Genome-Wide Screening of AP2 Transcription Factors Involving in Fruit Color and Aroma Regulation of Cultivated Strawberry.

Lixia Sheng,Jianwen Wang,Hongsheng Gao,Yue Chen,Cong Ma

doi:10.3390/genes12040530

Abstract

Fragaria × ananassa Duch, which among the youngest fruit crops, comprises many popular cultivars that are famous for their favored color and aroma. The regulation roles of AP2/ERF (APETALA2/ethylene-responsive element-binding factor) transcription factors in fruit flavor and color regulation have been studied in several fruit crops. The AP2 family of strawberry, which was ignored in recent AP2/ERF identification studies, was explored in this study. A total of 64 FaAP2 (Fragaria × ananassa AP2) transcription factors belonging to the euAP2, euANT (AINTEGUMENTA), and baselANT groups were identified with canonical insertion motifs in two AP2 domains. The motif identification illustrated that motifs 1, 5, and 2 indicated a corresponding AP2 domain repeat 1 with a linker region, and motifs 6, 4, 3 indicated a corresponding AP2 domain repeat 2, all of which were highly conserved. By synteny analysis, FaAP2 paralogs were identified in each sub-genome, and FaAP2 gene duplication and loss explained the unequal AP2 loci of sub-genomes. The expression profile in three cultivars indicated that six FaAP2 paralogs—four WRI (WRINKLED) gene homologs and two AP2 gene homologs—were candidate regulators of red fruit color and/or special fruit aroma. All these finds provide a basis for further investigations into role of AP2 in fruit color and aroma and would be helpful in the targeted selection of strawberry fruit quality to improve breeding.

Highlights

The cultivated strawberry (Fragaria × ananassa Duch.) with favored aromas and colors is one of the most popular soft fruits worldwide
From the proteome of cultivated strawberry, 498 candidates of the AP2/ethyleneresponsive element-binding factor (AP2/ERF) superfamily were predicted, and 64 FaAP2 transcription factor (TF) were distinguished from 23 FaRAV (RAV TFs of F. × ananassa) TFs and 411 FaERF TFs based on the corresponding topological lineages of an NJ tree with the reference of the A. thaliana AP2/ERF superfamily
According to the homology pairs of the FaAP2 and AtAP2 TFs (Figure 1), as well as their sub-genome locations (Table S2), the symbols of FaAP2 gene were named ‘FaAP2 homology’–‘sub-genomes i, ii, iii, or iv’–‘number’

Summary

Introduction

The cultivated strawberry (Fragaria × ananassa Duch.) with favored aromas and colors is one of the most popular soft fruits worldwide. Its earliest cultivar with complicated allooctoploid (2n = 8× = 56) was one of the youngest fruit species (approximately 300 years ago) that originated from spontaneous hybrids of two wild octoploid species Fragaria chiloensis subsp. The genomic backgrounds of favored strawberry cultivars were found to be more complicated due to the fact that octoploid and diploid species have been used as parents of many commercial varieties [8,9]. Though cultivated strawberry cultivars with important fruit quality traits are excellent material for detecting the genetic locus of interesting traits like fruit colors and aromas, homologs need to be carefully examined for more introgression or recombination events because their genomes are mosaics of phylogenetically diverse progenitors [5,8]

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