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Title: Promoting utilization of Saccharum spp. genetic resources though genetic diversity analysis and core collection construction

item NAYAK, SPURTHI - University Of Florida
item SONG, JIAN - University Of Florida
item VILLA, ANDREA - University Of Florida
item PATHAK, BHUVAN - University Of Florida
item Ayala-Silva, Tomas
item YANG, XIPING - University Of Florida
item Todd, James
item GLYNN, NEIL - Syngenta
item Kuhn, David
item Glaz, Barry
item GILBERT, ROBERT - University Of Florida
item Comstock, Jack
item WANG, JIANPING - University Of Florida

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/28/2014
Publication Date: 10/21/2014
Citation: Nayak, S.N., Song, J., Villa, A., Pathak, B., Ayala Silva, T., Yang, X., Todd, J.R., Glynn, N.C., Kuhn, D.N., Glaz, B.S., Gilbert, R., Comstock, J.C., Wang, J. 2014. Promoting utilization of Saccharum spp. genetic resources though genetic diversity analysis and core collection construction. PLoS One. 9(10):e110856. doi: 10.1371/journal.pone.0110856.

Interpretive Summary: Interpretive Summary: Biofuel feedstocks are being investigated for domestic sources of energy, and of these sugarcane and energy cane (hybrids of Saccharum spp.) have shown good potential for biomass production. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami at the Subtropical Horticultural Research Station where it is a repository of Saccharum spp. for sugarcane breeding. This collection is presumably diverse with many useful alleles but has not been fully characterized and has not been genotypically evaluated. Thus, 1002 genotypes were screened with 36 SSR markers that determined using principle component analysis that there were three clusters one for S. spontaneum, another for S. officinarum and hybrids and a third for non Saccharum species. This information will be useful to scientist and breeders to better understand the structure of the diversity within the collection. A core collection of 300 accessions was made from this information that maximized the diversity of the collection and enabling breeder to fully utilize it for crop improvement. Diverse core collections like this also could be used as a mapping panel to associate markers with traits of interest, which would assist breeders when making selections of superior parents and clones.

Technical Abstract: Technical Abstract: Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been useful to breeders due to its lack of characterization and large number of accessions. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all of its 1002 accessions to understand its genetic diversity and population structure, and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG was 0.304 on average in a range of 0 to 0.5. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in a second cluster, and mostly non-Saccharum spp. in a third cluster. A core collection of 300 accessions was identified, which captured the maximum genetic diversity of the entire WCSRG. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can serve as a diverse panel for association mapping of traits of agronomic and commercial importance.. ARS - 115