Skip to main content
SpringerLink
Log in

Mapping QTL for leaf area in oil palm using genotyping by sequencing

  • Original Article
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Leaf area is an important parameter in oil palm breeding as it is positively correlated with oil yield. However, measurement of leaf area is tedious and also destructive. In the present study, a breeding population with 145 palms derived from a cross between Deli Dura and Avros Pisifera was used to construct a high-density linkage map and identify quantitative trait loci (QTL) for leaf area in oil palm. Using genotyping by sequencing, a linkage map containing 2413 SNPs was constructed. The total length of the linkage map was 1161.89 cM, with an average marker spacing of 0.48 cM. Based on the continuous phenotyping of leaf area from 2010 to 2015, two suggestive QTL for leaf area were mapped on chromosomes (Chr) 3 and 9. The allelic effects of the QTL associated with leaf area in the mapping population were estimated by linear regression using ordinary least squares method. The QTL on Chr 9 explained 13.3% of phenotypic variation for leaf area. A candidate gene, ARC5, within the narrow interval of QTL on Chr 9 was identified. The gene was significantly higher expressed in leaf than root and fruit of oil palm. This high-quality and SNP-based map supplies a base to fine map QTL for agronomic traits in oil palm, and the markers closely linked to the stable QTL may be used in marker-assisted selection in oil palm breeding.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Agyei-Dwarko D, Ofori K, Kaledzi P (2012) Variation and correlation analysis of growth parameters in DXP oil palm (Elaeis guineensis J.) seedlings. Elixir Agri 946–8949

  • Al-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, Al-Azwani EK, Chaluvadi S, Pontaroli AC, DeBarry J (2011) De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera). Nat Biotechnol 29:521–527

    Article  CAS  PubMed  Google Scholar 

  • Awal M, Wan I (2008) Measurement of oil palm LAI by manual and LAI-2000 method. Asian J Sci Res 1:49–56

    Article  Google Scholar 

  • Awal M, Ismail W, Ishak W, Bockari-Gevao SM (2010) Determination of leaf area index for oil palm plantation using hemispherical photography technique. Pertanika J Sci Technol 18:23–32

    Google Scholar 

  • Bai B, Wang L, Lee M, Zhang Y, Rahmadsyah, Alfiko Y, Ye BQ, Wan ZY, Lim CH, Suwanto A, Chua N-H (2017) Genome-wide identification of markers for selecting higher oil content in oil palm. BMC Plant Biol 17:93

    Article  PubMed  PubMed Central  Google Scholar 

  • Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376

    Article  PubMed  PubMed Central  Google Scholar 

  • Billotte N, Marseillac N, Risterucci AM, Adon B, Brottier P, Baurens FC, Singh R, Herran A, Asmady H, Billot C, Amblard P, Durand-Gasselin T, Courtois B, Asmono D, Cheah SC, Rohde W, Ritter E, Charrier A (2005) Microsatellite-based high density linkage map in oil palm (Elaeis guineensis Jacq.) Theor Appl Genet 110:754–765

    Article  CAS  PubMed  Google Scholar 

  • Breure CJ (1985) Relevant factors associated with crown expansion in oil palm (Elaeis guineensis Jacq.) Euphytica 34:161–175

    Article  Google Scholar 

  • Breure CJ (1986) Parent selection for yield and bunch index in the oil palm in West New Britain. Euphytica 35:65–72

    Article  Google Scholar 

  • Breure CJ (2010) Rate of leaf expansion: a criterion for identifying oil palm (Elaeis guineensis Jacq.) types suitable for planting at high densities. NJAS Wageningen J Life Sci 57:141–147

    Article  Google Scholar 

  • Catchen JM, Amores A, Hohenlohe P, Cresko W, Postlethwait JH (2011) Stacks: building and genotyping loci de novo from short-read sequences. G3 (Bethesda) 1:171–182

    Article  CAS  Google Scholar 

  • Corley R, Tinker P (2016) The oil palm, Fifth edn. Wiley Blackwell, New Jersey

    Google Scholar 

  • Corley R, Gray B, Kee NS (1971a) Productivity of the oil palm (Elaeis guineensis Jacq.) in Malaysia. Exp Agric 7:129–136

    Article  Google Scholar 

  • Corley R, Hardon J, Tan G (1971b) Analysis of growth of the oil palm (Elaeis guineensisJacq.) I. Estimation of growth parameters and application in breeding. Euphytica 20:307–315

    Article  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fowler C, Rasmusson DC (1969) Leaf area relationships and inheritance in barley. Crop Sci 9:729–731

    Article  Google Scholar 

  • Gao H, Kadirjan-Kalbach D, Froehlich JE, Osteryoung KW (2003) ARC5, a cytosolic dynamin-like protein from plants, is part of the chloroplast division machinery. Proc Natl Acad Sci U S A 100:4328–4333

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gao Y, Liu H, An C, Shi Y, Liu X, Yuan W, Zhang B, Yang J, Yu C, Gao H (2013) Arabidopsis FRS4/CPD25 and FHY3/CPD45 work cooperatively to promote the expression of the chloroplast division gene ARC5 and chloroplast division. Plant J 75:795–807

    Article  CAS  PubMed  Google Scholar 

  • Hardon J, Williams C, Watson I (1969) Leaf area and yield in the oil palm in Malaya. Exp Agric 5:25–32

    Article  Google Scholar 

  • Holzinger A, Kwok EY, Hanson MR (2008) Effects of arc3, arc5 and arc6 mutations on plastid morphology and stromule formation in green and nongreen tissues of Arabidopsis thaliana. Photochem Photobiol 84:1324–1335

    Article  CAS  PubMed  Google Scholar 

  • Horton P (2000) Prospects for crop improvement through the genetic manipulation of photosynthesis: morphological and biochemical aspects of light capture. J Exp Bot 51:475–485

    Article  CAS  PubMed  Google Scholar 

  • Iqbal M, Khan K, Sher H, Al-Yemeni MN (2011) Genotypic and phenotypic relationship between physiological and grain yield related traits in four maize (Zea mays L.) crosses of subtropical climate. SRE 6:2864–2872

    Google Scholar 

  • Jin J, Lee M, Bai B, Sun Y, Qu J, Rahmadsyah AY, Lim CH, Suwanto A, Sugiharti M, Wong L (2016) Draft genome sequence of an elite Dura palm and whole-genome patterns of DNA variation in oil palm. DNA Res 23:527–533

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ku L, Ren Z, Chen X, Shi Y, Qi J, Su H, Wang Z, Li G, Wang X, Zhu Y (2016) Genetic analysis of leaf morphology underlying the plant density response by QTL mapping in maize (Zea mays L.) Mol Breed 36:63

    Article  Google Scholar 

  • Lambert RJ, Mansfield BD, Mumm RH (2014) Effect of leaf area on maize productivity. Maydica 59:58–64

    Google Scholar 

  • Leister D (2003) Chloroplast research in the genomic age. Trends Genet 19:47–56

    Article  CAS  PubMed  Google Scholar 

  • Li C, Li Y, Shi Y, Song Y, Zhang D, Buckler ES, Zhang Z, Wang T, Li Y (2015) Genetic control of the leaf angle and leaf orientation value as revealed by ultra-high density maps in three connected maize populations. PLoS One 10:e0121624

    Article  PubMed  PubMed Central  Google Scholar 

  • Metzker ML (2010) Sequencing technologies--the next generation. Nat Rev Genet 11:31–46

    Article  CAS  PubMed  Google Scholar 

  • Mickelson S, Stuber C, Senior L, Kaeppler S (2002) Quantitative trait loci controlling leaf and tassel traits in a B73× Mo17 population of maize. Crop Sci 42:1902–1909

    Article  CAS  Google Scholar 

  • Miyagishima S-Y, Froehlich JE, Osteryoung KW (2006) PDV1 and PDV2 mediate recruitment of the dynamin-related protein ARC5 to the plastid division site. Plant Cell 18:2517–2530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nicot N, Hausman J-F, Hoffmann L, Evers D (2005) Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot 56:2907–2914

    Article  CAS  PubMed  Google Scholar 

  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pootakham W, Jomchai N, Ruang-areerate P, Shearman JR, Sonthirod C, Sangsrakru D, Tragoonrung S, Tangphatsornruang S (2015) Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS). Genomics 105:288–295

    Article  CAS  PubMed  Google Scholar 

  • Pyke KA, Leech RM (1994) A genetic analysis of chloroplast division and expansion in Arabidopsis thaliana. Plant Physiol 104:201–207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rance K, Mayes S, Price Z, Jack P, Corley R (2001) Quantitative trait loci for yield components in oil palm (Elaeis guineensis Jacq.) Theor Appl Genet 103:1302–1310

    Article  CAS  Google Scholar 

  • Robertson EJ, Rutherford SM, Leech RM (1996) Characterization of chloroplast division using the Arabidopsis mutant arc5. Plant Physiol 112:149–159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sakamoto W, S-y M, Jarvis P (2008) Chloroplast biogenesis: control of plastid development, protein import, division and inheritance. Arabidopsis Book 6:e0110

    Article  PubMed  PubMed Central  Google Scholar 

  • Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using kompetitive allele specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14

    Article  CAS  Google Scholar 

  • Singh R, Ong-Abdullah M, Low ETL, Manaf MAA, Rosli R, Nookiah R, Ooi LCL, Ooi SE, Chan KL, Halim MA, Azizi N, Nagappan J, Bacher B, Lakey N, Smith SW, He D, Hogan M, Budiman MA, Lee EK, DeSalle R, Kudrna D, Goicoechea JL, Wing RA, Wilson RK, Fulton RS, Ordway JM, Martienssen RA (2013) Oil palm genome sequence reveals divergence of interfertile species in old and new worlds. Nature 500:335–339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tesso T, Tirfessa A, Mohammed H (2011) Association between morphological traits and yield components in the durra sorghums of Ethiopia. Hereditas 148:98–109

    Article  PubMed  Google Scholar 

  • Torkamaneh D, Laroche J, Belzile F (2016) Genome-wide SNP calling from genotyping by sequencing (GBS) data: a comparison of seven pipelines and two sequencing technologies. PLoS One 11:e0161333

    Article  PubMed  PubMed Central  Google Scholar 

  • Van Ooijen JW (2006) JoinMap®4, software for the calculation of genetic linkage maps in experimental populations. Kyazma B V, Wageningen

    Google Scholar 

  • Van Ooijen JW (2009) MapQTL®6. Software for the mapping of quantitative trait loci in experimental populations of diploid species. Kyazma BV, Wageningen

    Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  CAS  PubMed  Google Scholar 

  • Wan Ishake WI, Awal MA (2007) Leaf area index model for oil palm FFB yield prediction. Pertanika J Trop Agric Sci 30:51–56

    Google Scholar 

  • Wang L, Huang SQ, Xia JH, Liu P, Wan ZY, Yue GH (2015) Genome-wide discovery of gene-related SNPs in Barramundi Lates calcarifer. Conserv Genet Resour 7:605–608

    Article  Google Scholar 

  • Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407

    Article  Google Scholar 

  • Yang Y, Glynn JM, Olson BJ, Schmitz AJ, Osteryoung KW (2008) Plastid division: across time and space. Curr Opin Plant Biol 11:577–584

    Article  CAS  PubMed  Google Scholar 

  • Yang C, Tang D, Qu J, Zhang L, Zhang L, Chen Z, Liu J (2016a) Genetic mapping of QTL for the sizes of eight consecutive leaves below the tassel in maize (Zea mays L.) Theor Appl Genet 129:2191–2209

    Article  CAS  PubMed  Google Scholar 

  • Yang D, Liu Y, Cheng H, Chang L, Chen J, Chai S, Li M (2016b) Genetic dissection of flag leaf morphology in wheat (Triticum aestivum L.) under diverse water regimes. BMC Genet 17:94

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yin X, Kropff MJ, Stam P (1999) The role of ecophysiological models in QTL analysis: the example of specific leaf area in barley. Heredity 82:415–421

    Article  PubMed  Google Scholar 

  • Yue B, XUE W-Y, Luo L-J, XING Y-Z (2006) QTL analysis for flag leaf characteristics and their relationships with yield and yield traits in rice. Acta Genet Sin 33:824–832

    Article  CAS  PubMed  Google Scholar 

  • Zelitch I (1982) The close relationship between net photosynthesis and crop yield. Bioscience 32:796–802

    Article  Google Scholar 

Download references

Acknowledgements

This research has been financially supported by Wilmar International and the internal fund of the Temasek Life Sciences Laboratory, Singapore. We thank staff members of the R&D Department of Wilmar International Plantation for technical support.

Author information

Author notes

  1. Bin Bai and Ying Jun Zhang contributed equally to this work.

Authors and Affiliations

  1. Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore

    Bin Bai, Ying Jun Zhang, Le Wang, May Lee, Bao Qing Ye & Gen Hua Yue

  2. Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China

    Bin Bai

  3. Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China

    Ying Jun Zhang

  4. R & D Department, Wilmar International Plantation, Palembang, Indonesia

    Rahmadsyah

  5. Biotech Lab, Wilmar International, Jakarta, Indonesia

    Yuzer Alfiko, Sigit Purwantomo & Antonius Suwanto

  6. Bogor Agricultural University, Bogor, Jawa Barat, 16680, Indonesia

    Antonius Suwanto

  7. Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore

    Gen Hua Yue

  8. School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, Singapore, 637551, Singapore

    Gen Hua Yue

Authors
  1. Bin Bai
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ying Jun Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Le Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. May Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rahmadsyah
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bao Qing Ye
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yuzer Alfiko
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Sigit Purwantomo
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Antonius Suwanto
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Gen Hua Yue
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

GHY designed and supervised this study. BB performed SNP development, linkage map construction, and drafted the manuscript. YJZ assisted with DNA extraction, data analysis and gene expression study. LW conducted in RAD-seq data analysis and SNP calling. ML prepared DNA samples and carried out genotyping using microchip. BQY edited the paper. Rahmadsyah, CHL, YA, SP and AS managed the plants and recorded the traits in the field. GHY finalized the manuscript, and all authors read and approved the final manuscript.

Corresponding author

Correspondence to Gen Hua Yue.

Ethics declarations

Competing interests

The authors BB, YJZ, LW, ML, BQY, and GHY declare no competing financial interests. But the authors R, YA, SP and AS have financial competing interests due to they are employees of Wilmar International and Wilmar International funded this study.

Data archiving statement

The RAD-seq datasets supporting the conclusions of this article are available in the DDBJ database, accession number (BioProject Accession: PRJDB5817). Other data related to this paper are available in Supplementary Materials, Additional Tables S1, S2 and S3, as well as Additional Fig. S1.

Additional information

Communicated by W. Ratnam

Electronic supplementary material

Additional Table S1

All the RAD-seq markers and micro-chip array markers used in this study, with flanking sequences, linkage map and physical position. (XLSX 282 kb)

Additional Table S2

Descriptive statistics of leaf area in the mapping population of Deli Dura × Avros Pisifera (DOCX 13 kb)

Additional Table S3

Summary of annotated genes within QTL region on Chr 9 for leaf area in oil palm genome (DOCX 14 kb)

Additional Figure S1

Distribution of leaf area value (average across four periods) in the mapping population of Deli Dura × Avros Pisifera (JPEG 38 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Bai, B., Zhang, Y.J., Wang, L. et al. Mapping QTL for leaf area in oil palm using genotyping by sequencing. Tree Genetics & Genomes 14, 31 (2018). https://doi.org/10.1007/s11295-018-1245-1

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-018-1245-1

Keywords

Search

Navigation