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Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers

Planta volume 253, Article number: 63 (2021) Cite this article

Abstract

Main conclusion

Karyotyping using high-density genome-wide SNP markers identified various chromosomal aberrations in oil palm (Elaeis guineensis Jacq.) with supporting evidence from the 2C DNA content measurements (determined using FCM) and chromosome counts.

Abstract

Oil palm produces a quarter of the world’s total vegetable oil. In line with its global importance, an initiative to sequence the oil palm genome was carried out successfully, producing huge amounts of sequence information, allowing SNP discovery. High-capacity SNP genotyping platforms have been widely used for marker–trait association studies in oil palm. Besides genotyping, a SNP array is also an attractive tool for understanding aberrations in chromosome inheritance. Exploiting this, the present study utilized chromosome-wide SNP allelic distributions to determine the ploidy composition of over 1,000 oil palms from a commercial F1 family, including 197 derived from twin-embryo seeds. Our method consisted of an inspection of the allelic intensity ratio using SNP markers. For palms with a shifted or abnormal distribution ratio, the SNP allelic frequencies were plotted along the pseudo-chromosomes. This method proved to be efficient in identifying whole genome duplication (triploids) and aneuploidy. We also detected several loss of heterozygosity regions which may indicate small chromosomal deletions and/or inheritance of identical by descent regions from both parents. The SNP analysis was validated by flow cytometry and chromosome counts. The triploids were all derived from twin-embryo seeds. This is the first report on the efficiency and reliability of SNP array data for karyotyping oil palm chromosomes, as an alternative to the conventional cytogenetic technique. Information on the ploidy composition and chromosomal structural variation can help to better understand the genetic makeup of samples and lead to a more robust interpretation of the genomic data in marker–trait association analyses.

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Availability of data

The pseudo-chromosome positions and BAF for the SNP markers analysed in this study are included in this article as Supplementary Table S1.

Abbreviations

AP:

AVROS pisifera

BAF:

B-allele frequency

CMDV:

Centre for marker discovery and validation

CTAB:

Cetyltriammonium bromide

DD:

Deli dura

FCM:

Flow cytometry

FISH:

Fluorescent in situ hybridization

LOH:

Loss of heterozygosity

LTR:

Long terminal repeat

PI:

Propidium iodide

SNP:

Single nucleotide polymorphism

2C:

Nuclear DNA content in a diploid genome

θ :

Theta distribution (the allelic intensity ratio of SNP markers)

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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. We would also like to thank Zainab Anip, Maizura Azwanie Mohd Zarawi, Mohamad Razali Mohd Nor and MPOB Breeding and Quantitative Genetics Group for technical assistance in sampling and lab work.

Funding

The project was funded by Malaysian Palm Oil Board (ABBC23-2019).

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Author notes

  1. Ting Ngoot-Chin and Muhammad Azwan Zulkifli contributed equally.

Authors and Affiliations

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

    Ting Ngoot-Chin, Muhammad Azwan Zulkifli, Noorhariza Mohd Zaki, Norhalida Mohamed Serdari, Suzana Mustaffa, Nik Shazana Nik Mohd Sanusi, Eng Ti Leslie Low, Maizura Ithnin & Rajinder Singh

  2. Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands

    Eric van de Weg & Marinus J. M. Smulders

  3. Plant Breeding and Services Department, KULIM Plantations Berhad, 81900, Kota Tinggi, Johor, Malaysia

    Mohd Isa Zainol Abidin

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  1. Ting Ngoot-Chin
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Correspondence to Rajinder Singh.

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Communicated by Anastasios Melis.

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Electronic supplementary material

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425_2021_3567_MOESM1_ESM.xlsx

Supplementary Table S1. The oil palm (EG5) pseudo-chromosome positions and BAF for the SNP markers analysed in this study (xlsx 5732 kb)

Supplementary Table S2. Example of the FCM histogram statistics for two palms (docx 1880 kb)

Supplementary Table S3. Comparison 4.5 Mbp chromosomal region on CHR08 among diploids (xlsx 66 kb)

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Ngoot-Chin, T., Zulkifli, M.A., van de Weg, E. et al. Detection of ploidy and chromosomal aberrations in commercial oil palm using high-throughput SNP markers. Planta 253, 63 (2021). https://doi.org/10.1007/s00425-021-03567-7

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