Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding

A Genome-Wide Association Study Identifies Markers and Candidate Genes Affecting Tolerance to the Wheat Pathogen Zymoseptoria tritici

Plants defend themselves against pathogens using either resistance, measured as the host's ability to limit pathogen multiplication, or tolerance, measured as the host's ability to reduce the negative effects of infection. Tolerance is a promising trait for crop breeding, but its genetic basis has rarely been studied and remains poorly understood. Here, we reveal the genetic basis of leaf tolerance to the fungal pathogen Zymoseptoria tritici that causes the globally important septoria tritici blotch (STB) disease on wheat. Leaf tolerance to Z. tritici is a quantitative trait that was recently discovered in wheat by using automated image analyses that quantified the symptomatic leaf area and counted the number of pycnidia found on the same leaf. A genome-wide association study identified four chromosome intervals associated with tolerance and a separate chromosome interval associated with resistance. Within these intervals, we identified candidate genes, including wall-associated kinases similar to Stb6, the first cloned STB resistance gene. Our analysis revealed a strong negative genetic correlation between tolerance and resistance to STB, indicative of a trade-off. Such a trade-off between tolerance and resistance would hinder breeding simultaneously for both traits, but our findings suggest a way forward using marker-assisted breeding. We expect that the methods described here can be used to characterize tolerance to other fungal diseases that produce visible fruiting bodies, such as speckled leaf blotch on barley, potentially unveiling conserved tolerance mechanisms shared among plant species. [Formula: see text] Copyright © 2025 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Unveiling pepper immunity's robustness to temperature shifts: insights for empowering future crops

Boosting plant immunity is an effective alternative to pesticides. However, environmental variations, accentuated by climate change, can compromise immunity. The robustness of a trait corresponds to the absence (or low level) of variation in that trait in the face of an environmental change. Here, we examined two types of robustness, robustness of immunity mean and robustness of immunity variation, and proposed nine quantitative robustness estimators. We characterized the immunity of a set of accessions representative of the natural diversity of pepper (Capsicum annuum L.), to two major pathogens: the oomycete Phytophthora capsici Leon. and potato virus Y. For each pathogen, we measured the immunity of accessions in two contrasting environments in terms of temperature. For each type of robustness and each pathogen, the impact of temperature change on immunity varied between accessions. The robustness estimators proved to be complementary and differed in terms of heritability and ability to discriminate accessions. A positive and significant correlation was observed between immunity and robustness. There was no significant relationship between the robustness of immunity to the two pathogens, but some accessions showed high immunity and robustness against both pathogens. These results justify the need to consider both immunity and robustness to environmental variations in order to select varieties adapted to current and future climate conditions. Phenotypic robustness should also be considered when assessing the "value of sustainable cultivation and use" of future plant varieties, particularly during the application process for protection rights granted from the European Community Plant Variety Office.

Physiological and Genetic Aspects of Resistance to Abiotic Stresses in Capsicum Species

Abiotic stress is one of the key factors harming global agriculture today, seriously affecting the growth and yield of vegetables. Pepper is the most widely grown vegetable in the world, with both high nutritional and economic values. Currently, the increase in global extreme weather events has heightened the frequency of abiotic stresses, such as drought, high and low temperatures, waterlogging, and high salt levels, which impairs pepper growth and development, leading to its reduced yield and quality. In this review, we summarize the research progress on the responses of pepper to abiotic stress in recent years in terms of physiology, biochemistry, molecular level, and mitigation measures. We then explore the existing problems and propose future research directions. This work provides a reference for the cultivation and development of new pepper varieties resistant to abiotic stress.

Current knowledge and breeding strategies for management of aphid-transmitted viruses of pepper (Capsicum spp.) in Africa

Aphid-transmitted viruses cause significant losses in pepper production worldwide, negatively affecting yield and quality. The emergence of new aphid-transmitted viruses or development of variants as well as the occurrence in mixed infections make management a challenge. Here, we overview the current status of the distribution, incidence and phylogeny of aphids and the viruses they transmit in pepper in Africa; outline the available genetic resources, including sources of resistance, resistance genes and molecular markers; and discuss the recent advances in understanding the genetic basis of resistance to the predominant African viruses infecting pepper. Pepper veinal mottle virus (PVMV; Potyvirus); Potato virus Y (PVY; Potyvirus), Chili veinal mottle virus (ChiVMV; Potyvirus), Cucumber mosaic virus (CMV; Cucumovirus) and Pepper veins yellow virus (PeVYV; Polerovirus) have been reported to be the most widespread and devastating aphid-transmitted viruses infecting pepper across Africa. Co-infection or mixed infection between aphid-transmitted viruses has been detected and the interrelationship between viruses that co-infect chili peppers is poorly understood. Establishing and evaluating existing and new diversity sets with more genetic diversity is an important component of developing host resistance and implementing integrated management strategies. However, more work needs to be done to characterize the aphid-transmitted viral strains across Africa and understand their phylogeny in order to develop more durable host resistance. In addition, a limited number of QTLs associated with resistance to the aphid-transmitted virus have been reported and QTL data are only available for PVY, ChiVMV and CMV mainly against European and Asian strains, although PVMV is likely the most important aphid-transmitted viral disease in Africa. There is a need to identify germplasm resources with resistance against various aphid-transmitted virus strains, and subsequent pyramiding of the resistance using marker-assisted selection could be an effective strategy. The recent advances in understanding the genetic basis of the resistance to the virus and the new breeding techniques that can be leveraged to accelerate breeding for aphid-transmitted virus in pepper are proposed as strategies to more efficiently develop resistant cultivars. The deployment of multi-genetic resistances in pepper is an effective and desirable method of managing viral-diseases in Africa and limit losses for farmers in a sustainable manner.

Genome-wide association study and candidate gene identification for agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum

Pepper agronomic traits serve as pivotal indicators for characterizing germplasm attributes and correlations. It is important to study differential genotypic variation through phenotypic differences of target traits. Whole genome resequencing was used to sequence the whole genome among different individuals of species with known reference genomes and annotations, and based on this, differential analyses of individuals or populations were carried out to identify SNPs for agronomic traits related to pepper. This study conducted a genome-wide association study encompassing 26 key agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum. The population structure (phylogenetics, population structure, population principal component analysis, genetic relationship) and linkage disequilibrium analysis were realized to ensure the accuracy and reliability of GWAS results, and the optimal statistical model was determined. A total of 929 SNPs significantly associated with 26 agronomic traits, were identified, alongside the detection of 519 candidate genes within 100 kb region adjacent to these SNPs. Additionally, through gene annotation and expression pattern scrutiny, genes such as GAUT1, COP10, and DDB1 correlated with fruit traits in Capsicum frutescens and Capsicum annuum were validated via qRT-PCR. In the CH20 (Capsicum annuum) and YB-4 (Capsicum frutescens) cultivars, GAUT1 and COP10 were cloned with cDNA lengths of 1065 bp and 561 bp, respectively, exhibiting only a small number of single nucleotide variations and nucleotide deletions. This validation provides a robust reference for molecular marker-assisted breeding of pepper agronomic traits, offering both genetic resources and theoretical foundations for future endeavors in molecular marker-assisted breeding for pepper.

Multi-environment association study highlights candidate genes for robust agronomic quantitative trait loci in a novel worldwide Capsicum core collection

Investigating crop diversity through genome-wide association studies (GWAS) on core collections helps in deciphering the genetic determinants of complex quantitative traits. Using the G2P-SOL project world collection of 10 038 wild and cultivated Capsicum accessions from 10 major genebanks, we assembled a core collection of 423 accessions representing the known genetic diversity. Since complex traits are often highly dependent upon environmental variables and genotype-by-environment (G × E) interactions, multi-environment GWAS with a 10 195-marker genotypic matrix were conducted on a highly diverse subset of 350 Capsicum annuum accessions, extensively phenotyped in up to six independent trials from five climatically differing countries. Environment-specific and multi-environment quantitative trait loci (QTLs) were detected for 23 diverse agronomic traits. We identified 97 candidate genes potentially implicated in 53 of the most robust and high-confidence QTLs for fruit flavor, color, size, and shape traits, and for plant productivity, vigor, and earliness traits. Investigating the genetic architecture of agronomic traits in this way will assist the development of genetic markers and pave the way for marker-assisted selection. The G2P-SOL pepper core collection will be available upon request as a unique and universal resource for further exploitation in future gene discovery and marker-assisted breeding efforts by the pepper community.

Genome-Wide Association Studies Using 3VmrMLM Model Provide New Insights into Branched-Chain Amino Acid Contents in Rice Grains

Rice (Oryza sativa L.) is a globally important food source providing carbohydrates, amino acids, and dietary fiber for humans and livestock. The branched-chain amino acid (BCAA) level is a complex trait related to the nutrient quality of rice. However, the genetic mechanism underlying the BCAA (valine, leucine, and isoleucine) accumulation in rice grains remains largely unclear. In this study, the grain BCAA contents and 239,055 SNPs of a diverse panel containing 422 rice accessions were adopted to perform a genome-wide association study (GWAS) using a recently proposed 3VmrMLM model. A total of 357 BCAA-content-associated main-effect quantitative trait nucleotides (QTNs) were identified from 15 datasets (12 BCAA content datasets and 3 BLUP datasets of BCAA). Furthermore, the allelic variation of two novel candidate genes, LOC_Os01g52530 and LOC_Os06g15420, responsible for the isoleucine (Ile) content alteration were identified. To reveal the genetic basis of the potential interactions between the gene and environmental factor, 53 QTN-by-environment interactions (QEIs) were detected using the 3VmrMLM model. The LOC_Os03g24460, LOC_Os01g55590, and LOC_Os12g31820 were considered as the candidate genes potentially contributing to the valine (Val), leucine (Leu), and isoleucine (Ile) accumulations, respectively. Additionally, 10 QTN-by-QTN interactions (QQIs) were detected using the 3VmrMLM model, which were putative gene-by-gene interactions related to the Leu and Ile contents. Taken together, these findings suggest that the implementation of the 3VmrMLM model in a GWAS may provide new insights into the deeper understanding of BCAA accumulation in rice grains. The identified QTNs/QEIs/QQIs serve as potential targets for the genetic improvement of rice with high BCAA levels.

Virus Evolution Faced to Multiple Host Targets: The Potyvirus-Pepper Case Study

The wealth of variability amongst genes controlling immunity against potyviruses in pepper (Capsicum spp.) has been instrumental in understanding plant-virus co-evolution and major determinants of plant resistance durability. Characterization of the eukaryotic initiation factor 4E1 (eIF4E1), involved in mRNA translation, as the basis of potyvirus resistance in pepper initiated a large body of work that showed that recessive resistance to potyviruses and other single-stranded positive-sense RNA viruses resulted from mutations in eukaryotic initiation factors in many plant crop species. Combining mutations in different eIF4Es in the same pepper genotype had complex effects on the breadth of the resistance spectrum and on resistance durability, revealing a trade-off between these two traits. In addition, combining eIF4E1 mutations with a quantitatively resistant genetic background had a strong positive effect on resistance durability. Analysing the evolutionary forces imposed by pepper genotypes onto virus populations allowed identifying three key factors improving plant resistance durability: the complexity of mutational pathways involved in virus adaptation to the plant resistance, the decrease of competitivity induced by these mutations on the virus and the intensity of genetic drift imposed by plant genotypes on the virus during its infection cycle.

Germplasm Resources and Strategy for Genetic Breeding of Lycium Species: A Review

Lycium species (goji), belonging to Solanaceae, are widely spread in the arid to semiarid environments of Eurasia, Africa, North and South America, among which most species have affinal drug and diet functions, resulting in their potential to be a superior healthy food. However, compared with other crop species, scientific research on breeding Lycium species lags behind. This review systematically introduces the present germplasm resources, cytological examination and molecular-assisted breeding progress in Lycium species. Introduction of the distribution of Lycium species around the world could facilitate germplasm collection for breeding. Karyotypes of different species could provide a feasibility analysis of fertility between species. The introduction of mapping technology has discussed strategies for quantitative trait locus (QTL) mapping in Lycium species according to different kinds of traits. Moreover, to extend the number of traits and standardize the protocols of trait detection, we also provide 1,145 potential traits (275 agronomic and 870 metabolic) in different organs based on different reference studies on Lycium, tomato and other Solanaceae species. Finally, perspectives on goji breeding research are discussed and concluded. This review will provide breeders with new insights into breeding Lycium species.

Concurrent evolution of resistance and tolerance to potato virus Y in Capsicum annuum revealed by genome-wide association

We performed a genome-wide association study of pepper (Capsicum annuum) tolerance to potato virus Y (PVY). For 254 pepper accessions, we estimated the tolerance to PVY as the coefficient of regression of the fresh weight (or height) of PVY-infected and mock-inoculated plants against within-plant virus load. Small (strongly negative) coefficients of regression indicate low tolerance because plant biomass or growth decreases sharply as virus load increases. The tolerance level varied largely, with some pepper accessions showing no symptoms or fairly mild mosaics, whereas about half (48%) of the accessions showed necrotic symptoms. We found two adjacent single-nucleotide polymorphisms (SNPs) at one extremity of chromosome 9 that were significantly associated with tolerance to PVY. Similarly, in three biparental pepper progenies, we showed that the induction of necrosis on PVY systemic infection segregated as a monogenic trait determined by a locus on chromosome 9. Our results also demonstrate the existence of a negative correlation between resistance and tolerance among the cultivated pepper accessions at both the phenotypic and genetic levels. By comparing the distributions of the tolerance-associated SNP alleles and previously identified PVY resistance-associated SNP alleles, we showed that cultivated pepper accessions possess favourable alleles for both resistance and tolerance less frequently than expected under random associations, while the minority of wild pepper accessions frequently combined resistance and tolerance alleles. This divergent evolution of PVY resistance and tolerance could be related to pepper domestication or farmer's selection.

The INRAE Centre for Vegetable Germplasm: Geographically and Phenotypically Diverse Collections and Their Use in Genetics and Plant Breeding

The French National Research Institute for Agriculture, Food and the Environment (INRAE) conserves and distributes five vegetable collections as seeds: the aubergine* (in this article the word aubergine refers to eggplant), pepper, tomato, melon and lettuce collections, together with their wild or cultivated relatives, are conserved in Avignon, France. Accessions from the collections have geographically diverse origins, are generally well-described and fixed for traits of agronomic or scientific interest and have available passport data. In addition to currently conserving over 10,000 accessions (between 900 and 3000 accessions per crop), the centre maintains scientific collections such as core collections and bi- or multi-parental populations, which have also been genotyped with SNP markers. Each collection has its own merits and highlights, which are discussed in this review: the aubergine collection is a rich source of crop wild relatives of Solanum; the pepper, melon and lettuce collections have been screened for resistance to plant pathogens, including viruses, fungi, oomycetes and insects; and the tomato collection has been at the heart of genome-wide association studies for fruit quality traits and environmental stress tolerance.

Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances

Growing virus resistant varieties is a highly effective means to avoid yield loss due to infection by many types of virus. The challenge is to be able to detect resistance donors within plant species diversity and then quickly introduce alleles conferring resistance into elite genetic backgrounds. Until now, mainly monogenic forms of resistance with major effects have been introduced in crops. Polygenic resistance is harder to map and introduce in susceptible genetic backgrounds, but it is likely more durable. Genome wide association studies (GWAS) offer an opportunity to accelerate mapping of both monogenic and polygenic resistance, but have seldom been implemented and described in the plant-virus interaction context. Yet, all of the 48 plant-virus GWAS published so far have successfully mapped QTLs involved in plant virus resistance. In this review, we analyzed general and specific GWAS issues regarding plant virus resistance. We have identified and described several key steps throughout the GWAS pipeline, from diversity panel assembly to GWAS result analyses. Based on the 48 published articles, we analyzed the impact of each key step on the GWAS power and showcase several GWAS methods tailored to all types of viruses.

Association mapping reveals novel genomic regions controlling some root and stolon traits in tetraploid potato (Solanum tuberosum L.)

Tuber crops have measurable biological variation in root and stolon phenotyping and thus may be utilized to identify genomic regions associated with these variations. This is the first comprehensive association mapping study related to potato root and stolon traits. A diverse panel of 192 tetraploid potato (Solanum tuberosum L.) genotypes were grown in aeroponics to reveal a biologically significant variation and detection of genomic regions associated with the root and stolon traits. Phenotyping of root traits was performed by image analysis software "WinRHIZO" (a root scanning method), and stolon traits was measured manually, while SolCAP 25K potato array was used for genotyping. Significant variation was observed between the potato genotypes for root and stolon traits along with high heritabilities (0.80 in TNS to 0.95 in SL). For marker-trait associations, Q + K linear mixed model was implemented and 50 novel genomic regions were detected. Significantly associated SNPs with stolon traits were located on chr 4, chr 6, chr 7, chr 9, chr 11 and chr 12, while those linked to root traits on chr 1, chr 2, chr 3, chr 9, chr 11, and chr 12. Structure and PCA analysis grouped genotypes into four sub-populations disclosing population genetic diversity. LD decay was observed at 2.316 Mbps (r 2 = 0.29) in the population. The identified SNPs were associated with genes performing vital functions such as root signaling and signal transduction in stress environments (GT-2 factors, protein kinases SAPK2-like and protein phosphatases "StPP1"), transcriptional and post-transcriptional gene regulation (RNA-binding proteins), sucrose synthesis and transporter families (UGPase, Sus3, SuSy, and StSUT1) and PVY resistance (Ry sto). The findings of our study can be employed in future breeding programs for improvement in potato production.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02727-6.

Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics

Pepper (Capsicum spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant. The genus includes over 30 species, five of which (C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens) are domesticated and mainly grown for consumption as food and for non-food purposes (e.g., cosmetics). The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security, the growing consumers' demand for food. Furthermore, demographic trends and changes to climate require more efficient use of plant genetic resources in breeding programs. Increases in pepper consumption have been observed in the past 20 years, and for maintaining this trend, the development of new resistant and high yielding varieties is demanded. The range of pathogens afflicting peppers is very broad and includes fungi, viruses, bacteria, and insects. In this context, the large number of accessions of domesticated and wild species stored in the world seed banks represents a valuable resource for breeding in order to transfer traits related to resistance mechanisms to various biotic stresses. In the present review, we report comprehensive information on sources of resistance to a broad range of pathogens in pepper, revisiting the classical genetic studies and showing the contribution of genomics for the understanding of the molecular basis of resistance.