How to handle high subgenome sequence similarity in allopolyploid Fragaria x ananassa: linkage disequilibrium based variant filtering.

ABSTRACT:

Background

The allo-octoploid Fragaria x ananassa follows disomic inheritance, yet the high sequence similarity among its subgenomes can lead to misalignment of short sequencing reads (150 bp). This misalignment results in an increased number of erroneous variants during variant calling. To accurately associate traits with the appropriate subgenome, it is essential to filter out these erroneous variants. By classifying variants into correct (type 1) and erroneous types (homoeologous variants-type 2, and multi-locus variants-type 3), we can improve the reliability of downstream analyses.

Results

Our analysis reveals that while erroneous variant types often display skewed average allele balances (AAB) for heterozygous calls, this measure alone is insufficient. To mitigate the

SUBMITTER: Koorevaar T 

PROVIDER: S-EPMC11606298 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature