The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development

Germplasm collections are a crucial resource to conserve natural genetic diversity and provide a source of novel traits essential for sustained crop improvement.Optimal collection,preservation and utilization of these materials depends upon knowledge of the genetic variation present within the collection.Here we use the high-throughput genotyping-by-sequencing(GBS)technology to characterize the United States National Plant Germplasm System(NPGS)collection of cucumber(Cucumis sativus L.).The GBS data,derived from 1234 cucumber accessions,provided more than 23 K high-quality single-nucleotide polymorphisms(SNPs)that are well distributed at high density in the genome(~1 SNP/10.6 kb).The SNP markers were used to characterize genetic diversity,population structure,phylogenetic relationships,linkage disequilibrium,and population differentiation of the NPGS cucumber collection.These results,providing detailed genetic analysis of the U.S.cucumber collection,complement NPGS descriptive information regarding geographic origin and phenotypic characterization.We also identified genome regions significantly associated with 13 horticulturally important traits through genome-wide association studies(GWAS).Finally,we developed a molecularly informed,publicly accessible core collection of 395 accessions that represents at least 96%of the genetic variation present in the NPGS.Collectively,the information obtained from the GBS data enabled deep insight into the diversity present and genetic relationships among accessions within the collection,and will provide a valuable resource for genetic analyses,gene discovery,crop improvement,and germplasm preservation.

Molecularly tagged genes and quantitative trait loci in cucumber with recommendations for QTL nomenclature

Cucumber,Cucumis sativus L.(2n=2x=14),is an important vegetable crop worldwide.It was the first specialty crop with a publicly available draft genome.Its relatively small,diploid genome,short life cycle,and selfcompatible mating system offers advantages for genetic studies.In recent years,significant progress has been made in molecular mapping,and identification of genes and QTL responsible for key phenotypic traits,but a systematic review of the work is lacking.Here,we conducted an extensive literature review on mutants,genes and QTL that have been molecularly mapped or characterized in cucumber.We documented 81 simply inherited trait genes or major-effect QTL that have been cloned or fine mapped.For each gene,detailed information was compiled including chromosome locations,allelic variants and associated polymorphisms,predicted functions,and diagnostic markers that could be used for marker-assisted selection in cucumber breeding.We also documented 322 QTL for 42 quantitative traits,including 109 for disease resistances against seven pathogens.By alignment of these QTL on the latest version of cucumber draft genomes,consensus QTL across multiple studies were inferred,which provided insights into heritable correlations among different traits.Through collaborative efforts among public and private cucumber researchers,we identified 130 quantitative traits and developed a set of recommendations for QTL nomenclature in cucumber.This is the first attempt to systematically summarize,analyze and inventory cucumber mutants,cloned or mapped genes and QTL,which should be a useful resource for the cucurbit research community.

Transcriptomic and metabolomic analyses of cucumber fruit peels reveal a developmental increase in terpenoid glycosides associated with age-related resistance to Phytophthora capsici

The oomycete,Phytophthora capsici,infects cucumber(Cucumis sativus L.)fruit.An age-related resistance(ARR)to this pathogen was previously observed in fruit of cultivar‘Vlaspik’and shown to be associated with the peel.Young fruits are highly susceptible,but develop resistance at~10–12 days post pollination(dpp).Peels from resistant(16 dpp)versus susceptible(8 dpp)age fruit are enriched with genes associated with defense,and methanolic extracts from resistant age peels inhibit pathogen growth.Here we compared developing fruits from‘Vlaspik’with those of‘Gy14’,a line that does not exhibit ARR.Transcriptomic analysis of peels of the two lines at 8 and 16 dpp identified 80 genes that were developmentally upregulated in resistant‘Vlaspik’16 dpp versus 8 dpp,but not in susceptible‘Gy14’at 16 dpp.A large number of these genes are annotated to be associated with defense and/or specialized metabolism,including four putative resistance(R)genes,and numerous genes involved in flavonoid and terpenoid synthesis and decoration.Untargeted metabolomic analysis was performed on extracts from 8 and 16 dpp‘Vlaspik’and‘Gy14’fruit peels using Ultra-Performance Liquid Chromatography and Quadrupole Time-of-Flight Mass Spectrometry.Multivariate analysis of the metabolomes identified 113 ions uniquely abundant in resistant‘Vlaspik’16 dpp peel extracts.The most abundant compounds in this group had relative mass defects consistent with terpenoid glycosides.Two of the three most abundant ions were annotated as glycosylated nor-terpenoid esters.Together,these analyses reveal potential mechanisms by which ARR to P.capsici may be conferred.

植物抗病毒的遗传工程

植物抗病毒道传工程中利用病毒衣壳蛋白基因、弱毒株系的完整基因组、病毒反义RNA序列和RNA随体序列等方法获得作物抗病毒转基因植物,本文列举了这些方法的最新应用实例。

Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection

Melon(C.melo L.)is an economically important vegetable crop cultivated worldwide.The melon collection in the U.S.National Plant Germplasm System(NPGS)is a valuable resource to conserve natural genetic diversity and provide novel traits for melon breeding.Here we use the genotyping-by-sequencing(GBS)technology to characterize 2083 melon accessions in the NPGS collected from major melon production areas as well as regions where primitive melons exist.Population structure and genetic diversity analyses suggested that C.melo ssp.melo was firstly introduced from the centers of origin,Indian and Pakistan,to Central and West Asia,and then brought to Europe and Americas.C.melo ssp.melo from East Asia was likely derived from C.melo ssp.agrestis in India and Pakistan and displayed a distinct genetic background compared to the rest of ssp.melo accessions from other geographic regions.We developed a core collection of 383 accessions capturing more than 98%of genetic variation in the germplasm,providing a publicly accessible collection for future research and genomics-assisted breeding of melon.Thirty-five morphological characters investigated in the core collection indicated high variability of these characters across accessions in the collection.Genome-wide association studies using the core collection panel identified potentially associated genome regions related to fruit quality and other horticultural traits.This study provides insights into melon origin and domestication,and the constructed core collection and identified genome loci potentially associated with important traits provide valuable resources for future melon research and breeding.