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With 2 figures and 2 tables The purpose of this research was to identify the genetic basis of foliar and tuber resistance to Phytophthora infestans in a potato breeding population developed from a cross between two tetraploid Solanum tuberosum lines, NY121 and NY115. The parent with high foliar resistance, NY121, was highly susceptible to tuber blight. Foliar resistance was assessed in field trials, while tuber blight was assessed both in the field and in the laboratory. A quantitative trait locus (QTL) explaining ca. 50% of the phenotypic variance for foliar resistance was located on the lower arm of linkage group V, and was loosely associated with tuber blight resistance (significantly in one of two trials). This QTL was confirmed in a separate sample from the same population. Tuber blight detected via laboratory assays was not correlated with tuber blight incidence in the field. Most markers associated with tuber blight resistance were not associated with foliar resistance and most markers associated with foliar resistance were not associated with tuber blight resistance. [ABSTRACT FROM AUTHOR]

Phytophthora infestans, the causal agent of late blight, threatens potato production worldwide. An important tool in the management of the disease is the use of resistant varieties. Eleven major resistance genes have been identified and introgressed from Solanum demissum. However, new sources of resistance are continually sought. Here, we report the characterization and refined genetic localization of a resistance gene previously identified as Rber in a backcross progeny of Solanum tuberosum and Solanum berthaultii. In order to further characterize Rber, we developed a set of P. infestans isolates capable of identifying each of the 11 R-genes known to confer resistance to late blight in potato. Our results indicate that Rber is a new resistance gene, different from those recognized in S. demissum, and therefore, it has been named R Pi-ber according to the current system of nomenclature. In order to add new molecular markers around R Pi-ber , we used a PCR-based mapping technique, named MASP-map, which located R Pi-ber in a 3.9 cM interval between markers CT240 and TG63 on potato chromosome X. The location of R Pi-ber coincides with an area involved in resistance to different pathogens of potato and tomato. [ABSTRACT FROM AUTHOR]

Lettuce ( Lactuca sativa L.) is a popular leafy vegetable valued for its dietary fiber, antioxidants, and beneficial vitamins. This study presents a comprehensive spatio-temporal analysis of the lettuce metabolome, revealing complex dynamics in metabolite accumulation influenced by plant age, leaf position, proximodistal distribution within a leaf, and head closure. Samples were collected from plants at five maturity stages (ranging from baby leaf to full commercial maturity and eventually to bolting) and from five leaf positions (from the apex to the base of each plant). A widely targeted metabolomics approach identified 1905 compounds, with flavonoids, phenolic acids, and lipids as the largest classes. Younger plants exhibited higher levels of flavonoids, while older plants accumulated more saccharides and amino acids. Metabolites showed distinct proximodistal distributions, with flavonoids and vitamins concentrated at leaf tips and terpenoids declining from base to tip. Head closure significantly reduced levels of flavonoids, retinol (vitamin A1), and riboflavin (vitamin B2), while it was associated with increased content of other beneficial vitamins, such as thiamine (B1), pantothenate (B5), and pyridoxine (B6). Broad-sense heritability ( H 2 ) estimates for metabolites yielded mean H 2 values of 0.648 and 0.743 for plants at baby-leaf and commercial maturity stages, respectively. The overall highest heritability was observed in tannins ( H 2 = 0.909) in younger plants and chalcones ( H 2 = 0.894) in older plants, suggesting strong genetic control over specific metabolite classes and subclasses. These findings offer a robust framework for optimizing lettuce's nutritional profile by linking metabolite distributions to developmental processes, plant architecture, and genetic regulation. By leveraging these insights, breeders and producers can develop targeted strategies to enhance metabolite content through optimized breeding and harvesting strategies.

The impact of limited water availability on lettuce growth has been well documented. However, the mechanisms by which lettuce controls seed germination under water stress remain unknown. Germination percentage was evaluated in the cv. Salinas (Lactuca sativa) (L. sativa) × US96UC23 (Lactuca serriola) (L. serriola) recombinant inbred line (RIL) population and USDA germplasm collection using 10% polyethylene glycol (PEG). About 50% of both populations displayed less than 90% germination. The average broad-sense heritability (H 2 ) for germination percentage was 0.81 across both populations. Two quantitative trait loci (QTL) for germination percentage were identified on chromosomes 4 and 8 in the RIL population. The RNA-Seq and network analyses of wild lettuce, US96UC23, were performed using the control (distilled water, dH 2 O) and treatment (10% PEG) datasets. The number of differentially expressed genes (DEGs) was 4,095. The top 20 gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were assessed by enrichment analysis. The consensus network analysis captured 44 modules. Gene networks were constructed for the top 20 hub genes in 10 significant modules from each dataset. This study comprehensively explains QTL, GO terms, KEGG pathways, and gene networks associated with lettuce seed germination under osmotic stress., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Bacterial leaf spot (BLS) of lettuce ( Lactuca sativa L.) is caused by the bacterium Xanthomonas hortorum pv. vitians which is hypothesized to have at least three races of the pathogen present in North America as defined by their differential resistance phenotypes in lettuce cultivars/accessions. Though resistance to X. hortorum pv. vitians race 1 has been identified in cultivated lettuce, numerous other X. hortorum pv. vitians strains cause disease on cultivars carrying this resistance locus. Thus far, resistance to these 'additional' X. hortorum pv. vitians strains has not been adequately described in L. sativa or in any other wild Lactuca species sexually compatible with cultivated lettuce. We have performed an extensive screening of approximately 500 Lactuca accessions from L. sativa, L. serriola, L. saligna, L. virosa, L. aculeata, L. altaica , and L. perennis species to identify accessions resistant to these additional X. hortorum pv. vitians races. Following the initial screenings, greenhouse tests confirmed that X. hortorum pv. vitians race 2 and race 3 could be defined using Lactuca sativa accessions. Race 2 strain BS3217 had an incompatible response (hypersensitive response) on ten Lactuca serriola accessions including PI491114 and PI491108, while race 1 (BS0347) and race 3 (BS2861) strains of X. hortorum pv. vitians showed a compatible response (disease) on these genotypes. L. serriola accession ARM09-161 (and selections derived from it) was the only genotype resistant to the race 3 strain BS2861. L. serriola accessions identified in this study to be resistant to race 2 and race 3 of X. hortorum pv. vitians , together with race 1 resistant cultivars, can be used for pyramiding resistance loci against the three races of the BLS-causing pathogen.

Background: Sclerotinia spp. are generalist fungal pathogens, infecting over 700 plant hosts worldwide, including major crops. While host resistance is the most sustainable and cost-effective method for disease management, complete resistance to Sclerotinia diseases is rare. We recently identified soft basal stem as a potential susceptibility factor to Sclerotinia minor infection in lettuce (Lactuca sativa) under greenhouse conditions., Results: Analysis of stem and root cell wall composition in five L. sativa and one L. serriola accessions with varying growth habits and S. minor resistance levels revealed strong association between hemicellulose constituents, lignin polymers, disease phenotypes, and basal stem mechanical strength. Accessions resistant to basal stem degradation consistently exhibited higher levels of syringyl, guaiacyl, and xylose, but lower levels of fucose in stems. These findings suggest that stem cell wall polymers recalcitrant to breakdown by lignocellulolytic enzymes may contribute to stem strength-mediated resistance against S. minor., Conclusions: The lignin content, particularly guaiacyl and syringyl, along with xylose could potentially serve as biomarkers for identifying more resistant lettuce accessions and breeding lines. Basal stem degradation by S. minor was influenced by localized microenvironment conditions around the stem base of the plants., (© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Verticillium wilt, caused by Verticillium dahliae , is one of the most devastating soilborne diseases of lettuce ( Lactuca sativa L.). There are three races of V. dahliae , and each race has been characterized by markers representing race-specific effectors. Race 1 is differentiated by the presence of the functional secretory Ave1 effector. Similarly, races 2 and 3 are differentiated by effectors VdR2e and VdR3e , respectively. Although the presence of race 1 in coastal California was well established, the presence of effector-based races 2 and 3 was uncertain. This study therefore focused on characterizing 727 isolates collected from 142 ranches of symptomatic lettuce and other crops from coastal California. Based on this evaluation, 523 isolates were designated as race 1, 20 isolates as race 2, 23 isolates as race 3, and 17 as race undefined. Isolates representing other Verticillium species totaled 110, and 34 were non- Verticillium fungal species. Because the use of resistant cultivars is a key strategy to manage this disease, we evaluated 48 lettuce germplasm lines and 1 endive ( Cichorium endivia L.) line, comprising commercial cultivars and breeding lines, including the race 1-resistant heirloom cultivar La Brillante and the susceptible cultivar Salinas as controls. Resistance against races 1, 2, and 3 along with VdLs17, a virulent isolate of V. dahliae from lettuce that is currently not assigned to a race, was evaluated in replicated greenhouse experiments. Two crisphead lettuce lines, HL28 and HL29, exhibited resistance against race 1 and a partial resistance against race 2, whereas all other lines were highly susceptible to races 1 and 2 and VdLs17. The majority of lines exhibited higher resistance to race 3 relative to the other two races. This study documents the current distribution of the different races in coastal California. In addition, the sources of resistance currently being developed should be effective or partially effective against these races for targeted deployment as soon as they are available., Competing Interests: The author(s) declare no conflict of interest.

Stable neotetraploid lines of lettuce ( Lactuca sativa L.) were produced from three phenotypically distinct cultivars (Annapolis, Eruption, Merlot) and an advanced breeding line (SM13-L2) using colchicine treatment of seeds or young seedlings. When tested under the greenhouse and field conditions, neotetraploids initially grew more rapidly than their diploid progenitors, however they reached their reproductive stage (bolting, flower bud formation, and flowering) substantially later. Seeds production on neotetraploids was delayed by more than 30 days compared to diploids. Tetraploid plants had fewer, but larger stomata and leaves, less chlorophyll per area, higher photosystem II photochemical efficiency, generally lighter root system, and produced less than 1% of seeds in comparison with diploids. Field-grown neotetraploids of all lines displayed a significant reduction in tipburn (1.8% vs. 22.2%, respectively), a highly undesirable physiological disorder. Changes in leaf and root mineral composition were detected in neotetraploids. Several elements were found in lower abundance than in diploids, most notably iron, calcium, and silicon. Whole genome bisulfite sequencing (WGBS) revealed 498 differentially methylated regions (DMR), with 106 of these regions having at least 50% difference in the level of methylation between neotetraploids and their diploid progenitors. At least 18 of the most prominent DMR were detected in proximity to genes predicted to be involved in plant development or reaction to biotic and abiotic stressors. Because neotetraploid lines have low seed production, they are not suitable for commercial cultivation. They can be used, however, in research to study the factors contributing to tipburn, traits affected by stomata size or density, and the effect of ploidy on resistance to environmental stressors., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Simko and Zhao.)

Flavonoids are antioxidant phytochemicals that confer a beneficial effect on human health. We have previously developed and characterized eight lettuce ( Latuca sativa L.) lines that accumulated high levels of diverse flavonoids and their precursors in controlled environment conditions. Three Rutgers Scarlet lettuce (RSL) lines selected in tissue culture for deep-red color (RSL-NAR, RSL-NBR, RSL-NFR) accumulate anthocyanins and quercetin, three lines identified in a chemically mutagenized red lettuce population accumulate kaempferol (KfoA and KfoB) or naringenin chalcone (Nco), and two lines that were spontaneous green mutants derived from the red line RSL-NAR (GSL, GSL-DG) accumulate quercetin. These eight lines were field-grown in the Salinas Valley of California for four years together with seven control accessions of varying colors (light green, dark green, red, and dark red). At market maturity, a substantial variation in plant composition was observed, but the three RSL lines consistently accumulated high levels of cyanidin, GSL and GSL-DG accumulated the highest levels of quercetin, KfoA and KfoB accumulated kaempferol, and Nco amassed naringenin chalcone, confirming that these mutant lines produce high levels of beneficial phytochemicals under field conditions. Mutant lines and control accessions were also assessed for their biomass production (plant weight, height, and width), overall content of pigments (leaf chlorophyll and anthocyanins), resistance to diseases (downy mildew, lettuce drop, and Impatiens necrotic spot virus), postharvest quality of processed tissue (deterioration and enzymatic discoloration), and composition of 23 mineral elements. All but one mutant line had a fresh plant weight at harvest comparable to commercial leaf cultivars; only Nco plants were significantly ( p < 0.05) smaller. Therefore, except for Nco, the new, flavonoid hyperaccumulating lines can be considered for field cultivation.

Heritable cytosine methylation plays a role in shaping plant phenotypes; however, no information is available about DNA methylation in cultivated lettuce ( Lactuca sativa ), one of the most important leafy vegetables. Whole-genome bisulfite sequencing (WGBS) performed on seeds of 95 accessions from eight morphologically distinct horticultural types (Batavia, butterhead, iceberg, Latin, leaf, oilseed, romaine and stem) revealed a high level of methylation in lettuce genome with an average methylation of 90.6 % in the CG context, 72.9 % in the CHG context and 7.5 % in the CHH context. Although WGBS did not show substantial differences in overall methylation levels across eight horticultural types, 350 differentially methylated regions (DMR) were identified. Majority of the 41 pivotal DMR overlapped with genomic features predicted or confirmed to be involved in plant growth and development. These results provide the first insight into lettuce DNA methylation and indicate a potential role for heritable variation in cytosine methylation in lettuce morphology. The results reveal that differences in methylation profiles of morphologically distinct horticultural types are already detectable in seeds. Identified DMR can be a focus of the future functional studies., Competing Interests: The author declares no conflict of interest., (Published by Oxford University Press on behalf of the Annals of Botany Company 2023. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

Key Message: GWAS identified 19 QTLs for resistance to Sclerotinia minor, 11 of them co-locating with red leaf color. Lower disease incidence was observed in red and dark red accessions. Lettuce (Lactuca sativa L.), one of the most economically important vegetables grown primarily in moderate climates around the world, is susceptible to many diseases including lettuce drop caused by the soilborne fungus Sclerotinia minor. Complete resistance to S. minor has not been identified in cultivated lettuce or its wild relatives. We conducted five experiments over 4 years with the diversity panel of almost 500 lettuce accessions to evaluate their response to the pathogen in an artificially infested field. The lowest disease incidence (DI) was observed in cultivars Eruption, Infantry, and Annapolis (median DI of 12.1-17.5%), while the highest DI was recorded for cultivars Reine des Glaces, Wayahead, and line FL. 43007 (median DI of 81.0-95.2%). Overall, significantly lower DI was observed in red and dark red accessions compared to those with a lower anthocyanin content. Genome-wide association mapping identified 19 QTLs for resistance to S. minor, 21 for the presence of red leaf color or its variations caused by the anthocyanin content, and one for the green color intensity. Eleven of the QTLs for disease resistance were located within 10 Mb of the loci associated with red color or anthocyanin content identified in this diversity panel. The frequent, non-random co-location of QTLs, together with the lower DI observed in red and dark red accessions suggests that lettuce interaction with S. minor may be partly influenced by anthocyanins. We have identified RLL2 and ANS, the genes of the anthocyanin biosynthesis pathway that co-locate with resistance QTLs, as candidates for functional studies to ascertain the involvement of anthocyanins in lettuce resistance against S. minor. Resistance QTLs closely linked with QTLs for anthocyanin content could be used to develop lettuce with a relatively high partial resistance and red color, while those not associated with anthocyanins could be used to develop partially resistant cultivars of green color., (© 2023. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Lettuce is associated with seasonal outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections. Little is known about how various biotic and abiotic factors affect the lettuce microbiome, which in turn impacts STEC colonization. We characterized the lettuce phyllosphere and surface soil bacterial, fungal, and oomycete communities at harvest in late-spring and -fall in California using metagenomics. Harvest season and field type, but not cultivar, significantly influenced the microbiome composition of leaves and surface soil near plants. Phyllosphere and soil microbiome compositions were correlated with specific weather factors. The relative abundance of Enterobacteriaceae, but not E. coli, was enriched on leaves (5.2%) compared to soil (0.4%) and correlated positively with minimum air temperature and wind speed. Co-occurrence networks revealed seasonal trends in fungi-bacteria interactions on leaves. These associations represented 39%-44% of the correlations between species. All significant E. coli co-occurrences with fungi were positive, while all negative associations were with bacteria. A large proportion of the leaf bacterial species was shared with those in soil, indicating microbiome transmission from the soil surface to the canopy. Our findings provide new insight into factors that shape lettuce microbial communities and the microbial context of foodborne pathogen immigration events in the lettuce phyllosphere., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier Ltd.)

Lettuce ( Lactuca sativa L.) is an important leafy vegetable cultivated in moderate climates around the world. Based on phenotypic characteristics, such as formation and size of 'heads' (leaves arranged in a dense rosette), size, and texture of leaves, length of stems, and size and composition of seeds, lettuce cultivars can be classified into several distinct horticultural types (Batavia, butterhead, iceberg, Latin, leaf, oilseed, romaine, and stem). L. serriola , a wild progenitor of cultivated lettuce, is frequently utilized in breeding programs to introgress desirable genes and alleles (e.g., resistance to diseases) into lettuce gene pool. A diversity panel of ∼500 lettuce accessions was genotyped with tunable genotyping-by-sequencing (tGBS) method to identify single nucleotide polymorphism (SNP) sites. 115,261 SNPs were positioned on lettuce genome using the reference genome of cultivar Salinas. The described diversity panel together with the set of SNP markers can be used for mapping quantitative trait loci (QTL) and to develop marker assays for marker assisted selection (MAS). Identified SNP sites can also be used to identify F 1 hybrids, genotype gene bank collections, and in other areas of lettuce genetics and breeding., Competing Interests: The author declares no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Introduction: Impatiens necrotic spot virus (INSV) is a major pathogen currently threatening lettuce ( Lactuca sativa L.) production in the coastal areas of California. The virus is transmitted by the western flower thrips (Frankliniella occidentalis Pergande)., Methods: We have tested a diversity panel of almost 500 lettuce accessions for disease incidence (DI) in 12 field experiments performed over 7 years. This set of accessions was also assessed for thrips feeding damage (TFD), the rate of plant development (PD), and the content of chlorophyll (SPAD) and anthocyanins (ACI) to determine their effect on resistance to INSV. In addition, recombinant inbred lines from two biparental mapping populations were also evaluated for DI in field experiments., Results: The mean DI in 14 field experiments ranged from 2.1% to 70.4%. A highly significant difference in DI was observed among the tested accessions, with the overall lowest DI detected in the red color cultivars, Outredgeous Selection, Red Splash Cos, Infantry, Sweet Valentine, Annapolis, and Velvet. Multiple linear regression models revealed a small but significant effect ( p < 0.005) of the four analyzed determinants on DI. Accessions with lower DI values had slower plant development (PD, r = 0.352), higher ACI content ( r = -0.284), lower TFD ( r = 0.198), and lower SPAD content ( r = 0.125). A genome-wide association study revealed 13 QTLs for DI located on eight out of the nine lettuce chromosomes (the exception was chr. 8). The most frequently detected QTL ( qINSV2.1 ) was located on chr. 2. Several of the QTLs for DI were in the same genomic areas as QTLs for PD, ACI, and SPAD. Additional three QTLs for DI on chr. 5 and 8 were identified using linkage mapping performed on two biparental mapping populations., Conclusions: The work highlights the genetic basis of partial resistance to INSV and reveals the relationship between resistance, the host physiology, and the thrips vector. Results of this study are an important steppingstone toward developing cultivars with increased resistance against INSV., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Simko, Hasegawa, Peng and Zhao.)

Lettuce, a leafy vegetable used in cuisines worldwide, is a highly perishable product sensitive to postharvest losses caused by biotic and abiotic factors. The existing technologies and approaches used during plant cultivation, harvest, processing, transportation, and storage can limit the postharvest issues, but further improvements are needed to meet a growing demand for excellent product appearance, combined with superb quality, biosafety, and low economic and environmental cost. This review summarizes our current understanding of lettuce postharvest physiology and genetics with focus on enzymatic discoloration of wounded surfaces and rapid tissue deterioration. Discussed are existing and emerging integrated technologies and approaches that can facilitate achieving outstanding postharvest quality of lettuce products., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier Ltd.)

The concept of competitive balance is considered to be an essential aspect in the field of sport economics. This work describes a novel approach for measuring and evaluating competitive balance through concentration of championships. The concentration of championships was assessed using a sliding window approach with the length of five consecutive competitions (years) and a single competition (year) increment over the whole evaluated period. Because the sliding window was relatively short, the newly developed index, termed 'We Are the Champions' (WAC 5 ), is sensitive to rapid changes in competitive balance. The WAC 5 index, average WAC 5 (aWAC 5 ), expected WAC 5 (eWAC 5 ), and ΔWAC 5 (eWAC 5 - a WAC 5 ) were applied to data from 68 competitions of several individual and team sports collected for the 1960-2020 period. The significance of indices was tested by resampling (bootstrapping and permutation). The results of the study show a growth in competitive balance of several ice hockey competitions (national and international), but decreasing competitive balance in Formula 1 racing and in several European soccer competitions. In soccer competitions, there was a substantially lower competitive balance in a league than in a domestic cup competition within each country/federation. The difference between the overall competitive balance in the most popular, North American, professional leagues and the top European soccer leagues is growing. A significant grouping of champions was determined for all sports involving individual athletes, but also for several team competitions., Competing Interests: The authors declare no conflict of interest.

Spring mix is a popular packaged salad that contains lettuce ( Lactuca sativa L.) as one of its main ingredients. Plants for baby leaf lettuce (BLL) production are grown at very high densities, which enhances the occurrence of bacterial leaf spot (BLS) caused by Xanthomonas hortorum pv. vitians ( Xhv ), a disease that can make the crop unmarketable. The market demands disease-free, high-quality BLL all year round. Growing highly BLS-resistant cultivars will reduce loss of yield and quality, thus minimizing economic detriment to lettuce and spring mix growers. The research objectives were to identify lettuce accessions resistant to BLS and associated quantitative trait loci (QTL). A total of 495 lettuce accessions were screened with six isolates (BS0347, BS2861, BS3127, L7, L44, and Sc8B) of Xhv . Accessions showing overall high-level resistance to all tested Xhv isolates were 'Bunte Forellen', PI 226514, 'La Brillante', ARM09-161-10-1-4, 'Grenadier', 'Bella', PI 491210, 'Delight', and 'Romana Verde del Mercado'. Genome-wide association studies of BLS resistance by mixed linear model analyses identified significant QTLs on four lettuce chromosomes (2, 4, 6, and 8). The most significant QTL was on Chromosome 8 ( P = 1.42 × 10 -7 ), which explained 6.7% of total phenotypic variation for the disease severity. Accessions with a high level of resistance detected in this study are valuable resources for lettuce germplasm improvement. Molecular markers closely linked to QTLs can be considered for marker-assisted selection to develop new BLL lettuce cultivars with resistance to multiple races of Xhv .

Large amounts of nitrogen fertilizers applied during lettuce (Lactuca sativa L.) production are lost due to leaching or volatilization, causing severe environmental pollution and increased costs of production. Developing lettuce varieties with high nitrogen use efficiency (NUE) is the eco-friendly solution to reduce nitrogen pollution. Hence, in-depth knowledge of nitrogen metabolism and assimilation genes and their regulation is critical for developing high NUE varieties. In this study, we performed comparative transcriptomic analysis of the cultivated lettuce (L. sativa L.) and its wild progenitor (L. serriola) under high and low nitrogen conditions. A total of 2,704 differentially expressed genes were identified. Key enriched biological processes included photosynthesis, oxidation-reduction process, chlorophyll biosynthetic process, and cell redox homeostasis. The transcription factors (TFs) belonging to the ethylene responsive factor family and basic helix-loop-helix family were among the top differentially expressed TFs. Using weighted gene co-expression network analysis we constructed nine co-expression modules. Among these, two modules were further investigated because of their significant association with total nitrogen content and photosynthetic efficiency of photosystem II. Three highly correlated clusters were identified which included hub genes for nitrogen metabolism, secondary metabolites, and carbon assimilation, and were regulated by cluster specific TFs. We found that the expression of nitrogen transportation and assimilation genes varied significantly between the two lettuce species thereby providing the opportunity of introgressing wild alleles into the cultivated germplasm for developing lettuce cultivars with more efficient use of nitrogen., (© 2022. The Author(s).)

Key Message: GWAS identified 63 QTLs for resistance to downy mildew. Though QTLs were distributed across all chromosomes, the genomic regions frequently associated with resistance were located on chromosomes 4 and 5. Lettuce downy mildew is one of the most economically important diseases of cultivated lettuce worldwide. We have applied the genome-wide association mapping (GWAS) approach to detect QTLs for field resistance to downy mildew in the panel of 496 accessions tested in 21 field experiments. The analysis identified 131 significant marker-trait associations that could be grouped into 63 QTLs. At least 51 QTLs were novel, while remaining 12 QTLs overlapped with previously described QTLs for lettuce field resistance to downy mildew. Unlike race-specific, dominant Dm genes that mostly cluster on three out of nine lettuce chromosomes, QTLs (qDMR loci) for polygenic resistance are randomly distributed across all nine chromosomes. The genomic regions frequently associated with lettuce field resistance to downy mildew are located on chromosomes 4 and 5 and could be used for detailed study of the mechanism of polygenic resistance. The most resistant accessions identified in the current study (cvs. Auburn, Grand Rapids, Romabella, PI 226514, and PI 249536) are being incorporated into our breeding program. Markers closely linked to the resistance QTLs could be potentially used for marker-assisted selection, or in combination with other markers in the genome, for a combined genomic and marker-assisted selection. Up to date this is the most comprehensive study of QTLs for field resistance to downy mildew and the first study that uses GWAS for mapping disease resistance loci in lettuce., (© 2022. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

Background: Lettuce is linked to recurrent outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections, the seasonality of which remains unresolved. Infections have occurred largely from processed lettuce, which undergoes substantial physiological changes during storage. We investigated the microbiome and STEC O157:H7 (EcO157) colonization of fresh-cut lettuce of two cultivars with long and short shelf life harvested in the spring and fall in California and stored in modified atmosphere packaging (MAP) at cold and warm temperatures., Results: Inoculated EcO157 declined significantly less on the cold-stored cultivar with short shelf life, while multiplying rapidly at 24 °C independently of cultivar. Metagenomic sequencing of the lettuce microbiome revealed that the pre-storage bacterial community was variable but dominated by species in the Erwiniaceae and Pseudomonadaceae. After cold storage, the microbiome composition differed between cultivars, with a greater relative abundance (RA) of Erwiniaceae and Yersiniaceae on the cultivar with short shelf life. Storage at 24 °C shifted the microbiome to higher RAs of Erwiniaceae and Enterobacteriaceae and lower RA of Pseudomonadaceae compared with 6 °C. Fall harvest followed by lettuce deterioration were identified by recursive partitioning as important factors associated with high EcO157 survival at 6 °C, whereas elevated package CO 2 levels correlated with high EcO157 multiplication at 24 °C. EcO157 population change correlated with the lettuce microbiome during 6 °C storage, with fall microbiomes supporting the greatest EcO157 survival on both cultivars. Fall and spring microbiomes differed before and during storage at both temperatures. High representation of Pantoea agglomerans was a predictor of fall microbiomes, lettuce deterioration, and enhanced EcO157 survival at 6 °C. In contrast, higher RAs of Erwinia persicina, Rahnella aquatilis, and Serratia liquefaciens were biomarkers of spring microbiomes and lower EcO157 survival., Conclusions: The microbiome of processed MAP lettuce evolves extensively during storage. Under temperature abuse, high CO 2 promotes a lettuce microbiome enriched in taxa with anaerobic capability and EcO157 multiplication. In cold storage, our results strongly support a role for season and lettuce deterioration in EcO157 survival and microbiome composition, suggesting that the physiology and microbiomes of fall- and spring-harvested lettuce may contribute to the seasonality of STEC outbreaks associated with lettuce grown in coastal California., (© 2021. The Author(s).)

Key Message: Photoperiod and temperature conditions elicit different genetic regulation over lettuce bolting and flowering. This study identifies environment-specific QTLs and putative genes and provides information for genetic marker assay. Bolting, defined as stem elongation, marks the plant life cycle transition from vegetative to reproductive stage. Lettuce is grown for its leaf rosettes, and premature bolting may reduce crop quality resulting in economic losses. The transition to reproductive stage is a complex process that involves many genetic and environmental factors. In this study, the effects of photoperiod and ambient temperature on bolting and flowering regulation were studied by utilizing a lettuce mapping population to identify quantitative trait loci (QTL) and by gene expression analyses of genotypes with contrasting phenotypes. A recombinant inbred line (RIL) population, derived from a cross between PI 251246 (early bolting) and cv. Salinas (late bolting), was grown in four combinations of short (8 h) and long (16 h) days and low (20 °C) and high (35 °C) temperature. QTL models revealed both genetic (G) and environmental (E) effects, and GxE interactions. A major QTL for bolting and flowering time was found on chromosome 7 (qFLT7.2), and two candidate genes were identified by fine mapping, homology, and gene expression studies. In short days and high temperature conditions, qFLT7.2 had no effect on plant development, while several small-effect loci on chromosomes 2, 3, 6, 8, and 9 were associated with bolting and flowering. Of these, the QTL on chromosome 2, qBFr2.1, co-located with the Flowering Locus T (LsFT) gene. Polymorphisms between parent genotypes in the promotor region may explain identified gene expression differences and were used to design a genetic marker which may be used to identify the late bolting trait., (© 2021. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

Background: Plant pathogens and their hosts undergo adaptive changes in managed agricultural ecosystems, by overcoming host resistance, but the underlying genetic adaptations are difficult to determine in natural settings. Verticillium dahliae is a fungal pathogen that causes Verticillium wilt on many economically important crops including lettuce. We assessed the dynamics of changes in the V. dahliae genome under selection in a long-term field experiment., Results: In this study, a field was fumigated before the Verticillium dahliae race 1 strain (VdLs.16) was introduced. A derivative 145-strain population was collected over a 6-year period from this field in which a seggregating population of lettuce derived from Vr1/vr1 parents were evaluated. We de novo sequenced the parental genome of VdLs.16 strain and resequenced the derivative strains to analyze the genetic variations that accumulate over time in the field cropped with lettuce. Population genomics analyses identified 2769 single-nucleotide polymorphisms (SNPs) and 750 insertion/deletions (In-Dels) in the 145 isolates compared with the parental genome. Sequence divergence was identified in the coding sequence regions of 378 genes and in the putative promoter regions of 604 genes. Five-hundred and nine SNPs/In-Dels were identified as fixed. The SNPs and In-Dels were significantly enriched in the transposon-rich, gene-sparse regions, and in those genes with functional roles in signaling and transcriptional regulation., Conclusions: Under the managed ecosystem continuously cropped to lettuce, the local adaptation of V. dahliae evolves at a whole genome scale to accumulate SNPs/In-Dels nonrandomly in hypervariable regions that encode components of signal transduction and transcriptional regulation.

Lettuce ( Lactuca sativa ) is one of the most economically important vegetables in the United States, with approximately 50% of the domestic production concentrated in the Salinas Valley of California. Verticillium wilt, caused by races 1 and 2 of the fungal pathogen Verticillium dahliae , poses a major threat to lettuce production in this area. Although resistance governed by a single dominant gene against race 1 has previously been identified and is currently being incorporated into commercial cultivars, identification of resistance against race 2 has been challenging and no lines with complete resistance have been identified. In this study, we screened germplasm for resistance and investigated the genetics of partial resistance against race 2 using three mapping populations derived from crosses involving L. sativa × L. sativa and L. serriola × L. sativa. The inheritance of resistance in Lactuca species against race 2 is complex but a common quantitative trait locus (QTL) on linkage group 6, designated qVERT6.1 ( quantitative Verticillium dahliae resistance on LG 6, first QTL ), was detected in multiple populations. Additional race 2 resistance QTLs located in several linkage groups were detected in individual populations and environments. Because resistance in lettuce against race 2 is polygenic with a large genotype by environment interaction, breeding programs to incorporate these resistance genes should be aware of this complexity as they implement strategies to control race 2.

Lettuce downy mildew, caused by Bremia lactucae Regel, is the most economically important foliar disease of lettuce ( Lactuca sativa L.). The deployment of resistant cultivars carrying dominant resistance genes ( Dm genes) plays a crucial role in integrated downy mildew disease management; however, high variability in pathogen populations leads to the defeat of plant resistance conferred by Dm genes. Some lettuce cultivars exhibit field resistance that is only manifested in adult plants. Two populations of recombinant inbred lines (RILs), originating from crosses between the field resistant cultivars Grand Rapids and Iceberg and susceptible cultivars Salinas and PI491224, were evaluated for downy mildew resistance under field conditions. In all, 160 RILs from the Iceberg × PI491224 and 88 RILs from the Grand Rapids × Salinas populations were genotyped using genotyping by sequencing, which generated 906 and 746 high-quality markers, respectively, that were used for quantitative trait locus (QTL) analysis. We found a QTL in chromosome 4 that is present in both Grand Rapids × Salinas and Iceberg × PI491224 populations that has a major effect on field resistance. We also found two additional significant QTLs in chromosomes 2 and 5 in the Iceberg × PI491224 RIL population. Marker-assisted gene pyramiding of multiple Dm genes in combination with QTLs for field resistance provide the opportunity to develop cultivars with more durable resistance to B. lactucae .

Deep understanding of genetic architecture of water-stress tolerance is critical for efficient and optimal development of water-stress tolerant cultivars, which is the most economical and environmentally sound approach to maintain lettuce production with limited irrigation. Lettuce ( Lactuca sativa L.) production in areas with limited precipitation relies heavily on the use of ground water for irrigation. Lettuce plants are highly susceptible to water-stress, which also affects their nutrient uptake efficiency. Water stressed plants show reduced growth, lower biomass, and early bolting and flowering resulting in bitter flavors. Traditional phenotyping methods to evaluate water-stress are labor intensive, time-consuming and prone to errors. High throughput phenotyping platforms using kinetic chlorophyll fluorescence and hyperspectral imaging can effectively attain physiological traits related to photosynthesis and secondary metabolites that can enhance breeding efficiency for water-stress tolerance. Kinetic chlorophyll fluorescence and hyperspectral imaging along with traditional horticultural traits identified genomic loci affected by water-stress. Supervised machine learning models were evaluated for their accuracy to distinguish water-stressed plants and to identify the most important water-stress related parameters in lettuce. Random Forest (RF) had classification accuracy of 89.7% using kinetic chlorophyll fluorescence parameters and Neural Network (NN) had classification accuracy of 89.8% using hyperspectral imaging derived vegetation indices. The top ten chlorophyll fluorescence parameters and vegetation indices selected by sequential forward selection by RF and NN were genetically mapped using a L. sativa × L. serriola interspecific recombinant inbred line (RIL) population. A total of 25 quantitative trait loci (QTL) segregating for water-stress related horticultural traits, 26 QTL for the chlorophyll fluorescence traits and 34 QTL for spectral vegetation indices (VI) were identified. The percent phenotypic variation (PV) explained by the horticultural QTL ranged from 6.41 to 19.5%, PV explained by chlorophyll fluorescence QTL ranged from 6.93 to 13.26% while the PV explained by the VI QTL ranged from 7.2 to 17.19%. Eight QTL clusters harboring co-localized QTL for horticultural traits, chlorophyll fluorescence parameters and VI were identified on six lettuce chromosomes. Molecular markers linked to the mapped QTL clusters can be targeted for marker-assisted selection to develop water-stress tolerant lettuce., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Kumar, Eriksen, Simko and Mou.)