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Title: Genetic diversity in a collection of Saccharum spontaneum genotypes and their contribution to the Louisiana commercial breeding program as revealed using AFLP markers

Author
item PINNAMANENI, S - LSU Agcenter
item SUMAN, A - LSU Agcenter
item KIMBENG, C - LSU Agcenter
item PONTIF, M - LSU Agcenter
item Hale, Anna
item GRAVOIS, K - LSU Agcenter

Submitted to: American Society of Sugar Cane Technologists
Publication Type: Abstract Only
Publication Acceptance Date: 5/18/2017
Publication Date: 6/14/2017
Citation: Pinnamaneni, S.R., Suman, A., Kimbeng, C.A., Pontif, M.J., Hale, A.L., Gravois, K.A. 2017. Genetic diversity in a collection of Saccharum spontaneum genotypes and their contribution to the Louisiana commercial breeding program as revealed using AFLP markers [abstract]. Journal of the American Society of Sugar Cane Technologists. 37:55.

Interpretive Summary:

Technical Abstract: Saccharum spontaneum has been the most important source of wild germpalsm for sugarcane cultivar development in Louisiana, particularly in improving traits such as mosaic virus resistance, vigor, ratooning ability and cold tolerance. A collection of 51 S. spontaneum genotypes maintained at the Sugarcane Research Unit at Houma, LA, were genotyped using amplified fragment length polymorphism (AFLP) markers along with 66 commercial hybrids and parents used for cultivar development. The objective was to characterize the diversity present within this S. spontaneum collection and to assess their past, and potential contribution to diversity in the Louisiana sugarcane cultivar development program. This information will help instruct where the diversity was coming from, if enough of the diversity had been tapped or if there are gaps in the collection that need to be addressed via collection or introgression. We used the Model-Based Bayesian Clustering (MBBC) approach to study the genetic diversity and structure in the populations. The 51 S. spontaneum genotypes in the collection grouped into two main clusters largely according to their geographical origin namely, Central (India) and Eastern (Thailand) zones. On average, the proportion of inferred ancestry of the Louisiana cultivars/parents with the S. spontaneum clusters was about 0.69 % with the Eastern and 0.31 % with Central zone cluster. Not surprising, the clone with the highest proportion of inferred ancestry with the S. spontaneum clusters was CP77-407 (24 % with the Eastern zone cluster and 4.4 % with the Central zone cluster). This clone (CP77-407) is a parent of cultivar LCP 85-384 and a progeny of US 56-15-8, one of the S. spontaneum clones in the collection. The average proportion of inferred ancestry between the Louisiana cultivars/parents and the two S. spontaneum clusters dropped to 0.30 % when CP77-407 was removed from the analysis indicating that most of the S. spontaneum genome shared between cultivars/parents and the Eastern zone cluster came from US 56-15-8. Previously a very important cultivar in Louisiana, LCP 85-384 is a BC4 derivative of US 56-15-8. LCP 85-384 had a proportion of inferred ancestry of 0.2 with the Eastern zone cluster and 0.1 with the Central zone cluster, which was no more different from the values obtained for other cultivars of similar or later generations, and even among progenies of LCP 85-384. This may suggest that the desired S. spontaneum alleles were already fixed in the cultivar/parent population by the BC4 generation as TucCP 77-42, a BC1 cultivar was the only other clone with > 3% of inferred ancestry with the two clusters. In recent years, more effort has been put into breeding with clones from the Central zone. The AFLP markers were instructive in deducing the relationships among the S. spontaneum and cultivars/parents. However, given the size of the sugarcane genome and abundant polymorphism in S. spontaneum clones, the marker information was not sufficient in determining the actual proportion of genome shared by these defined groups.