QTL Mapping And Candidate Gene Screening Of Parthenocarpy In Cucumber

Parthenocarpy is a valuable trait to be used to improve both fruit quality and productivity in horticultural species grown for the value of their fruit,and is a target trait for breeding as well.Cucumber(Cucumis sativus L.)is one of the main vegetables cultivated in China.Parthenocarpy is a common phenomenon in cucumber germplasm,thus cucumber has the advantage to carry out research on it.There were different views on inheritance of parthenocarpy in cucumber.One QTL mapping was performed and the QTLs controlling parthenocarpy in cucumber,however,were not physically mapped since the markers used for linkage map construction were not based on the genome of cucumber.Moreover,the linked markers were AFLP markers that were neither user friendly nor confirmed.Therefore,inheritance analysis of parthenocarpy in cucumber was conducted using two F2 progeny derived from two crosses between EC1,a parthenocarpic inbred line and 8419s-1 and 14519,two non-parthenocarpic lines.QTL mapping was performed with F2:3 population derived from a cross between EC1 and 8419s-1;RHL97-5 was used for confirmation of the major-effect QTL and F3 4 population derived from the same cross and 21 inbred lines were used to validate the linked marker;Candidate genes were screening with combined analysis of re-sequencing and RNA-seq.The results were as follows:1.Parthenocarpy in cucumber was inherited quantitatively but segregated towards different parents in two F2 progenies.A linkage map containing 7 chromosomes,133 SSR and 9 InDel markers was constructed with F2(EC1×8419s-1)population.The total length of which was 808.1 cM and average distance between two markers was 5.7 cM.QTL analysis identified 7 QTLs distributing on chromosome 1,2,3,5 and 7 in spring and fall 2013.The QTL,Parth2.1,locating between SSR00684-SSR22083 on chromosome 2 was the only locus detected in two seasons,having R2 over than 10%and considered as the major-effect QTL,the others were minor-effect QTLs.2.The inden:sity of linakage map was increased using newly developed InDel markers by re-sequencing.This map covered 13.5 cM and contained 6 SSR and 7 InDel markers.Residual heterozygous line(RHL97-5)was used to confirm the major-effect QTL Parth2.1 and the results proved that a QTL existed in this region and was narrowed down between Indel-T-8 and Indel-T-32 within 674kb,having a LOD score of 9.1 and R2 of 24.4%.Indel-T-47 was a peak marker and closely linked to Parth2.1.This marker was validated by F3:4 population and 21 cucumber inbred lines.It showed that the marker was significantly related to parthenocapy and could be used in MAS for parthenocarpy in cucumber.3.All genes within 674kb of Parth 2.1 were analyzed using re-sequencing and RNA-seq data.There were 59 genes in this region and 24 of them contained the polymorphic SNPs/InDels in coding sequence region that led to missense or frameshift mutations.Among them,three genes such as Csa2M068680(CsARF19),an ortholog of auxin response factor(ARF),Csa2M070230(CsWD40),an ortholog of cytokinin response factor,Csa2M070880(CsEINl),an ortholog of ethylene insensitive gene,were hormone related genes.Seven genes were differentially expressed between parthenocapic fruit of EC1 and aborted fruit of 8419s-1 based on the transcriptome data within 674 kb.qRT-PCR suggested that transcription of Csa2M070230(CsWD40),Csa2M070330(CsPPR)and Csa2M073000(CsHEXO3)were continuously up-regulated during the parthenocarpic fruit set.Re-sequencing combined with RNA-seq data,five genes such as Csa2M068680(CsARF19),Csa2M070230(CsWD40),Csa2M070880(CsEIN1),Csa2M070330(CsPPR)and Csa2M073000(CsHEXO3)were considered as candidate genes for parthenocarpy in cucumber.