Development of candidate markers for high oil yield in oil palm

Name: Nipha Chuenpom

LCSH: Kasetsart University -- Dissertations. Ph.D. (Agricultural Biotechnology) 2017

Classification :.LCCS: SB299.P3

LCSH: Kasetsart University. Interdisciplinary Graduate Program -- Dissertations

LCSH: Oil palm

Abstract: Oil palm is an important oil crop for human consumption and as a transportation fuel. Selection for oil yield traits in an oil palm breeding program is difficult as oil palm is a highly heterozygous out-crossing crop with a long life cycle and large size. This research aims to develop Single Nucleotide Polymorphism (SNP) markers in oil palm using high throughput sequencing of reduced representation (RR) libraries in a set of progenies selected for contrasting phenotypes. Twenty four samples from 12 progenies (Dura X Pisifera) with contrasting bunch numbers (12 high and 12 average) were analyzed by sequencing of size selected insert libraries generated by restriction enzyme digestion. An average of 15.53 million 100 bp reads from each of the 24 samples were generated, for a total of 37 Gb. The forward and reverse reads were combined into complete fragment sequences with median length of 183 bp. All fragment sequences were combined into a RR reference sequences with differing level of allowed mismatch varying in length from 388 Mbp to 634 Mbp. For SNP detection, the individual fragment sequences were re-aligned to the RR reference sequence. Twenty loci showed correlation with oil yield traits using Fisher exact test for non-random distribution in an allelic/additive gene action model in a case-control setting. Additionally, the individual sequences were clustered with CD-HIT and clusters with 2 alleles at a locus were identified. To confirm allelism of the loci identified by sequencing, 226 loci were genotyped by CAPS or by SSCP. All 24 trees were then genotyped for these loci based on the individual read sequences. An additional 9 loci were then identified based on significant allele frequency differences between the selected and average trees. To confirm the candidate markers 52 loci were tested with 499 individual palms from an unrelated set of 32 families using association testing for quantitative traits. 9 SSR markers were used to estimate population structure and kinship relationships. The results indicated that the genotypes at 14 markers might be associated with oil yield traits (BN, ABW, FFB and PH combined) at significant statistical P-value, corrected for multiple testing. There might be a confounding effect of a fertility or moisture gradient in the plantation which still has to be investigated.

Kasetsart University. Office of the University Library

Address: Bangkok

Email: tdckulib@ku.ac.th

Name: Hugo Volkaert

Role: Thesis Advisor

Name: Patcharin Tanya

Role: Thesis Co-Advisor

Created: 2017

Modified: 2023-06-21

Issued: 2023-06-21

วิทยานิพนธ์/Thesis

application/pdf

URL: https://kasetsart.idm.oclc.org/login?url=https://www.lib.ku.ac.th/KUthesis/2560/nipha-chu-all.pdf

CallNumber: SB299.P3.N56

eng

DegreeName: Doctor of Philosophy

Level: Doctoral Degree

Descipline: Agricultural Biotechnology

Grantor: Kasetsart University

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