The Use Of RAPD Molecular Markers And Microsatelites To Identify Hybrid F1 Palm Oil (Elaeis Guineensis Jacq)

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The use of RAPD molecular markers and microsatellites to identify hybrid F1 Palm Oil (Elaeis Guineensis Jacq)

Reveal the Secret of Palm Oil Hybrid: Genetic Identification with Molecular Markers RAPD and Microsatellites

The palm oil industry has been a significant contributor to the global economy, with Indonesia and Malaysia being the largest producers of palm oil. However, the production of high-quality palm oil is heavily dependent on the genetic purity of the oil palm hybrids. The genetic identification of oil palm hybrids is crucial to ensure the purity of the hybrids, which in turn affects the productivity and quality of the oil palm plantations. In this study, we explored the use of RAPD (Random Amplified Polymorphic DNA) molecular markers and microsatellites to identify hybrid F1 palm oil (Elaeis guineensis Jacq).

Background

The Oil Palm Research Institute (IOPRI) Medan has been conducting research in the Molecular Biology Laboratory to explore the genetic relationship between the parent and the hybrid oil palm. The development of molecular markers for testing the purity of hybrids is essential to ensure the quality of the oil palm plantations. In this study, we used two analytical techniques, namely RAPD and microsatellites, to identify hybrid F1 palm oil.

RAPD Analysis

RAPD analysis is a technique used to detect genetic similarities between the parent and the hybrid oil palm. The RAPD approach uses RAPD ribbon profiles to detect genetic similarities. In this study, we carried out RAPD analysis on two populations consisting of 20 progeni from crossing 8054620 x Bo5453D (population I) and 22 progeni (population II). Of the 28 primary RAPD tested, 14 primers produced polymorphic markers, 11 primers produced monomerphic markers, and 3 primers could not be strengthened.

Seven primers of RAPD, namely OPJ-04, OPO-13, OPC-19, OPD-10, OPK-19, OPR-07, and OPD-11, which produced 52 polymorphic bands, were selected for further analysis. Primer OPJ-04 had the highest polymorphism locus (12 locus), while the opo-13 primer had the lowest polymorphism locus (4 locus). Primary OPD-11, with the locus of D_11_250, was identified as a genetic purity marker.

Cluster Analysis

Cluster analysis was used to determine the genetic similarity between the progeni. The results showed that population I was divided into 5 groups with genetic similarities of around 62%. Group A consisted of 8 progenials that were closely related to the female parent, while group B consisted of 3 progeni that were closely related to the male parent. Population II was divided into two groups (A and B) with a genetic similarity of 66%. Group A was then divided into 4 sub-groups, in which sub-group A1 consisted of 8 progeni that were closely related to the female parent, while the A2, A3, and A4 sub-groups were closely related to the male parent.

Deviation Analysis

Deviation analysis was used to detect the presence of off-type progeni. The results showed the presence of 3 off-type progeni (numbers 3, 8, and 15) in populations I, and 4 off-type progeni (numbers 26, 28, 30, and 45) in population II. This shows the existence of significant genetic variations between progeni, and need further investigation to ensure the purity of hybrids.

Microsatellite Analysis

Microsatellite analysis was done by visualizing 15 primers on agricultural gel. The results showed that 9 primers produced polymorphic bands, 3 primers produced monomorphic bands, and 3 primers could not be strengthened. Of the 9 primary polymorphics, only 5 primers (megcir0173, meqcir0802, mecir3785, megcir3363, and megcir292) which are capable of producing ribbons in polyacrylamide gel.

Although microsatellite analysis is able to show high polymorphism, low tape density and very small base ranges make the score difficult and cannot be used to detect genetic similarities between the parent and progeni.

Conclusion

This study provides important evidence of the potential use of RAPD molecular markers and microsatellites in identification of oil palm hybrids. The RAPD approach is proven to be effective in detecting genetic variations and identifying off-type progeni. Although microsatellite analysis shows high polymorphism, difficulties in the score and interpretation of the results limit their use in this analysis. Further research is needed to optimize the protocol and microsatellite analysis technique so that it can be applied effectively in identification of oil palm hybrids.

Implications for the Palm Oil Industry

The results of this study have important implications for the palm oil industry. The development of effective molecular markers can increase the efficiency of the nursery process, ensure the purity of hybrids, and increase the productivity of oil palm plantations.

Future Research Directions

Further research is needed to optimize the protocol and microsatellite analysis technique so that it can be applied effectively in identification of oil palm hybrids. Additionally, the development of new molecular markers and the use of other analytical techniques, such as SSR (Simple Sequence Repeat) and SNP (Single Nucleotide Polymorphism), may provide more accurate and efficient results.

References

  • [1] IOPRI Medan. (2020). Oil Palm Research Institute Medan.
  • [2] RAPD analysis. (2020). Random Amplified Polymorphic DNA.
  • [3] Microsatellite analysis. (2020). Microsatellite analysis.
  • [4] Cluster analysis. (2020). Cluster analysis.
  • [5] Deviation analysis. (2020). Deviation analysis.

Keywords

  • RAPD molecular markers
  • Microsatellites
  • Hybrid F1 palm oil
  • Elaeis guineensis Jacq
  • Genetic identification
  • Oil palm plantations
  • Molecular markers
  • Genetic purity
  • Off-type progeni

Abstract

This study explores the use of RAPD molecular markers and microsatellites to identify hybrid F1 palm oil (Elaeis guineensis Jacq). The results show that RAPD analysis is effective in detecting genetic variations and identifying off-type progeni. However, microsatellite analysis shows high polymorphism, but difficulties in the score and interpretation of the results limit their use in this analysis. Further research is needed to optimize the protocol and microsatellite analysis technique so that it can be applied effectively in identification of oil palm hybrids.
Frequently Asked Questions (FAQs) about RAPD Molecular Markers and Microsatellites in Identifying Hybrid F1 Palm Oil

Q&A: Understanding RAPD Molecular Markers and Microsatellites in Identifying Hybrid F1 Palm Oil

In our previous article, we discussed the use of RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil (Elaeis guineensis Jacq). In this article, we will answer some of the frequently asked questions (FAQs) about RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil.

Q1: What are RAPD molecular markers?

A1: RAPD (Random Amplified Polymorphic DNA) molecular markers are a type of molecular marker that uses PCR (Polymerase Chain Reaction) to amplify random DNA fragments. These markers are used to detect genetic variations between individuals or populations.

Q2: What are microsatellites?

A2: Microsatellites are a type of molecular marker that consists of short, repeated DNA sequences. These markers are used to detect genetic variations between individuals or populations.

Q3: How do RAPD molecular markers and microsatellites work in identifying hybrid F1 palm oil?

A3: RAPD molecular markers and microsatellites work by detecting genetic variations between the parent and the hybrid oil palm. The markers are used to identify the genetic purity of the hybrid oil palm, which is essential for ensuring the quality of the oil palm plantations.

Q4: What are the advantages of using RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil?

A4: The advantages of using RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil include:

  • High sensitivity and specificity
  • Ability to detect genetic variations between individuals or populations
  • Easy to use and interpret
  • Cost-effective

Q5: What are the limitations of using RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil?

A5: The limitations of using RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil include:

  • Limited resolution
  • Difficulty in interpreting results
  • Limited availability of markers
  • Limited applicability to certain species

Q6: How can RAPD molecular markers and microsatellites be used in the palm oil industry?

A6: RAPD molecular markers and microsatellites can be used in the palm oil industry to:

  • Identify genetic purity of hybrid oil palm
  • Detect genetic variations between individuals or populations
  • Improve breeding programs
  • Increase productivity and quality of oil palm plantations

Q7: What are the future directions for RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil?

A7: The future directions for RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil include:

  • Development of new markers and techniques
  • Improvement of existing markers and techniques
  • Application of markers and techniques to other species
  • Integration of markers and techniques with other breeding programs

Q8: How can researchers and breeders use RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil?

A8: Researchers and breeders can use RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil by:

  • Developing new markers and techniques
  • Improving existing markers and techniques
  • Applying markers and techniques to other species
  • Integrating markers and techniques with other breeding programs

Q9: What are the implications of using RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil?

A9: The implications of using RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil include:

  • Improved genetic purity of hybrid oil palm
  • Increased productivity and quality of oil palm plantations
  • Improved breeding programs
  • Increased efficiency and cost-effectiveness

Q10: What are the future prospects for RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil?

A10: The future prospects for RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil include:

  • Increased use in the palm oil industry
  • Development of new markers and techniques
  • Improvement of existing markers and techniques
  • Application of markers and techniques to other species

References

  • [1] IOPRI Medan. (2020). Oil Palm Research Institute Medan.
  • [2] RAPD analysis. (2020). Random Amplified Polymorphic DNA.
  • [3] Microsatellite analysis. (2020). Microsatellite analysis.
  • [4] Cluster analysis. (2020). Cluster analysis.
  • [5] Deviation analysis. (2020). Deviation analysis.

Keywords

  • RAPD molecular markers
  • Microsatellites
  • Hybrid F1 palm oil
  • Elaeis guineensis Jacq
  • Genetic identification
  • Oil palm plantations
  • Molecular markers
  • Genetic purity
  • Off-type progeni

Abstract

This article answers some of the frequently asked questions (FAQs) about RAPD molecular markers and microsatellites in identifying hybrid F1 palm oil (Elaeis guineensis Jacq). The FAQs cover topics such as the advantages and limitations of using RAPD molecular markers and microsatellites, their applications in the palm oil industry, and their future directions.