Genomics Analyses On The Population Diversity,Quality Domestication And Improvement In Apple

As one of the most economically and representative fruit trees of Rosaceae,apple(Malus × domestica Borkh.),which with a huge cultivation area in temperate regions of the world.The origin of apple is the Tianshan Mountains in Central Asia.The aliases of apple are either ‘Nai’ or ‘Lin Qin’.Based on the fossil collected results,the domestication history of apple has been at least 4,000 years.One of the ancestral varieties of cultivated apple is Malus sieversii,which originated in the Tianshan region of Central Asia and was widely spread between Asia and Europe along the Silk Road.The modern cultivated apple is formed by hybridization between Malus sieversii and Malus sylvestris.Morphological and genetic evidence also indicated that Malus sieversii and Malus sylvestris were the ancestors of modern cultivated apples.According to historical research,the history of European domestication of apples can be traced back to the Neolithic Age and the Bronze Age 4,000 years ago.Apples with high acid and high tannin content were domesticated for brewing cider,but genetic evidence is unclear.The history of apple breeding can be classified into two stages: domestication and improvement.Significant changes have taken place in the phenotypes of different stages,such as the larger fruit size,the sweeter and richer taste,etc.However,the genetic control of these important qualities and the biological mechanism for biotic stress response of development remain elusive.In this paper,through the systematic analysis of 497 representative apple sample sequencing data from all over the world combined with 16 phenotypic data,the independent domestication events of ancient wine and ancient sweet apples and the important genes affecting the evolution of apple flavor were revealed for the first time.Candidate variation sites for important agronomic quality traits such as apple fruit taste,flavor,and size were identified by genome-wide association analysis.At the same time,based on multi-omics data,the MATE transporter gene family was identified and analyzed at the genome-wide level,revealing the important role of MATE gene family members in the process of apple biotic stress response.The main results are as follows:1.About 23 million single nucleotide polymorphisms(SNPs)were identified from 497 apple resequencing samples,and a high-resolution and-quality apple SNP variation map was constructed,which provided a basis for the genetic diversity study,breeding markers development and candidate gene fine mapping of apples.2.Genome-wide association analysis was carried out based on the mixed linear model of the apple SNP variation map,and 5,796 candidate gene loci were identified.Combined with the transcriptomic data of typical samples,the candidate genes were further screened to reduce false positives,and the results were verified experimentally.3.The results of population structure analysis provided support for the important ancestral status of Xinjiang Malus sieversii apple and European forest apple.An event of erosion of genetic diversity in apple populations was discovered,which was caused by multiple artificial selections in the long breeding process.Further research on cultivated populations found that the diversity of genetic information in the original heirloom populations was higher than that of modern cultivated apples.Genomic introgression analysis results showed that no genetic introgression was observed between the ancient apple varieties used for winemaking and the dessert heirloom used for fresh food in East Asia,indicating for the first time that the domestication of these two varieties was independent,Genetic evidence supports the early record of domestication of apples for cider production by Europeans.4.Analysis of candidate genes which identified by genome-wide association analysis and genetic characteristics during domestication and improvement found that the evolution of apple fruit taste is mainly attribute to the selection of fruit organic acid content,while the soluble sugar candidate genes experience little selective pressure.This is the reason of apple fruit with pleasant taste.It is clear the there is no hitchhiking effect between fruit flavor and fruit size.During the domestication and improvement of apple,the domestication of taste related traits such as fruit acidity,organic acid composition and sorbitol content depends on the selection of one major gene,while the changes of apple fruit size involve the selection of multiple quantitative trait loci.An evolutionary model of apple fruit taste and size was proposed for the first time based on the above results.5.A high-confidence apple copy number variation(CNV)map was constructed based on346 samples with high sequencing depth.It was found that CNV is a genetic variation resource independent of SNP.Functional enrichment analysis found that the CNV related genes were mainly involved in stress response and metabolism.Comparison of CNV in cultivars and wild relatives identified 127 genes with higher copy number differences.6.Based on the hidden Markov model,for the first time,66 genes encoding MATE transporters were accurately excavated from the apple genome.Synteny analysis found that doubling events were the main driving force for the expansion of the apple MATE gene family.Transcriptome data analysis of multiple tissues showed that the apple MATE gene family has diverse expression patterns and specific expression at the tissue level.Analysis of cis-regulatory elements in the upstream promoter region of MATE members in the apple genome revealed that the apple MATE genes are mainly related to the organisms response to exogenous stress.Transcriptome analysis before and after infection by various pathogens supported that MATE was involved in the biotic stress response process of apple.In summary,this paper uses the apple genome sequencing data to carry out a systematic analysis on the evolutionary history of apple species,fruit quality improvement and other related issues.It reveals the great potential of apple germplasm resources for breeding improvement,provides a good reference for further research on the genetic basis of apple quality traits,and provides a rich resource for the study of quality improvement of apple and other fruit trees.