A SNP variation in an expansin (EgExp4) gene affects height in oil palm

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Plant Biology

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Introduction

Materials and Methods

Plant material and phenotype details

DNA extraction

Oil palm samples, PCR amplification and barcoding preparation for PacBio SMRT sequencing

Sequence data analysis

SNP Marker designing for high through-put PACE™ SNP genotyping

Population structure, statistical and association analyses

Results

Details for height phenotype of the GT population

Primer testing for amplification of full-length genomic DNA sequences of the height-related genes

Sample preparation for PacBio SMRT sequencing of the height-related genes

Analysis of sequence variations among short and tall oil palm groups

High through-put genotyping by PACE™ SNP genotyping

ANOVA and association analysis of mEgExp4_SNP118 with height

Discussion

Conclusions

Supplemental Information

Comparison of height distribution in short (St) and tall (Tt) oil palm groups from height data, including HT-1, HT-2, HT-3 and HT-4, of the GT population. cm = centimeters.

DOI: 10.7717/peerj.13046/supp-1

Example of PCR products amplified from the height-related genes by the gene-specific primers, including EgDELLA1-P1, EgGRF1-P2, EgGA20ox1-P2, EgAPG1-P1 and EgExp4-P1 with sizes from 2,516 to 3,015 bp (shown by red arrows). M = 1 Kb Plus DNA ladder.

DOI: 10.7717/peerj.13046/supp-2

Example of PCR products amplified from EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4 with bands close to the expected sizes from 2,516 to 3,015 bp (shown by red arrows) by the M13-tagged primers (Gel images on the left side) and.

DOI: 10.7717/peerj.13046/supp-3

The insertion and SNP variations are illustrated on the EgDELLA1 reference gene sequence, which has a full-length of 3,015 bp (oil palm draft sequences of Malaysian Palm Oil Board (MPOB) (http://genomsawit.mpob.gov.my/genomsawit/).

DOI: 10.7717/peerj.13046/supp-4

The insertion and deletion variations are illustrated on the EgGRF1 reference gene sequence, which has a full-length of 2,516 bp (oil palm draft sequences of Malaysian Palm Oil Board (MPOB) (http://genomsawit.mpob.gov.my/genomsawit/).

DOI: 10.7717/peerj.13046/supp-5

The insertion and deletion variations are illustrated on the EgGA20ox1 reference gene sequence, which has a full-length of 2,759 bp (oil palm draft sequences of Malaysian Palm Oil Board (MPOB) (http://genomsawit.mpob.gov.my/genomsawit/).

DOI: 10.7717/peerj.13046/supp-6

The insertion and deletion variations are illustrated on the EgExp4 reference gene sequence, which has a full-length of 2,586 bp (oil palm draft sequences of Malaysian Palm Oil Board (MPOB) (http://genomsawit.mpob.gov.my/genomsawit/).

DOI: 10.7717/peerj.13046/supp-7

The insertion and deletion variations are illustrated on the EgAPG1 reference gene sequence, which has a full-length of 2,917 bp (oil palm draft sequences of Malaysian Palm Oil Board (MPOB) (http://genomsawit.mpob.gov.my/genomsawit/).

DOI: 10.7717/peerj.13046/supp-8

Details of gene-specific primers designed from the height-related genes, including EgDELLA1, EgGRF1, EgGA20ox1, EgAPG1 and EgExp4.

The specified primers were selected based on their size amplification in the expected size. The amplification sites were from 5′ UTR to 3′ UTR sites of the genes.

DOI: 10.7717/peerj.13046/supp-9

Details of M13-tagged primers for full-length genomic DNA amplification, including M13-tagged EgDELLA1-P1, EgGRF1-P2, EgGA20ox1-P2, EgAPG1-P1 and EgExp4-P1 primers.

Sequences in red letters represent forward M13 sequence (18 bp) while sequences in blue letters represent reverse M13 sequence (18 bp).

DOI: 10.7717/peerj.13046/supp-10

Details of barcode (BC)-tagged M13 primer sets for both BC forward and BC reverse primers.

DOI: 10.7717/peerj.13046/supp-11

Details of SNP primers designed from the 4 SNP variations of the three genes, including EgDELLA1, EgGA20ox1 and EgExp4.

To amplify each SNP position, three primers, including two forward primers that are specific for each SNP (red letters and yellow highlights) and 1 common reverse primer, were designed. Sequences in blue letters represent sequences for FAM emission while sequences in green letters represent sequences for HEX emission.

DOI: 10.7717/peerj.13046/supp-12

Height details of three mEgExp4-SNP118 genotypes, including C/C, T/C and T/T, for height-recordings HT-1, HT-2, HT-3 and HT-4 from the GT population.

Genotype C/C was shown to be tallest, at 210 cm for HT-1, 250 cm for HT-2, 278 cm for HT-3 and 409 cm for HT-4. Genotype T/T was shown to be shortest, 185 cm for HT-1, 224 cm for HT-2, 257 cm for HT-3 and 370 cm for HT-4.

DOI: 10.7717/peerj.13046/supp-13

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Suthasinee Somyong conceived and designed the experiments, performed the experiments, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Phakamas Phetchawang performed the experiments, prepared figures and/or tables, and approved the final draft.

Abdulloh Kafa Bihi performed the experiments, prepared figures and/or tables, and approved the final draft.

Chutima Sonthirod analyzed the data, prepared figures and/or tables, and approved the final draft.

Wasitthee Kongkachana analyzed the data, prepared figures and/or tables, and approved the final draft.

Duangjai Sangsrakru performed the experiments, prepared figures and/or tables, and approved the final draft.

Nukoon Jomchai performed the experiments, prepared figures and/or tables, and approved the final draft.

Wirulda Pootakham conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Sithichoke Tangphatsornruang conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The sequences and raw data are available in the Supplemental Files and at NCBI: PRJNA760254.

Funding

This research was supported by the Agricultural Research Development Agency (ARDA), Thailand (grant numbers: PRP6105020780 and PRP6305030940). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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