title: Transcript Quantification by RNA-Seq Reveals Differentially Expressed Genes in the Red and Yellow Fruits of Fragaria vesca.
abstract: Fragaria vesca (2n = 2x = 14), the woodland strawberry, is a perennial herbaceous plant with a small sequenced genome (240 Mb). It is commonly used as a genetic model plant for the Fragaria genus and the Rosaceae family. Fruit skin color is one of the most important traits for both the commercial and esthetic value of strawberry. Anthocyanins are the most prominent pigments in strawberry that bring red, pink, white, and yellow hues to the fruits in which they accumulate. In this study, we conducted a de novo assembly of the fruit transcriptome of woodland strawberry and compared the gene expression profiles with yellow (Yellow Wonder, YW) and red (Ruegen, RG) fruits. De novo assembly yielded 75,426 unigenes, 21.3% of which were longer than 1,000 bp. Among the high-quality unique sequences, 45,387 (60.2%) had at least one significant match to an existing gene model. A total of 595 genes, representing 0.79% of total unigenes, were differentially expressed in YW and RG. Among them, 224 genes were up-regulated and 371 genes were down-regulated in the fruit of YW. Particularly, some flavonoid biosynthetic pathway genes, including C4H, CHS, CHI, F3H, DFR and ANS, as well as some transcription factors (TFs), including MYB (putative MYB86 and MYB39), WDR and MADS, were down-regulated in YW fruit, concurrent with a reduction in anthocyanin accumulation in the yellow pigment phenotype, whereas a putative transcription repressor MYB1R was up-regulated in YW fruit. The altered expression levels of the genes encoding flavonoid biosynthetic enzymes and TFs were confirmed by quantitative RT-PCR. Our study provides important insights into the molecular mechanisms underlying the yellow pigment phenotype in F. vesca.
authors.affiliation: College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China.|Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 139 Shiqiao Road, Hangzhou 310021, China.
authors.forename: Yuchao
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China.
authors.forename: Weijia
authors.initials: W
authors.lastname: Li
authors.affiliation: College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China.|Institute of Soil and Water Conservation of Liaoning Province, Chaoyang 122000, China.
authors.forename: Yujuan
authors.initials: Y
authors.lastname: Dou
authors.affiliation: College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China.
authors.forename: Junxiang
authors.initials: J
authors.lastname: Zhang
authors.affiliation: Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 139 Shiqiao Road, Hangzhou 310021, China.
authors.forename: Guihua
authors.initials: G
authors.lastname: Jiang
authors.affiliation: Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, 139 Shiqiao Road, Hangzhou 310021, China.
authors.forename: Lixiang
authors.initials: L
authors.lastname: Miao
authors.affiliation: College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China.
authors.forename: Guofen
authors.initials: G
authors.lastname: Han
authors.affiliation: College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China.
authors.forename: Yuexue
authors.initials: Y
authors.lastname: Liu
authors.affiliation: College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China.
authors.forename: He
authors.initials: H
authors.lastname: Li
authors.affiliation: College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, China.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D031985:Fragaria / Q000235:genetics / Q000378:metabolism*; D005638:Fruit / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D010858:Pigmentation / Q000502:physiology*; D010940:Plant Proteins / Q000096:biosynthesis* / Q000235:genetics; D018749:RNA, Plant / Q000096:biosynthesis* / Q000235:genetics; D014158:Transcription, Genetic / Q000502:physiology
chemical_list: D010940:Plant Proteins; D018749:RNA, Plant