Identification of QTLs conferring resistance to downy mildew in legacy cultivars of lettuce

LsMybW-encoding R2R3-MYB transcription factor is responsible for a shift from black to white in lettuce seed

KEY MESSAGE

We identified LsMybW as the allele responsible for the shift in color from black to white seeds in wild ancestors of lettuce to modern cultivars. Successfully selected white seeds are a key agronomic trait for lettuce cultivation and breeding; however, the mechanism underlying the shift from black-in its wild ancestor-to white seeds remains uncertain. We aimed to identify the gene/s responsible for white seed trait in lettuce. White seeds accumulated less proanthocyanidins than black seeds, similar to the phenotype observed in Arabidopsis TT2 mutants. Genetic mapping of a candidate gene was performed with double-digest RAD sequencing using an F2 population derived from a cross between "ShinanoPower" (white) and "Escort" (black). The white seed trait was controlled by a single recessive locus (48.055-50.197 Mbp) in linkage group 7. Using five PCR-based markers and numerous cultivars, eight candidate genes were mapped in the locus. Only the LG7_v8_49.251Mbp_HinfI marker, employing a single-nucleotide mutation in the stop codon of Lsat_1_v5_gn_7_35020.1, was completely linked to seed color phenotype. In addition, the coding region sequences for other candidate genes were identical in the resequence analysis of "ShinanoPower" and "Escort." Therefore, we proposed Lsat_1_v5_gn_7_35020.1 as the candidate gene and designated it as LsMybW (Lactuca sativa Myb White seeds), an ortholog encoding the R2R3-MYB transcription factor in Arabidopsis. When we validated the role of LsMybW through genome editing, LsMybW knockout mutants harboring an early termination codon showed a change in seed color from black to white. Therefore, LsMybW was the allele responsible for the shift in seed color. The development of a robust marker for marker-assisted selection and identification of the gene responsible for white seeds have implications for future breeding technology and physiological analysis.

Identification and characterization of Glycolate oxidase gene family in garden lettuce (Lactuca sativa cv. 'Salinas') and its response under various biotic, abiotic, and developmental stresses

Glycolate oxidase (GLO) is an FMN-containing enzyme localized in peroxisomes and performs in various molecular and biochemical mechanisms. It is a key player in plant glycolate and glyoxylate accumulation pathways. The role of GLO in disease and stress resistance is well-documented in various plant species. Although studies have been conducted regarding the role of GLO genes from spinach on a microbial level, the direct response of GLO genes to various stresses in short-season and leafy plants like lettuce has not been published yet. The genome of Lactuca sativa cultivar 'Salinas' (v8) was used to identify GLO gene members in lettuce by performing various computational analysis. Dual synteny, protein-protein interactions, and targeted miRNA analyses were conducted to understand the function of GLO genes. The identified GLO genes showed further clustering into two groups i.e., glycolate oxidase (GOX) and hydroxyacid oxidase (HAOX). Genes were observed to be distributed unevenly on three chromosomes, and syntenic analysis revealed that segmental duplication was prevalent. Thus, it might be the main reason for GLO gene diversity in lettuce. Almost all LsGLO genes showed syntenic blocks in respective plant genomes under study. Protein-protein interactions of LsGLO genes revealed various functional enrichments, mainly photorespiration, and lactate oxidation, and among biological processes oxidative photosynthetic carbon pathway was highly significant. Results of in-depth analyses disclosed the interaction of GLO genes with other members of the glycolate pathway and the activity of GLO genes in various organs and developmental stages in lettuce. The extensive genome evaluation of GLO gene family in garden lettuce is believed to be a reference for cloning and studying functional analyses of GLO genes and characterizing other members of glycolate/glyoxylate biosynthesis pathway in various plant species.

Phytochemical and Agronomic Characterization of High-Flavonoid Lettuce Lines Grown under Field Conditions

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.

Genetic determinants of lettuce resistance to drop caused by Sclerotinia minor identified through genome-wide association mapping frequently co-locate with loci regulating anthocyanin content

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.

Genetic and physiological determinants of lettuce partial resistance to Impatiens necrotic spot virus

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.

LettuceGDB: The community database for lettuce genetics and omics

As a globally popular leafy vegetable and a representative plant of the Asteraceae family, lettuce has great economic and academic significance. In the last decade, high-throughput sequencing, phenotyping, and other multi-omics data in lettuce have accumulated on a large scale, thus increasing the demand for an integrative lettuce database. Here, we report the establishment of a comprehensive lettuce database, LettuceGDB (https://www.lettucegdb.com/). As an omics data hub, the current LettuceGDB includes two reference genomes with detailed annotations; re-sequencing data from over 1000 lettuce varieties; a collection of more than 1300 worldwide germplasms and millions of accompanying phenotypic records obtained with manual and cutting-edge phenomics technologies; re-analyses of 256 RNA sequencing datasets; a complete miRNAome; extensive metabolite information for representative varieties and wild relatives; epigenetic data on the genome-wide chromatin accessibility landscape; and various lettuce research papers published in the last decade. Five hierarchically accessible functions (Genome, Genotype, Germplasm, Phenotype, and O-Omics) have been developed with a user-friendly interface to enable convenient data access. Eight built-in tools (Assembly Converter, Search Gene, BLAST, JBrowse, Primer Design, Gene Annotation, Tissue Expression, Literature, and Data) are available for data downloading and browsing, functional gene exploration, and experimental practice. A community forum is also available for information sharing, and a summary of current research progress on different aspects of lettuce is included. We believe that LettuceGDB can be a comprehensive functional database amenable to data mining and database-driven exploration, useful for both scientific research and lettuce breeding.

Identification of Quantitative Trait Loci Associated with Bacterial Leaf Spot Resistance in Baby Leaf Lettuce

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.

Identification of genetic loci in lettuce mediating quantitative resistance to fungal pathogens

KEY MESSAGE

We demonstrate genetic variation for quantitative resistance against important fungal pathogens in lettuce and its wild relatives, map loci conferring resistance and predict key molecular mechanisms using transcriptome profiling. Lactuca sativa L. (lettuce) is an important leafy vegetable crop grown and consumed globally. Chemicals are routinely used to control major pathogens, including the causal agents of grey mould (Botrytis cinerea) and lettuce drop (Sclerotinia sclerotiorum). With increasing prevalence of pathogen resistance to fungicides and environmental concerns, there is an urgent need to identify sources of genetic resistance to B. cinerea and S. sclerotiorum in lettuce. We demonstrated genetic variation for quantitative resistance to B. cinerea and S. sclerotiorum in a set of 97 diverse lettuce and wild relative accessions, and between the parents of lettuce mapping populations. Transcriptome profiling across multiple lettuce accessions enabled us to identify genes with expression correlated with resistance, predicting the importance of post-transcriptional gene regulation in the lettuce defence response. We identified five genetic loci influencing quantitative resistance in a F6 mapping population derived from a Lactuca serriola (wild relative) × lettuce cross, which each explained 5-10% of the variation. Differential gene expression analysis between the parent lines, and integration of data on correlation of gene expression and resistance in the diversity set, highlighted potential causal genes underlying the quantitative trait loci.

Genome-wide association mapping reveals genomic regions frequently associated with lettuce field resistance to downy mildew

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.

Identification of Major Quantitative Trait Loci Controlling Field Resistance to Downy Mildew in Cultivated Lettuce (Lactuca sativa)

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.

Innovative breeding technologies in lettuce for improved post-harvest quality

Societal awareness of healthy eating is increasing alongside the market for processed bagged salads, which remain as one of the strongest growing food sectors internationally, including most recently from indoor growing systems. Lettuce represents a significant proportion of this ready-to-eat salad market. However, such products typically have a short shelf life, with decay of post-harvest quality occurring through complex biochemical and physiological changes in leaves and resulting in spoilage, food waste and risks to health. We review the functional and quantitative genetic understanding of lettuce post-harvest quality, revealing that few findings have translated into improved cultivar development. We identify (i) phytonutrient status (for enhanced antioxidant and vitamin status, aroma and flavour) (ii) leaf biophysical, cell wall and water relations traits (for longer shelf life) (iii) leaf surface traits (for enhanced food safety and reduced spoilage) and (iv) chlorophyll, other pigments and developmental senescence traits (for appearance and colour), as key targets for future post-harvest breeding. Lettuce is well-placed for rapid future exploitation to address postharvest quality traits with extensive genomic resources including the recent release of the lettuce genome and the development of innovative breeding technologies. Although technologies such as CRISPR/Cas genome editing are paving the way for accelerated crop improvement, other equally important resources available for lettuce include extensive germplasm collections, bi-parental mapping and wide populations with genotyping for genomic selection strategies and extensive multiomic datasets for candidate gene discovery. We discuss current progress towards post-harvest quality breeding for lettuce and how such resources may be utilised for future crop improvement.

Comparative analysis of the rhizomicrobiome of the wild versus cultivated crop: insights from rice and soybean

Plant domestication was a pivotal accomplishment in human history, which led to a reduction in genetic diversity of crop species; however, there was less research focus on how this reduced genetic diversity of crops in affecting rhizosphere microbial communities during crop domestication process. Here, we used high-throughput sequencing to explore the different effects of crops domestication on rhizosphere microbial community structure of rice (Oryza sativa L. and Oryza rufipogon Griff.) and soybean (Glycine max L. and Glycine soja Sieb. et Zucc.). Results indicated that rhizosphere fungal communities are more strongly influenced by crop domestication than bacterial communities. There was a stronger relationship for fungi and bacteria in the cultivated crops than in the wild relatives. Results also showed that the wild varieties had a higher abundance of beneficial symbionts and a lower abundance of pathogens comparing with the cultivated varieties. There was a similar tendency for both rice and soybean in rhizosphere microbial communities by comparing wild crops and their cultivated varieties. In conclusion, crop domestication had a stronger effect on the fungal communities than on the bacterial communities and had improved the microbial relationship in rhizosphere of cultivated crops.

The genetics of resistance to lettuce drop (Sclerotinia spp.) in lettuce in a recombinant inbred line population from Reine des Glaces × Eruption

KEY MESSAGE

Two QTLs for resistance to lettuce drop, qLDR1.1 and qLDR5.1, were identified. Associated SNPs will be useful in breeding for lettuce drop and provide the foundation for future molecular analysis. Lettuce drop, caused by Sclerotinia minor and S. sclerotiorum, is an economically important disease of lettuce. The association of resistance to lettuce drop with the commercially undesirable trait of fast bolting has hindered the integration of host resistance in control of this disease. Eruption is a slow-bolting cultivar that exhibits a high level of resistance to lettuce drop. Eruption also is completely resistant to Verticillium wilt caused by race 1 of Verticillium dahliae. A recombinant inbred line population from the cross Reine des Glaces × Eruption was genotyped by sequencing and evaluated for lettuce drop and bolting in separate fields infested with either S. minor or V. dahliae. Two quantitative trait loci (QTLs) for lettuce drop resistance were consistently detected in at least two experiments, and two other QTLs were identified in another experiment; the alleles for resistance at all four QTLs originated from Eruption. A QTL for lettuce drop resistance on linkage group (LG) 5, qLDR5.1, was consistently detected in all experiments and explained 11 to 25% of phenotypic variation. On LG1, qLDR1.1 was detected in two experiments explaining 9 to 12% of the phenotypic variation. Three out of four resistance QTLs are distinct from QTLs for bolting; qLDR5.1 is pleiotropic or closely linked with a QTL for early bolting; however, the rate of bolting shows only a small effect on the variance in resistance observed at this locus. The SNP markers linked with these QTLs will be useful in breeding for resistance through marker-assisted selection.

Genetic architecture of tipburn resistance in lettuce

KEY MESSAGE

Two major QTLs for tipburn were identified in LGs 1 and 5 contributing to resistance in cv. Salinas. The findings suggest pleiotropic effects between leaf crinkliness/savoy and tipburn. Tipburn is a physiological disorder in lettuce that is thought to be caused by a localized deficiency of calcium in leaf tissues. To elucidate the genetic architecture of resistance to tipburn in lettuce, seven recombinant inbred line populations were analyzed in multiple environments and years to identify quantitative trait loci (QTLs) for tipburn. Core height, head firmness, head closure, leaf crinkliness, plant fresh weight, and leaf savoy were also analyzed to investigate whether QTLs for these morphological traits collocated with QTLs for tipburn, which would be indicative of pleiotropic effects. Twenty-three major, intermediate, and minor unique QTLs for tipburn were identified in one or more populations scattered throughout the genome. Two major QTLs for tipburn incidence were identified in linkage groups (LGs) 1 and 5, which determined up to 45 and 66% of the phenotypic variance. The major QTL in LG 1 collocated with the head firmness QTL. The major QTL in LG 5 collocated with the QTL for core height, leaf crinkliness, and head firmness. Further research is needed to determine whether these associations are due to pleiotropic effects of the same gene or if the genes determining these traits are tightly linked. The beneficial alleles at the QTLs in LGs 1 and 5 are present in Lactuca sativa cv. Salinas, the genotype sequenced for the reference genome assembly. Therefore, these QTLs are good targets to identify genes causing tipburn as well as regions for marker-assisted selection to improve resistance to tipburn in lettuce.

Variation within Lactuca spp. for Resistance to Impatiens necrotic spot virus

Lettuce (Lactuca sativa L.) production in coastal California, one of the major lettuce-producing areas of the United States, is regularly affected by outbreaks of Impatiens necrotic spot virus (INSV), a member of the genus Orthotospovirus. Transmission of INSV among lettuce crops in this growing region has been attributed predominantly to the western flower thrips (Frankliniella occidentalis). INSV is acquired by first- or second-instar thrips nymphs feeding on infected host plants (not necessarily lettuce). The virus replicates within the insect vector, and is transmitted to new plants by adult thrips as they feed on epidermal and mesophyll cells of susceptible host plants. All currently grown cultivars of lettuce are susceptible to the disease. Screening lettuce for resistance to INSV under field conditions is problematic because natural infections appear sporadically and the virus is not evenly distributed across infected fields. We have developed a greenhouse-based assay that uses viruliferous thrips in combination with mechanical inoculation that allows dependable, year-round screening for resistance. In all, 89 cultivars, breeding lines, and plant introductions of cultivated lettuce, together with 53 accessions from 11 other Lactuca spp., 4 accessions from two dandelion (Taraxacum) species, and 4 tomato (Solanum lycopersicum L.) lines were evaluated for resistance to INSV. All tested material was susceptible to INSV to varying degrees, with the exception of two tomato lines that carry the Sw-5 gene that confers resistance to Tomato spotted wilt virus, a virus closely related to INSV. In cultivated lettuce, a partial resistance to INSV was observed in cultivars Amazona, Ancora, Antigua, Commodore, Eruption, Iceberg, La Brillante, Merlot, Telluride, and Tinto. Limited comparison of the greenhouse-based screening results with the data from opportunistic evaluations of resistance on 775 lettuce accessions from six field trials indicates consistency of results from both greenhouse and field environments. The most resistant lettuce accessions are being incorporated into our breeding program for introgression of resistance into lettuce breeding lines.

A first linkage map and downy mildew resistance QTL discovery for sweet basil (Ocimum basilicum) facilitated by double digestion restriction site associated DNA sequencing (ddRADseq)

Limited understanding of sweet basil (Ocimum basilicum L.) genetics and genome structure has reduced efficiency of breeding strategies. This is evidenced by the rapid, worldwide dissemination of basil downy mildew (Peronospora belbahrii) in the absence of resistant cultivars. In an effort to improve available genetic resources, expressed sequence tag simple sequence repeat (EST-SSR) and single nucleotide polymorphism (SNP) markers were developed and used to genotype the MRI x SB22 F2 mapping population, which segregates for response to downy mildew. SNP markers were generated from genomic sequences derived from double digestion restriction site associated DNA sequencing (ddRADseq). Disomic segregation was observed in both SNP and EST-SSR markers providing evidence of an O. basilicum allotetraploid genome structure and allowing for subsequent analysis of the mapping population as a diploid intercross. A dense linkage map was constructed using 42 EST-SSR and 1,847 SNP markers spanning 3,030.9 cM. Multiple quantitative trait loci (QTL) model (MQM) analysis identified three QTL that explained 37-55% of phenotypic variance associated with downy mildew response across three environments. A single major QTL, dm11.1 explained 21-28% of phenotypic variance and demonstrated dominant gene action. Two minor QTL dm9.1 and dm14.1 explained 5-16% and 4-18% of phenotypic variance, respectively. Evidence is provided for an additive effect between the two minor QTL and the major QTL dm11.1 increasing downy mildew susceptibility. Results indicate that ddRADseq-facilitated SNP and SSR marker genotyping is an effective approach for mapping the sweet basil genome.

Identification of downy mildew resistance gene candidates by positional cloning in maize (Zea mays subsp. mays; Poaceae)

PREMISE OF THE STUDY

Positional cloning in combination with phenotyping is a general approach to identify disease-resistance gene candidates in plants; however, it requires several time-consuming steps including population or fine mapping. Therefore, in the present study, we suggest a new combined strategy to improve the identification of disease-resistance gene candidates.

METHODS AND RESULTS

Downy mildew (DM)-resistant maize was selected from five cultivars using a spreader row technique. Positional cloning and bioinformatics tools were used to identify the DM-resistance quantitative trait locus marker (bnlg1702) and 47 protein-coding gene annotations. Eventually, five DM-resistance gene candidates, including bZIP34, Bak1, and Ppr, were identified by quantitative reverse-transcription PCR (RT-PCR) without fine mapping of the bnlg1702 locus.

CONCLUSIONS

The combined protocol with the spreader row technique, quantitative trait locus positional cloning, and quantitative RT-PCR was effective for identifying DM-resistance candidate genes. This cloning approach may be applied to other whole-genome-sequenced crops or resistance to other diseases.

Inflorescence Development and the Role of LsFT in Regulating Bolting in Lettuce (Lactuca sativa L.)

Lettuce (Lactuca sativa L.) is one of the most important leafy vegetable that is consumed during its vegetative growth. The transition from vegetative to reproductive growth is induced by high temperature, which has significant economic effect on lettuce production. However, the progression of floral transition and the molecular regulation of bolting are largely unknown. Here we morphologically characterized the inflorescence development and functionally analyzed the FLOWERING LOCUS T (LsFT) gene during bolting regulation in lettuce. We described the eight developmental stages during floral transition process. The expression of LsFT was negatively correlated with bolting in different lettuce varieties, and was promoted by heat treatment. Overexpression of LsFT could recover the late-flowering phenotype of ft-2 mutant. Knockdown of LsFT by RNA interference dramatically delayed bolting in lettuce, and failed to respond to high temperature. Therefore, this study dissects the process of inflorescence development and characterizes the role of LsFT in bolting regulation in lettuce.

Mapping quantitative trait loci responsible for resistance to Bakanae disease in rice

BACKGROUND

Bakanae or foot rot disease caused by Fusarium fujikuroi [teleomorph: Gibberella fujikuroi (Sawada) Ito] is emerging as a serious disease in rice. The disease causes both quantitative and qualitative losses to the grains under the field conditions. Breeding for resistance to Bakanae disease is a promising strategy to manage this emerging disease. In this study, we used a population of 168 F14 recombinant inbred lines (RILs) derived from two indica rice parents Pusa 1342, a highly resistant variety and Pusa Basmati 1121, a highly susceptible variety to map quantitative trait loci (QTLs) governing resistance against Bakanae disease.

RESULTS

The disease reaction of 168 F14 RILs were measured on the seedlings inoculated using Fusarium fujikuroi culture using high-throughput screening protocol under glasshouse conditions. Utilizing inclusive composite interval mapping, three QTLs governing resistance to Bakanae were identified, namely qBK1.1, qBK1.2 and qBK1.3 which accounted 4.76, 24.74 and 6.49 % of phenotypic variation, respectively. The major effect QTL designated qBK1.2 was mapped in 0.26 Mb region between RM5336 and RM10153. A total of 55 annotated genes were identified within the identified QTL region qBK1.2.

CONCLUSIONS

The novel QTLs identified in this study are useful resource for efficiently breeding rice cultivars resistant to Bakanae disease. This is the first report on identification of QTLs governing resistance against Bakanae in rice using inclusive composite interval mapping strategy in a RIL population.

Molecular Mapping of High Resistance to Bacterial Leaf Spot in Lettuce PI 358001-1

Lettuce (Lactuca sativa L.) is a diploid (2n = 18) with a genome size of 2,600 Mbp, and belongs to the family Compositae. Bacterial leaf spot (BLS), caused by Xanthomonas campestris pv. vitians, is a major disease of lettuce worldwide. Leaf lettuce PI 358001-1 has been characterized as an accession highly resistant to BLS and has white seed. In order to understand inheritance of the high resistance in this germplasm line, an F3 population consisting of 163 families was developed from the cross PI 358001-1 × 'Tall Guzmaine' (a susceptible Romaine lettuce variety with black seed). The segregation ratio of reaction to disease by seedling inoculation with X. campestris pv. vitians L7 strain in the F3 families was shown to be 32:82:48 homozygous resistant/heterozygous/homozygous susceptible, fitting to 1:2:1 (n = 162, χ2 = 3.19, P = 0.20). The segregation ratio of seed color by checking F2 plants was 122:41 black/white, fitting to 3:1 (n = 163, χ2 = 0.002, P = 0.96). The results indicated that both BLS resistance and seed color were inherited as a dominant gene mode. A genetic linkage map based on 124 randomly selected F2 plants was developed to enable molecular mapping of the BLS resistance and the seed color trait. In total, 199 markers, comprising 176 amplified fragment length polymorphisms, 16 simple-sequence repeats, 5 resistant gene candidate markers, and 2 cleaved amplified polymorphic sequences (CAPS) markers were assigned to six linkage groups. The dominant resistance gene to BLS (Xcvr) was mapped on linkage group 2 and the gene locus y for seed color was identified on linkage group 5. Due to the nature of a single gene inheritance, the high-resistance gene should be readily transferred to adapted lettuce cultivars to battle against the devastating disease of lettuce.

Impact of plant domestication on rhizosphere microbiome assembly and functions

The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a "back to the roots" framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication.

Comparing the Predictive Abilities of Phenotypic and Marker-Assisted Selection Methods in a Biparental Lettuce Population

Breeding for traits with polygenic inheritance is a challenging task that can be done by phenotypic selection, marker-assisted selection (MAS) or genome-wide selection. We comparatively evaluated the predictive abilities of four selection models on a biparental lettuce ( L.) population genotyped with 95 single nucleotide polymorphisms and 205 amplified fragment length polymorphism markers. These models were based on (i) phenotypic selection, (ii) MAS (with quantitative trait locus (QTL)-linked markers), (iii) genomic prediction using all the available molecular markers, and (iv) genomic prediction using molecular markers plus QTL-linked markers as fixed covariates. Each model's performance was assessed using data on the field resistance to downy mildew (DMR, mean heritability ∼0.71) and the quality of shelf life (SL, mean heritability ∼0.91) of lettuce in multiple environments. The predictive ability of each selection model was computed under three cross-validation (CV) schemes based on sampling genotypes, environments, or both. For the DMR dataset, the predictive ability of the MAS model was significantly lower than that of the genomic prediction model. For the SL dataset, the predictive ability of the genomic prediction model was significantly lower than that for the model using QTL-linked markers under two of the three CV schemes. Our results show that the predictive ability of the selection models depends strongly on the CV scheme used for prediction and the heritability of the target trait. Our study also shows that molecular markers can be used to predict DMR and SL for individuals from this cross that were genotyped but not phenotyped.

MADS-Box Genes and Gibberellins Regulate Bolting in Lettuce (Lactuca sativa L.)

Bolting in lettuce is promoted by high temperature and bolting resistance is of great economic importance for lettuce production. But how bolting is regulated at the molecular level remains elusive. Here, a bolting resistant line S24 and a bolting sensitive line S39 were selected for morphological, physiological, transcriptomic and proteomic comparisons. A total of 12204 genes were differentially expressed in S39 vs. S24. Line S39 was featured with larger leaves, higher levels of chlorophyll, soluble sugar, anthocyanin and auxin, consistent with its up-regulation of genes implicated in photosynthesis, oxidation-reduction and auxin actions. Proteomic analysis identified 30 differentially accumulated proteins in lines S39 and S24 upon heat treatment, and 19 out of the 30 genes showed differential expression in the RNA-Seq data. Exogenous gibberellins (GA) treatment promoted bolting in both S39 and S24, while 12 flowering promoting MADS-box genes were specifically induced in line S39, suggesting that although GA regulates bolting in lettuce, it may be the MADS-box genes, not GA, that plays a major role in differing the bolting resistance between these two lettuce lines.

Resistance to Downy Mildew in Lettuce 'La Brillante' is Conferred by Dm50 Gene and Multiple QTL

Many cultivars of lettuce (Lactuca sativa L.) are susceptible to downy mildew, a nearly globally ubiquitous disease caused by Bremia lactucae. We previously determined that Batavia type cultivar 'La Brillante' has a high level of field resistance to the disease in California. Testing of a mapping population developed from a cross between 'Salinas 88' and La Brillante in multiple field and laboratory experiments revealed that at least five loci conferred resistance in La Brillante. The presence of a new dominant resistance gene (designated Dm50) that confers complete resistance to specific isolates was detected in laboratory tests of seedlings inoculated with multiple diverse isolates. Dm50 is located in the major resistance cluster on linkage group 2 that contains at least eight major, dominant Dm genes conferring resistance to downy mildew. However, this Dm gene is ineffective against the isolates of B. lactucae prevalent in the field in California and the Netherlands. A quantitative trait locus (QTL) located at the Dm50 chromosomal region (qDM2.2) was detected, though, when the amount of disease was evaluated a month before plants reached harvest maturity. Four additional QTL for resistance to B. lactucae were identified on linkage groups 4 (qDM4.1 and qDM4.2), 7 (qDM7.1), and 9 (qDM9.2). The largest effect was associated with qDM7.1 (up to 32.9% of the total phenotypic variance) that determined resistance in multiple field experiments. Markers identified in the present study will facilitate introduction of these resistance loci into commercial cultivars of lettuce.

Genetic analysis and molecular mapping of QTLs for resistance to rice black-streaked dwarf disease in rice

Rice black-streaked dwarf disease, caused by rice black-streaked dwarf virus (RBSDV), is transmitted by small brown planthoppers (Laodelphax striatellus Fallén, SBPH) and causes severe yield loss in epidemic years in China and other East Asian countries. Breeding for resistance to RBSDV is a promising strategy to control the disease. We identified Tetep that showed resistance to RBSDV using a field test and artificial inoculation test. An evaluation of the resistance mechanism revealed that Tetep was resistant to RBSDV but not to SBPH. Genetic analysis showed that the resistance of Tetep to RBSDV was controlled by quantitative trait loci (QTLs). Three new QTLs for RBSDV resistance were identified in this study, i.e., qRBSDV-3, qRBSDV-10 and qRBSDV-11. The LOD scores of qRBSDV-3, qRBSDV-10 and qRBSDV-11 were 4.07, 2.24 and 2.21, accounting for 17.5%, 0.3% and 12.4% of the total phenotypic variation, respectively. All the resistance loci identified in this study were associated with virus resistance genes. The alleles for enhancing resistance on chromosomes 3 and 11 originated from Tetep, whereas the other allele on chromosome 10 originated from a susceptible parent. The identified new resistance QTLs in this study are useful resources for efficiently breeding resistant rice cultivars to RBSDV.

Bremia lactucae Infection Efficiency in Lettuce is Modulated by Temperature and Leaf Wetness Duration Under Quebec Field Conditions

More than 80% of Canadian lettuce production is located in the province of Quebec. Yet most of our knowledge on the epidemiology of lettuce downy mildew (Bremia lactucae) is derived from controlled-condition experiments or field experiments conducted in subtropical climates and, thus, cannot readily be applied to Quebec lettuce production. The influence of temperature and leaf wetness duration on the infection efficiency (IE) of B. lactucae was studied for 4 years (2003, 2004, 2012, and 2013) under field and growth-chamber conditions. IE was defined as the ratio of the number of lesions/leaf to the airborne conidia concentration (ACC). B. lactucae ACC was measured with rotating-arm samplers three times/week. In addition, 72 lettuce trap plants/sampling day were exposed to the potential airborne B. lactucae inoculum and disease intensity was assessed after 7 days of incubation in greenhouse. Under growth-chamber conditions, an ACC of 1 conidium/m³ was sufficient to cause 1 lesion/leaf, and IE ranged from 0.25 to 1.00. Under field conditions, an ACC of 10 to 14 conidia/m³ was required to cause 1 lesion/leaf, and IE ranged from 0.02 to 0.10, except in 2004, when IE ranged from 0.03 to 1.00. IE increased with increasing leaf wetness duration but decreased with increasing temperature. Also, considering an observed average temperature range from 10 to 20°C in the area of Quebec, 2 h of leaf wetness was sufficient for infection by B. lactucae. Therefore, under Quebec lettuce production conditions, a leaf wetness period of 2 h and an ACC of 10 to 14 conidia/m³ can be used as risk indicators to facilitate disease management decisions. Also, under typical Quebec weather conditions, measuring both morning and evening leaf wetness events could be used to improve the reliability of leaf wetness duration as a downy mildew risk indicator. Further research is needed to validate these risk indicators for integration into management strategies.

Downy mildew disease promotes the colonization of romaine lettuce by Escherichia coli O157:H7 and Salmonella enterica

BACKGROUND

Downy mildew, a plant disease caused by the oomycete Bremia lactucae, is endemic in many lettuce-growing regions of the world. Invasion by plant pathogens may create new portals and opportunities for microbial colonization of plants. The occurrence of outbreaks of Escherichia coli O157:H7 (EcO157) and Salmonella enterica Typhimurium (S. Typhimurium) infections linked to lettuce prompted us to investigate the role of downy mildew in the colonization of romaine lettuce by these human pathogens under controlled laboratory conditions.

RESULTS

Whereas both EcO157 and S. Typhimurium population sizes increased 10(2)-fold on healthy leaf tissue under conditions of warm temperature and free water on the leaves, they increased by 10(5)-fold in necrotic lesions caused by B. lactucae. Confocal microscopy of GFP-EcO157 in the necrotic tissue confirmed its massive population density and association with the oomycete hyphae. Multiplication of EcO157 in the diseased tissue was significantly lower in the RH08-0464 lettuce line, which has a high level of resistance to downy mildew than in the more susceptible cultivar Triple Threat. qRT-PCR quantification of expression of the plant basal immunity gene PR-1, revealed that this gene had greater transcriptional activity in line RH08-0464 than in cultivar Triple Threat, indicating that it may be one of the factors involved in the differential growth of the human pathogen in B. lactucae lesions between the two lettuce accessions. Additionally, downy mildew disease had a significant effect on the colonization of EcO157 at high relative humidity (RH 90-100%) and on its persistence at lower RH (65-75%). The latter conditions, which promoted overall dryness of the lettuce leaf surface, allowed for only 0.0011% and 0.0028% EcO157 cell survival in healthy and chlorotic tissue, respectively, whereas 1.58% of the cells survived in necrotic tissue.

CONCLUSIONS

Our results indicate that downy mildew significantly alters the behavior of enteric pathogens in the lettuce phyllosphere and that breeding for resistance to B. lactucae may lower the increased risk of microbial contamination caused by this plant pathogen.