Abstract Sweet potato (Ipomoea batatas (L.) Lam.) is a vital global crop, with breeding focused on both high starch and high yield. Hybrid populations are crucial for genetic improvement, but research on sweet potato hybrid F1 populations remains limited. To explore the genetic laws of important traits in hybrid progenies, this study investigates the genetic diversity and efficient selection methods of the hybrid F1 population from crossing between Yushu No.12 (high starch content) and Luoxushu No.9 (high yield) using phenotypic detection and SSR markers. Coefficients of variation, genetic distances, and similarity coefficients results showed that the F1 population has rich genetic diversity. The parents and F1 progenies could be clustered into 4 and 6 categories based on phenotypic detection and SSR markers, respectively. The results of transgressive inheritance analysis and cluster analysis showed that the hybrid F1 population of sweet potato was closer to the female parent and might exhibit matroclinous inheritance. Based on the principal component analysis (PCA) results, a comprehensive scoring model was developed to select superior progeny. Correlation analysis revealed a strong link (r = 0.6420) between the hardness and starch content of storage root, suggesting hardness could be used for rapid screening high-starch materials. Mantel test showed SSR markers as more reliable for evaluating genetic diversity than phenotypic analysis. These findings uncover the genetic diversity information of sweet potato F1 generation, and provide strategies for the rapid and accurate selection of hybrid progenies, and lay theoretical foundation for deciphering the genetic mechanisms of important traits in sweet potato.

The development of novel improved varieties adapted to unstable environmental conditions is possible through the genetic diversity of breeding materials. Potato is among the most important food crops worldwide; however, there are still significant hindrances to breeding gains attributed to its autotetraploid and highly heterozygous genome. Bacterial wilt caused by the Ralstonia solanacearum species complex is an important disease affecting potato among many economically important crops worldwide. No cultivated potato genotypes have shown a satisfactory level of resistance to bacterial wilt. Nevertheless, resistance can play a crucial role in effective integrated disease management. To understand the genetic landscape of bacterial wilt resistance in cultivated potato, we evaluated the diversity of 192 accessions from the International Potato Center (CIP) using 9,250 single-nucleotide polymorphisms and their associations with the response to bacterial wilt disease evaluated over two independent trials. Twenty-four accessions showed high resistance throughout both trials. Genetic diversity analysis revealed three major clusters whose subgroups were mostly represented by CIP clones derived from common parents. Genome-wide association analyses identified six major hits: two on chromosome 8 and one on each chromosome 2, 4, 5, and 9. These results facilitate genetic dissection of bacterial wilt resistance and enable marker-assisted breeding in elite genotypes for potato breeding initiatives.

Abstract Background Sweet potato is an important root crop cultivated in different countries of the world. Its production and productivity are limited by factors such as the use of unimproved local varieties, pests, disease, and drought. To overcome these constraints, diversity in sweet potato genotypes could be a prerequisite for breeding programs. The present study aimed to determine the genetic diversity and nutritional composition of sweet potato accessions. One hundred accessions of sweet potato were collected from Nigeria and Niger for agro-morphological characterization and 50 of them were used for nutritional and molecular analysis. Eleven quantitative traits, six nutritional traits, and ten SSR markers were used for diversity analysis. Results Analysis of variance (ANOVA) revealed significant differences (p < 0.01) among the sweet potato varieties for all the agro-morphological and nutritional traits studied. Accessions with orange flesh color had higher beta-carotene content compared to those with white, cream, and yellow flesh color. From the molecular diversity analysis, a total of 20 alleles were detected in 50 sweet potato accessions using 10 SSR markers. The average values for Na, Ne, I, Ho, He, and PIC were 2, 1.62, 0.55, 0.40, 0.37, and 0.30 respectively. Cluster analysis based on dissimilarity matrix grouped the accessions into two major clusters. Analysis of molecular variance (AMOVA) revealed 11% variation among the populations and 89% variation within the population, indicating low genetic variation among the populations and high genetic variation within population at p < 0.001. Conclusion Overall, variability was observed among the studied sweet potato accessions based on agro-morphological, nutritional traits and the SSR markers used. This will help breeding in using these genotypes for further improvement of the studied traits.

Different cross-selection (CS) methods incorporating genomic selection (GS) have been used in diploid species to improve long-term genetic gain and preserve diversity. However, their application to heterozygous and autotetraploid crops such as potato (Solanum tuberosum L.) is lacking so far. The objectives of our study were to (i) assess the effects of different CS methods and the incorporation of GS and genetic variability monitoring on both short- and long-term genetic gains compared to strategies using phenotypic selection (PS); (ii) evaluate the changes in genetic variability and the efficiency of converting diversity into genetic gain across different CS methods; and (iii) investigate the interaction effects between different genetic architectures and CS methods on long-term genetic gain. In our simulation results, implementing GS with optimal selected proportions had increased short- and long-term genetic gain compared to any PS strategy. The CS method considering additive and dominance effects to predict progeny mean based on simulated progenies (MEGV-O) achieved the highest long-term genetic gain among the assessed mean-based CS methods. Compared to MEGV-O and usefulness criteria (UC), the linear combination of UC and genome-wide diversity (called EUCD) maintained the same level of genetic gain but resulted in higher diversity and a lower number of fixed QTLs. Moreover, EUCD had a relatively high degree of efficiency in converting diversity into genetic gain. However, choosing the most appropriate weight to account for diversity in EUCD depends on the genetic architecture of the target trait and the breeder&#39;s objectives. Our results provide breeders with concrete methods to improve their potato breeding programs.

Abstract: Heat stress reduces potato productivity by restricting photosynthesis, assimilation production, and sink partitioning. Potato wild relatives (Solanum sect. Petota, Solanaceae) possess abiotic stress resistance characteristics. However, we must assess physiological parameters like gas exchange, chlorophyll index, and fuorescence to determine whether wild potato genotypes can boost crop yield under adverse conditions. We utilized a factorial experimental design to fnd substantial trait-based genotype diferences. The mixed-model technique ranked the genotypes according to their performance in terms of predicted true genotypic values. For potato breeding, we used PCA and cluster analysis on genotypic values to identify critical features and heat-stress-tolerant genotypes. Ranking by best linear unbiased prediction (BLUP) values and heat comprehensive evaluation values for assessed characteristics indicated that predominantly S. chacoense genotypes performed well. Some of the most important physiological characteristics for investigating heat resistant germplasm genetic diversity are net photosynthetic rates, transpiration rates, stomatal conductance, intracellular/ambient CO2, water usage efciency, photosystem II operational efciency, photochemical quenching, and dry matter content. We were able to fnd genotypes (BGB083, BGB102, BGB103, BGB109, BGB113, BGB444, BGB451, BGB467, and BGB472) that have a mix of these traits and are better at keeping up their photosynthetic performance, water use efciency, and chlorophyll content. They also have better photoprotective mechanisms that work better when they are under heat stress. Heat stress is most likely to afect BGB008, BGB096, and BGB107. These characteristics are highly valuable for breeding heat-tolerant potato cultivars that can sustain growth, yield, and tuber quality under the increasing threat of heat stress.

The genetic diversity of tomato in Italy and the growing interest in high-quality food products highlight the importance of establishing varietal distinctiveness through molecular strategies to ensure agrifood product quality and traceability. In this study, four Italian potato-like leaf (PL) landraces were analyzed: “Spagnoletta di Formia e di Gaeta” (SPA) from southern Lazio, “Giagiù” (GIA) and “Patanara” (PTN) from Campania, and “Pomodoro di Mola” (MOL) from Apulia. These landraces were genotyped for the potato leaf gene (C), with two PL American genotypes and a non-allelic PL mutant line included as outgroups. Nagcarlang served as control. An allelism test confirmed C as determinant gene. The SCAR marker for C revealed that the Italian landraces presented determinants other than the most representative one responsible for PL. Whole-genome sequencing of SPA identified a private novel nonsense SNP variant allele, confirmed through dCAPS marker analysis. Additionally, two novel PL alleles responsible for missense variations were identified in GIA/PTN and MOL. In silico protein analysis suggested that novel C alleles could be functional determinants for the protein activity. Overall, PL mutations identified for the first time could serve as molecular tools for agrifood chain traceability, enabling early differentiation and recognition of genotypically similar varieties.

BackgroundEffectors are critical in the antagonistic interactions between plants and pathogens. However, knowledge of mutation mechanisms and evolutionary processes of effectors remains fragmented despite its importance for the sustainable management of plant diseases. Here, we used a population genetic approach to explore the evolution of the effector gene Pi04314 in Phytophthora infestans, the causal agent of potato blight.ResultsWe found that Pi04314 gene exhibits a low genetic variation generated by point mutations mainly occurring in the signal peptide. Two of the 14 amino acid isoforms completely abolished the secretion functions of signal peptides. The effector is under purifying selection, supported by the comparative analyses between its population differentiation with that of SSR marker loci as well as by negative Tajima's D (-1.578, p = 0.040) and Fu's FS (-10.485, p = 0.000). Furthermore, we found that the nucleotide diversity of Pi04314 is significantly correlated with the annual mean temperature at the collection sites.ConclusionThese results suggest that the evolution of effector genes could be influenced by local air temperature and signal peptides may contribute to the ecological adaptation of pathogens. The implications of these results for agricultural and natural sustainability are discussed.

The amount of genetic variability is the foundation for genetic change in any plant breeding program, and the amount of double reduction can influence genetic gain and the amount of future genetic diversity in polyploid species. Our study investigates these factors using variance components analysis on a dataset comprising 13,131 potato breeding lines and phenotypic data from Scandinavian environments spanning 17 years (2003 to 2021). Pedigree information was used in quantitative genetic models to estimate additive genetic variance and the relative importance of additive and non-additive genetic variance. We used two models, a baseline model (M1) without effects due to specific combining ability (SCA) and M2 (including SCA due to interaction between parental genomes). Two cross-validation (CV) schemes [5-Fold and leave-one-breeding-cycle-out (LBCO)] were used to evaluate the prediction ability (PA) of each model. We estimated the rate of double reduction phenomenon (DRP) by determining the rate best fitting the data using a marginal likelihood approach. Our findings showed a wide range of variation in different traits, with very large proportion of additive genetic variance in dry matter content (DMC), but intermediate additive genetic variance for relative yield (RY), germination (GR), and withering (WNG). All traits showed modest non-additive genetic variance. Furthermore, genotype x environment interaction played a significant role in trait variability but is still much smaller than the additive genetic variance. After using different DRP rates, we found that a model with a 0.05 DRP rate provided the best fit to the data. Heritability estimates indicated a strong genetic basis for DMC, while other traits showed more moderate heritability, which shows contributions from both additive and interaction factors. Model comparison by 5-Fold CV and LBCO and the log likelihood ratio test (LRT) highlighted the importance of considering SCA when capturing trait variability. In 5-Fold CV, PA ranged from 0.296 to 0.812 in M1 and 0.300 to 0.813 in M2. Under LBCO CV, PA ranged from 0.180 to 0.726 in M1 and 0.180 to 0.728 in M2. However, an increase in PA in Model 2, which incorporates SCA, compared to Model 1, can be attributed to the inclusion of SCA effects. Furthermore, the LRT results indicated a highly significant difference between the models. CV and LRT suggest the need for genetic models that account for both additive and SCA effects. Our analysis also showed that genotype x environment interactions should be accounted for in order to maximize the accuracy of predicted breeding values of tetraploid potato clones. The rate of double reductions was small and insignificant.

ABSTRACT. Potato late blight, caused by Phytophthora infestans, remains a substantial threat to global food security. European P. infestans populations are generally divided into Northern (genetically diverse) and Western (mainly clonal) populations. However, new genotypes have recently emerged and successfully established themselves in Northern Europe. Additionally, new strains that are more aggressive and more virulent or exhibit fungicide sensitivity to widely used active ingredients emerge frequently. The main objectives of this thesis were to study the drivers of new invasive lineages of P. infestans in Europe and the reason behind the shift in Northern European populations. Samples were collected from potato plants from conventional production fields, organic fields and trap nurseries in Estonia, Denmark, Norway, the UK, and France in ten growing seasons (between 2005-¬2022). DNA acquired from all the samples was genotyped through simple sequence repeat analysis. Phenotypic experiments were performed for samples collected in 2016 and 2017 and involved testing the isolates’ fungicide sensitivity to active ingredients widely used in Europe and evaluating their virulence to assess the ability of P. infestans to damage potato plants. Various population genetic indices were calculated to characterise the genetic diversity and dynamics of the pathogen in Estonia. Results showed that the Western European genotype EU_37_A2 exhibits fluazinam resistance, likely aiding its invasiveness. Genotype EU_41_A2 has successfully been established in Northern Europe, possibly due to higher virulence combined with other fitness traits or changes in environmental conditions not examined in this study. Substantial genetic and genotypic diversity persists in Estonia, suggesting a high likelihood of random mating. Still, monitoring results showed introductions of clonal lineages to the country, which creates a potential risk for future establishment. Our findings underscore the importance of continuous pathogen population monitoring to enable timely adjustments in control strategies. | LÜHIKOKKUVÕTE. Kartuli-lehemädaniku tekitaja Phytophthora infestans on otsene oht globaalsele toidujulgeolekule. Lääne-Euroopas on lehemädaniku tekitaja populatsioonid peamiselt klonaalsed, samas kui Põhja-Euroopas esineb suuremat geneetilist mitmekesisust. Viimastel aastatel on siiski täheldatud muutusi põhjapoolsemates populatsioonides, kus klonaalsed genotüübid on muutunud sagedasemaks. Tihti kerkivad Euroopas esile ka tüved, mis on agressiivsemad, virulentsemad või kasutusel olevate fungitsiidide toimeainete suhtes resistentsed. Käesoleva doktoritöö eesmärk on uurida uute invasiivsete P. infestans genotüüpide levikut mõjutavaid tegureid Euroopas. Uuringute läbiviimiseks koguti P. infestans proovid Eesti, Taani, Norra, Ühendkuningriigi ja Prantsusmaa tava- ja mahetootmispõldudelt ning püünistaimlatest kümne kasvuperioodi vältel aastate vahemikus 2005-2022 ning need genotüpiseeriti. Aastatel 2016 ja 2017 kogutud proovidel viidi lisaks läbi fenotüübilised katsed: fungitsiiditundlikkuse katse, kasutades Euroopas enamlevinud nelja fungitsiidi toimeainet ning virulentsuskatsed, kasutades 11 kartuligenotüüpi, mis sisaldavad erinevaid resistentsusgeene. Eesti proovide genotüpiseerimise tulemuste põhjal arvutati erinevad populatsioonigeneetilised indeksid, et iseloomustada patogeeni geneetilist mitmekesisust ja dünaamikat Eestis. Lääne-Euroopas levival uuel invasiivsel genotüübil EU_37_A2 esines osaliselt fluasinaamiresistentsus. Põhja-Euroopas leviva uue invasiivse genotüübi EU_41_A2 edukust võib seostada kõrgema virulentsusega. Eesti P. infestans populatsioonis on jätkuvalt märkimisväärne geneetiline ja genotüübiline mitmekesisus, kuigi seireandmed näitavad, et kohati esineb ka klonaalseid genotüüpe. Kuigi statistiliste analüüside põhjal ei ole hetkel tõendeid klonaalsete genotüüpide püsimisest Eestis, kujutab nende esinemine erinevates piirkondades potentsiaalset riski nende edaspidiseks levikuks. Käesolev doktoritöö näitlikustab patogeenide seire tähtsust, et kohandada vastavalt tõrjestrateegiaid.