Genome-wide association mapping in a sweet cherry germplasm collection(Prunus avium L.)reveals candidate genes for fruit quality traits

In sweet cherry(Prunus avium L.),large variability exists for various traits related to fruit quality.There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands.With this objective,a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomic fruit quality traits over 2-6 years,and characterized using a genotyping-by-sequencing approach.The SNP coverage collected was used to conduct a genome-wide association study using two multilocus models and three reference genomes.We identified numerous SNP-trait associations for global fruit size(weight,width,and thickness),fruit cracking,fruit firmness,and stone size,and we pinpointed several candidate genes involved in phytohormone,calcium,and cell wall metabolisms.Finally,we conducted a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker-trait associations.This study brings new knowledge of the genetic control of important agronomic traits related to fruit quality,and to the development of marker-assisted selection strategies targeted towards the facilitation of breeding efforts.

Genetic characterization of worldwide Prunus domestica(plum)germplasm using sequence-based genotyping

Prunus domestica commonly known as European plum is a hexaploid fruit tree species cultivated around the world.Locally it is used for fresh consumption,in jams or jellies,and the production of spirits while commercially the fruit is primarily sold dried(prunes).Despite its agricultural importance and long history of cultivation,many questions remain about the origin of this species,the relationships among its many pomological types,and its underlying genetics.Here,we used a sequence-based genotyping approach to characterize worldwide plum germplasm including the potential progenitor Eurasian plum species.Analysis of 405 DNA samples established a set of four clades consistent with the pomological groups Greengages,Mirabelles,European plums,and d’Agen(French)prune plums.A number of cultivars from each clade were identified as likely clonal selections,particularly among the“French”type prune germplasm that is widely cultivated today.Overall,there was relatively low genetic diversity across all cultivated plums suggesting they have been largely inbred and/or derived from a limited number of founders.The results agree with P.domestica having originated as an interspecific hybrid of a diploid P.cerasifera and a tetraploid P.spinosa that itself may have been an interspecific hybrid of P.cerasifera and an unknown Eurasian plum species.The low genetic diversity and lack of true wild-types coupled with the known cultivation history of Eurasian plums imply that P.domestica may have been a product of inter-specific cross breeding and artificial selection by early agrarian Eurasian societies.

Prediction of genetic value for sweet cherry fruit maturity among environments using a 6K SNP array

The timing of fruit maturity is an important trait in sweet cherry production and breeding.Phenotypic variation for phenology of fruit maturity in sweet cherry appears to be under strong genetic control,but that control might be complicated by phenotypic instability across environments.Although such genotype-by-environment interaction(G×E)is a common phenomenon in crop plants,knowledge about it is lacking for fruit maturity timing and other sweet cherry traits.In this study,1673 genome-wide SNP markers were used to estimate genomic relationships among 597 weakly pedigree-connected individuals evaluated over two seasons at three locations in Europe and one location in the USA,thus sampling eight‘environments’.The combined dataset enabled a single meta-analysis to investigate the environmental stability of genomic predictions.Linkage disequilibrium among marker loci declined rapidly with physical distance,and ordination of the relationship matrix suggested no strong structure among germplasm.The most parsimonious G×E model allowed heterogeneous genetic variance and pairwise covariances among environments.Narrow-sense genomic heritability was very high(0.60–0.83),as was accuracy of predicted breeding values(>0.62).Average correlation of additive effects among environments was high(0.96)and breeding values were highly correlated across locations.Results indicated that genomic models can be used in cherry to accurately predict date of fruit maturity for untested individuals in new environments.Limited G×E for this trait indicated that phenotypes of individuals will be stable across similar environments.Equivalent analyses for other sweet cherry traits,for which multiple years of data are commonly available among breeders and cultivar testers,would be informative for predicting performance of elite selections and cultivars in new environments.

Prunus genetics and applications after de novo genome sequencing:achievements and prospects

Prior to the availability of whole-genome sequences,our understanding of the structural and functional aspects of Prunus tree genomes was limited mostly to molecular genetic mapping of important traits and development of EST resources.With public release of the peach genome and others that followed,significant advances in our knowledge of Prunus genomes and the genetic underpinnings of important traits ensued.In this review,we highlight key achievements in Prunus genetics and breeding driven by the availability of these whole-genome sequences.Within the structural and evolutionary contexts,we summarize:(1)the current status of Prunus whole-genome sequences;(2)preliminary and ongoing work on the sequence structure and diversity of the genomes;(3)the analyses of Prunus genome evolution driven by natural and man-made selection;and(4)provide insight into haploblocking genomes as a means to define genome-scale patterns of evolution that can be leveraged for trait selection in pedigree-based Prunus tree breeding programs worldwide.Functionally,we summarize recent and ongoing work that leverages whole-genome sequences to identify and characterize genes controlling 22 agronomically important Prunus traits.These include phenology,fruit quality,allergens,disease resistance,tree architecture,and self-incompatibility.Translationally,we explore the application of sequence-based marker-assisted breeding technologies and other sequence-guided biotechnological approaches for Prunus crop improvement.Finally,we present the current status of publically available Prunus genomics and genetics data housed mainly in the Genome Database for Rosaceae(GDR)and its updated functionalities for future bioinformatics-based Prunus genetics and genomics inquiry.

中国华北和东北地区杏种质资源遗传多样性分析

利用核果类8条染色体连锁群上均匀分布的55对SSR引物,对中国华北和东北地区的51份杏(Prunus armeniaca L.)种质进行贝叶斯聚类、遗传多样性和稀有位点分析。结果表明,贝叶斯聚类K=5时,反映了最可能的5个遗传基础构成。在整体遗传水平上,华北和东北地区的杏种质所涵盖的遗传基础构成相似,但也有一定的差异。依据遗传成分比例划分亚组,并通过遗传多样性比较发现,亚组Ⅱ和Ⅴ的种质多来自东北地区,其他亚组的种质多来自华北地区。亚组Ⅳ的Shannon’s多样性指数(I)最高,为1.568,亚组Ⅴ最低(1.181)。亚组间遗传距离(Genetic distance)平均为0.262,亚组Ⅲ与亚组Ⅳ间的遗传距离最短(0.156),亚组Ⅴ与杂合组的遗传距离最长(0.398),亚组Ⅴ同其他亚组间的遗传渗透和交流频率最低,其次为亚组Ⅱ。主坐标分析表明,大多数华北和东北地区的种质个体间遗传差异较小,归入东北地区的亚组Ⅱ和亚组Ⅴ的遗传基础差别明显。对供试材料的稀有等位基因位点统计和比较发现,86.27%供试杏种质检测到140个稀有位点,平均每个样品2.74个。种质‘李蜜杏’含稀有位点数最多(11个),占其位点总数的10%;而‘吨葫芦’、‘新世纪’和‘关音脸’等种质中未检测到稀有位点。

The SlSHN2 transcription factor contributes to cuticle formation and epidermal patterning in tomato fruit

Tomato(Solanum lycopersicum)is an established model for studying plant cuticle because of its thick cuticle covering and embedding the epidermal cells of the fruit.In this study,we screened an EMS mutant collection of the miniature tomato cultivar Micro-Tom for fruit cracking mutants and found a mutant displaying a glossy fruit phenotype.By using an established mapping-by-sequencing strategy,we identified the causal mutation in the SlSHN2 transcription factor that is specifically expressed in outer epidermis of growing fruit.The point mutation in the shn2 mutant intro-duces a K to N amino acid change in the highly conserved‘mm’domain of SHN proteins.The cuticle from shn2 fruit showed a~fivefold reduction in cutin while abundance and composition of waxes were barely affected.In addition to alterations in cuticle thickness and properties,epidermal patterning and polysaccharide composition of the cuticle were changed.RNAseq analysis further highlighted the altered expression of hundreds of genes in the fruit exocarp of shn2,including genes associated with cuticle and cell wall formation,hormone signaling and response,and transcrip-tional regulation.In conclusion,we showed that a point mutation in the transcriptional regulator SlSHN2 causes major changes in fruit cuticle formation and its coordination with epidermal patterning.