Characterization and QTL identification in eggplant introgression lines under two N fertilization levels

Lowering nitrogen inputs is a major goal for sustainable agriculture.In the present study,a set of 10 Solanum melongena introgression lines(ILs)developed using Solanum incanum as the exotic donor parent were grown under two nitrogen fertilization doses supplied with the irrigation system:1)8.25 mmol·L-1NH4NO3,corresponding to the high nitrogen treatment(HN),and 2)no external nitrogen supply,corresponding to the low nitrogen treatment(LN).Twenty traits,including plant growth and yield parameters,fruit size and morphology,nitrogen and carbon content in leaf and fruit,and phenolics content in fruit,were evaluated.The aim was to select of potential materials for eggplant breeding under low N inputs,as well as to identify and locate putative QTLs associated with the traits evaluated.No significant differences were observed between the soil characteristics of the HN and LN treatments,except for nitrogen and iron content,which was slightly lower in the HN,probably as a consequence of higher nutrient removal from soil by plants in the latter group.Analysis of variance showed that lowering nitrogen inputs did not significantly affect the final yield,fruit morphology,size and phenolics content.Most agronomic traits were highly and positively correlated with each other under both treatments,as well as total phenolics with chlorogenic acid content.The assessment of the differences between each IL and the recipient parent resulted in the identification of 36 QTLs associated with most of the traits—12 were specific to the HN,17 specific to the LN,and 7 were stable across treatments.The introgressed fragment of S.incanum generally had a negative effect on the trait,except for QTLs for fruit dry matter,for fruit length on chromosome 10 under the HN,and for fruit pedicel length on chromosome 9 under the LN.The increase over AN-S-26 of the allele of S.incanum for the QTLs detected ranged between-73.98% and 26.03% in HN and-73.67%and 34.43% in LN.These findings provide useful tools for the utilization of S.incanum in eggplant breeding under lower nitrogen fertilization.

Evaluation of three sets of advanced backcrosses of eggplant with wild relatives from different gene pools under low N fertilization conditions

The development of new cultivars with improved nitrogen use efficiency(NUE)is key for implementing sustainable agriculture practices.Crop wild relatives(CWRs)provide valuable genetic resources for breeding programs aimed at achieving this goal.In this study,three eggplant(Solanum melongena)accessions together with their advanced backcrosses(ABs;BC3 to BC5 generations)were evaluated for 22 morpho-agronomic,physiological,and NUE traits under low nitrogen(LN)fertilization conditions.The ABs were developed with introgressions from the wild relatives Solanum insanum,Solanum dasyphyllum,and Solanum elaeagnifolium.The AB population comprised a total of 25,59,and 59 genotypes,respectively,with overall donor wild relative genome coverage percentages of 58.8%,46.3%,and 99.2%.The three S.melongena recurrent parents were also evaluated under control(normal)N fertilization.Reduction of N fertilization in the parents resulted in decreased chlorophyll content-related traits,aerial biomass,stem diameter,and yield and increased NUE,nitrogen uptake efficiency(NUpE),and nitrogen utilization efficiency(NUtE).However,the decrease in yield was moderate,ranging between 62.6%and 72.6%.A high phenotypic variation was observed within each of the three sets of ABs under LN conditions,with some individuals displaying improved transgressive characteristics over the recurrent parents.Using the single primer enrichment technology 5 k probes platform for high-throughput genotyping,we observed a variable but high degree of recurrent parent genome recovery in the ABs attributable to the lines recombination,allowing the successful identification of 16 quantitative trait loci(QTL).Different allelic effects were observed for the introgressed QTL alleles.Several candidate genes were identified in the QTL regions associated with plant growth,yield,fruit size,and NUE-related parameters.Our results show that eggplant materials with introgressions from CWRs can result in a dramatic impact in eggplant breeding for a more sustainable agriculture.

Genetic diversity,population structure,and relationships in a collection of pepper(Capsicum spp.)landraces from the Spanish centre of diversity revealed by genotypingby-sequencing(GBS)

Pepper(Capsicum spp.)is one of the most important vegetable crops;however,pepper genomic studies lag behind those of other important Solanaceae.Here we present the results of a high-throughput genotyping-by-sequencing(GBS)study of a collection of 190 Capsicum spp.accessions,including 183 of five cultivated species(C.annuum,C.chinense,C.frutescens,C.baccatum,and C.pubescens)and seven of the wild form C.annuum var.glabriusculum.Sequencing generated 6,766,231 high-quality read tags,of which 40.7%were successfully aligned to the reference genome.SNP calling yielded 4083 highly informative segregating SNPs.Genetic diversity and relationships of a subset of 148 accessions,of which a complete passport information was available,was studied using principal components analysis(PCA),discriminant analysis of principal components(DAPC),and phylogeny approaches.C.annuum,C.baccatum,and C.chinense were successfully separated by all methods.Our population was divided into seven clusters by DAPC,where C.frutescens accessions were clustered together with C.chinense.C.annuum var.glabriusculum accessions were spread into two distinct genetic pools,while European accessions were admixed and closely related.Separation of accessions was mainly associated to differences in fruit characteristics and origin.Phylogeny studies showed a close relation between Spanish and Mexican accessions,supporting the hypothesis that the first arose from a main genetic flow from the latter.Tajima’s D statistic values were consistent with positive selection in the C.annuum clusters,possibly related to domestication or selection towards traits of interest.This work provides comprehensive and relevant information on the origin and relationships of Spanish landraces and for future association mapping studies in pepper.

Morphoagronomic characterization and wholegenome resequencing of eight highly diverse wild and weedy S.pimpinellifolium and S.lycopersicum var.cerasiforme accessions used for the first interspecific tomato MAGIC population

The wild Solanum pimpinellifolium(SP)and the weedy S.lycopersicum var.cerasiforme(SLC)are largely unexploited genetic reservoirs easily accessible to breeders,as they are fully cross-compatible with cultivated tomato(S.lycopersicum var.lycopersicum).We performed a comprehensive morphological and genomic characterization of four wild SP and four weedy SLC accessions,selected to maximize the range of variation of both taxa.These eight accessions are the founders of the first tomato interspecific multi-parent advanced generation inter-cross(MAGIC)population.The morphoagronomic characterization was carried out with 39 descriptors to assess plant,inflorescence,fruit and agronomic traits,revealing the broad range of diversity captured.Part of the morphological variation observed in SP was likely associated to the adaptation of the accessions to different environments,while in the case of SLC to both human activity and adaptation to the environment.Whole-genome resequencing of the eight accessions revealed over 12 million variants,ranging from 1.2 to 1.9 million variants in SLC and from 3.1 to 4.8 million in SP,being 46.3%of them(4,897,803)private variants.The genetic principal component analysis also confirmed the high diversity of SP and the complex evolutionary history of SLC.This was also reflected in the analysis of the potential footprint of common ancestors or old introgressions identified within and between the two taxa.The functional characterization of the variants revealed a significative enrichment of GO terms related to changes in cell walls that would have been negatively selected during domestication and breeding.The comprehensive morphoagronomic and genetic characterization of these accessions will be of great relevance for the genetic analysis of the first interspecific MAGIC population of tomato and provides valuable knowledge and tools to the tomato community for genetic and genomic studies and for breeding purposes.