AveDissR: An R function for assessing genetic distinctness and genetic redundancy

Area of Science:

• Plant genetics
• Bioinformatics
• Germplasm characterization

Background:

• Assessing genetic distinctness and redundancy is crucial for plant germplasm characterization.
• A previously introduced marker-based approach using average dissimilarity lacked widespread adoption due to the absence of integrated software.
• The lack of integrated software for dissimilarity calculation, analysis of molecular variance, and principal coordinates analysis hindered the application of this approach.

Purpose of the Study:

• To develop an integrated software solution for assessing genetic distinctness and redundancy in plant germplasm.
• To overcome the limitations of previous marker-based approaches by providing a user-friendly tool.
• To facilitate the application of average dissimilarity for germplasm characterization.

Main Methods:

• Development of an R function named AveDissR.
• Integration of three separate analyses: dissimilarity calculation, analysis of molecular variance (AMOVA), and principal coordinates analysis (PCoA).
• The function is designed to handle large datasets of dominant or codominant markers.

Main Results:

• The AveDissR function successfully integrates key analyses for assessing genetic distinctness and redundancy.
• It supports various marker types, including amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and single-nucleotide polymorphisms (SNPs).
• The function generates comprehensive output files beneficial for germplasm assessment and is platform-independent.

Conclusions:

• The developed AveDissR function makes the assessment of genetic distinctness and redundancy in plant germplasm more feasible.
• This tool enhances the utility of marker-based approaches for germplasm characterization.
• AveDissR promotes more efficient and effective management of plant genetic resources.