Construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield-related quantitative trait loci
Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops that provide great nutritional value and high economic returns. Genotyping-by-sequencing (GBS) provides a platform to accelerate the discovery of single nucleotide polymorphisms (SNP) and insertion and deletions (InDel) ma...
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| Format: | Thesis |
| Language: | English |
| Published: |
2020
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| Online Access: | http://psasir.upm.edu.my/id/eprint/104318/ http://psasir.upm.edu.my/id/eprint/104318/1/FAKHRUR%20RAZI%20BIN%20MOHD%20SHAHA%20-%20IR.pdf |
| _version_ | 1848864256263454720 |
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| author | Mohd Shaha, Fakhrur Razi |
| author_facet | Mohd Shaha, Fakhrur Razi |
| author_sort | Mohd Shaha, Fakhrur Razi |
| building | UPM Institutional Repository |
| collection | Online Access |
| description | Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops that provide
great nutritional value and high economic returns. Genotyping-by-sequencing (GBS)
provides a platform to accelerate the discovery of single nucleotide polymorphisms
(SNP) and insertion and deletions (InDel) markers for the construction of a genetic
linkage map. The genetic linkage map facilitates the identification of quantitative trait
loci (QTL) associated with the trait of interest. Together these approaches will speed up
the process in identifying markers for marker-assisted selection (MAS) in oil palm
breeding programmes. A total of 112 full sibling mapping population from a cross of a
Deli dura and a Serdang pisifera was used in this study. Reduced representation libraries
(RRL) of 112 F1 progeny and the two parents were sequenced, and the reads were
mapped against E. guineensis reference genome. A total of 2.5 million SNPs and 153,547
InDels were identified. However, only a subset of 5,278 markers comprising 4,838 SNPs
and 440 InDels were informative for the construction of linkage map. The sixteen linkage
groups spanned 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map
with the average marker densities of one marker per 2.9 cM and 2.0 cM, respectively.
Phenotypic data were correlated with polymorphic markers to discover markers flanking
QTL regions for fresh-fruit-bunch yield (FFB), oil yield (OY), oil-to-bunch (O/B), oilto-
dry mesocarp (O/DM), oil-to-wet mesocarp (O/WM), mesocarp-to-fruit (M/F),
kernel-to-fruit (K/F), shell-to-fruit (S/F), and fruit-to-bunch (F/B) ratio. Two significant
QTLs for M/F were detected with PVE value of 20.6% and 23.9%, four markers for K/F
were detected with PVE value range from 19.4% to 25.6%, and a marker for S/F was
successfully detected with PVE value of 18.1%. The QTL peaks detected for K/F, M/F
and S/F were significant with the logarithm of odds (LOD) value ranging from 4.51 to
6.24, which surpassed the genome-wide LOD threshold. Meanwhile, the allele effect
analysis showed alleles associated with these three traits could contribute to the trait
improvement from 4.6% to 20.7%. These findings, including a dense linkage map and
identification of significant QTL regions associated with K/F, M/F and S/F that could be
applied in MAS in the oil palm breeding programme. In addition, these approaches using
the oil palm genetic linkage map and QTL analysis could fast-track the process of
generating new oil palm varieties as compared to the oil palm conventional breeding
method. |
| first_indexed | 2025-11-15T13:45:55Z |
| format | Thesis |
| id | upm-104318 |
| institution | Universiti Putra Malaysia |
| institution_category | Local University |
| language | English |
| last_indexed | 2025-11-15T13:45:55Z |
| publishDate | 2020 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | upm-1043182023-08-08T02:10:01Z http://psasir.upm.edu.my/id/eprint/104318/ Construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield-related quantitative trait loci Mohd Shaha, Fakhrur Razi Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops that provide great nutritional value and high economic returns. Genotyping-by-sequencing (GBS) provides a platform to accelerate the discovery of single nucleotide polymorphisms (SNP) and insertion and deletions (InDel) markers for the construction of a genetic linkage map. The genetic linkage map facilitates the identification of quantitative trait loci (QTL) associated with the trait of interest. Together these approaches will speed up the process in identifying markers for marker-assisted selection (MAS) in oil palm breeding programmes. A total of 112 full sibling mapping population from a cross of a Deli dura and a Serdang pisifera was used in this study. Reduced representation libraries (RRL) of 112 F1 progeny and the two parents were sequenced, and the reads were mapped against E. guineensis reference genome. A total of 2.5 million SNPs and 153,547 InDels were identified. However, only a subset of 5,278 markers comprising 4,838 SNPs and 440 InDels were informative for the construction of linkage map. The sixteen linkage groups spanned 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map with the average marker densities of one marker per 2.9 cM and 2.0 cM, respectively. Phenotypic data were correlated with polymorphic markers to discover markers flanking QTL regions for fresh-fruit-bunch yield (FFB), oil yield (OY), oil-to-bunch (O/B), oilto- dry mesocarp (O/DM), oil-to-wet mesocarp (O/WM), mesocarp-to-fruit (M/F), kernel-to-fruit (K/F), shell-to-fruit (S/F), and fruit-to-bunch (F/B) ratio. Two significant QTLs for M/F were detected with PVE value of 20.6% and 23.9%, four markers for K/F were detected with PVE value range from 19.4% to 25.6%, and a marker for S/F was successfully detected with PVE value of 18.1%. The QTL peaks detected for K/F, M/F and S/F were significant with the logarithm of odds (LOD) value ranging from 4.51 to 6.24, which surpassed the genome-wide LOD threshold. Meanwhile, the allele effect analysis showed alleles associated with these three traits could contribute to the trait improvement from 4.6% to 20.7%. These findings, including a dense linkage map and identification of significant QTL regions associated with K/F, M/F and S/F that could be applied in MAS in the oil palm breeding programme. In addition, these approaches using the oil palm genetic linkage map and QTL analysis could fast-track the process of generating new oil palm varieties as compared to the oil palm conventional breeding method. 2020-12 Thesis NonPeerReviewed text en http://psasir.upm.edu.my/id/eprint/104318/1/FAKHRUR%20RAZI%20BIN%20MOHD%20SHAHA%20-%20IR.pdf Mohd Shaha, Fakhrur Razi (2020) Construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield-related quantitative trait loci. Masters thesis, Universiti Putra Malaysia. Oil palm - Genetics Plant genome mapping |
| spellingShingle | Oil palm - Genetics Plant genome mapping Mohd Shaha, Fakhrur Razi Construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield-related quantitative trait loci |
| title | Construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield-related quantitative trait loci |
| title_full | Construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield-related quantitative trait loci |
| title_fullStr | Construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield-related quantitative trait loci |
| title_full_unstemmed | Construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield-related quantitative trait loci |
| title_short | Construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield-related quantitative trait loci |
| title_sort | construction of oil palm (elaeis guineensis jacq.) genetic linkage map and mapping of yield-related quantitative trait loci |
| topic | Oil palm - Genetics Plant genome mapping |
| url | http://psasir.upm.edu.my/id/eprint/104318/ http://psasir.upm.edu.my/id/eprint/104318/1/FAKHRUR%20RAZI%20BIN%20MOHD%20SHAHA%20-%20IR.pdf |