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United States Department of Agriculture

Agricultural Research Service

Research Project: Genetic Improvement of Sugarcane for Temperate Climates

Location: Sugarcane Research Unit

Title: Allelic divergence in sugarcane cultivars revealed through capillary electrophoregrams of fluorescence-labeled microsatellite markers

Authors
item Chandra, Amaresh -
item Grisham, Michael
item Pan, Yong-Bao

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: November 1, 2013
Publication Date: January 13, 2014
Citation: Chandra, A., Grisham, M.P., Pan, Y-B. 2014. Allelic divergence in sugarcane cultivars revealed through capillary electrophoregrams of fluorescence-labeled microsatellite markers [abstract]. Plant and Animal Genome XXII Program. Available online: https://pag.confex.com/pag/xxii/webprogram/Paper11195.html.

Technical Abstract: Though sugarcane cultivars (Saccharum spp. hybrids) are complex aneu-polyploid hybrids, genetic evaluation and tracking of clone- or cultivar-specific alleles become possible due to capillary electerophoregrams (CE) using fluorescence-labeled SSR primer pairs. Twenty-four sugarcane cultivars, 12 each from India and the U.S., were genetically assessed using 21 fluorescence-labeled polymorphic microsatellite markers. These markers primed the amplification of 213 alleles. Of these alleles, 161 were common to both Indian and US cultivars, 25 were specific to the Indian cultivars, and the rest 27 were observed only in the US cultivars. Only 10 alleles were monomorphic among all 24 cultivars. A high level of heterozygosity was observed among the Indian cultivars as 159 alleles (82.4%) were polymorphic resulting in an average PIC value of 0.66 and marker index (MI) value of 5.07. The Pearson correlation between PIC and MI was found to be significant (r = 0.56). The unweighted pair group method with arithmetic mean clustering dendrogram separated the Indian and the US cultivars into two distinct clusters with 59% homology. These results propose the potential utility of six cultivar-specific SSR alleles [CoJ64 (mSSCIR3_182), CoLk8001 (SMC486CG_229, SMC36BUQ_125, mSSCIR74_216), CoLk94184 (SMC334BS_154) and CoSe92423 (mSSCIR43_238)] in sugarcane breeding vis a vis transporting CE-based evaluation in clone/variety identity testing, cross fidelity assessments, and genetic relatedness among Saccharum species and related genera.

Last Modified: 8/22/2014
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