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Putative regulatory candidate genes for QTL linked to fruit traits in oil palm (Elaeis guineensis Jacq.)

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Abstract

Palm oil is among the most important vegetable oils, contributing to a quarter of the world’s oils and fats market. The oil palm (Elaeis guineensis Jacq.) fruitlets, which are the source of palm oil, vary from 8 to 20 g in weight. Palm oil content in the fruitlets is approximately 45–50% by weight and an increase in the percentage of mesocarp-to-fruit is likely to have a positive effect on oil yield. In this study, we report a quantitative trait loci (QTL) associated with two yield related components, namely fruit and mesocarp content in a commercial breeding population (Deli dura × Yangambi pisifera). The QTL confidence interval of about 12 cM (~ 6.7 Mbp) was fine-mapped with 31 markers (17 SNPs and 14 SSRs) consisting of 20 nuclear markers derived from the maternal parent, six paternal and five co-segregating markers. Interestingly, inheritance of the paternal alleles leads to a larger difference in both fruit and mesocarp weight, when comparing genotypes in the progeny palms. Candidate genes and transcription factors were mined from the QTL region by positioning markers on the oil palm EG5 genome build. Putative genes and transcription factors involved in various biological processes including flower organ development, flowering, photosynthesis, microtubule formation, nitrogen and lipid metabolism were identified within this QTL interval on pseudo-chromosome 3. This genome-based approach allowed us to identify a number of potential candidate gene markers associated with oil palm fruit and mesocarp weight which can be further evaluated for potential use in marker-assisted breeding.

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Abbreviations

BLASTN:

Similarity search of the NCBI nucleotide database using a nucleotide query

BLASTX:

Similarity search of the NCBI protein database using a translated nucleotide query

CCT4 :

T-complex protein 1 subunit delta

CHR03:

Pseudo-chromosome 3

CHS :

Chalcone synthase

COP1 :

Constitutively photomorphogenic 1

cM:

Centimorgan map distance

DPF:

Dry mesocarp/fruit ratio

EG5:

E. guineensis 5th genome build as published as Singh et al. (2013)

FB:

Fruit/bunch ratio

FELDA:

Federal Land Development Authority Malaysia

FFB:

Fresh fruit bunch

GM:

G model

GS :

Glutamine synthetase nodule isozyme

IM:

Interval Mapping

KCS6 :

3-Ketoacyl-CoA synthase 6

KW:

Kruskal–Wallis test

Lhcb1 :

Chlorophyll a-b binding protein of LHCII type 1

LG:

Linkage group

LOD:

Logarithm of odds

LPP2 :

Lipid phosphate phosphatase 2

MAP70.1 :

Microtubule-associated protein 70-1

MAS:

Marker-assisted selection

Mbp:

Million base-pairs

MFW:

Mean fruit weight

MKW:

Mean kernel weight

MPW:

Mean mesocarp weight

MQM:

Multiple-QTL Model

MSW:

Mean shell weight

MTF:

Mesocarp/fruit ratio

MYB21 :

TF MYB21

nr:

NCBI non-redundant protein sequences database

nt:

NCBI nucleotide collection

NUC :

Zinc finger protein NUTCARACKER

ORP1C :

Oxysterol-binding protein-related protein 1C

OTDP:

Oil/dry mesocarp ratio

QTL:

Quantitative trait loci

refseq_protein:

NCBI reference proteins database

RFLP:

Restriction fragment length polymorphism

SF and STF:

Shell/fruit ratio

SLR1 :

DELLA protein SLR1

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

TF:

Transcription factor

TPS6 :

α,α-Trehalose-phosphate synthase [UDP-forming] 6

TUBB :

Tubulin beta chain

VAC14 :

Protein VAC14 homolog

WPF:

Wet mesocarp/fruit ratio

YC:

Yield components

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Acknowledgements

The authors would like to thank the Director-General of Malaysian Palm Oil Board for permission to publish this paper. Part of the work was carried out at Biometris, Wageningen University and Research Centre, the Netherlands. The authors thank Dr. Rex Bernardo from University of Minnesota for permission to use the G Model software. We would also like to extend our appreciation to Ms. Maizura Azwanie Mohd Zarawi for her technical assistance in PCR. We thank Bioinformatics team at Malaysian Palm Oil Board for providing the automatic computational pipeline used for sequence homology search and sequence extraction.

Funding

This study was funded by the Malaysian Palm Oil Board.

Author information

Author notes

  1. Tzer-Ying Seng

    Present address: IOI Palm Biotech Sdn. Bhd, IOI Resort, 62502, Putrajaya, Malaysia

Authors and Affiliations

  1. Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000, Kajang, Selangor, Malaysia

    Ngoot-Chin Ting, Ravigadevi Sambanthamurthi, Maizura Ithnin & Rajinder Singh

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

    Sean Mayes

  3. Biotechnology Research Centre, School of Biosciences, University of Nottingham Malaysia Campus, Jalan Broga, 43500, Semenyih, Selangor, Malaysia

    Ngoot-Chin Ting & Festo Massawe

  4. Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC, Wageningen, The Netherlands

    Johannes Jansen

  5. FELDA Global Ventures Research and Development Sdn. Bhd. (FGV R&D), Kuala Lumpur, Wilayah Persekutuan, Malaysia

    Sharifah Shahrul Rabiah Syed Alwee & Tzer-Ying Seng

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  7. Tzer-Ying Seng
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  8. Maizura Ithnin
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  9. Rajinder Singh
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Correspondence to Rajinder Singh.

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Ting, NC., Mayes, S., Massawe, F. et al. Putative regulatory candidate genes for QTL linked to fruit traits in oil palm (Elaeis guineensis Jacq.). Euphytica 214, 214 (2018). https://doi.org/10.1007/s10681-018-2296-y

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  • DOI: https://doi.org/10.1007/s10681-018-2296-y

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