Identifying Genome-Wide Sequence Variations and Candidate Genes Implicated in Self-Incompatibility by Resequencing Fragaria viridis

International Journal of Molecular Sciences
Jianke DuYushan Qiao

Abstract

It is clear that the incompatibility system in Fragaria is gametophytic, however, the genetic mechanism behind this remains elusive. Eleven second-generation lines of Fragaria viridis with different compatibility were obtained by manual self-pollination, which can be displayed directly by the level of fruit-set rate. We sequenced two second-generation selfing lines with large differences in fruit-set rate: Ls-S₂-53 as a self-incompatible sequencing sample, and Ls-S₂-76 as a strong self-compatible sequencing sample. Fragaria vesca was used as a completely self-compatible reference sample, and the genome-wide variations were identified and subsequently annotated. The distribution of polymorphisms is similar on each chromosome between the two sequencing samples, however, the distribution regions and the number of homozygous variations are inconsistent. Expression pattern analysis showed that six candidate genes were significantly associated with self-incompatibility. Using F. vesca as a reference, we focused our attention on the gene FIP2-like (FH protein interacting protein), associated with actin cytoskeleton formation, as the resulting proteins in Ls-S₂-53 and Ls-S₂-76 have each lost a number of different amino acids. Suppressi...Continue Reading

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Datasets Mentioned

BETA
PRJNA510489

Methods Mentioned

BETA
monoclonal sequencing
antisense oligonucleotides
PCR

Software Mentioned

GATK
SnpEff
CDD Tool
Burrows Alignment
UnifedGenotyper
DNAMAN8
SAMtools

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