Abstract
Marker-assisted selection (MAS) is the process of using morphological, biochemical, or DNA markers as indirect selection criteria for selecting agriculturally important traits in crop breeding. This process is used to improve the effectiveness or efficiency of selection for the traits of interest in breeding programs. The significance of MAS as a tool for crop improvement has been extensively investigated in different crop species and for different traits. The use of MAS for manipulating simple/qualitative traits is straightforward and has been well reported. However, MAS for the improvement of complex/polygenic traits, including plant tolerance/resistance to abiotic stresses, is more complicated, although its usefulness has been recognized. With the recent advances in marker technology, including high-throughput genotyping of plants, together with the development of nested association mapping populations, it is expected that the utility of MAS for breeding for stress tolerance traits will increase. In this chapter, we describe the basic procedure for using MAS in crop breeding for salt tolerance.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Flowers TJ (2004) Improving crop salt tolerance. J Exp Bot 55:307–319
Foolad MR (2004) Recent advances in genetics of salt tolerance in tomato. Plant Cell Tissue Organ Cult 76:101–119
Richards RA (1983) Should selection for yield in saline regions be made on saline or non-saline soils. Euphytica 32:431–438
Foolad MR (1999) Comparison of salt tolerance during seed germination and vegetative growth in tomato by QTL mapping. Genome 42:727–734
Foolad MR, Chen FQ, Lin GY (1998) RFLP mapping of QTLs conferring salt tolerance during germination in an interspecific cross of tomato. Theor Appl Genet 97:1133–1144
Greenway H, Munns R (1980) Mechanism of salt tolerance in nonhalophytes. Annu Rev Plant Physiol 31:149–190
Maas EV (1986) Salt tolerance of plants. Appl Agric Res 1:12–26
Forster BP, Russell JR, Ellis RP et al (1997) Locating genotype and genes for abiotic stress tolerance in barley: a strategy using maps, markers and the wild species. New Phytol 137:141–147
Koyama H, Kawamura A, Kihara T et al (2000) Overexpression of mitochondrial citrate synthase in Arabidopsis thaliana improved growth on a phosphorus-limited soil. Plant Cell Physiol 41:1030–1037
Foolad MR, Zhang LP, Lin GY (2001) Identification and validation of QTLs for salt tolerance during vegetative growth in tomato by selective genotyping. Genome 44:444–454
Bonilla P, Dvorak J, Mackill D et al (2002) RLFP and SSLP mapping of salinity tolerance genes in chromosome 1 of rice (Oryza sativa L.) using recombinant inbred lines. Philipp Agric Sci 85:68–76
Takehisa H, Shimodate T, Fukuta Y et al (2004) Identification of quantitative trait loci for plant growth of rice in paddy field flooded with salt water. Field Crops Res 89:85–95
Monforte AJ, Asins MJ, Carbonell EA (1996) Salt tolerance in Lycopersicon species. IV. Efficiency of marker-assisted selection for salt tolerance improvement. Theor Appl Genet 93:765–772
Foolad MR (1997) Genetic basis of physiological traits related to salt tolerance in tomato, Lycopersicon esculentum Mill. Plant Breed 116:53–58
Munns R, Hare RA, James RA et al (2000) Genetic variation for improving the salt tolerance of durum wheat. Aust J Agric Res 51:69–74
Rahman M, Ullah I, Ashraf M et al (2008) Genotypic variation for drought tolerance in cotton. Agron Sustain Dev 28:439–447
Sabouri H, Rezai AM, Moumeni A et al (2009) QTLs mapping of physiological traits related to salt tolerance in young rice seedlings. Biol Plantarum 53:657–662
Siahsar BA, Narouei M (2010) Mapping QTLs of physiological traits associated with salt tolerance in ‘Steptoe’ × ‘Morex’ doubled haploid lines of barley at seedling stage. Food Agric Environ 8:751–759
Doyle JJ, Doyle JL (1990) A rapid total DNA preparation procedure for fresh plant tissue. Focus Cited 12:13–15
Williams JG, Kubelik AR, Livak KJ et al (1990) DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res 18:6531–6535
Saiki RK, Gelfand DH, Stoffel S et al (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491
Saiki RK (1989) The design and optimization of the PCR. In: Erlich HA (ed) PCR technology—principles and applications for DNA amplification. Stockton, New York, pp 7–16
Vos P, Hogers R, Blecker M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucl Acids Res 23:4407–4414
Zhang S, Chen QZ, Lu L et al (2006) Assessment of the variety resistance to Pyricularia grisea and Rhizoctonia solani induced under the natural condition in Hubei Province. J Huazhoung Agric Univ 25:236–240
Zhan AB, Bao ZM, Wang XL et al (2005) Microsatellite markers derived from bay scallop Argopecten irradians expressed sequence tags. Fish Sci 71:1341–1346
Lander G, Barlow A, Lincoln D et al (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181
Semagn K, Bjornstad A, Ndjiondjop MN (2006) An overview of molecular marker methods for plants. Afr J Biotechnol 5:2540–2568
Chakravarti A, Lasher LK, Reefer JE (1991) A maximum likelihood method for estimating genome length using generic linkage data. Genetics 128:183–193
Postlethwait JH, Johnson SL, Midson CN et al (1994) A genetic linkage map for the zebrafish. Science 264:699–703
Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B 363:557–572
Singh RK, Mishra B (1997) Stable genotypes of rice for sodic soils. Indian J Genet 57:431–438
Heggie L, Jansen MAK, Burbridge EM et al (2005) Transgenic tobacco (Nicotiana tabacum L. cv. Samsun-NN) plants over-expressing a synthetic HRP-C gene are altered in growth, development and susceptibility to abiotic stress. Plant Physiol Biochem 43:1067–1073
Riehle MM, Bennett AF, Long AD (2005) Differential patterns of gene expression and gene complement in laboratory-evolved lines of E. coli. Integr Comp Biol 45:532–538
Robbins M (2011) Introduction to inbred backcross (IBC) lines and populations. Plant Breeding and Genomics Home, http://www.extension.org/pages/32448/introduction-to-inbred-backcross-c-lines-and-populations
Khurana P, Chauhan H (2011) Doubled haploid bread wheat engineered for drought tolerance. ISB News Report, http://www.vt.edu
Doerge RW (2002) Multifactorial genetics: mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3:43–52
Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10:156–161
Yu J, Holland JB, McMullen MD et al (2008) Genetic design and statistical power of nested association mapping. Genetics 178:539–551
Hunter RL, Merkert CL (1957) Histochemical demonstration of enzymes separated by zone electrophoresis in starch gels. Science 125:1294–1295
Tanksley SD (1983) Mapping polygenes. Annu Rev Genet 27:205–233
Patra N, Chawla HS (2010) Biochemical and RAPD molecular markers for establishing distinctiveness of basmati rice (Oryza sativa L.) varieties as additional descriptors for plant variety protection. Indian J Biotechnol 9:371–377
Helentjaris T, King G, Slocum M et al (1985) Restriction fragment polymorphisms as probes for plant diversity and their development as tools for applied plant breeding. Plant Mol Biol 5:109–118
Paterson AH, Damon S, Hewitt JD et al (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127:181–197
Mullis K, Faloona F, Scharf S et al (1986) Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol 51:263–273
Foolad MR, Arulsekar S, Rodriguez RL (1995) Applications of PCR to plant genome analysis. In: Gamborg OL, Phillips GC (eds) Plant cell, tissue, and organ culture. Springer, Berlin, pp 281–298
Shinde VM, Dhalwal K, Mahadik KR et al (2007) RAPD analysis for determination of components in herbal medicine. Evid Based Complement Alternat Med 4:21–23
Rahman M, Hussain D, Zafar Y (2002) Estimation of genetic divergence among elite cotton (Gossypium hirsutum L.) cultivars/genotypes by DNA fingerprinting technology. Crop Sci 42:2137–2144
Saunders JA, Mischke S, Hemeida AA (2000) The use of AFLP techniques for DNA fingerprinting in plants. Application Information Beckman Coulter
Oliveira EJ, Padua JG, Zucchi MI et al (2006) Origin, evolution and genome distribution of microsatellites. Genet Mol Biol 29:294–307
Rahman M, Zafar Y, Paterson AH (2009) Gossypium DNA markers types, number and uses. In: Paterson AH (ed) Genomics of cotton. Springer, Dordrecht
Ding X, Zhengtao W, Kaiya Z et al (2003) Allele-specific primers for diagnostic PCR authentication of Dendrobium officinale. Planta Med 69:587–588
Qutob D, Hraber PT, Sobral BW et al (2000) Comparative analysis of expressed sequences in Phytopthora sojae. Plant Physiol 123:243–253
Shaheen T, Rahman M, Zafar Y (2006) Chloroplast RPS8 gene of cotton reveals the conserved nature through out taxa. Pak J Bot 38:1467–1476
Shaheen T, Asif M, Zafar Y et al (2009) Single nucleotide polymorphism analysis of MT-SHSP gene of Gossypium arboreum and its relationship with other diploid cotton genomes G. hirsutum and Arabidopsis thaliana. Pak J Bot 41(1):117–183
Ganal MW, Altmann T, Röder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12:211–217
Yong-Jun S, Yong L, Na-La-Hu W et al (2010) Mining and identification of SNPs from EST sequences in soybean and converting SNP markers into CAPS. Acta Agron Sin 36:574–579
de Souza GA, Softeland T, Koehler CJ et al (2009) Validating divergent ORF annotation of the Mycobacterium leprae genome through a full translation data set and peptide identification by tandem mass spectrometry. Proteomics 9:3233–3243
Jafari-Shabestari J, Corke H, Qualset CO (1995) Field evaluation of tolerance to salinity stress in Iranian hexaploid wheat landrace accessions. Genet Resour Crop Evol 42:147–156
Houshmand S, Arzani A (2005) Evaluation of grain yield and its component under drought stress during grain filling period in durum wheat. In: Proceedings of the 2nd International conference on integrated approaches to sustain and improve plant production under drought stress, Rome, Italy, vol 2, p. 45
Yamaguchi T, Blumwald E (2005) Developing salt-tolerant crop plants: challenges and opportunities. Trends Plant Sci 10:615–620
Singh RK, Flowers TJ (2010) The physiology and molecular biology of the effects of salinity on rice. In: Pessarakli M (ed) Handbook of plant and crop stress, 3rd edn. Taylor and Francis, Florida, pp 901–942
Munns R (2010) Approaches to identifying genes for salinity tolerance and the importance of timescale. Methods Mol Biol 639:25–38
Schon CC, Friedrich UH, Susanne G et al (2004) Quantitative trait loci mapping based on resampling in a vast maize testcross experiment and its relevance to quantitative genetics for complex traits. Genetics 167:485–498
Paterson AH (1998) QTL mapping in DNA marker-assisted plant and animal improvement. In: Paterson AH (ed) Molecular dissection of complex traits. CRC Press, Boca Raton, pp 131–143
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Ashraf, M., Akram, N.A., Mehboob-ur-Rahman, Foolad, M.R. (2012). Marker-Assisted Selection in Plant Breeding for Salinity Tolerance. In: Shabala, S., Cuin, T. (eds) Plant Salt Tolerance. Methods in Molecular Biology, vol 913. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-986-0_21
Download citation
DOI: https://doi.org/10.1007/978-1-61779-986-0_21
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61779-985-3
Online ISBN: 978-1-61779-986-0
eBook Packages: Springer Protocols