Comparative Population Genomic Analysis Of Apple Organelle

Apple is an important cash crop.Researchers have long been trying to improve the yield and flavor of apples.The Malus sylvestris and the Malus sieversii,which originated from the Mount Tianshan in Central Asia,are the ancestors of the modern cultivated apple.They continued to spread along the Silk Road,and their genomic components continued to change,eventually forming a wide variety of cultivated apples.The study of apple genome mainly focuses on the nuclear genome,and the analysis of chloroplast and mitochondrial genome in the domestication process of apple has not been carried out on a large scale.As two important semiautomous in eukaryotic cells,chloroplast and mitochondria are the site of many important biochemical reactions.Among them,photosynthesis in chloroplast involves the generation of carbohydrates,and ATP produced by respiration in mitochondria provides essential energy for life activities.In this paper,461 apple re-sequencing data and phenotypic data from public databases were used to conduct the following studies: 1.Using high-quality SNPs and indels from chloroplast and mitochondria,pan-genome analyses of apple organelle genome were performed.2.Based on the high quality SNPs of chloroplast and mitochondrial genome,combined with the fruit phenotype data,the relationship between SNPs of apple organelle genome and phenotype was basically analyzed.3.Seven apple samples were found to show some properties of subpopulations in transition state during apple domestication.In conclusion,this study preliminarily explored the variation of chloroplast and mitochondrial genomes of several apple subpopulation and their association with apple fruit traits,which provided resources and reference for apple breeding and quality improvement at the organelle genome level.