The development and application of molecular markers for linkage mapping and quantitative trait loci analysis of important agronomic traits in oil palm (Elaeis guineensis Jacq.)

Gan, Siou Ting (2014) The development and application of molecular markers for linkage mapping and quantitative trait loci analysis of important agronomic traits in oil palm (Elaeis guineensis Jacq.). PhD thesis, University of Nottingham.

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Oil palm (Elaeis guineensis) produces over five times more oil/year/hectare than oil seed rape and accounted for 33% of world vegetable oil production in 2011. Being a cross-pollinated perennial tree crop with long breeding cycles (typically 12 years) and a large planting area requirement (usually 143 palms/hectare), utilization of molecular technology could greatly improve the efficiency of oil palm breeding. In the present study, various approaches were used to develop molecular markers for genetic linkage mapping and QTL analysis, with the ultimate goal of marker-assisted selection in oil palm.

Firstly, Representational Difference Analysis (RDA) and Amplified Fragment Length Polymorphism (AFLP) were coupled with Bulked Segregant Analysis (BSA) to try to identify marker(s) closely linked to the important shell-thickness gene. A novel combination of RDA with Roche 454 pyrosequencing enabled a more comprehensive study of the enrichment profiles compared to Sanger sequencing. Identification of >35% redundant sequences, repetitive sequences and organelle DNA suggested that subtractive hybridization and target enrichment of RDA were inefficient here, with the lack of elimination of common sequences masking the real difference products. The use of the AFLP method identified 29 primer pairs that yielded 49 putative shell-thickness related-polymorphic bands. A detailed analysis will need to be carried out to fully evaluate and validate these markers.

The use of the relatively new Diversity Array Technology “Genotyping-By-Sequencing” (DArTSeq) platform through genotyping of two closely-related tenera self-pollinated F2 populations, 768 (n=44) and 769 (n=57), generated a total of 11,675 DArTSeq polymorphic markers of good quality. These markers were used in the construction of the first reported DArTSeq based high-density linkage maps for oil palm. Both genetic maps consist of 16 major independent linkage groups (total map length of 1874.8 and 1720.6 cM, with an average marker density of one marker every 1.33 and 1.62 cM, respectively), corresponding well with the 16 homologous chromosome pairs of oil palm (2n = 2x = 32; 14/16 chromosomes were confirmed by known location SSR markers). Preliminary quantitative trait loci (QTL) mapping of the yield and vegetative growth traits detected four significant and 34 putative as well as two significant and 30 putative QTLs for these small 768 and 769 populations, respectively. No common significant QTL were detected between the two closely-related controlled crosses which could have allowed combination of QTL across the two populations.

Saturation of the shell-thickness (Sh) region with all available DArTSeq markers, as well as map integration around the Sh regions for both populations, identified 32 Single Nucleotide Polymorphism (SNP) and DArT markers mapped within a 5 cM flanking region of the Sh gene. Homology search of the DArTSeq marker sequence tag (64 bp) against the recently published oil palm genome assembly confirmed that 23 out of the 32 (72%) DArTSeq markers were located on the p5_sc00060 scaffold in which the SHELL gene was identified. The identified shell-thickness markers could be useful as molecular screening tools. This study demonstrated the potential and feasibility of using genomic resources available for genetic improvement of oil palm breeding programmes.

Item Type: Thesis (University of Nottingham only) (PhD)
Supervisors: Massawe, Festo
Mayes, Sean
Subjects: S Agriculture > SB Plant culture
Faculties/Schools: University of Nottingham, Malaysia > Faculty of Science and Engineering — Science > School of Biosciences
Item ID: 14197
Depositing User: EP, Services
Date Deposited: 12 Feb 2015 07:47
Last Modified: 13 Oct 2017 08:53

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