Genomic Variation,evolution History,and Agronomic Trait Association Analysis In Peach

Peach(Prunus persica L.)is an important temperate deciduous fruit crop in Rosaceae family which is widely cultivated around the world,with high economic and nutritive values.Peach originates from southwestern China and the natural population of its wild relatives are extensive in China.After domesticated at approximately 5000 years ago,peach has spread to different regions of China,subsequently Japan,Korea,Europe,and North America.Compared with wild peaches,the cultivated peaches harbor remarkable changes in the phenotypes,for instance,the enlargement of fruit size and the increase of fruit taste.The genetic bases underlying the changes remain largely unknown.In addition,the peach has generated different ecotypes that adaptation to different climate conditions during domestication and subsequent spread,but genetic bases underlying the adaptation to different climate keep unknown.To explore the genetic bases of domestication and adaptation,here we constructed a large variation map based on sequencing of 480 wild and cultivated peach accessions.Using the resources,we identified the footprints underlying the genetic bases of domestication and improvement at molecular level using genome-wide association studies(GWAS)and comparative genomic approaches.We also deciphered adaptive patterns across genomes by combining signatures of selective sweeps with genome-wide association studies of environmental variables and adaptive traits,providing new insights into the adaptive evolution history of peach.Overall,we have obtained the following results:1.Based on the sequencing of 480 wild and cultivated accessions collected from around the world,we constructed the biggest variation map for peach in the world consisting of 5 M SNP,1 M INDELs,and 150 K SVs.This variation map provides new resources for peach genetics and breeding marker development.2.We performed GWAS on 14 agronomic traits and identified a total of 31 novel loci or candidate genes that were highly associated with these traits in peach genome.3.Combining the phylogenetic construction and model-based population structure analyses,we assigned the 480 peach accessions into three major groups: wild,landrace,and improved cultivars.The landrace can be further divided into seven subgroups,which are consistent with their geographic information.The improved cultivars can be assigned into western improved and eastern improved subgroup that biased towards improved cultivars from Asia as well as North American and Europe,respectively.Based on comparison of genetic diversity and demographic history analyses,we found a narrow bottleneck during domestication resulting from integrated reasons which is different with other perennial fruit species.Through model-based population structure analyses,the extensive admixture was found among landrace and improved subgroups,indicating the historical gene flow.4.Through genetic diversity comparison among wild,landrace,and improved cultivar groups,we elucidate the genomic footprints during peach domestication and improvement.A total of 142 domestication sweeps and 104 improvement sweeps were identified(jointly 42.4 Mb,?18.6%).A series of QTLs related to fruit size,fruit appearance,and fruit taste were located at selective sweeps,conferring the remarkable changes of agronomic traits during peach domestication and improvement.Fruit size was predominantly selected during domestication(domestication:8 QTLs,3 GWAS associations,improvement:4 QTLs),and that selection for large fruits has led to the loss of genetic diversity in several fruit weight QTLs.In contrast,fruit taste related QTLs were successively selected for by domestication and improvement,with more QTLs selected for during improvement(domestication: 29 QTLs,1 GWAS association,improvement: 32 QTLs,4 GWAS associations).The allele associated with fruit bitterness was nearly swept during domestication and nearly fixed in domestication groups.GWAS on chilling requirement identified novel loci associated chilling requirement.CR is the major factor that restricts distributions of peach.We discovered genome regions underlying low CR breeding that contributes to the extension of harvest season and adaptation to low-chill zones,as well as adaptation to future climate(global warming).Moreover,we developed a molecular marker that can be used to select low CR varieties.Finally,we found that fruit texture and flavors showed distinct patterns between peach cultivars from eastern and western countries,reflecting divergent selection and local breeding in different continents.5.We revealed the adaptive evolution history to different climates based on the identification of genomic loci showed selection signals.Using multi-omics analyses,we found that selection on ABA pathway related genes play an important role in adaptation to highly drought regions for peach.Drought-mediated interactions between the ABA-responsive element-binding factors and the sucrose phosphate synthase(Pp SPS1)could be an important mechanism underlying the sweeter taste of peach fruits under drought conditions.The yellow-fleshed peach also could be an important adaptive evolution driven by highly drought conditions.Analyses on Tibet groups revealed two candidate genes,Pp CHS1 and Pp EPF1,that associated with adaptation to strong UV-B and hypoxia in Tibet.6.Genome-wide environmental association studies(GWEAS)on 51 climate variables identified a number of loci or candidate genes that were highly associated with these environmental variables.Of which,five temperature related environment variables association hotspots and six precipitation association hotspots were identified.Combining with GWAS and genomic selection scan,we identified a candidate gene and its potential causative variants for cold hardiness.7.Using GWAS and latent factor mixed-effect model(LFMM)analyses,we identified novel loci associated with bloom date and an SVP locus on chromosome 8underlying the adaption of bloom date and chilling requirement to different climates.Based on a 30-year observation on bloom date(from 1983 to 2011),we identified a genomic locus associated with bloom date advance under global warming.Moreover,the candidate gene,Pp LNK1,was verified using a simulation experiment and transgenic analyses.8.This study provides a comprehensive understanding on how natural selection and human selection shape the peach genomes.And a series of candidate genes controlling importantly agronomic traits were mined.These results will be helpful for peach genomic research and future molecular breeding.