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Candidate genes linked to QTL regions associated with fatty acid composition in oil palm

Biologia volume 76, pages 267–279 (2021)Cite this article

Abstract

The present study searched for candidate genes in five linkage groups (LGs) - T2, T3, OT4, OT6 and T9 hosting the QTLs associated with iodine value (IV) and fatty acid composition (FAC) in an oil palm interspecific hybrid population. Each of the five LGs was successfully anchored to its corresponding chromosomal segment where, a wider repertoire of candidate genes was identified. This study further revealed a total of 19 candidate genes and four transcription factors involved in biosynthesis of fatty acids, lipids (including triacylglycerol) and acetyl-CoA, glycosylation and degradation of fatty acids. Their possible involvement in regulating the levels of saturation are discussed. In addition, 22 candidate genes located outside the QTL intervals were also identified across the interspecific hybrid genome. A total of 92 SSR markers were developed to tag the presence of these candidate genes and 50 were successfully mapped onto their respective positions on the genome. The data obtained here complements the previous studies, and collectively, these QTL-linked candidate gene markers could help breeders in more precisely selecting palms with the desired FAC.

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Fig. 1
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Abbreviations

4CLL1:

4-coumarate--CoA ligase 1

AACT :

acetoacetyl-CoA thiolase

acbd4:

acyl-CoA-binding domain-containing protein 4

ACX4:

acyl-CoA oxidase 4

C14:0:

myristic acid

C16:0:

palmitic acid

C16:1:

palmitoleic acid

C18:0:

stearic acid

C18:1:

oleic acid

C18:2:

linoleic acid

CHR :

pseudo-chromosome

cM :

centiMorgans

CP :

cross pollinator

CPO:

crude palm oil

CTAB:

cetyltriammonium bromide

DNA:

deoxyribonucleic acid

EG5:

E. guineensis genome build

ER :

endoplasmic reticulum

FA:

fatty acid

FAC:

fatty acid composition

FAD3/7/8:

omega-3 fatty acid desaturase

FBA :

fructose-bisphosphate aldolase

Fwd :

forward primer

GLABRA :

homeobox protein GLABRA

GPAT3:

glycerol-3-phosphate acyltransferase 3

GPDH :

glycerol-3-phosphate dehydrogenase

HAGH :

hydroxyacyl glutathione hydrolase

HD-Zip :

TF homeobox-leucine zipper protein ATHB-13

IV:

iodine value

KAR :

beta-ketoacyl-ACP reductase

KASII, III :

beta-ketoacyl-ACP synthases II, III

LG:

linkage group

LIPT2:

triacylglycerol lipase 2

LOD :

logarithm of odds

LPAAT1:

lysophosphatidic acid acyltransferase 1

M13 :

primer 5’CACGACGTTGTAAAACGAC3’

MACP/MAT :

malonyl-CoA:ACP transacylase

MAS:

marker-assisted selection

MDH :

malate dehydrogenase

MYB :

TF myb family PHL8

NCBI:

National center for biotechnology information

OxG:

the E. oleifera x E. guineensis interspecific hybrid population

OEP163:

outer envelope pore protein 16–3

OTE/FATA :

oleoyl-ACP thioesterase

PATE/FATB :

palmitoyl-ACP thioesterase

PVE :

phenotypic variation explained

QTLs:

quantitative trait loci

rf :

recombination frequency

Rvs :

reverse primer

SAD :

stearoyl-ACP desaturase

sn :

stereospecific number

SNP :

single nucleotide polymorphism

SSR :

simple sequence repeats

T128:

Nigerian E. guineensis paternal palm

TAG:

triacylglycerol

TCP15:

TF TCP15

TF:

transcription factor

TPE:

tris-phosphate buffer

UGT :

UDP-glycosyltransferase

Uniprot :

Universal protein resource database

UP1026:

Colombian E. oleifera maternal palm

References

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Acknowledgments

The authors would like to thank the Director-General of Malaysian Palm Oil Board (MPOB) for permission to publish this paper.

Availability of data

The sequence information for the candidate SSR markers is available at http://genomsawit.mpob.gov.my.

Funding

This study was funded by the Malaysian Palm Oil Board (MPOB).

Author information

Authors and Affiliations

  1. Malaysian Palm Oil Board (MPOB), P.O. Box 10620, 50720, Kuala Lumpur, Malaysia

    Ngoot-Chin Ting, Ravigadevi Sambanthamurthi, Kuang-Lim Chan & Rajinder Singh

  2. School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Malaysia

    Ngoot-Chin Ting & Festo Massawe

  3. Plant and Crop Sciences, Sutton Bonington Campus, University of Nottingham, Sutton Bonington, Loughborough, LE12 5RD, UK

    Sean Mayes

  4. United Plantations Bhd, Jendarata Estate, 36009, Teluk Intan, Perak, Malaysia

    Kandha Sritharan

Authors
  1. Ngoot-Chin Ting
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  2. Sean Mayes
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  3. Festo Massawe
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  4. Ravigadevi Sambanthamurthi
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  5. Kuang-Lim Chan
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  6. Kandha Sritharan
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  7. Rajinder Singh
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Contributions

All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by Ting Ngoot-Chin. Bioinformatics analysis was supported by Chan Kuang-Lim and the plant materials used in this study was provided by Kandha Sritharan. The first draft of the manuscript was written by Ting Ngoot-Chin and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Rajinder Singh.

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Conflict of interest

The authors declare that they have no conflict of interest.

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Electronic supplementary material

Online Resource 1

Fig. 1. The polymorphism profiles observed for the segregating SSR alleles in the OxG mapping population. (DOCX 30.5 kb)

Online Resource 2

Table 1. Putative biological function for the candidate genes and transcription factors (TFs) identified from various QTL regions associated with palm oil iodine value (IV) and fatty acid composition (FAC) on the OxG genetic linkage map (Ting et al. 2016). (DOCX 54.5 kb)

Online Resource 3

Fig. 2. Mapping candidate SSR markers (in blue font) onto the OxG linkage map in linkage groups (LGs) T5, OT10, OT12, T14, OT15 and T16. These candidate SSR markers were developed from QTLs associated with FAC and oil yield published previously by Bourgis et al. (2011), Montoya et al. (2013) and Jeennor and Volkaert (2014). The updated OxG LGs (Mapping candidate markers) are aligned to the previous map (Before mapping candidate markers) published by Ting et al. (2016). Candidate genes and transcription factors are indicated in italic red. (DOCX 1.57 mb)

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Ting, NC., Mayes, S., Massawe, F. et al. Candidate genes linked to QTL regions associated with fatty acid composition in oil palm. Biologia 76, 267–279 (2021). https://doi.org/10.2478/s11756-020-00563-2

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