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United States Department of Agriculture

Agricultural Research Service


item Glynn, Neil
item Mccorkle, Katherine
item Comstock, Jack

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/13/2009
Publication Date: 7/1/2009
Citation: Glynn, N.C., Mccorkle, K., Comstock, J.C. 2009. Diversity Among Mainland USA Sugarcane Cultivars Examined by SSR Genotyping. Amer. Soc. of Sugar Cane Technol. 29:36-52.

Interpretive Summary: The fundamental objectives of plant breeding are the improvement and or maintenance of genetic diversity within new cultivars in order to enhance or preserve productivity. In sugarcane new cultivars for the US mainland states of Florida, Louisiana and Texas are developed by selection from the progeny of crosses made between existing, successful cultivars. Generally cultivars adapted to one state are not successful in the other two states however, the progeny of crosses between cultivars from each state sometimes produce successful cultivars for other states. Crosses are selected based on phenotypic knowledge of each cultivar. Concerns exist over the erosion of diversity through this system of recurrent selection, therefore determination of the diversity that exists between the cultivars used in the crossing programs for each of the three states would aid breeders in selecting potentially productive crosses. SSR genotyping has been widely applied in breeding of many crops their application however relies on the efficient identification of informative markers that can be easily analyzed efficiently. The identification of useful markers is difficult in sugarcane due to it’s complex polyploidy genome. The objectives of this study were 1) to examine the amplification characteristics of 181 previously designed SSR primers 2) to use a sub-set of primers to obtain the fingerprints of varieties used in the crossing programs for the US states of Florida, Louisiana and Texas 3) to examine diversity within and between the cultivars used in each state. The SSR’s examined proved highly informative and polymorphic, each of 65 varieties examined could be uniquely identified using the SSR fingerprints from 12 primer pairs. Groupings of varieties were evident and generally the cultivars grown in Florida could be distinguished from those grown in Louisiana. Groupings of cultivars grown in each state were evident some of the groups identified were consistent with parentage information.

Technical Abstract: SSR’s have been effective in examining diversity to improve plant breeding strategies however, the identification of useful SSR’s is critical and can be difficult especially in the complex sugarcane genome. Diversity among the cultivars grown and used for the sugarcane breeding programs of Florida, Louisiana and Texas was examined using twelve informative SSR’s identified from an initial screen of 181. Amplification characteristics were evaluated against DNA from Saccharum officinarum (Green German), S. spontaneum (IND 81-146) and from hybrid clones produced from a cross between these two. The number of alleles observed varied from 1 to 24, 176 (97%) primer pairs proved polymorphic. The variation accounted for between states was small (3.4%) however significant differences were observed between Florida and Louisiana. Cluster analysis and PCOORDA showed some general groups of varieties which in some cases were consistent with pedigree information and in some cases were not. The information generated from this study will prove valuable in the selection of crosses and the maintenance and improvement of genetic diversity in sugarcane cultivars in the US mainland.

Last Modified: 06/24/2017
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