Abstract
The advent of molecular markers (particularly RFLP- and PCR-derived) for use as probes for genomic DNA has revolutionized the genetic analysis of crop plants and provided not only geneticists, but also physiologists, agronomists and breeders with valuable new tools to identify traits of importance in improving resistance to abiotic stresses. For the breeder, a genetic map saturated with molecular markers allows selection for certain characters to be carried out much more efficiently and effectively than was possible previously. Two areas of molecular marker technology that are proving particularly useful in identifying traits of value for stress resistance and introducing them into improved varieties are in situ hybridization with fluorescent-labelled molecular probes and quantitative trait locus (QTL) analysis with either radioactively- or cold-labelled probes. Fluorescence in situ hybridization (FISH) takes out much of the cytological tedium previously associated with monitoring the introgression of chromosomes and DNA fragments from one species to another. Labelled DNA can be prepared that is specific to a particular species and used to visualize in chromosome preparations the presence of chromosomes or chromosomal fragments from that species amongst the recipient's chromosomes. This is being used to help transfer genes for drought resistance and salt tolerance from alien species into Graminaceous crops. DNA probes showing polymorphism between the donor and recipient species can also be used to monitor the incorporation of alien genes from chromosome addition lines into the recipient species. High density molecular maps allow the location of all major genes regulating the expression of a particular trait to be determined. Statistical methods have been developed to allow QTL for the trait to be identified. Not only does this allow the complexity of genetic control of any trait to be determined, but by comparing the extent to which confidence intervals of QTL for different traits overlap it is possible to examine the likelihood that traits are pleiotropically linked. Thus, the traits most likely to be important in determining yield under droughted conditions can be identified. Examples are given of traits that could be incorporated into breeding programmes to improve drought resistance using techniques of marker-assisted selection.
Similar content being viewed by others
References
Abbo S, Dunford RP, Miller TE, Reader SM and King IP (1993) Primer-mediated in situ detection of the B-hordein gene cluster on barley chromosome 1H. Proc Natl Acad Sci USA 90: 11821–11824
Ahn S and Tanksley SD (1993) Comparative linkage maps of the rice and maize genomes. Proc Natl Acad Sci USA 90: 7980–7984
Alonso-Blanco C, Pendás AM, Garcia-Suarez R, Roca A, Goicoechea PG and Giraldez R (1995) Physical mapping of 5S rDNA reveals a new locus on 3R and unexpected complexity in a rye translocation used in chromosome mapping. Chromosoma 103: 331–337
Austin RB (1994) Plant breeding opportunities. In: Physiology and Determination of Crop Yield, pp 567–585. Madison, WI, USA: American Society of Agronomy, Crop Science Society of America, Soil Science Society of America
Austin RB, Morgan CL, Ford MA, Roscoe TJ and Miller TE (1988) Increasing the photosynthetic capacity of wheat by incorporating genes from A genome diploid species. In: Proc. Seventh International Wheat Genetics Symposium, pp 203–208. Cambridge, UK. 13–19 July, 1988
Beavis WD, Smith OS, Drant D and Fincher R (1994) Identification of quantitative trait loci using a small sample of topcrossed and F4 progeny from maize. Crop Sci 34: 882–896
Blum A (1988) Plant Breeding for Stress Environments. Boca Raton, FL, USA: CRC Press
Bolaños J and Edmeades GO (1991) Value of selection for osmotic potential in tropical maize. Agron J 83: 948–956
Camussi A, Sari-Gorla M, Villa M, Greco R and Stefanini FM (1994) Effect of microclimate variations on the estimate of relationships between RFLP markers and low heritability traits in maize. Maydica 39: 127–132
Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, Second G, McCouch SR, Tanksley SD (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138: 1251–1274
Champoux MC, Wang G, Sarkarung S, Mackill DJ, O'Toole JC, Huang N and McCouch SR (1995) Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers. Theor Appl Genet 90: 969–981
Chinoy CN, Koebner RMD, Mills ENC and Morgan MRA (1995) Monoclonal antibodies: A novel source of genetic markers. In: Proc. Eighth International Wheat Genetics Symposium, pp 573–576. Beijing, China. 20–25 July, 1993
Cho YG, Eun MY, McCouch SR and Chae YA (1994) The semidwarf gene, sd-1, of rice (Oryza sativa L.). II. Molecular mapping and marker-assisted selection. Theor Appl Genet 89: 54–59
Curtis CA and Lukaszewski AJ (1991) Genetic linkage between C-bands and storage protein genes in chromosome 1B of tetraploid wheat. Theor Appl Genet 81: 245–252
Delaney DE, Friebe BR, Hatchett JH, Gill BS and Hulbert SH (1995) Targeted mapping of a hessian fly resistance gene from rye by representational difference analysis. Abstracts of Plant Genome III, San Diego, January, 1995, p 33
D'Ovidio R, Tanzarella OA, Cenci A, Iacono E and Porceddu E (1994) RFLP analysis in wheat. Isolation and chromosomal assignment of digoxigenin-labelled clones. J Genet Breed 48: 73–80
Edmeades GO, Bolaños J and Lafitte HR (1993) Progress in breeding for drought tolerance in maize. In: Proceedings of the 47th Annual Corn and Sorghum Conference, pp 93–111. 1992
Edwards MD, Stuber CW and Wendel JF (1987) Molecular-marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics 116: 113–125
Ehdaie B, Barnhart D and Waines JG (1993) Genetic analysis of transpiration efficiency, carbon isotope discrimination, and growth characters in bread wheat. In: Ehleringer JR, Hall AE and Farquhar GD (eds) Stable Isotopes and Plant Carbon-water Relations, pp 419–434. San Diego, USA: Academic Press
Farquhar GD and Richards RA (1984) Isotopic composition of plant carbon correlates with water-use efficiency of wheat genotypes. Aust J Plant Physiol 11: 539–552
Fedak G (1980) Production, morphology and meiosis of reciprocal barley-wheat hybrids. Can J Genet Cytol 22: 117–123
Fernández-Calvin B, Benavente E and Orellana J (1995) Meiotic pairing in wheat-rye derivatives detected by genomic in situ hybridization and C-banding — A comparative analysis. Chromosoma 103: 554–558
Fuchs J and Schubert I (1995) Localization of seed protein genes on metaphase chromosomes of Vicia faba via fluorescence in situ hybridization. Chromosome Res 3: 94–100
Gale MD, Atkinson MD, Chinoy CN, Harcourt RL, Jia J, Li QY and Devos KM (1995) Genetic maps of hexaploid wheat. In: Proc. Eighth International Wheat Genetics Symposium, pp 29–40. Beijing, China. 20–25 July, 1993
Gale MD and Miller TE (1987) The introduction of alien genetic variation in wheat. In: Lupton FGH (ed) Wheat Breeding. Its Scientific Basis, pp 173–210. London, New York: Chapman and Hall
Gall JG and Pardue ML (1969) Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci USA 63: 378–383
Gallais A and Rives M (1993) Detection, number and effects of QTLs for a complex character. Agronomie 13: 723–738
Gimelfarb A and Lande R (1994) Simulation of marker assisted selection for non-additive traits. Genet Res, Camb 64: 127–136
Giovannoni JJ, Wing RA, Ganal MW and Tanksley SD (1991) Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations. Nucl Acids Res 19: 6553–6558
Handley LL, Nevo E, Raven JA, Martinez-Carrasco R, Scrimgeour CM, Pakniyat H and Forster BP (1994) Chromosome 4 controls potential water use efficiency (δ13C) in barley. J Exp Bot 45: 1661–1663
Heslop-Harrison JS (1991) The molecular cytogenetics of plants. J Cell Sci 100, 15–21
Humphreys MW and Thomas H (1993) Improved drought resistance in introgression lines derived from Lolium multiflorum × Festuca arundinacea hybrids. Plant Breed 111: 155–161
Humphreys MW, Thomas HM, Morgan WG, Meredith MR, Harper JA, Thomas H, Zwierzykowski Z and Ghesquière M (1995) Discriminating the ancestral progenitors of hexaploid Festuca arundinacea using genomic in situ hybridization. Heredity 75: 171–174
Jansen RC (1994) Controlling the Type I and Type II errors in mapping quantitative trait loci. Genetics 138: 871–881
Jansen RC and Stam P (1994) High resolution of quantitative traits into multiple loci via interval mapping. Genetics 136: 1447–1455
Jiang J and Gill BS (1994) Nonisotopic in situ hybridization and plant genome mapping: the first 10 years. Genome 37: 717–725
Kearsey MJ and Hyne V (1994) QTL analysis: A simple ‘marker regression’ approach. Theor Appl Genet 89: 698–702
King IP, Purdie KA, Orford SE, Reader SM and Miller TE (1993) Detection of homoeologous chiasma formation in Triticum durum × Thinopyrum bessarabicum hybrids using genomic in situ hybridization. Heredity 71: 369–372
Knapp SJ and Bridges WC (1990) Using molecular markers to estimate quantitative trait locus parameters: Power and genetic variances for unreplicated and replicated progeny. Genetics 126: 769–777
Koebner RMD, Devos KM and Gale MD (1994) Advances in the application of genetic markers in plant breeding. Technical Report No. 3. Asian Seed '94 Conference, Chiang Mai, Thailand. 27–29 Sept, 1994, pp 1–13. Asia and Pacific Seed Association
Kurata N, Nagamura Y, Yamamoto K, Harushima Y, Sue N, Wu J, Antonio BA, Shomura A, Shimizu T, Lin S-Y, Inoue T, Fukuda A, Shimano T, Kuboki Y, Totama T, Miyamoto Y, Kirihara T, Hayasaka K, Mitao A, Monna L, Zhong HS, Tamura Y, Wang Z-X, Momma T, Umehara Y, Yano M, Sasaki T and Minobe Y (1994) A 300 kilobase interval genetic map of rice including 883 expressed sequences. Nature Genet 8: 365–372
Lande R and Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124: 743–756
Lander ES and Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185–199
Lebreton C, Lazić-Jančić V, Steed A, Pekić S and Quarrie SA (1995) Identification of QTL for drought responses in maize and their use in testing causal relationships between traits. J Exp Bot 46: 853–865
Lehfer H, Busch W, Martin R and Herrmann RG (1993) Localization of the B-hordein locus on barley chromosomes using fluorescence in situ hybridization. Chromosoma 102: 428–432
Leitch AR and Heslop-Harrison JS (1993) Physical mapping of four sites of 5s rDNA sequences and one site of the α-amylase-2 gene in barley (Hordeum vulgare). Genome 36: 517–523
Leitch AR, Schwarzacher T, Jackson D and Leitch IJ (1994) In situ Hybridization: A Practical Guide. Royal Microscopical Society Microscopy Handbooks 27. Oxford, UK: Bios Scientific Publishers
Liang YL and Richards RA (1994) Coleoptile tiller development is associated with faster early vigour in wheat. Euphytica 80: 119–124
Lilley JM, Ludlow MM, McCouch SR, Champoux MC and O'Toole JC (1996) Locating QTL for osmotic adjustment and dehydration tolerance in rice. J Exp Bot 47 (in press)
Lisitsyn N, Lisitsyn N and Wigler M (1993) Cloning the differences between two complex genomes. Science 259: 946–951
López-Castañeda C, Richards RA and Farquhar GD (1995) Variation in early vigor between wheat and barley. Crop Sci 35: 472–479
Martin B, Nienhuis J, King G and Schaefer A (1989) Restriction fragment length polymorphisms associated with water use efficiency in tomato. Science 243: 1725–1728
Matz EC, Burr FA and Burr B (1994) Molecular map based on T×Cm and Co×Tx recombinant inbred families. Maize Gen Coop Newsl 68: 198–208
Michelmore RW, Paran I and Kesseli RV (1991) Identification of markers linked to disease-resistance genes 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
Miller TE and Koebner RMD (eds) (1988) Seventh International Wheat Genetics Symposium, Volume 2. Cambridge, UK: Institute of Plant Science Research
Miller TE, Reader SM, Purdie KA and King IP (1994) Determination of the frquency of wheat-rye hybrids with and without chromosome 5B. Theor Appl Genet 89: 255–258
Moore G, Devos KM, Wang Z and Gale MD (1995) Grasses, line up and form a circle. Curr Biol 5: 737–739
Morgan JM (1991) A gene controlling differences in osmoregulation in wheat. Aust J Plant Physiol 18: 249–257
Morgan JM (1995) Growth and yield of wheat lines with differing osmoregulative capacity at high soil water deficit in seasons of varying evaporative demand. Field Crops Res 40: 143–152
Mukai Y and Gill BS (1991) Detection of barley chromatin added to wheat by genomic in situ hybridization. Genome 34: 448–452
Nguyen HT, Xu W, Crasta O, Rosenow DT and Mullet JM (1995) Molecular mapping of stay-green and other drought resistance traits in sorghum. In: Proc Interdrought 95, Integrated Study on Drought Tolerance of Higher Plants, pp XI B1-5. Montpellier, France. 31 August–2 September, 1995
Paterson AH, Tanksley SD and Sorrells ME (1991) DNA markers in plant improvement. Adv Agron 46: 39–90
Price AH and Tomos AD (1995) The use of RFLP analysis in the promotion of drought tolerance in upland rice. J Exp Bot (Suppl): 55
Quarrie SA (1991) Implications of genetic differences in ABA accumulation for crop production. In: Davies WJ and Jones HG (eds) Abscisic Acid Physiology and Biochemistry, pp 227–243. Oxford, UK: Bios Scientific Publishers
Quarrie SA, Gulli M, Calestani C, Steed A and Marmiroli N (1994) Location of a gene regulating drought-induced abscisic acid production on the long arm of chromosome 5A of wheat. Theor Appl Genet 89: 794–800
Quarrie SA, Heyl A, Steed A, Lebreton C and Lazić-Jančić V (1996) QTL analysis of stress responses as a method to study the importance of stress-induced genes. In: Leone A and Nover L (eds) Genes and Their Products for Tolerance to Physical Stresses in Plants. ESF Meeting, Maratea, Italy, 24–27 September, 1995: Springer-Verlag (in press)
Quarrie SA, Steed A, Lebreton C, Gulli M, Calestani C and Marmiroli N (1994) QTL analysis of ABA production in wheat and maize and associated physiological traits. Russ J Plant Physiol 41: 565–571
Quarrie SA, Steed A, Semikhodski A, Lebreton C, Calestani C, Clarkson DT, Tuberosa R, Sanguineti MC, Melchiorre R and Prioul J-L (1995) Identification of quantitative trait loci regulating water- and nitrogen-use efficiency in wheat. In: Proceedings of STRESSNET meeting, Salsomaggiore, Sept 1995. European Commission, Luxembourg, pp 175–180
Ragot M, and Hoisington DA (1993) Molecular markers for plant breeding: comparisons of RFLP and RAPD genotyping costs. Theor Appl Genet 86: 975–984
Rayburn AL and Gill BS (1985) Use of biotin-labeled probes to map specific DNA sequences on wheat chromosomes. J Hered 76: 78–81
Reader SM, Miller TE and Purdie KA (1995) Cytological analysis of plant chromosomes using rapid in situ hybridization. Euphytica 85: 275–279
Ribaut J-M, Gonzalez-de-Leon D, Edmeades G, Huerta E and Hoisington D (1995) Changes in allelic frequencies in a tropical maize population under selection for drought tolerance. In: Proc Interdrought 95, Integrated Study on Drought Tolerance of Higher Plants, pp XI A1-7. Montpellier, France. 31 August–2 September, 1995
Ribaut J-M, Hoisington DA, Deutsch JA, Jiang C and Gonzalez-de-Leon D (1996) Identification of quantitative trait loci under drought conditions in tropical maize. 1. Flowering parameters and the anthesis-silking interval. Theor Appl Genet 92: 905–914
Richards RA, López-Castañeda C, Gomez-Macpherson H and Condon AG (1993) Improving the efficiency of water use by plant breeding and molecular biology. Irrig Sci 14: 93–104
Rosenberg M, Przybylska M and Straus D (1994) “RFLP subtraction”: A method for making libraries of polymorphic markers. Proc Natl Acad Sci USA 91: 6113–6117
Sanguineti MC, Tuberosa R, Stefanelli S, Noli E, Blake TK and Hayes PM (1994) Utilization of a recombinant inbred population to localize QTLs for abscisic acid content in leaves of drought-stressed barley (Hordeum vulgare L.). Russ J Plant Physiol 41: 572–576
Schwarzacher T, Anamthawat-Jónsson K, Harrison GE, Islam AKMR, Jia JZ, King IP, Leitch AR, Miller TE, Reader SM, Rogers WJ, Shi M and Heslop-Harrison JS (1992) Genomic in situ hybridization to identify alien chromosomes and chromosome segments in wheat. Theor Appl Genet 84: 778–786
Schwarzacher T, Leitch AR, Bennet MD and Heslop-Harrison JS (1989) In situ localization of parental genomes in a wide hybrid. Ann Bot 64: 315–324
Shepherd KW and Islam AKMR (1988) Fourth compendium of wheat-alien chromosome lines. In: Proc. Seventh International Wheat Genetics Symposium, pp 1373–1398. Cambridge, UK. 13–19 July, 1988
Snape JW, Law CN, Parker BB and Worland AJ (1985) Genetical analysis of chromosome 5A of wheat and its influence on important agronomic traits. Theor Appl Genet 71: 518–526
Soller M, Brody T and Genizi A (1976) On the power of experimental designs for the detection of linkage between marker loci and quantitative loci in crosses between inbred lines. Theor Appl Genet 47: 35–39
Stromberg LD, Dudley JW and Rufener GK (1994) Comparing conventional early generation selection with molecular marker assisted selection in maize. Crop Sci 34: 1221–1225
Tangpremsri T, Fukai S and Fischer KS (1995) Growth and yield of sorghum lines extracted from a population for differences in osmotic adjustment. Aust J Agri Res 46: 61–74
Tanksley SD and Rick CM (1980) Isozyme linkage map of the tomato: applications in genetics and breeding. Theor Appl Genet 57: 161–170
Tanksley SD, Medina-Filho H and Rick CM (1982) Use of naturally-occurring enzyme variation to detect and map genes controlling quantitative traits in an interspecific backcross of tomato. Heredity 49: 11–25
Tanksley SD, Ganal MW and Martin GB (1995) Chromosome landing: A paradigm for map-based gene cloning in plants with large genomes. Trends Genet 11: 63–68
Tauer CG, Hallgren SW and Martin B (1992) Using markeraided selection to improve growth response to abiotic stress. Can J For Res 22: 1018–1030
Thomas H and Evans C (1989) Effects of divergent selection for osmotic adjustment on water relations and growth of plants of Lolium perenne. Ann Bot 64: 581–587
Thomas H, Humphreys MW, Ghesquiere M, Humphreys MO and Mousset C (1995) Introgression of drought resistance in Lolium by introgression from Festuca. In: Proc Interdrought 95, Integrated Study on Drought Tolerance of Higher Plants, pp II A1-5. Montpellier, France. 31 August–2 September, 1995
Thomas HM, Morgan WG, Meredith MR, Humphreys MW, Thomas H and Legget JM (1994) Identification of parental and recombined chromosomes in hybrid derivatives of Lolium multiforum×Festuca pratensis by genomic in situ hybridization. Theor Appl Genet 88: 909–913
VanDeynze AE, Nelson JC, Yglesias ES, Harrington SE, Braga DP, McCouch SR and Sorrels ME (1995) Comparative mapping in grasses. Wheat relationships. Mol Gen Genet 248: 744–754
Virk PS, Ford-Lloyd BV, Jackson MT, Pooni HS, Clemeno TP and Newbury HJ (1996) Predicting quantitative variation within rice germplasm using molecular markers. Heredity 76: 296–304
William MDHM and Mujeeb-Kazi A (1995) Biochemical and molecular diagnosis of Thinopyrum bessarabicum chromosomes in Triticum aestivum germ plasm. Theor Appl Genet 90: 952–956
Wu WR and Li WM (1995) A new approach for mapping quantatitive trait loci using complete genetic marker linkage maps. Theor Appl Genet 89: 535–539
Xu W, Crasta O, Rosenow D, Mullet J and Nguyen H (1995) Major QTLs for post-flowering drought resistance in grain sorghum. Abstracts of Plant Genome III, San Diego, January, 1995, p 22
Zeng Z-B (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457–1468
Zivy M, Prioul JL, Cornic G, Westhoff P, Lacroix B and de Vienne D (1995) Characterizing proteins induced by drought in maize and search for their QTLs. In: Proc Interdrought 95, Integrated Study on Drought Tolerance of Higher Plants, pp XI C1-5. Montpellier, France. 31 August–2 September, 1995
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Quarrie, S.A. New molecular tools to improve the efficiency of breeding for increased drought resistance. Plant Growth Regul 20, 167–178 (1996). https://doi.org/10.1007/BF00024013
Issue Date:
DOI: https://doi.org/10.1007/BF00024013