Identification Of Gene Markers For Fruit Sugar Contents And Development Of Genome Based Selection Array For Fruit Quality Traits And Disease-resistance In Apple

The self-incompatibility,long juvenile phase and highly heterozygous genome severely hinder the efficiency of apple breeding.In this study,by conducting successively phenotyping in year 2014-2016,fruit sugar content related QTLs were identified using MapQTL and BSA-seq methods,combining with whole genome re-sequencing of hybrid parents,molecular markers were developed.Meanwhile,reported makers related to peel color,sugar content,malic acid content,fruit texture and disease-resistance were collected.After validating in different genetic background hybrid crosses and germplasms,a genome-based selection array was constructed.Detailed results were as follows:(1)By analyzing the phenotypic data of individuals from ’Zisai Pearl’ × ’Red Fuji’ and its reciprocal cross,’Zisai Pearl’×’Golden Delicious’ and its reciprocal cross,and ’Jonathan’× ’Golden Delicious’ in year 2014-2016,we found that apple fruit sugar traits were quantitatively inherited and segregated extensively among individuals.The broad sense heritability of the five hybrid crosses were more than 70%,indicated that the variation of sugar traits was determined mainly by genetic effect,which was the basis of genetic deciphering by means of QTL characterization.(2)Totally four QTLs were detected for fruit soluble solid content(SSC)by MapQTL method,one of which was firstly reported on LG01 of ’Jonathan’,others were stably located on LG16 of ’Red Fuji’across years,spanning from 1.57 Mb to 7.08 Mb,explaining 11.3%～13.2%of the total phenotypic variation.Besides,five QTLs related to fruit sucrose content were also identified on LG01 of’Jonathan’,spanning from 11.11 Mb to 28.09 Mb,explaining 16.7%～22.7%of the total phenotypic variation.While using whole genome re-sequencing-based method BSA-seq,eight QTLs for fruit fructose content were detected on LG01,LG06,LG08,and LG15;ten QTLs for fruit sucrose content were identified on LG01,LG03,and LG09.Notably,QTLs for SSC,fructose,and sucrose on LG01 of Jonathan were perfected overlapped,implied a QTL hotspot on LG01.(3)For fruit fructose content,three markers,PLT5-cds1213,E3UPFH-utr33 and HKl-utr232 were developed,contained in gene PLT5(encode a sugar alcohol transporter),gene E3UPFH(encode an E3 ubiquitin ligase),and gene HK1(encode a hexose kinase),respectively.A model for fructose content prediction was established(CF = F1×F2×F3×10.65).For fruit sucrose content,three markers,E3UPSH-cds4367,MYB-up604 and FK4-up713 were developed,contained in gene E3UPSH(encode an E3 ubiquitin ligase),gene MYB1(encode a MYB family transcription factor),and gene FK4(encode a gene fructokinase),respectively.A model for sucrose content prediction was established(Cs = S1×S2×S3×3.51).While put the above-mentioned markers together,a model was established for the prediction of total soluble sugar content(CT =T1×T2×T3×T4×T5×T6×18.59).(4)In total,25 markers were collected for apple fruit peel color,sugar content,malic acid content,fruit texture and resistance to fruit ring rot.After validating for accuracy and applicability in different genetic background hybrid crosses ’Qinguan’ × ’Honey Crisp’,’Gala’ × ’Fuji’,’Meiguo No.8’ ×’Pink Lady’,’Starkrimson’× ’Miyazaki Spur Fuji’ and germplasms,significant correlation was found between predicted and observed phenotypes,subsequently,based on Microfluidic SNP Biochip Detection System,Apple GBS Array v1.0 was developed with the 25 markers,enabling the early selection for fruit traits in apple.