The transcriptional landscape of cultivated strawberry (Fragaria×ananassa) and its diploid ancestor (Fragaria vesca) during fruit development

doi:10.1016/S2095-3119(20)63376-7

摘要/Abstract

摘要：

栽培草莓（Fragaria×ananassa）来自四个二倍体祖先：F. vesca，F. viridis，F .iinumae和F. nipponica。其中，F. vesca是栽培草莓最主要的亚基因组。目前，基因表达如何促进二倍体和八倍体草莓之间的果实发育过程中的差异的机制沿不清楚。在这里，我们对F. vesca和F.×ananassa的转录组进行全面分析，以研究水果发育不同阶段的基因表达。通过二倍体和八倍体之间的成对比较，我们总共获得了3,741个（转色期）和3,960个（成熟期）差异表达的基因。类黄酮生物合成中涉及的基因在八倍体的转色阶段被显著上调，并且我们还通过加权共表达网络（WGCNA）分析发现了与几种类黄酮生物合成基因（包括FveMYB10，FveMYB9/11和FveRAP）相关的成熟果实特异性模块。此外，我们确定了八倍体和二倍体果实中的物种特异调控网络。值得注意的是，我们发现WAK和F-box基因分别在八倍体和二倍体果实中富集。总体而言，这项研究有助于阐明草莓的类黄酮生物合成和果实大小，这对栽培草莓的未来分子育种具有重要意义。

Abstract:

Cultivated strawberry (Fragaria×ananassa) originated from four diploid ancestors: F. vesca, F. viridis, F. iinumae and F. nipponica. Among them, F. vesca is the dominant subgenome for cultivated strawberry. It is not well understood how differences in gene expression between diploid and octoploid strawberry contribute to differences during fruit development. In this study, we used comprehensive transcriptomic analyses of F. vesca and F.×ananassa to investigate gene expression at the different stages of fruit development. In total, we obtained 3 508 (turning stage) and 3 958 (red stage) differentially expressed genes with pairwise comparisons between diploid and octoploid. The genes involved in flavonoid biosynthesis were almost upregulated in the turning stages of octoploid, and we also discovered a ripe fruit-specific module associated with several flavonoid biosynthetic genes, including FveMYB10, FveMYB9/11, and FveRAP, using weighted gene coexpression network analysis (WGCNA). Furthermore, we identified the species-specific regulated networks in the octoploid and diploid fruit. Notably, we found that the WAK and F-box genes were enriched in the octoploid and diploid fruits, respectively. This study elucidates new findings on flavonoid biosynthesis and fruit size of strawberry with important implications for future molecular breeding in cultivated strawberry.

Key words: strawberry , Fragaria vesca , Fragaria×ananassa , RNA-Seq , fruit , development , anthocyanin

. [J]. Journal of Integrative Agriculture, 2021, 20(6): 1540-1553.

LI Yong-ping, LIU Tian-jia, LUO Hui-feng, LIU Sheng-cai . The transcriptional landscape of cultivated strawberry (Fragaria×ananassa) and its diploid ancestor (Fragaria vesca) during fruit development[J]. Journal of Integrative Agriculture, 2021, 20(6): 1540-1553.

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