To elucidate the mechanisms underlying the differences in yield formation among two parents (P₁ and P₂) and their F₁ hybrid of cucumber, biomass production and whole source–sink dynamics were analyzed using a functional–structural plant model (FSPM) that simulates both the number and size of individual organs.  Observations of plant development and organ biomass were recorded throughout the growth periods of the plants.  The GreenLab Model was used to analyze the differences in fruit setting, organ expansion, biomass production and biomass allocation.  The source–sink parameters were estimated from the experimental measurements.  Moreover, a particle swarm optimization algorithm (PSO) was applied to analyze whether the fruit setting is related to the source–sink ratio.  The results showed that the internal source–sink ratio increased in the vegetative stage and reached a peak until the first fruit setting.  The high yield of hybrid F₁ is the compound result of both fruit setting and the internal source–sink ratio.  The optimization results also revealed that the incremental changes in fruit weight result from the increases in sink strength and proportion of plant biomass allocation for fruits.  The model-aided analysis revealed that heterosis is a result of a delicate compromise between fruit setting and fruit sink strength.  The organ-level model may provide a computational approach to define the target of breeding by combination with a genetic model.

 

Tomato (Solanum lycopersicum) stress resistance and fruit total soluble solid (TSS) content have changed dramatically during selective breeding, and transcriptome variation has played a critical role in this rewiring.  However, the single tomato reference genome impedes characterization of whole-transcriptome variation during domestication and breeding at the population level.  Here, we constructed a pan-transcriptome of orange-stage tomato fruit, and investigated global expression presence/absence variation (ePAV) and differentially expressed genes (DEGs) based on RNA sequencing (RNA-seq) data from 399 tomato accessions.  A total of 7 181 genes absent from the reference genome were identified, 6 122 of which were ePAV genes during tomato domestication and breeding including resistance genes such as late blight resistance gene PIM_DN29746_c0_g3_i1 and peroxidase P7-like gene PIM_DN30274_c0_g2_i1.  In addition, 3 629 genes were significantly differentially expressed during tomato selection, among which 19 genes were associated with the reduced fruit TSS content of modern tomato cultivars, including LIN5, TIV1, and seven novel sugar transporter genes.  Our results indicate that natural and artificial selection greatly shaped the tomato transcriptome, thereby altering the fruit TSS content and resistance to abiotic and biotic stresses.

Potato (Solanum tuberosum L.) is the third most important food crop worldwide after wheat and rice in terms of human consumption.  A critical domestication trait for potato was the decrease of toxic steroidal glycoalkaloids (SGAs) in tuber flesh.  Here, we used a diploid F2 segregating population derived from a cross between S. tuberosum and the wild potato species Solanum chacoense to map the quantitative trait loci (QTLs) associated with the regulation of SGAs content in tuber flesh.  In a three-year study, we identified two QTLs on chromosomes 2 and 8 affecting SGAs content in tuber flesh.  The QTL on chromosome 8 harbors 38 genes that are co-expressed with the GLYCOALKALOID METABOLISM genes.  These findings lay the foundation for exploiting the genes controlling SGAs content in tuber flesh and they provide a theoretical basis for the use of wild germplasm in potato breeding.

 

Cucumber is an important vegetable crop and a model crop for the study of sex expression in plants.  However, the genomic resources and tools for functional genomics studies in cucumber are still limited.  In this paper, we conducted ethyl methyl sulfone (EMS) mutagenesis in the northern China ecotype cucumber inbred line 406 to construct a mutant library.  We optimized the conditions of EMS mutagenesis on inbred line 406 which included treatment of seeds at 1.5% EMS for 12 h.  We obtained a number of mutant lines showing inheritable morphological changes in plant architecture, leaves, floral organs, fruits and other traits through M1, M2 and M3 generations.  The F2 segregating populations were constructed and analyzed.We found that a short fruit mutant and a yellow-green fruit peel mutant were both under the control of a single recessive gene, respectively.  These results provide valuable germplasm resources for the improvement of cucumber genetics and functional genomic research.