Identification Of The Genome-wide Sequence Variations By Genome Resequencing And Mapping Of The QTLs Related To Fruit Size And Shape In Two Cucumber Inbred Lines With Different Fruit Size And Shape

Cucumber（Cucumis sativus L.）is an economically important vegetable worldwide.Fruit size and shape are important agronomic traits that affect yield and external quality of cucumber,but their genetic basis remains poorly understood.To investigate the inheritance and quantitative trait loci underlying the fruit size and shape,we developed two inbred lines:CNS21 and RNS7 with fruit index（length/dimeter）being about 10 and 1,respectively.CNS21 bears long fruits,while RNS7 bears“round ball”.In addition,these two inbred lines are significantly different in plant structure（the internode in CNS21 is longer and thinner than RNS7）,leaf shape（there are more unfolded margin of leaf in RNS7 than CNS21）,especially in fruit external characters（CNS21 with white spines,dark green immature skin,yellow mature skin,and three seed cavities,while RNS7 with black spine,yellow-green immature skin,reddish brown mature skin,no less than four seed cavities）.The main findings in this study are as follows:（1）The two inbred lines were re-sequenced.A total of 71,497,784 and 65,875,278 clean reads were obtained in CNS21 and RNS7,respectively,over 80%of them were above Q30 in both samples.88.73%and 89.2%of the obtained clean reads were successfully mapped onto the reference genome,Chinese long 9930,in CNS21 and RNS7,respectively.The average sequencing depth was approximately 18-fold and 19-fold,and the resulting consensus sequences with no less than 10-fold covered approximately 89%and 91%of the reference genome in CNS21 and RNS7,respectively.A total of 158,957 and 220,841 SNPs,51,860 and70,578 In Dels,11,340 and 10,894 SVs were detected between CNS21 and 9930,and between RNS7 and 9930,respectively.A total of 186,669 SNPs,51,478 InDels and 898 SVs between CNS21 and RNS7 were identified by bioinformatics analysis.To verify the accuracy of these SNPs and InDels identified,a total of 122 SNPs and 105 InDels were randomly selected in all seven chromosomes,as a result,98.4%and 90.3%were consistent with the re-sequencing data.（2）The proportions of transitions（Ts）were all significantly higher than the proportions of transversions（Tv）.Almost 40%of In Dels were monobase,and decrease in number with increasing in size.The total number and density of polymorphisms（SNPs,InDels and SVs）which have been detected varies across different chromosomes,and the distribution of polymorphisms was uneven within chromosomes.（3）These proportions of polymorphisms in CDS were little,and the proportions in CDS in cucumber（less than 2%SNPs and almost 0.5%InDels）lower than other grass family species,such as rice（4%SNPs and 3%InDels）and foxtail millet（5.01%SNPs and 2.23%InDels）.Furthermore,IDPs that are multiples of 3 bp so as to can not produce frame-shift mutations are common in coding regions,suggesting that IDPs with multiples of 3 bp were also easier to be preserved in cucumber evolution because of their subtle impact on genes.（4）Gene ontology（GO）terms enrichment analysis were conducted to classify all of the variational genes between CNS21 and RNS7 in primary structure.GO items that enriched the most number differential genes were“metabolic process”and“cellular process”in the biological process group,“cell part”and“cell”in the cellular component group,“catalytic activity”and“binding”in the molecular function group,respectively,which corresponds to the character divergence between CNS21 and RNS7.（5）3 populations were constructed for mapping quantitative trait loci related to cucumber fruit size and shape.There were 202 plants,665 ovaries and 322 commercial fruits data were collected in F₂ population in autumn of 2015;220 plants,1733 ovaries and 1433commercial fruits data were collected in F₂ population in spring of 2016;201 plants,531ovaries and 589 commercial fruits data were collected in BC₁F₁ population in autumn of2016.（6）A total of 84 InDel markers that easy to use in populations during PCR were developed,which cover 7 chromosomes uniformly and no less than 10 markers per chromosome.These markers were used to genotype the 3 populations,then QTLs for fruit length（FL）,fruit diameter（FD）,fruit shape（L/D）were mapped.A total of 58 QTLs,32 of which QTLs explained more than 10%of the total phenotypic variations,were detected.This study resequenced two advanced inbred cucumber lines,and analysed the characteristics of the obtained polymorphersm.A total of 84 markers easy to use were developed to genotype the two F₂ and one BC₁F₁ populations that planted in greenhouse and arched shed during autumn,spring and autumn of 2015-2016,respectively.And phenotype data about fruit shape were collected in the 3 population.A total of 58 QTLs,32 of which having more than 10%contribution ratio,were detected.and through combining re-sequencing data and mapped QTLs,5 candidate genes controlling fruit size and shape were found.These work provided important information for further study in the genetic basis and gene cloning of fruit size and shape.