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

• Main Authors: Jianke Du, Yan Lv, Jinsong Xiong, Chunfeng Ge, Shahid Iqbal, Yushan Qiao
• Format: Article
• Language: English
• Published: MDPI AG 2019-02-01
• Series: International Journal of Molecular Sciences
• Subjects: <i>Fragaria viridis</i>; genome; variations; resequencing; self-incompatibility; <i>FIP2-like</i>
• Online Access: https://www.mdpi.com/1422-0067/20/5/1039

It is clear that the incompatibility system in <i>Fragaria</i> is gametophytic, however, the genetic mechanism behind this remains elusive. Eleven second-generation lines of <i>Fragaria viridis</i> 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. <i>Fragaria vesca</i> 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 <i>F. vesca</i> as a reference, we focused our attention on the gene <i>FIP2-like</i> (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. Suppression of <i>FIP2-like</i> to some extent inhibits germination of pollen grains and growth of pollen tubes by reducing F-actin of the pollen tube tips. Our results suggest that the differential distribution of homozygous variations affects <i>F. viridis</i> fruit-set rate and that the fully encoded FIP2-like can function normally to promote F-actin formation, while the new FIP2-like proteins with shortened amino acid sequences have influenced the (in)compatibility of two selfing lines of <i>F. viridis</i>.