM Stanca G Valè (2003) ArticleTitleThe PCR-based marker MWG2018 linked to the Rdg2a leaf stripe resistance gene is a useful tool for assesing barley resistance in breeding programs Crop Sci. 43 1036–1042
RC Babu BD Nguyen V Chamarerk P Shanmugasundaram P Chezhian P Jeyaprakash SK Ganesh A Palchamy S Sadasivam S Sarkarung LJ Wade HT Nguyen (2003) ArticleTitleGenetic analysis of drought resistance in rice by molecular markers Crop Sci. 43 1457–1469
B Baker P Zambryski B Staskawicz SP Dinesh-Kumar (1997) ArticleTitleSignaling in plant-microbe interactions Science 276 726–733 Occurrence Handle10.1126/science.276.5313.726 Occurrence Handle9115193
AR Barr SP Jefferies P Warner DB Moody KJ Chalmers P Langridge (2000) ArticleTitleMarker assisted selection in theory and pratice Proceedings VIII Barley Genetic Symposium. Vol.I 167–178
E Barzen R Stahl E Fuchs DC Borchardt F Salamini (1997) ArticleTitleDevelopment of coupling-repulsion-phase SCAR markers diagnostic for the sugar beet Rr1 allele conferring resistance to rhizomania Mol. Breed. 3 231–238 Occurrence Handle10.1023/A:1009626214058
MP Boer CJF Ter Braak Jansen (2002) ArticleTitleA penalized likelihood method for mapping epistatic quantitative trait loci with one-dimensional genome searches Genetics 162 951–960 Occurrence Handle12399402
HJ Bohnert RG Jensen (1996) ArticleTitleStrategies for engineering water-stress tolerance in plants Trends Biotechnol. 14 89–97 Occurrence Handle10.1016/0167-7799(96)80929-2
J Bolanos GO Edmeades (1996) ArticleTitleThe importance of the anthesis-silking interval in breeding for drought tolerance in tropical maize Field Crop Res. 48 65–80 Occurrence Handle10.1016/0378-4290(96)00036-6
A Bouchez F Hospital M Causse A Gallais A Charcosset (2002) ArticleTitleMarker-assisted introgression of favorable alleles at Quantitative Trait Loci between maize elite lines Genetics 162 1945–1959 Occurrence Handle12524362
SR Boutin ND Young T Olson Z-H Yu RC Shoemaker C Vallejos (1995) ArticleTitleGenome conservation among three legume genera detected with DNA markers Genome 38 928–937
ES Buckler SuffixIV JM Thornsberry (2002) ArticleTitlePlant molecular diversity and application to genomics Curr. Opin. Plant Biol. 5 107–111 Occurrence Handle10.1016/S1369-5266(02)00238-8 Occurrence Handle11856604
R Büschges K Hollricher R Panstruga G Simons M Wolter A Frijters R Daelen Particlevan T Lee Particlevan der P Diergaarde J Groenendijk S Töpsch P Vos F Salamini P Schulze-Lefert (1997) ArticleTitleThe barley Mlo gene: a novel control element of plant pathogen resistance Cell 88 695–705 Occurrence Handle10.1016/S0092-8674(00)81912-1 Occurrence Handle9054509
L Cattivelli P Baldi C Crosatti N Di Fonzo P Faccioli M Grossi AM Mastrangelo N Pecchioni AM Stanca (2002) ArticleTitleChromosome regions and stress-related sequences involved in resistance to abiotic stress in Triticeae Plant. Mol. Biol. 48 IssueID5– 6 649–665 Occurrence Handle10.1023/A:1014824404623 Occurrence Handle11999841
S Ceccarelli E Acevedo S Grando (1991) ArticleTitleBreeding for yield stability in unpredictable environments: single traits, interaction between traits, and architecture of genotypes Euphytica 56 169–185 Occurrence Handle10.1007/BF00042061
V Chaguè T Fahima A Dahan GL Sun AB Korol YI Ronin A Grama ME Röder E Nevo (1999) ArticleTitleIsolation of microsatellite and RAPD markers flanking the Yr15 gene of wheat using NILs and bulked segregant analysis Genome 42 1050–1056 Occurrence Handle10.1139/gen-42-6-1050 Occurrence Handle10659769
FS Cheng NF Weeden SK Brown HS Aldwinckle SE Gardiner VG Bus (1998) ArticleTitleDevelopment of a DNA marker for Vm, a gene conferring resistance to apple scab Genome 41 208–214 Occurrence Handle10.1139/gen-41-2-208
VC Concibido BL Vallee P Mclaird N Pineda J Meyer L Hummel J Yang K Wu X Delannay (2003) ArticleTitleIntrogression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars Theor. Appl. Genet. 106 575–582 Occurrence Handle12595984
PB Cregan J Mudge EW Fickus D Danesh R Denny ND Young (2000) ArticleTitleTwo simple sequence repeat markers to select for soybean cyst nematode resistance conditioned by the rhg1locus Theor. Appl. Genet. 99 811–818 Occurrence Handle10.1007/s001220051300
J Crossa M Vargas FA Eeuwijk Particlevan C Jang GO Edmeades D Hoisington (1999) ArticleTitleInterpreting genotype × environment interaction in tropical maize using linked molecular markers and environmental covariables Theor. Appl. Genet. 99 611–625 Occurrence Handle10.1007/s001220051276
JCM Dekkers F Hospital (2002) ArticleTitleThe use of molecular genetics in the improvement of agricultural populations Nat. Rev. Genet. 3 22–32 Occurrence Handle10.1038/nrg701 Occurrence Handle11823788
S Doganlar J Dodson B Gabor T Beck-Bunn C Crossman SD Tanksley (1998) ArticleTitleMolecular mapping of the py-1 gene for resistance to corky root rot (Pyrenochaeta lycopersici) in tomato Theor. Appl. Genet. 97 784–788 Occurrence Handle10.1007/s001220050956
TM Donald F Pellerone A-F Adam-Blondon A Bouquet MR Thomas IB Dry (2002) ArticleTitleIdentification of resistance gene analogs linked to a powdery mildew resistance locus in grapevine Theor. Appl. Genet. 104 610–618 Occurrence Handle10.1007/s00122-001-0768-1 Occurrence Handle12582665
CM Dussle M Quint ML Xu AE Melchinger T Lübberstedt (2002) ArticleTitleConversion of AFLP fragments tightly linked to SCMV resistance genes Scmv1 and Scmv2 into simple PCR-based markers Theor. Appl. Genet. 105 1190–1195 Occurrence Handle10.1007/s00122-002-0964-7 Occurrence Handle12582898
SR Eathington JW Dudley GK Rufener (1997) ArticleTitleUsefulness of marker-QTL associations in early generation selection Crop Sci. 37 1686–1693
B Ehdaie AE Hall GD Farquhar HT Nguyen JG Waines (1991) ArticleTitleWater-use efficiency and carbon isotope discrimination in wheat Crop Sci. 31 1282–1288
C Feuillet S Travella N Stein L Albar A Nublat B Keller (2003) ArticleTitleMap-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome Proc. Natl. Acad. Sci. USA 100 15253–15258 Occurrence Handle10.1073/pnas.2435133100 Occurrence Handle14645721
R Fjellstrom C Conaway-Bormans AM McClung MA Marchetti AR Shank WD Park (2004) ArticleTitleDevelopment of DNA markers suitable for marker assisted selection of three Pi genes conferring resistance to multiple Pyricularia griseapathotypes Crop Sci. 44 1790–1798
MR Foolad LP Zhang P Subbiah (2002) ArticleTitleGenetics of drought tolerance during seed germination in tomato: inheritance and QTL mapping Genome 46 536–545 Occurrence Handle10.1139/g03-035
GP Fox JF Panozzo CD Li PA LanceRCM Inkerman RJ Henry (2003) ArticleTitleMolecular basis of barley quality Aust. J. Agricult. Res. 54 1081–1101 Occurrence Handle10.1071/AR02237
PN Fox J Crossa I Romagosa (1997) Genotype × environment and adaptation R Kempton P Fox (Eds) Statistical Methods for Plant Variety Evaluation. Chapman&Hall London 117–138
E Francia F Rizza L Cattivelli AM Stanca G Galiba B Toth PM Hayes JS Skinner N Pecchioni (2004) ArticleTitleTwo loci on chromosome 5H determine low-temperature tolerance in a ‘Nure’ (winter) × ‘Tremois’ (spring) barley map Theor. Appl. Genet. 108 670–680 Occurrence Handle10.1007/s00122-003-1468-9 Occurrence Handle14576984
A Frary TC Nesbitt A Frary S Grandillo E Knaap Particlevan der B Cong JP Liu J Meller R Elber KB Alpert SD Tanksley (2000) ArticleTitlefw2.2: A quantitative trait locus key to the evolution of tomato fruit size Science 289 85–88 Occurrence Handle10884229
A Frary S Doganlar A Frampton T Fulton J Uhlig H Yates S Tanksley (2003) ArticleTitleFine mapping of quantitative trait loci for improved fruit characteristics from Lycopersicon chmielewskii chromosome 1 Genome 46 235–243 Occurrence Handle10.1139/g02-122 Occurrence Handle12723039
E Fridman T Pleban D Zamir (2000) ArticleTitleA recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene Proc. Natl. Acad. Sci. USA 97 4718–4723 Occurrence Handle10.1073/pnas.97.9.4718 Occurrence Handle10781077
M Frisch M Bohn AE Melchinger (1999) ArticleTitleComparison of selection strategies for marker-assisted selection backcrossing of a gene Crop Sci. 39 1285–1301
MD Gale KM Devos (1998) ArticleTitleComparative genetics in the grasses Proc. Natl. Acad. Sci. USA 95 1971–1794 Occurrence Handle10.1073/pnas.95.5.1971 Occurrence Handle9482816
LF Gao RL Jing NX Huo Y Li XP Li RH Zhou XP Chang JF Tang ZY Ma JZ Jia (2004) ArticleTitleOne hundred and one new microsatellite loci derived from ESTs (EST-SSRs) in bred wheat Theor. Appl. Genet. 108 1392–1400 Occurrence Handle10.1007/s00122-003-1554-z Occurrence Handle14968301
C Gebhardt JPT Valkonen (2001) ArticleTitleOrganization of genes controlling disease resistance in the potato genome Annu. Rev. Phytopathol. 39 79–102 Occurrence Handle10.1146/annurev.phyto.39.1.79 Occurrence Handle11701860
AC Gleeson (1997) Spatial analysis RA Kempton PN Fox (Eds) Statistical Mathods for Plant Variety Evaluation. Chapman & Hall London 68–85
SA Goff D Ricke T-H Lan G Presting R Wang M Dunn J Glazebrook A Sessions P Oeller H Varma D Hadley D Hutchison C Martin F Katagiri BM Lange T Moughamer Y Xia P Budworth J Zhong T Miguel U Paszkowski S Zhang M Colbert W-L Sun L Chen B Cooper S Park TC Wood L Mao P Quail R Wing R Dean Y Yu A Zharkikh R Shen S Sahasrabudhe A Thomas R Cannings A Gutin D Pruss J Reid S Tavtigian J Mitchell G Eldredge T Scholl RM Miller S Bhatnagar N Adey T Rubano N Tusneem R Robinson J Feldhaus T Macalma A Oliphant S Briggs (2002) ArticleTitleA draft sequence of the rice genome (Oryza sativa L ssp japonica) Science 296 92–100 Occurrence Handle10.1126/science.1068275 Occurrence Handle11935018
S Grandillo HM Ku SD Tanksley (1999) ArticleTitleIdentifying the loci responsible for natural variation in fruit size and shape in tomato Theor. Appl. Genet. 99 978–987 Occurrence Handle10.1007/s001220051405
A Graner S Streng A Kellermann A Schiemann E Baner R Waugh B Pellio F Ordon (1999) ArticleTitleMolecular mapping of the rym5 locus encoding resistance to different strains of the barley yellow mosaic virus complex Theor. Appl. Genet. 98 285–290 Occurrence Handle10.1007/s001220051070
A Graner S Streng A Drescher Y Jin I Borovkova B Steffenson (2000) ArticleTitleMolecular mapping of the leaf rust resistance gene Rph7 in barley Plant Breed. 119 389–392 Occurrence Handle10.1046/j.1439-0523.2000.00528.x
Graner A, Kota R, Perovic D, Potokina E, Prasad M, Scholz U, Stein N, Thiel T, Varshney RK, Zhang H (2004) Molecular mapping: shifting from the structural to the functional level. Proc. 9th International Barley Genetic Symposium (pp. 49–57).
KE Hammond-Kosack JE Parker (2003) ArticleTitleDeciphering plant– pathogen communication: fresh perspectives for molecular resistance breeding Curr. Opin. Biotec. 14 177–193 Occurrence Handle10.1016/S0958-1669(03)00035-1
F Han I Romagosa SE Ullrich BL Jones PM Hayes DM Wesenberg (1997) ArticleTitleMolecular marker-assisted selection for malting quality traits in barley Mol. Breed. 3 427–437 Occurrence Handle10.1023/A:1009608312385
BIG Haussmann V Mahalakshmi BVS Reddy N Seetharama CT Hash HH Geiger (2002) ArticleTitleQTL mapping of stay-green in two sorghum recombinant inbred populations Theor. Appl. Genet. 106 133–142 Occurrence Handle12582881
K Hayashi N Hashimoto M Daigen I Ashikawa (2004) ArticleTitleDevelopment of PCR-based SNP markers for rice blast resistance genes at the Piz locus Theor. Appl. Genet. 108 1212–1220 Occurrence Handle10.1007/s00122-003-1553-0 Occurrence Handle14740086
M Helguera IA Khan Dubcavsky (2000) ArticleTitleDevelopment of PCR markers for wheat leaf rust resistance gene Lr47 Theor. Appl. Genet. 101 625–631 Occurrence Handle10.1007/s001220051524
S Hittalmani A Parco TV Mew RS Zeigler N Huang (2000) ArticleTitleFine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice Theor. Appl. Genet 100 1121–1128 Occurrence Handle10.1007/s001220051395
CC Huang YY Cui CR Weng P Zabel P Lindhout (2000) ArticleTitleDevelopment of diagnostic PCR markers closely linked to the tomato powdery mildew resistance gene Ol-1 on chromosome 6 of tomato Theor. Appl. Genet 101 918–924 Occurrence Handle10.1007/s001220051562
L Huang BS Gill (2001) ArticleTitleAn RGA-like marker detects all known Lr21 leaf rust resistance gene family members in Aegilops tauschii and wheat Theor. Appl. Genet. 103 1007–1013 Occurrence Handle10.1007/s001220100701
XQ Huang LX Wang MX Xu MS Röder (2003) ArticleTitleMicrosatellite mapping of the powdery mildew resistance gene Pm5e in common wheat (Triticum aestivum L.). Theor Appl. Genet. 106 858–865
E Igartua M Edney BG Rossnagel D Spaner WG Legge GJ Scoles PE Eckstein GA Penner NA Tinker KG Briggs DE Falk DE Mather (2000) ArticleTitleMarker-based selection of QTL affecting grain and malt quality in two-row barley Crop Sci. 40 1426–1433
K Ishimaru (2003) ArticleTitleIdentification of a locus increasing rice yield and physiological analysis of its function Plant Physiol. 133 1083–1090 Occurrence Handle10.1104/pp.103.027607 Occurrence Handle14576284
AM Ismail AE Hall TJ Close (1999) ArticleTitleAllelic variation of a dehydrin gene co-segregates with chilling tolerance during seedling emergence Proc. Natl. Acad. Sci. USA 96 13566–13570 Occurrence Handle10.1073/pnas.96.23.13566 Occurrence Handle10557361
KR Jaglo-Ottosen SJ Gilmour DG Zarka O Schabenberger MF Thomashow (1998) ArticleTitleArabidopsis CBF1 overexpression induces COR genes and enhances freezing tolerance Science 280 104–106 Occurrence Handle10.1126/science.280.5360.104 Occurrence Handle9525853
N Jannoo L Grivet A Dookum A D’Hont JC Glaszmann (1999) ArticleTitleLinkage disequilibrium among modern sugarcane cultivars Theor. Appl. Genet. 99 1053–1060 Occurrence Handle10.1007/s001220051414
J-S Jeon D Chen G-H Yi GL Wang PC Ronald (2003) ArticleTitleGenetic and physical mapping of Pi5(t), a locus associated with broad-spectrum resistance to rice blast Mol. Gen. Genom. 269 280–289
C Jiang Z-B Zeng (1995) ArticleTitleMultiple trait analysis of genetic mapping for quantitative trait loci Genetics 140 1111–1127 Occurrence Handle7672582
GJ King S Tartarini L Brown F Gennari S Sansavini (1999) ArticleTitleIntrogression of the Vf source of scab resistance and distribution of linked marker alleles within the Malus gene pool Theor. Appl. Genet. 99 1039–1046 Occurrence Handle10.1007/s001220051412
FJ Kloppers ZA Pretorius (1997) ArticleTitleEffects of combinations amongst genes Lr13, Lr34 and Lr37 on components of resistance in wheat to leaf rust Plant Pathol. 46 737–750 Occurrence Handle10.1046/j.1365-3059.1997.d01-58.x
SJ Knapp (1998) ArticleTitleMarker-assisted selection as a strategy for increasing the probability of selecting superior genotypes Crop Sci 38 1164–1174
JA Kolmer (1996) ArticleTitleGenetics of resistance to wheat leaf rust Annu. Rev. Phytopathol. 34 435–455 Occurrence Handle10.1146/annurev.phyto.34.1.435 Occurrence Handle15012551
T Kraft M Hansen NO Nilsson (2000) ArticleTitleLinkage disequilibrium and fingerprinting in sugar beet Theor. Appl. Genet. 101 323–326 Occurrence Handle10.1007/s001220051486
R Lande R Thompson (1990) ArticleTitleEfficiency of marker-assisted selection in the improvement of quantitative traits Genetics 124 743–756 Occurrence Handle1968875
L Lecomte P Duffè M Buret B Servin F Hospital M Causse (2004) ArticleTitleMarker-assisted introgression of five QTLs controlling fruit quality traits into three tomato lines revealed interactions between QTLs and genetic backgrounds Theor. Appl. Genet. 109 658–668 Occurrence Handle10.1007/s00122-004-1674-0 Occurrence Handle15112037
KS Lee WY Choi JC Ko TS Kim GB Gregorio (2003) ArticleTitleSalinity tolerance of japonica and indica rice (Oryza sativa L.) at the seedling stage Planta 216 1043–1046 Occurrence Handle12687373
D Leister J Kurth DA Laurie M Yano T Sasaki A Graner P Schulze-Lefert (1999) ArticleTitleRFLP- and physical mapping of resistance gene homologues in rice (O. sativa) and barley (H. vulgare) Theor. Appl. Genet. 98 509–520 Occurrence Handle10.1007/s001220051099
JM Lilley MM Ludlow SR McCouch JC O’Toole (1996) ArticleTitleLocating QTL for osmotic adjustment and deydration tolerance in rice J. Exp. Bot. 47 1427–1436
HX Lin MZ Zhu M Yano JP Gao ZW Liang WA Su XH Hu ZH Ren DY Chao (2004) ArticleTitleQTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance Theor. Appl. Genet. 108 253–260 Occurrence Handle10.1007/s00122-003-1421-y Occurrence Handle14513218
JP Liu J Van Eck B Cong SD Tanksley (2002) ArticleTitleA new class of regulatory genes underlying the cause of pear-shaped tomato fruit Proc. Natl. Acad. Sci. USA 99 13302–13306 Occurrence Handle10.1073/pnas.162485999 Occurrence Handle12242331
S Liu CA Griffey MA Shagai Maroof (2001) ArticleTitleIdentification of molecular markers associated with adult plant resistance to powdey mildew in common wheat cultivar Massey Crop Sci. 41 1268–1275
KD Livingstone VK Lackney JR Blauth R Wijk Particlevan MK Jahn (1999) ArticleTitleGenome mapping in Capsicumand the evolution of genome structure in the Solanaceae Genetics 152 1183–1202 Occurrence Handle10388833
Z-X Lu K Sossey-Alaoui GL Reighard WMV Baird AG Abbot (1999) ArticleTitleDevelopment and characterization of a codominat marker linked to root-knot nematode resistance, and its application to peach rootstock breeding Theor. Appl. Genet. 99 115–122 Occurrence Handle10.1007/s001220051215
W Ma W Zhang KR Gale (2003) ArticleTitleMultiplex-PCR typing of high molecular weight glutenin alleles in wheat Euphytica 134 51–60 Occurrence Handle10.1023/A:1026191918704
ZQ Ma JB Wei SH Cheng (2004) ArticleTitlePCR-based markers for the powdery mildew resistance gene Pm4a in wheat Theor. Appl. Genet. 109 140–145 Occurrence Handle10.1007/s00122-004-1605-0 Occurrence Handle14985977
LH Madsen NC Collins M Rakwalska G Backes N Sandal L Krusell J Jensen EH Waterman A Jahoor M Ayliffe AJ Pryor P Langridge P Schulze-Lefert J Stougaard (2003) ArticleTitleBarley disease resistance gene analogs of the NBS-LRR class: identification and mapping Mol. Gen. Genomics 269 150–161
R Mago W Spielmeyer GJ Lawrence ES Lagudah JG Ellis A ·Pryor (2002) ArticleTitleIdentification and mapping of molecular markers linked to rust resistance genes located on chromosome 1RS of rye using wheat-rye translocation lines Theor. Appl. Genet. 104 1317–1324 Occurrence Handle10.1007/s00122-002-0879-3 Occurrence Handle12582587
O Merah E Deléens B Teulat P Monneveux (2001) ArticleTitleProductivity and carbon isotope discrimination of different durum wheat organs under Mediterranean conditions CR Acad. Sci. Paris, Science de la vie, Série III 324 51–57
R Michelmore (2000) ArticleTitleGenomic approaches to plant disease resistance Curr. Opin. Plant Biol. 3 125–131 Occurrence Handle10.1016/S1369-5266(99)00050-3 Occurrence Handle10712954
RW Michelmore (2003) ArticleTitleThe impact zone: genomics and breeding for durable disease resistance Curr. Opin. Plant Biol. 6 397–404 Occurrence Handle10.1016/S1369-5266(03)00067-0 Occurrence Handle12873536
RW Michelmore I Paran RV Kesseli (1991) ArticleTitleIdentification of markers linked to disease-resistance gene by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations Proc. Natl. Acad. Sci. USA 88 9828–9832 Occurrence Handle1682921
G Miftahudin J Scoles JP Gustafson (2002) ArticleTitleAFLP markers tightly linked to the aluminium tolerance gene Alt3 in rye (Secale cereale L.) Theor. Appl. Genet. 104 626–631 Occurrence Handle10.1007/s00122-001-0782-3
M Mohan S Nair A Bhagwat TG Krishna M Yano CR Bhatia T Sasaki (1997) ArticleTitleGenome mapping, molecular markers and marker-assisted selection in crop plants Mol. Breed. 3 87–103 Occurrence Handle10.1023/A:1009651919792
JM Morgan MK Tan (1996) ArticleTitleChromosomal location of a wheat osmoregulation gene using RFLP analysis Aust. J. Plant Physiol. 23 803–806
M Morgante F Salamini (2003) ArticleTitleFrom plant genomics to breeding practice Curr. Opin. Biotechnol. 14 214–219 Occurrence Handle10.1016/S0958-1669(03)00028-4 Occurrence Handle12732323
M Morgante M Hanafey W Powell (2002) ArticleTitleMicrosatellites are preferentially associated with nonrepetitive DNA in plant genomes Nat. Genet. 30 194–200 Occurrence Handle10.1038/ng822 Occurrence Handle11799393
H Murai Z Hashimoto PN Sharma T Shimizu K Murata S Takumi N Mori S Kawasaki C Nakamura (2001) ArticleTitleConstruction of a high-resolution linkage map of a rice brown planthopper (Nilaparvata lugens Stal) resistance gene bph2 Theor. Appl. Genet. 103 526–532 Occurrence Handle10.1007/s001220100598
SK Naess JM Bradeen SM Wielgus GT Haberlach JM McGrath JP Helgeson (2000) ArticleTitleResistance to late blight in Solanum bulbocastaneum is mapped to chromosome 8 Theor. Appl. Genet. 101 697–704 Occurrence Handle10.1007/s001220051533
BD Nguyen DS Brar BC Bui TV Nguyen LN Pham HT Nguyen (2003) ArticleTitleIdentification and mapping of the QTL for aluminium tolerance introgressed from the new source, Oryza rufipogonGriff., into indica rice (Oryza sativa L.) Theor. Appl. Genet. 106 583–593 Occurrence Handle12595985
TTT Nguyen N Klueva V Chamareck A Aarti G Magpantay ACM Millena MS Pathan HT Nguyen (2004) ArticleTitleSaturation mapping of QTLs regions and identification of putative candidate genes for drought resistance in rice Mol. Gen. Genomics 272 35–46 Occurrence Handle10.1007/s00438-004-1025-5
M Nordborg S Tavarè (2002) ArticleTitleLinkage disequilibrium: what history has to tell us Trends Genet. 18 83–90 Occurrence Handle11818140
KM Olsen SS Halldorsdottir JR Stinchombe C Weinig J Schmitt MD Purugganan (2004) ArticleTitleLinkage disequilibrium mapping of Arabidopsis CRY2 flowering time alleles Genetics 167 1361–1369 Occurrence Handle10.1534/genetics.103.024950 Occurrence Handle15280248
Q Pan J Wendel R Fluhr (2000) ArticleTitleDivergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes J. Mol. Evol. 50 203–213 Occurrence Handle10754062
AH Paterson JE Bowers MD Burow X Draye CG Elsik C-X Jang CS Katsar T-H Lan Y-R Lin R Ming RJ Wright (2000) ArticleTitlegenomics of plant chromosomes Plant Cell 12 1523–1539 Occurrence Handle11006329
AH Paterson Y Saranga M Menz CX Jiang RJ Wright (2003) ArticleTitleQTL analysis of genotype × environment interactions affecting cotton fiber quality Theor. Appl. Genet. 106 384–396 Occurrence Handle12589538
J Pauquet A Bouquet P This A-F Adam-Blondon (2001) ArticleTitleEstablishment of a local map of AFLP markers around the powdery mildew resistance gene Run1 in grapevine and assessment of their usefulness for marker assisted selection Theor. Appl. Genet. 103 1201–1210 Occurrence Handle10.1007/s001220100664
JD Peleman JR Voort Particlevan der (2003) ArticleTitleBreeding by design Trends Plant Sci. 8 330–334 Occurrence Handle10.1016/S1360-1385(03)00134-1 Occurrence Handle12878017
DW Podlich CR Winkler M Cooper (2004) ArticleTitleMapping as you go: an effective approach for marker-assisted selection of complex traits Crop Sci. 44 1560–1571
N Radovanovic S Cloutier (2003) ArticleTitleGene-assisted selection for high molecular weight glutenin subunits in wheat doubled haploid breeding programs Mol. Breed. 12 51–59 Occurrence Handle10.1023/A:1025484523771
JA Rafalski (2002) ArticleTitleApplications of single nucleotide polymorphisms in crop genetics Curr. Opin. Plant Biol. 5 94–100 Occurrence Handle10.1016/S1369-5266(02)00240-6 Occurrence Handle11856602
H Raman A Karakousis JS Moroni R Raman BJ Read DF Garvin LV Kochian ME Sorrels (2003) ArticleTitleDevelopment and allele diversity of microsatellite markers linked to the aluminium toloerance gene Alp in barley Aust. J. Agric. Res. 54 1315–1321 Occurrence Handle10.1071/AR02226
JM Ribaut J Betran (1999) ArticleTitleSingle large-scale marker-assisted selection (SLS-MAS) Mol. Breed. 5 531–541 Occurrence Handle10.1023/A:1009631718036
JM Ribaut C Jiang D Gonzales-de Leon GO Edmeades DA Hoisington (1997) ArticleTitleIdentification of quantitative trait loci under drought conditions in tropical maize 2-yield components and marker-assisted selection strategies Theor. Appl. Genet. 94 887–896 Occurrence Handle10.1007/s001220050492
RA Richards (1996) ArticleTitleDefining selection criteria to improve yield under drought Plant Growth Regul. 20 157–166 Occurrence Handle10.1007/BF00024012
CR Riede JA Anderson (1996) ArticleTitleLinkage of RFLP markers to an aluminum tolerance gene in wheat Crop Sci. 36 905–909
M Robert MAL West S Inai A Caines L Arntzen JK Smith DA St. Clair (2001) ArticleTitleMarker-assisted introgression of blackmold resistance QTL alleles from wild Lycopersicon cheesmanii to cultivated tomato (L. esculentum) and evaluation of QTL phenotypic effects Mol. Breed. 8 217–233 Occurrence Handle10.1023/A:1013734024200
S Robin MS Pathan B Courtois R Lafitte S Carandang S Lanceras M Amante HT Nguyen Z Li (2003) ArticleTitleMapping osmotic adjustment in an advanced back-cross inbred population of rice Theor. Appl. Genet. 107 1288–1296 Occurrence Handle10.1007/s00122-003-1360-7 Occurrence Handle12920518
K Saito Y Hayano-Saito W Maruyama-Funatsuki Y Sato A Kato (2004) ArticleTitlePhysical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice Theor. Appl. Genet. 109 515–522 Occurrence Handle10.1007/s00122-004-1667-z Occurrence Handle15114474
AC Sanchez PK Subudhi DT Rosenow HT Nguyen (2002) ArticleTitleMapping QTLs associated with drought resistance in sorghum (Sorghum bicolor L.Moench) Plant Mol. Biol. 48 713–726 Occurrence Handle10.1023/A:1014894130270 Occurrence Handle11999845
N Sardesai A Kumar KR Rajyashri S Nair M Mohan (2002) ArticleTitleIdentification of an AFLP marker linked to Gm7, a gall midge resistance gene and its conversion to a SCAR marker for its utility in marker aided selection in rice Theor. Appl. Genet. 105 691–698 Occurrence Handle10.1007/s00122-002-1035-9 Occurrence Handle12582482
Schmierer DA, Kandemir N, Kudrna DA, Jones BL, Ullrich SE,Kleinhofs A (2004) Molecular marker-assisted selection for enhanced yield in malting barley. Mol. Breed. Published on line.
KA Schneider ME Brothers JD Kelly (1997) ArticleTitleMarker-assisted selection to improve drought resistance in common bean Crop Sci. 37 51–60
EM Septiningsih Septiningsih KR Trijatmiko S Moeljopawiro SR McCouch (2003) ArticleTitleIdentification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon Theor. Appl. Genet. 107 1419–1432 Occurrence Handle10.1007/s00122-003-1373-2 Occurrence Handle14513215
R Seyfarth C Feuillet G Schachermayr M Winzeler B Keller (1999) ArticleTitleDevelopment of molecular marker for the adult plant leaf rust resistance gene Lr35 in wheat Theor. Appl. Genet. 99 554–560 Occurrence Handle10.1007/s001220051268
L Shen B Courtois KL McNally S Robin Z Li (2001) ArticleTitleEvaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection Theor. Appl. Genet. 103 75–83 Occurrence Handle10.1007/s001220100538
RP Singh A Mujeeb-Kazi J Huerta-Espino (1998) ArticleTitleLr46: a gene conferring slow-rusting resistance to leaf rust in wheat Phytopathology 88 890–894
S Singh JS Sidhu N Huang Y Vikal Z Li DS Brar HS Dhaliwal GS Khush (2001) ArticleTitlePyramiding three bacterial blight resistance genes (xa5, xa13 and Xa21) using marker-assisted selection into indica rice cultivar PR106 Theor. Appl. Genet. 102 1011–1015 Occurrence Handle10.1007/s001220000495
PH Smith RMD Koebner LA Boyd (2002) ArticleTitleThe development of a STS marker linked to a yellow rust resistance derived from the wheat cultivar Moro Theor. Appl. Genet. 104 1278–1282 Occurrence Handle10.1007/s00122-002-0895-3 Occurrence Handle12582581
J Song JM Bradeen SK Naess JA Raasch SM Wielgus GT Halberlach J Liu H Kuang S Austin-Phillips CR Buell JP Hengelson J Jang (2003) ArticleTitleGene RB cloned from Solanum bulbocastaneum confers broad spectrum resistance to potato late blight Proc. Natl. Acad. Sci USA 100 9128–9133 Occurrence Handle10.1073/pnas.1533501100 Occurrence Handle12872003
CW Stuber (1994) ArticleTitleSuccess in the use of molecular markers for yield enhancement in corn.Proc. 49th Annual Corn and Sorghum Industry Res.Conf. American Seed Trade Assoc. 49 232–238
CW Stuber SE Lincoln DW Wolff T Helentjaris ES Lander (1992) ArticleTitleIdentification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers Genetics 132 823–839 Occurrence Handle1468633
CW Stuber M Polacco Senior Lynn M (1999) ArticleTitleSynergy of empirical breeding, marker-assisted selection, and genomics to increase crop yield potential Crop Sci. 39 1571–1583
K Suenaga RP Singh J Huerta-Espino HM William (2003) ArticleTitleMicrosatellite markers for genes Lr34/Yr18 and other quantitative loci for leaf rust and stripe rust resistance in bread wheat Phytopathology 93 881–890
BE Tabashnik (2001) ArticleTitleBreaking the code of resistance.Two reports shed light on the molecular basis of resistance to Bt toxins Nat. Biotechnol. 19 922–924 Occurrence Handle10.1038/nbt1001-922 Occurrence Handle11581654
Y Tang ME Sorrels LV Kochian DF Garvin (2000) ArticleTitleIdentification of RFLP markers linked to barley aluminum tolerance gene Alp Crop Sci. 40 778–782
SD Tanksley JC Nelson (1996) ArticleTitleAdvanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines Theor. Appl. Genet. 92 191–203 Occurrence Handle10.1007/s001220050114
SD Tanksley MW Ganal GB Martin (1995) ArticleTitleChromosome landing: a paradigm for map-based gene cloning in plants with large genomes Trends Genet. 11 63–68 Occurrence Handle10.1016/S0168-9525(00)88999-4 Occurrence Handle7716809
S Tartarini L Gianfranceschi S Sansavini C Gessler (1999) ArticleTitleDevelopment of reliable PCR markers for the selection of the Vf gene conferring scab resistance in apple Plant Breed. 118 183–186 Occurrence Handle10.1046/j.1439-0523.1999.118002183.x
B Teulat O Merah X Sirault C Borries R Waugh D This (2002) ArticleTitleQTLs for grain carbon isotope discrimination in field-grown barley Theor. Appl. Genet. 106 118–126 Occurrence Handle12582879
B Teulat N Zoumarou-Wallis B Rotter M Ben Salem H Bahri D This (2003) ArticleTitleQTL for relative water content in field-grown barleys and their stability across Mediterranean environments Thoer. Appl. Genet. 108 181–188 Occurrence Handle10.1007/s00122-003-1417-7
InstitutionalAuthorNameThe Arabidopsis Genome Initiative (2000) ArticleTitleAnalysis of the genome of the flowering plant Arabidopsis thaliana Nature 408 796–815
MJ Thomson TH Tai AM McClung ME Hinga KB Lobos Y Xu C Martinez SR McCouch (2003) ArticleTitleMapping 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 Occurrence Handle12736777
JM Thornsberry MM Goodman J Doebley S Kresovich D Nielsen ES Buckler SuffixIV (2001) ArticleTitleDwarf8 polymorphisms associate with variation in flowering time Nat. Genet. 28 286–289 Occurrence Handle10.1038/90135 Occurrence Handle11431702
Tóth B, Francia E, Rizza F, Stanca AM, Galiba G, Pecchioni N (2004) Development of PCR-based markers on chromosome 5H for assisted selection of frost-tolerant genotypes in barley. Mol. Breed. Published on line.
NC Turner (1997) ArticleTitleFurther progress in crop water relations Adv. Agron. 58 293–338
A Vagujfalvi G Galiba L Cattivelli J Dubcovsky (2003) ArticleTitleThe cold-regulated transcriptional activator Cbf3 is linked to the frost-tolerance locus Fr-A2 on wheat chromosome 5A Mol. Genet. Genom. 269 60–67
D Wang GL Graef AM Procopiuk BW Diers (2004) ArticleTitleIdentification of putative QTL that underlie yield in interspecific soybean backcross populations Theor. Appl. Genet. 108 458–467 Occurrence Handle14504749
JS Weerasena BJ Steffenson AB Falk (2004) ArticleTitleConversion of an amplified fragment lenght polymorphism marker into a co-dominant marker in the mapping of the Rph15 gene conferring resistance to barley leaf rust, Puccinia hordei Otth Theor. Appl. Genet. 108 712–719 Occurrence Handle10.1007/s00122-003-1470-2 Occurrence Handle14523515
F Wei RA Wing RP Wise (2002) ArticleTitleGenome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley Plant Cell 14 1903–1917 Occurrence Handle12172030
K Werner W Friedt E Laubach R Waugh F Ordon (2003) ArticleTitleDissection of resistance to soil-borne yellow-mosaic-inducing viruses of barley (BaMMV, BaYMV, BAYMV-2) in a complex breeders’ cross by means of SSR and simultaneous mapping of BaYMV/BaYMV-2 resistance of var.“Chikurin Ibaraki 1” Theor. Appl. Genet. 106 1425–1432 Occurrence Handle12750785
KJ Williams (2003) ArticleTitleThe molecular genetics of disease resistance in barley Aust. J. Agric. Res. 54 1065–1079 Occurrence Handle10.1071/AR02219
VM Williamson J-Y Ho FF Wu N Miller I Kaloshian (1994) ArticleTitleA PCR-based marker tightly linked to the nematode resistance gene, Mi, in tomato Theor. Appl. Genet. 87 757–763 Occurrence Handle10.1007/BF00221126
JC Wittaker RN Curnow CS Haley R Thompson (1995) ArticleTitlemarker-maps in marker-assisted selection Genet. Res. 66 255–265 Occurrence Handle8600020
DJ Wolyn JO Borevitz O Loudet C Scwartz J Maloof JR Ecker CC Berry J Chory (2004) ArticleTitleLight-response quantitative trait loci identified by composite interval mapping and eXtreme array mapping in Arabidopsis thaliana Genetics 167 907–917 Occurrence Handle10.1534/genetics.103.024810 Occurrence Handle15238539
J Wu T Maehara T Shimokawa S Yamamoto C Harada Y Takazaki N Ono Y Mukai K Koike J Yazaki F Fujii A Shomura T Ando I Kono K Waki K Yamamoto M Yano T Matsumoto T Sasaki (2002) ArticleTitleA comprehensive rice transcript map containing 6591 expressed sequence tag sites Plant Cell 14 525–535 Occurrence Handle10.1105/tpc.010274 Occurrence Handle11910001
J Xu T Narabu T Mizukubo T Hibi (2001) ArticleTitleA molecular marker correlated with selected virulence against the tomato resistance gene Mi in Meloidogyne incognita , M. javanica and M. arenaria Phytopathology 91 377–382
J Yaghoobi I Kaloshian Y Wen VM Williamson (1995) ArticleTitleMapping a new nematode resistance locus in Lycopersicon peruvianum Theor. Appl. Genet. 91 457–464 Occurrence Handle10.1007/BF00222973
X Yin P Stam MJ Kropff HCM Schapendonk (2003) ArticleTitleCrop modeling, QTL mapping, and their complementary role in plant breeding Agron. J 95 90–98
ND Young (1999) ArticleTitleA cautiously optimistic vision for marker-assisted breeding Mol. Breed. 5 505–510 Occurrence Handle10.1023/A:1009684409326
GG Yousef JA Juvik (2001) ArticleTitleComparison of phenotypic and marker-assisted selection for quantitative traits in sweet corn. Crop Sci. 41 645–655
Z Zhang J Xu Q Xu P Larkin Z Xin (2004) ArticleTitleDevlopment of novel PCR markers linked to the BYDV resistance gene Bdv2 useful in wheat for marker-assisted selection Theor. Appl. Genet. 109 433–439 Occurrence Handle10.1007/s00122-004-1649-1 Occurrence Handle15067508
J Zhang HG Zheng A Aarti G Pantuwan TT Nguyen JN Tripathy AK Sarial S Robin RC Babu BD Nguyen S Sarkarung A Blum HT Nguyen (2001) ArticleTitleLocating genomic regions associated with components of drought resistance in rice: Comparative mapping within and across species Theor. Appl. Genet. 103 19–29 Occurrence Handle10.1007/s001220000534
JX Zhang HT Nguyen A Blum (1999) ArticleTitleGenetic analysis of osmotic adjustment in crop plants J. Exp. Bot. 50 291–302 Occurrence Handle10.1093/jexbot/50.332.291
TZ Zhang YL Yuan J Yu WZ Guo RJ Kohel (2003) ArticleTitleMolecular tagging of a major QTL for fiber strength in Upland cotton and its marker-assisted selection Theor. Appl. Genet. 106 262–268 Occurrence Handle12582851
BS Zheng L Yang WP Zhang CZ Mao YR Wu KK Yi FY Liu P Wu (2003) ArticleTitleMapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations Theor. Appl. Genet. 107 1505–1515 Occurrence Handle10.1007/s00122-003-1390-1 Occurrence Handle12920516
F Zhou J Kurth F Wei C Elliot G Valè N Yahiaoui B Keller S Somerville R Wise P Schulze-Lefert (2001) ArticleTitleCell-autonomous expression of barley Mla1 confers race-specific resistance to the powdery mildew fungus via a Rar1-independent signaling pathway Plant Cell 13 337–350 Occurrence Handle10.1105/tpc.13.2.337 Occurrence Handle11226189
PH Zhou YF Tan YQ He CG Xu Q Zhang (2003) ArticleTitleSimultaneous improvement for four quality traits of Zhenshan 97, an elite parent of hybrid rice, by molecular marker-assisted selection Theor. Appl. Genet. 106 326–331 Occurrence Handle12582859
YL Zhu QJ Song DL Hyten CP Van Tassel LK Matukumalli DR Grimm SM Hyatt EW Fickus ND Young PB Cregan (2003) ArticleTitleSingle nucleotide polymorphisms (SNPs) in soybean Genetics 163 1123–1134 Occurrence Handle12663549
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Francia, E., Tacconi, G., Crosatti, C. et al. Marker assisted selection in crop plants. Plant Cell Tiss Organ Cult 82, 317–342 (2005). https://doi.org/10.1007/s11240-005-2387-z
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DOI: https://doi.org/10.1007/s11240-005-2387-z