Mapping of fruit apex shape related QTLs across multi-genetic backgrounds in cucumber(Cucumis sativus L.)

The shape of fruit apex is critical to appearance quality in cucumber(Cucumis sativus L.),of which the genetic basis was poorly understood,and the use of marker-assisted breeding for fruit apex improvement is not available yet.In this study,the variation of fruit apex in different cucumber ecotypes was evaluated by fruit apex angle(variation coefficient from 7.1%to 15.7%)and fruit apex index(variation coefficient from 8.8%to 22.6%).Fruit apex associated QTLs were mapped by using 145 F_(2:3) families and 155 F_(2:6) population that were derived from the cross of different ecotype cucumbers.Phenotyping of the mapping populations were conducted in four experiments in 2 years.Four majoreffect QTLs,Bfal4.1,Bfai4.1,Bfad6.1 and Bfai6.1 were consistently and reliably detected across two environments which could explain 11.6%-33.6%phenotypic variations(R^(2))in the F_(2:3) families.Three major-effect QTLs,Ofai4.1(R^(2)=13.4%-15.5%),Ofal4.1(R^(2)=10.7%-12.8%),and Ofad6.1(R^(2)=11.6%-12.4%)were stably detected in the F_(2:6) population in two experiments.Bfai4.1,Bfal4.1,Ofai4.1 and Ofal4.1 were integrated to be consensus QTL fa4.1,within which 11 candidate genes were predicted.Bfai6.1 and Bfad6.1 were integrated to be consensus QTL fa6.1.QTL interaction analysis showed that Bfai6.1 has epistatic effect with Bfai4.1.This study revealed two reliable major-effect fruit apex related QTLs across multi-genetic backgrounds and environments in cucumber.The possible candidate genes regulating the shape of fruit apex,and the relationship between cell division and fruit apex morphogenesis were discussed.

Chromosome-scale genome assembly of Cucumis hystrix-a wild species interspecifically cross-compatible with cultivated cucumber

Cucumis hystrix Chakr.(2n=2x=24)is a wild species that can hybridize with cultivated cucumber(C.sativus L.,2n=2x=14),a globally important vegetable crop.However,cucumber breeding is hindered by its narrow genetic base.Therefore,introgression from C.hystrix has been anticipated to bring a breakthrough in cucumber improvement.Here,we report the chromosome-scale assembly of C.hystrix genome(289 Mb).Scaffold N50 reached 14.1 Mb.Over 90%of the sequences were anchored onto 12 chromosomes.A total of 23,864 genes were annotated using a hybrid method.Further,we conducted a comprehensive comparative genomic analysis of cucumber,C.hystrix,and melon(C.melo L.,2n=2x=24).Whole-genome comparisons revealed that C.hystrix is phylogenetically closer to cucumber than to melon,providing a molecular basis for the success of its hybridization with cucumber.Moreover,expanded gene families of C.hystrix were significantly enriched in“defense response,”and C.hystrix harbored 104 nucleotide-binding site-encoding disease resistance gene analogs.Furthermore,121 genes were positively selected,and 12(9.9%)of these were involved in responses to biotic stimuli,which might explain the high disease resistance of C.hystrix.The alignment of whole C.hystrix genome with cucumber genome and self-alignment revealed 45,417 chromosome-specific sequences evenly distributed on C.hystrix chromosomes.Finally,we developed four cucumber-C.hystrix alien addition lines and identified the exact introgressed chromosome using molecular and cytological methods.The assembled C.hystrix genome can serve as a valuable resource for studies on Cucumis evolution and interspecific introgression breeding of cucumber.

口蹄疫病毒等小RNA病毒可通过一种共性机制操纵细胞加速病毒复制

小RNA病毒是RNA病毒中最小的类群。这种病毒的颗粒为直径22~30 nm的正二十面体,无包膜,并且含有29%~32%的连续线型单链RNA。小RNA病毒科的主要成员包括口蹄疫病毒(FMDV)、脊髓灰质炎病毒(PV)、塞内卡病毒(SVA)、埃可病毒、柯萨奇病毒等,能引起多种人或动物传染性疾病,对人和动物的健康构成威胁。小RNA病毒的VP3蛋白是病毒结构中的关键组成部分,尤其在口蹄疫病毒、脊髓灰质炎病毒和塞内卡病毒等病毒中,VP3蛋白被视为病毒复制和致病过程中的关键毒力因子。

Comparative Cyto-molecular Analysis of Repetitive DNA Provides Insights into the Differential Genome Structure and Evolution of Five Cucumis Species

The genus Cucumis, includes the cucumber(2n = 14), melon(2n = 24), and other wild species, which is a good model for studying genome organization and evolution due to their variation in genome size and basic chromosome number. In this study, five Cucumis species with different geographical origins and basic chromosome numbers(i.e., C. sativus, C. hystrix, C. melo, C. anguria, and C. metuliferus) were used to identify and characterize the repetitive DNA in detail using a phylogenetic method. Comparative cyto-molecular genetic analysis of repetitive DNA was carried out using a graph-based clustering method, construction of Neighbor-Joining tree and fluorescence in situ hybridization(FISH).The results revealed that the five Cucumis species had differences in the repeat content of their genome, as well as in the composition of repetitive DNA and their genomic proportions. Three species from subgenus Melo showed a decreased tendency in both repeat types and genomic proportions, while two species from subgenus Cucumis also showed a decreased tendency in repeat types, but an increased tendency in genomic proportions. Phylogenic analysis of Cucumis Ty1/Copia, Ty3/Gypsy, and 45 S rDNA ITS regions revealed that C. sativus, C. hystrix, and C. melo were closely related species, which C. sativus and C. hystrix were closer, while C. anguria and C. metuliferus were closer to each other and further from the other three species. Differential accumulation and elimination of different repeat types divergently shaped the genomic architecture of these five Cucumis species, contributing to the genome’s evolution and diversification. Overall, these results enhance our understanding of the genomes of these five Cucumis species, and contribute to a more holistic view of genome evolution and phylogenetics of this genus.