Register      Login
Crop and Pasture Science Crop and Pasture Science Society
Plant sciences, sustainable farming systems and food quality
RESEARCH ARTICLE

Simple sequence repeat (SSR) markers reveal low levels of polymorphism between cotton (Gossypium hirsutum L.) cultivars

D. Rungis A B C , D. Llewellyn A , E. S. Dennis A and B. R. Lyon B
+ Author Affiliations
- Author Affiliations

A Australian Cotton Cooperative Research Centre, CSIRO) Division of Plant Industry, PO Box 1600, Canberra, ACT 2601, Australia.

B Australian Cotton Cooperative Research Centre, School of Biological Sciences A12, The University of Sydney, Sydney, NSW 2006, Australia.

C Corresponding author; Present Address: Department of Forest Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada.

Australian Journal of Agricultural Research 56(3) 301-307 https://doi.org/10.1071/AR04190
Submitted: 23 August 2004  Accepted: 8 February 2005   Published: 23 March 2005

Abstract

Since their discovery in the 1980s microsatellite or simple sequence repeat (SSR) markers have been widely used in many species to generate relatively dense genetic maps or framework maps on which to anchor more abundant, but anonymous, markers such as amplified fragment length polymorphisms (AFLPs). They are typically highly polymorphic, robust, and often portable, particularly among different mapping populations or crosses and often to related species. They have been useful in species where low levels of genetic diversity limit the use of other markers. Cultivated cotton (Gossypium hirsutum L.) has a history of genetic bottlenecks that have considerably reduced its diversity, with the consequence that most molecular marker genetic linkage studies are done with inter-specific crosses. In this study we evaluated the potential for SSR markers to be used in marker-assisted selection (MAS) breeding in cotton by quantifying the level of polymorphism detected with a set of commercially available SSR markers between and within a collection of cotton cultivars being used in our breeding programs. Although the majority of these markers are polymorphic between the 2 tetraploid species of cotton, G. barbadense and G. hirsutum, they are not highly polymorphic (~5%) either among or within G. hirsutum cultivars. However, 6 of the 8 cultivars studied were found to be segregating for alleles of these SSR markers. This suggests that where polymorphisms exist, heterozygosity within cultivars is maintained by the breeding strategies adopted by many modern cotton breeders. Although SSRs clearly have utility in genetic studies using inter-specific crosses or in the introgression of wild germplasm, they will be more difficult to use for standard cotton breeding until greater numbers are available. The utility of some markers may be reduced in some breeding populations where heterozygosity remains in the parental material.

Additional keywords: microsatellite markers, marker-assisted breeding.


Acknowledgments

This work is part of a PhD project funded by the Australian Cotton Cooperative Research Centre. We thank Dr G. Constable for providing the cotton cultivars used in this study, and Dr Curt Brubaker for invaluable discussions.


References


Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36, 181–186. open url image1

Blair MW, Hedetale V, McCouch SR (2002) Fluorescent-labelled microsatellite panels useful for detecting allelic diversity in cultivated rice (Oryza sativa L.). Theoretical and Applied Genetics 105, 449–457.
Crossref | GoogleScholarGoogle Scholar | PubMed | open url image1

Cousins YL, Lyon BR, Llewellyn DJ (1991) Transformation of an Australian cotton cultivar – prospects for cotton improvement through genetic engineering. Australian Journal of Plant Physiology 18, 481–494. open url image1

Endrizzi JE, Turcotte EL, Kohel RJ (1995) Genetics, cytology, and evolution of Gossypium. Advances in Genetics 23, 271–375. open url image1

Felsenstein, J (1995). ‘PHYLIP, phylogeny inference package (Version 3.5c).’ (Department of Genetics, University of Washington: Seattle)

Gupta PK, Balyan HS, Sharma PC, Ramesh B (1996) Microsatellites in plants: a new class of molecular markers. Current Science 70, 45–54. open url image1

Gutierrez OA, Basu S, Saha S, Jenkins JN, Shoemaker DB, Cheatham CL, McCarty JC (2002) Genetic distance among selected cotton genotypes and its relationship with F2 performance. Crop Science 42, 1841–1847. open url image1

Harker N, Rampling LR, Shariflou MR, Hayden MJ, Holton TA, Morell MK, Sharp PJ, Henry RJ, Edwards KJ (2001) Microsatellites as markers for Australian wheat improvement. Australian Journal of Agricultural Research 52, 1121–1130.
Crossref | GoogleScholarGoogle Scholar | open url image1

Heckenberger M, Bohn M, Ziegle JS, Joe LK, Hauser JD, Hutton M, Melchinger AE (2002) Variation of DNA fingerprints among accessions within maize inbred lines and implications for identification of essentially derived varieties. I. Genetic and technical sources of variation in SSR data. Molecular Breeding 10, 181–191.
Crossref | GoogleScholarGoogle Scholar | open url image1

Hudcovicova M, Kraic J (2003) Utilisation of SSRs for characterisation of the soybean (Glycine max (L.) Merr) genetic resources. Czech Journal of Genetics and Plant Breeding 39, 120–126. open url image1

Iqbal MJ, Reddy OUK, El-Zik KM, Pepper AM (2001) A genetic bottleneck in the ‘evolution under domestication' of Upland cotton Gossypium hirsutum L. examined using DNA fingerprinting. Theoretical and Applied Genetics 103, 547–554. open url image1

Keim P, Beavis W, Schupp J, Freestone R (1992) Evaluation of soybean RFLP marker diversity in adapted germplasm. Theoretical and Applied Genetics 85, 205–212.
Crossref | GoogleScholarGoogle Scholar | open url image1

Kochman J, Moore N, Obst N, O’Neill W, Salmond G, Bentley S (2000) Management strategies for Fusarium wilt of cotton. ‘Proceedings: ACGRA 2000 Australian Cotton Conference’. Brisbane, Qld. (Australian Cotton Growers Research Association: Wee Waa, NSW)


Liu S, Cantrell RG, McCarty JC, Stewart JM (2000) Simple sequence repeat-based assessment of genetic diversity in cotton race stock accessions. Crop Science 40, 1459–1469. open url image1

May OL, Bowman DT, Calhoun DS (1995) Genetic diversity of U.S. Upland cotton cultivars released between 1980 and 1990. Crop Science 35, 1570–1574. open url image1

Minch, E , Ruiz-Linares, A , Goldstein, D , Feldman, M ,  and  Cavalli-Sforza, LL (1995). ‘Microsat (version 1.5b): a computer program for calculating various statistics on microsatellite allele data.’ (WWW: http://hpgl.stanford.edu/projects/microsat/)

Multani DS, Lyon BR (1995) Genetic fingerprinting of Australian cotton cultivars with RAPD markers. Genome 38, 1005–1008. open url image1

Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Molecular Biology Reporter 11, 122–127. open url image1

Reid P, Constable G (2000) Three new CSIRO varieties. ‘Proceedings: ACGRA 2000 Australian Cotton Conference’. Brisbane, Qld. (Australian Cotton Growers Research Association: Wee Waa, NSW)


Rungis D (2002) Development of Molecular Markers in Cotton. PhD thesis, Faculty of Science, University of Sydney, NSW, Australia.

Saha S, Karaca M, Jenkins JN, Zipf AE, Reddy OUK, Kantety RV (2003) Simple sequence repeats as useful resources to study transcribed genes of cotton. Euphytica 130, 355–364.
Crossref | GoogleScholarGoogle Scholar | open url image1

Small RL, Ryburn JA, Wendel JF (1999) Low levels of nucleotide diversity at homoeologous Adh loci in allotetraploid cotton (Gossypium L.). Molecular Biology and Evolution 16, 491–501.
PubMed |
open url image1

Van Esbroeck GA, Bowman DT (1998) Cotton germplasm diversity and its importance to cultivar development. Journal of Cotton Science 2, 121–129. open url image1

Van Esbroeck GA, Bowman DT, May OL, Calhoun DS (1999) Genetic similarity indices for ancestral cotton cultivars and their impact on genetic diversity estimates of modern cultivars. Crop Science 39, 323–328. open url image1

Wendel JF, Brubaker CL, Percival AD (1992) Genetic diversity in Gossypium hirsutum and the origin of Upland cotton. American Journal of Botany 79, 1291–1310. open url image1

Young ND (1999) A cautiously optimistic vision for marker-assisted breeding. Molecular Breeding 5, 505–510.
Crossref | GoogleScholarGoogle Scholar | open url image1