ARS | Publication request: Development of a core set of SSR markers for the characterization of Gossypium germplasm

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 11, 2012
Publication Date: August 29, 2012
Citation: Yu, J., Fang, D.D., Kohel, R.J., Ulloa, M., Hinze, L.L., Percy, R.G., Zhang, J., Chee, P., Scheffler, B.E., Jones, D.C. 2012. Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica. 187(2):203-213.

Interpretive Summary: Systematic characterization of plant germplasm requires effective genomic tools that reveal the genetic diversity for crop improvement. In cotton, less than 1 percent of potential genetic diversity in the U.S. Cotton Germplasm Collection has been exploited due to the shortage of effective genomic tools that are yet to be developed. Although fragmentary data and useful information on cotton germplasm studies were produced in recent years, systematic characterization and comparative analysis of the cotton germplasm collections were hindered by the lack of a common set of core DNA markers that are portable among different laboratories and/or research projects. This paper reports a core set of 105 such markers as simple sequence repeats (SSR) that are evenly distributed on every one of the 26 cotton chromosomes (at least four markers per chromosome). This core set of SSR markers that represent ten different research groups in marker development were labeled with one of the three fluorescent dyes to make 35 triplex marker bins and were evaluated on a standardized 12-cotton germplasm panel. Results from the study validated high values of the core marker set to reveal DNA polymorphism within cotton accessions and between cotton species. The core marker set provides the cotton research community with a robust genomic tool for systematic characterization and simultaneous comparison of cotton germplasm among other genetic studies.

Technical Abstract: Molecular markers such as simple sequence repeats (SSR) are a useful tool for characterizing genetic diversity of Gossypium germplasm collections. Genetic profiles by DNA fingerprinting of cotton accessions can only be compared among different collections if a common set of molecular markers are used by different laboratories and/or research projects. Herein, we propose and report a core set of 105 SSR markers with wide genome coverage that were identified from a constructed saturated genetic map using a recombinant inbred line population developed between Gossypium hirsutum L. cv. Upland TM-1 and G. barbadense L. Pima 3-79 double haploid. At least four markers evenly distributed on each chromosome were selected from the 26 tetraploid cotton chromosomes. The core set of 105 SSR markers represents ten research groups involved in marker development and were systematically evaluated on 12 genotypes belonging to six Gossypium species posted at the cotton marker database (CMD). Labeled with one of three fluorescent dyes (FAM, HEX, and NED), a total of 35 marker bins in triplex sets were arranged from the 105 markers. Results from this study indicated that the core marker set was robust in revealing DNA polymorphism within accessions and between species. Average value of polymorphism information content (PIC) among the CMD panel was 0.65, and that within the cultivated cotton species G. hirsutum was 0.29. Species-specific alleles were identified to track introgression of wild species into cultivated accessions. Based on the similarity matrix and phylogenetic analysis of the CMD panel, the core set of SSR markers appeared to be sufficient to characterize the diversity within G. hirsutum and many other Gossypium species. The portability of this core marker set would facilitate the systematic characterization and the simultaneous comparison among various research efforts involved in genetic resources and diversity.