QTL Analysis And Candidate Gene Prediction For Apple Resistance To Valsa Canker

Apple Valsa canker is one of the most destructive fungal diseases for apple industry in China.The disease leads to serious harm and is difficult to control.Most cultivars used commercially are susceptible to the disease.Therefore,it could lay the foundation for resistance breeding of apple Valsa canker and is important to apple industry in China that identifying apple's resistant loci to Valsa canker and studying the resistance candidate genes.Valsa mali isolate 03-8 was used to inoculate five apple germplasm resources at the periods of dormant,pre-emergence,new shoot rapid growth,new shoot slow growth and pre-deciduous.The five germplasm resources were relatively resistant in dormancy period and showed the biggest resistance differences in the new shoot rapid growth period.Valsa mali isolates 03-8 and xc56 were used to inoculate 1486 hybrids of 'Jonathan'(Males domestica)x 'Golden Delicious'(M.domestica)in dormant period(February?March)of 2012?2015 and in new shoot growth period(June to July)of 2016.The same two isolates were used to inoculate 1667 hybrids of 'Zisai Pearl'(M.asiatica)x 'Fuji'(M.domestica)in dormant period(March)of 2010-2011.The lesion lengths of progenies showed continuous variation in each population,indicating that the resistance to V.mali was controlled by multiple genes of additive effects.A high-density SNP genetic map of 'Jonathan' x 'Golden Delicious' has been constructed in our laboratory.The genetic map and lesion length phenotypes of `Jonathan' x 'Golden Delicious' hybrids were used to identify QTLs for the resistance to Valsa canker.A total of 32 QTLs were identified in the dormant period and seven QTLs were detected in the new shoot growth period.No overlapping or adjacent QTLs were found between the two periods,suggesting that the population resistance to Valsa canker was controlled by different resistance loci in different periods.A high density genetic linkage map of 'Zisai Pearl' × 'Fuji' has been constructed in our laboratory.The genetic map and lesion length phenotypes of 'Zisai Pearl' × 'Fuji' hybrids were used to identify QTLs for the resistance.A total of two QTLs were identified.No overlapping or adjacent QTLs were found between the two populations,indicating that the resistance to Valsa canker was controlled by different resistance loci in different populations.Furthermore,all QTLs identified in this paper accounted for 4.4%?13.3%of the phenotypic variance,suggesting that the resistance to Valsa canker was determined by multiple minor genes.Among the 41 QTLs mentioned above,three year and isolate stable loci were found,which were used as the basis of gene prediction for apple resistance to Valsa canker.They were G13-1,G13-2 and J15-1,and 568 genes were involved in the three loci.According to the resequencing databases of'Jonathan' and 'Golden Delicious',149 genes were selected for they included non-synonymous SNP or indel between parents.The gene function annotations showed that 19 genes may be involved in the resistance to Valsa canker.After cloning and sequencing of the 19 genes in 'Jonathan' and 'Golden Delicious',eighteen non-synonymous SNPs between 'Jonathan' and 'Golden Delicious' in nine genes were verified.The eighteen non-synonymous SNPs were amplified and sequenced in the hybrids.Five SNPs were selected for they matched the 1:1 ratio in the random population and showed partial separation in the resistant and susceptible hybrids.SNP7 in MDP0000156108 and SNP11 in MDP0000629440 cloud led to non-synonymous substitution,the two genes were selected as the candidate genes for the resistance to Valsa canker.SNP1,SNP2/SNP3 were in the upstream regions of genes MDP0000127348 and MDP0000748479,which could change predicted cis-element.The expression of MDP0000748479 and MDP0000127348 were studied.No difference of expression patterns in MDP0000127348 was found between the resistant and susceptible hybrids,and MDP0000127348 was excluded.At last,a splicing factor MdCC1(MDP0000748479),a receptor-like serine/threonine kinase gene MdRLK(MDP0000156108)and a transcription factor MdoMYB194(MDP0000629440)were considered as the candidate genes for the resistance to Valsa canker.In conclusion,three year and isolate stable loci were mapped,and three candidate genes were predicted for the resistance to Valsa canker using the forward genetics method,which is important for the resistant breeding.