Title page for ETD etd-01202005-134859

Type of Document Master's Thesis
Author Arro, Jie Alojado
Author's Email Address jarro1@paws.lsu.edu
URN etd-01202005-134859
Title Genetic Diversity among Sugarcane Clones Using Target Region Amplification Polymorphism (TRAP) Markers and Pedigree Relationships
Degree Master of Science (M.S.)
Department Agronomy & Environmental Management
Advisory Committee
Advisor Name Title
Collins Kimbeng Committee Chair
Kenneth Gravois Committee Member
Prasanta Subudhi Committee Member
  • molecular markers
  • trap
  • coefficient of parentage
  • genetic diversity
  • sugarcane
Date of Defense 2004-12-15
Availability unrestricted
Genetic diversity is indispensable to sustain genetic gain in breeding programs. Cultivated sugarcane is a highly heterozygous hybrid derived from crossing two highly heterozygous parents. Sugarcane breeders traditionally rely on pedigree records to select parents. Molecular markers now make it possible to assess genetic diversity at the DNA level. Sixty three sugarcane clones were characterised using Target Region Amplification Polymorphism (TRAP) markers and pedigree relationship (Coefficient of parentage (COP)). The TRAP is a PCR-based marker with a fixed primer designed from Expressed Sequence Tag (EST) sequences paired with an arbitrary primer. It is supposed to unravel trait based polymorphism in the intronic- or exonic-regions of the genome. Ten genes evidently involved in sucrose accumulation (SUC), cold tolerance (CT) and trichome development (TRICH) were paired with four arbitrary primers. A total of 3,170 bands were scored of which 2,684 (85%) were polymorphic. Cluster and Multi Dimensional Scaling (MDS) analyses revealed a very narrow genetic diversity among the entries with genetic similarity (GS) ranging from 78 to 94%. Parentage did not seem to contribute to the grouping pattern in either the overall or individual gene family (SUC, CT and TRICH) clusters which was confirmed by the lack of correlation (r = -0.008) between the TRAP and COP-derived GS matrices. The complex genome of sugarcane and the strict assumptions inherent with estimating COP may account for this disparity. Analysis of Molecular Variance (AMOVA) revealed no structure in the population with regards to era of release (Pre- versus post-1980) with among clones accounting for up to 99% of the total variation and only 1% of variation attributable to era of release. Mixed Model Analysis on the MDS axes generally revealed no significant differences among era of release. Thus, pedigree records can enhance interpretation of marker-derived information especially in an interspecific crop like sugarcane where ancestral species possess and contribute different characteristics. Results from this study needs to be supplemented with sequence analysis of TRAP fragments to definitively relate the derived information to trait variation.
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