home icon user icon
Welcome to International Network for Natural Sciences | INNS Pub.
Home My Account
Submit Manuscript
double_slash
breadcumb_bg

An overview of marker assisted selection and QTL mapping in cotton

Paper Details

Research Paper 01/01/2016
Views (571) Download (11)
current_issue_feature_image
publication_file

An overview of marker assisted selection and QTL mapping in cotton

Makiya Rafiq, Shoaib Liaqat, Rana Imtiaz Ahmed, Muhammad Najeebullah, Rana Touqeer Ahmad, Abdul Karim, Abdul Jabbar
Int. J. Agron. Agri. Res.8( 1), 71-80, January 2016.
Certificate: IJAAR 2016 [Generate Certificate]
Key: CottonMarker-assisted selectionMolecular markersQTL mapping

Abstract

DNA markers are rapidly being developed for almost all the major crops. The most important markers are restriction fragment length polymorphisms (RFLPs), polymerase chain reaction (PCR) based markers such as random amplified polymorphic DNA (RAPD), and fingerprinting markers. DNA markers can supplement isozyme markers for monitoring trait improvement activities such as estimating genetic diversity in breeding populations, germplasm identification, verifying controlled crosses, and estimating seed efficiencies. As the number of DNA markers is potentially limitless, it should be possible to map individual quantitative trait loci (QTL) by linkage analysis with high-density maps. Twenty-first century agriculture will face frightening challenges to provide mankind with an appropriate level of food security while enhancing the sustainability of agricultural practices, lowering their environmental impact and preserving the remaining biodiversity. Marker assisted selection (MAS) have been widely adopted to improve resistance to biotic stresses, more modest results have been reported for the improvement of resistance to biotic constraints particularly drought and yield, mainly due to the elusive nature of the applicable quantitative trait loci (QTLs) and the unpredictability of their effects. In this article, what Marker assisted selection (MAS) is and why it is a good idea is described. MAS will probably exhaust genetic variation more hurriedly than phenotypic selection because many more cycles of selection are possible in a given time period using genomic compared to phenotypic selection.

VIEWS 37
Cover PDF

Abdallah AM, Reddy OUK, El-Zik KM, Pepper AE. 2001. Genetic diversity and relationships of diploid and tetraploid cottons revealed using AFLP. Theoretical and Applied Genetics 102, 222-229.

Brubaker CL, Wendel JF. 1994. Reevaluating the origin of domesticated cotton (Gossypium hirsutum L.) using nuclear restriction fragment length polymorphism (RFLPs). American Journal of Botany 81, 1309-1326.

Campbell B, Saha S, Percy R, Frelichowski J, Jenkins J, Park W, Mayee C, Gotmare V, Dessauw D, Giband M. 2010. Status of the Global Cotton Germplasm Resources. Crop Science 50, 1161-1179.

Cherry JP, Katterman FRH, Endrizzi JE. 1972. Seed esterases, leucine, and catalases of species of the genus Gossypium. Theoretical and Applied Genetics 42, 218–226.

Connell JP, Pammi S, Iqbal MJ, Huizinga T, Reddy AS. 1998. A high through put procedure for capturing microsatellites from complex plant genomes. Plant Molecular Biology 16, 341-349.

Ellegien H. 1993. Genomic analysis with microsatellite markers. Ph.D Dissertation. University of Agricultural Science, Swedish (Unpublished).

El-Zik KM, Thaxton PM. 1989. Genetic improvement for resistance to pests and stresses in cotton. In: Integrated Pest Management Systems and Cotton Production. John Wiley and Sons, NY pp. 191-224.

Geldermann H. 1975. Investigations on inheritance of quantitative characters in animals by gene markers methods. Theoretical and Applied Genetics 46, 319-330.

Geng CD, Gong ZZ, Huang JQ, Zhang ZC. 1995. Identification of difference between cotton cultivars (G. hirsutum) using the RAPD method. Jiangsu Journal of Agricultural Sciences 11, 21-24.

Han Z, Guo W, Song X, Zhang T. 2004. Genetic mapping of ESTderived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton. Molecular Genetics and Genomics 272, 308-327.

He DH, Lin ZX, Zhang XL, Nie YC, Guo XP, Zhang YX, Li W. 2007. QTL mapping for economic traits based on a dense genetic map of cotton with PCR-based markers using the interspecific cross of Gossypium hirsutum Vs Gossypium barbadense. Euphytica 153(1-2), 181-197.

Jeuken M, Wijk V, Peleman J, Lindhout. 2001. An integrated interspecific AFLP map of lettuce (Lactuca) based on two L. sativa L. saligna F2 populations. Theoretical and Applied Genetics 103, 638-647.

Khan SA, Hussain D, Askari E, Stewart JM, Malik KA, Zafar Y. 2000. Molecular phylogeny of Gossypium sp. by DNA fingerprinting and cotton Gossypium hirsutum examined using DNA fingerprinting. Theoretical and Applied Genetics 103, 547-554.

Kumar P, Singh K, Vikal Y, Radhawa LS, Chahal GS. 2003. Genetic diversity studies of elite cotton germplasm lines using RAPD markers and morphological characteristics. Indian Journal of Genetics and Plant Breeding 63(1), 5-10.

Lee M. 1995. DNA markers and plant breeding programs. Advances in Agronomy 55, 265-344.

Li G, Quiros CF. 2001. Sequence – related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theoretical and Applied Genetics 103, 455-461.

Lin Z, He D, Zhang X, Nie Y, Guo X, Feng C, Stewart JMCD. 2005. Linkage map construction and mapping QTL for cotton fibre quality using SRAP,,SSR and RAPD. Plant Breeding 124, 180-187.

Liu B, Wendel JF. 2001. Intersimple sequence repeats (ISSR) polymorphisms as a genetic marker system in cotton. Molecular ecology 1, 201-205.

Liu S, Cantrell RG, McCarty JC, Stewart JM. 2000. Simple sequence repeat-based assessment of genetic diversity in cotton race stock accessions. Crop Sciences 40, 1459–1469.

Meredith WR. 1992. Contributions of introductions to cotton improvement. In: Shands HL, Weisner LE (eds) Use of plant introductions in cultivar development. Part I. Crop Science Society of America, Madison, WI p 127–146.

Meredith WR. 2000. Cotton yield progress-why has it reached a plateau. Better Crops 84, 6–9.

Michaelson MJ, Price HJ, Ellison JR, Johnston  JS.  1991.  Comparison  of  plant  DNA contents determined by Feulgen microspectrophotometry and laser flow cytometry. American Journal of Botany 78, 183-188.

Miklas PN, Delorme R, Riley R. 2003. Identification of QTL conditioning resistance to white mold in a snap bean population. Journal of the American Society for Horticultural Science 128, 564– 570.

Ordon F, Wenzel W, Friedt W. 1998. Recombination: Molecular markers for resistance genes in major grain crops. Progress in Botany 59, 49-79.

Park YH, Alabady MS, Ulloa M, Sickler B, Wilkins TA, Yu J, Stelly DM, Kohel RJ, El-Shiny OM, Cantrell RG. 2005. Genetic mapping of new cotton fibre loci using EST-derived microsatellites in an interspecific recombinant inbred (RIL) cotton population. Molecular Genetics and Genomics 274, 428-441.

Pillay M, Meyers GO. 1999. Genetic diversity assessed by variation in ribosomal RNA genes and AFLP markers. Crop Science 39, 1881-1886.

Prioul JL, Quarrie S, Causse M, Vienne D. 1997. Dissecting complex physiological functions through the use of molecular quantitative genetics. Journal of Experimental Botany 48, 1151-1163.

Qureshi SN, Saha S, Kantety RV, Jenkins JN. 2004. EST-SSR:a new class of genetic markers in cotton. Journal of Cotton Science 8, 112-123.

Rafalski JA. 1997. Randomly amplified polymorphic DNA (RAPD) analysis. In : DNA markers : Protocols, Applications and Overviews (eds. G.C.Anolles and P.M. Gresshoff), Wiley-Liss, Inc. USA, p. 364.

Reddy OUK, Pepper AE, Ibrokhim A, Saha S, Jenkins JN, Brooks T, Bolek Y, El-Zik KM. 2001. New dinucleotide and trinucleotide microsatellite marker resources for cotton genome research. Journal of Cotton Science 5,103–113.

Ribaut JM, Hoisington D. 1998. Marker-assisted selection: new tools and strategies. Trends in Plant Science 3, 236-238.

Roder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganel MA. 1998. A microsatellite map of wheat. Genetics 149, 2007-2023.

Saha S, Karaca M, Jenkins JN, Zipf AE, Reddy UK, Kantey RV. 2003. Simple sequence repeats as useful resources to study transcribed genes of cotton. Euphytica 130, 355-364.

Sarang Y, Menz M, Jiang CX, Wright RJ, Yakir D, Paterson AH. 2001. Genomic dissection of genotype x environment interactions conferring adaptation of cotton to arid conditions. Genome Research 11, 1988-1995.

Semagn K, Bjornstad A, Skinnes H, Maroy AG, Tarkegne T, William M. 2006. Distribution of DArT, AFLP, and SSR markers in a genetic linkage map of a doubled haploid hexaploid wheat population. Genome 49, 545–555.

Shappley ZW, Jenkins JN, Meredith WR, McCarty JC. 1998b. An RFLP linkage map of upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics 97, 756–761.

Shappley ZW, Jenkins JN, Watson CE, Kahler AL, Meredith WR. 1996b. Establishment of molecular markers and linkage groups in two F2 populations of upland cotton. Theoretical and Applied Genetics 92, 915–919.

Soller M, Brody T, 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. Theoretical and Applied Genetics 47, 35-39.

Tanksley SD, Rick CM. 1980. Isozyme gene linkage map of the tomato: Applications in genetics and breeding. Theoretical and Applied Genetics 57, 161–170.

Tanksley SD. 1993. Mapping polygenes. Annuual Review of Genetics 27, 205-233.

Van Esbroeck GA, Bowman DT, Calhoun DS, OL May. 1998. Changes in the genetic diversity of cotton in the U.S. from 1970 to 1995. Crop Science 38, 33-37.

Vos P, Hogers R, Blecker M, Reijans M, Van de Lee T, Hornes M, Fritjters A, Pot J, Peleman J, Kuiper M, M Zabeau. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Research 23, 4407- 4414.

Wajahatullah MK, Stewart JM, Zhang J. 1997. Use of RAPD markers to analyse genomic affinity among Australian Gossypium species. Special Report -Agricultural Experiment Station, Division of Agriculture, University of Arkansas 183, 150-152.

Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Research 18, 6531–6535.

Zhang J, Guo W, Zhang T. 2002. Molecular linkage map of allotetraploid cotton (Gossypium hirsutum L. x Gossypium barbadense L.) with a haploid population. Theoretical and Applied Genetics 105(8), 1166-1174.

Zhang ZS, Xiao YH, Luo M, Li XB, Luo XY, Hou L, Li DM, Pei Y. 2005. Construction of a genetic linkage map and QTL analysis of fibre related traits in upland cotton. Euphytica 144, 91-99.

Submit Manuscript