Construction of high density genetic linkage maps and fine mapping of quantitative trait loci associated with yield components and fatty acid composition in oil palm

Ting, Ngoot Chin (2018) Construction of high density genetic linkage maps and fine mapping of quantitative trait loci associated with yield components and fatty acid composition in oil palm. PhD thesis, University of Nottingham.

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The African oil palm (Elaeis guineensis Jacq.) is a highly valued oil producing perennial crop with a productive lifespan of about 25 years. Although benefiting from a long productivity period, oil palm genetic improvement is a slow and tedious process which requires between 10 to 12 years to complete one selection cycle. As such, marker-assisted selection (MAS) is an invaluable tool for yield improvement in oil palm. In particular, MAS could be used to facilitate efforts to increase the unsaturated fatty acid content of palm oil by introgression of desired alleles from the American species, E. oleifera which produces highly unsaturated oil.

In order to help achieve this, high density genetic linkage maps were constructed for a commercial Deli dura (maternal) x Yangambi pisifera (paternal) breeding population (P2) and a Colombian E. oleifera (maternal) x Nigerian E. guineensis (paternal) interspecific hybrid population (OxG). The P2 and OxG mapping populations were screened with approximately 700 oil palm SSR primer-pairs and genotyped with a 4.5K customized oil palm SNP array to identify informative markers. The P2 and OxG populations consisted of 87 and 108 palms, respectively. Genetic linkage maps were first constructed for the individual parental palms of the mapping populations and followed by integration of the two

parental maps. A P2 integrated map with 1,331 markers spanning 1,867 cM over the 16 linkage groups was constructed, representing the 16 chromosome pairs in oil palm. This study for the first time reports the genetic map for the Colombian E. oleifera, although the map only comprises of ten linkage groups with 65 markers spanning 471 cM. The Colombian E. oleifera map was also successfully integrated with the Nigerian E. guineensis parental map, resulting in a partial integrated map for OxG. The genetic maps and the available phenotypic data were successfully used to identify 22 quantitative trait loci (QTLs) associated with various yield components (YC) in the P2 population and 12 QTLs for fatty acid composition (FAC) in the OxG population. The QTLs identified for FAC include the total unsaturation levels via iodine value (IV), myristic (C14:0), palmitic (C16:0), palmitoleic (C16:1), stearic (C18:0), oleic (C18:1) and linoleic (C18:2) acids. On the P2 integrated map, QTLs for YC were associated with mean bunch number (MBN), mean fruit weight (MFW), oil/bunch ratio (OTB), oil/wet mesocarp ratio (OTWP), oil/dry mesocarp ratio (OTDP), mean mesocarp weight (MPW), wet mesocarp weight (WPWT), kernel yield (KY), mean kernel weight (MKW), mean shell weight (MSW), shell to fruit (STF), total oil (TOT), oil yield (OY) and dry mesocarp weight (DPWT). The closely linked markers demonstrated significant allelic effects associated with the YC and FAC phenotypes analysed. The genetic effects (estimated by G Model) for the identified QTLs can be ranked from high for C16:0, C18:1 and IV (ranging from 2.16 – 2.46) to medium for OTWP, DPWT, MPW, WPWT, OTB, MFW, OTDP, MBN and STF (0.50 – 2.14) and low (< 0.5) for KY, MKW, MSW, C18:2, C18:0, C16:1 and C14:0. The three major QTLs for C16:0, C18:1 and IV were also successfully cross-mapped on two interspecific BC2 populations, which adds confidence on the association of the markers with the traits concerned and reflecting their potential utility in a MAS programme. This study also identified candidate regulatory genes and transcription factors (TFs) within the QTL confidence intervals by aligning to the oil palm (EG5) genome build. A set of five candidate genes (HIBCH, PATE/FATB, BASS2, LACS4 and DGAT1) and a TF (WRI1) were identified within the QTL confidence interval associated with genetic effects for C16:0, C18:1, C14:0, C18:0 and IV in LGOT1, which was supported by the significant differential expression patterns observed for the candidate genes and TF in RNA sequencing (RNA-seq) and real-time PCR (qRT-PCR) experiments. The RNA-seq and qRT-PCR experiments included palms from OxG and two independent interspecific backcross populations. Clear differential expression patterns were observed for some of the genes and their putative isoforms, which requires further validation in future studies.

The high-density SNP and SSR-based genetic maps developed in this study have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP, RFLP and SSR markers. The improved maps with reduced gap between markers were aligned to the EG5 genome build, which proved useful for mining of candidate genes associated with the QTLs from the targeted regions. The closely linked markers and candidate genes associated with FAC and YC provide a good starting point for other genetic improvement studies in oil palm including whole genome association mapping studies. The candidate gene approach as used in the present study is useful for identifying the potential causal genes linked to QTLs. Finally, the markers closely linked to specific traits, specially IV, C16:0 and C18:1, MFW, MPW and OTDP have great potential and should be prioritized for further validation in the effort towards their adoption for MAS to introduce greater unsaturation and improve oil yield in commercial oil palm.

Item Type: Thesis (University of Nottingham only) (PhD)
Supervisors: Massaw, Festo
Mayes, Sean
Sambanthamurthi, Ravigadevi
Singh, Rajinder
Keywords: oil palm, plant breeding, plant genome mapping, genetic
Subjects: S Agriculture > SB Plant culture
Faculties/Schools: University of Nottingham, Malaysia > Faculty of Science and Engineering — Science > School of Biosciences
Item ID: 52227
Depositing User: TING, NGOOT CHIN
Date Deposited: 18 Aug 2018 04:40
Last Modified: 21 Jul 2020 04:30

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