gsrc: an R package for genome structure rearrangement calling.

Area of Science:

• Genomics
• Plant Breeding
• Bioinformatics

Background:

• Genome structure rearrangements (GSRs) are prevalent in allopolyploids, impacting phenotypic traits.
• GSRs like deletions, duplications, and homeologous non-reciprocal translocations (HNRTs) occur between similar subgenomes.
• Current methods for genome-wide GSR detection are costly (sequencing) or unreliable (genotyping data).

Purpose of the Study:

• To develop a novel R-package, gsrc, for detecting GSRs in allopolyploid species.
• To enable reliable, genome-wide identification of GSRs, including subgenome exchanges, from high-density genotyping data.
• To provide a cost-effective alternative to sequencing-based approaches for GSR analysis.

Main Methods:

• Development of the R-package 'gsrc'.
• Utilizing high-density array genotyping data as input.
• Algorithm designed to detect deletions, duplications, and homeologous translocations.

Main Results:

• gsrc successfully detects genome structure rearrangements from genotyping data.
• The package can identify GSRs, including exchanges between subgenomes.
• Exemplary application on a Brassica napus dataset demonstrated the package's utility.

Conclusions:

• gsrc offers a reliable and accessible method for detecting GSRs in allopolyploids.
• The R-package facilitates large-scale genomic studies in polyploid species.
• This tool can advance research on the impact of GSRs on phenotypic variation.