Key message Eleven new major resistance genes for lettuce downy mildew were introgressed from wild Lactuca species and mapped to small regions in the lettuce genome. Abstract Downy mildew, caused by the oomycete pathogen Bremia lactucae Regel, is the most important disease of lettuce ( Lactuca sativa L.). The most effective method to control this disease is by using resistant cultivars expressing dominant resistance genes ( Dm genes). In order to counter changes in pathogen virulence, multiple resistance genes have been introgressed from wild species by repeated backcrosses to cultivated lettuce, resulting in numerous near-isogenic lines (NILs) only differing for small chromosome regions that are associated with resistance. Low-pass, whole genome sequencing of 11 NILs was used to identify the chromosome segments introgressed from the wild donor species. This located the candidate chromosomal positions for resistance genes as well as additional segments. F 2 segregating populations derived from these NILs were used to genetically map the resistance genes to one or two loci in the lettuce reference genome. Precise knowledge of the location of new Dm genes provides the foundation for marker-assisted selection to breed cultivars with multiple genes for resistance to downy mildew.

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.

Seedlings of 213 accessions representing 9, 14, and 10 Israeli natural populations of the wild Lactuca serriola, L. saligna, and L. aculeata, respectively, were initially screened for their resistance to a pathotype CAVIII isolate of Bremia lactucae. All 60 L. serriola accessions were susceptible while all 83 accessions of L. saligna were resistant. Out of the 69 L. aculeata accessions, 36 (52.2 %) were resistant. From those resistant accessions, 56 L. saligna and 23 L. aculeata accessions were then tested at the seedling stage for their reaction against five highly virulent isolates originating from California and representing the two current major pathotypes and a novel type of B. lactucae; true leaves of adult plants were also tested with two out of these five isolates. Our study supports previous observations that L. saligna is highly resistant to B. lactucae. However, our results provide additional evidence that L. saligna may not be an absolutely non-host plant for B. lactucae at least at a seedling stage, which is in agreement with other recent data for this species. Sixteen (69.6 %) out of the 23 L. aculeata accessions expressed resistance against all isolates tested, even in seedling stage as well as in true leaves of adult plants. This study is probably the first report of detailed screening of resistance to some B. lactucae isolates in natural populations of L. aculeata. These patterns of resistance reactions show that L. aculeata, a species within the primary lettuce gene pool, should be considered as an attractive source of germplasm for resistance breeding of cultivated lettuce (L. sativa).

Many cultivars of lettuce (Lactuca sativa L.), the most popular leafy vegetable, are susceptible to downy mildew disease caused by Bremia lactucae. Cultivars Iceberg and Grand Rapids that were released in the 18th and 19th centuries, respectively, have high levels of quantitative resistance to downy mildew. We developed a population of recombinant inbred lines (RILs) originating from a cross between these two legacy cultivars, constructed a linkage map, and identified two QTLs for resistance on linkage groups 2 (qDM2.1) and 5 (qDM5.1) that determined resistance under field conditions in California and the Netherlands. The same QTLs determined delayed sporulation at the seedling stage in laboratory experiments. Alleles conferring elevated resistance at both QTLs originate from cultivar Iceberg. An additional QTL on linkage group 9 (qDM9.1) was detected through simultaneous analysis of all experiments with mixed-model approach. Alleles for elevated resistance at this locus originate from cultivar Grand Rapids.

Fusarium wilt of lettuce, caused by the soilborne fungus Fusarium oxysporum f. sp. lactucae, affects all major lettuce production areas in California and Arizona. In trials at UC Davis, we found that lettuce cultivars differ significantly in susceptibility to the disease, with some leaf and romaine types highly resistant under all test conditions. For more susceptible cultivars, disease severity is strongly influenced by inoculum levels and ambient temperature. Management of Fusarium wilt requires an integrated approach that includes crop rotation to reduce soil inoculum levels and the use of resistant cultivars during the warmest planting windows.

Thermoinhibition, or failure of seeds to germinate when imbibed at warm temperatures, can be a significant problem in lettuce (Lactuca sativa L.) production. The reliability of stand establishment would be improved by increasing the ability of lettuce seeds to germinate at high temperatures. Genes encoding germination- or dormancy-related proteins were mapped in a recombinant inbred line population derived from a cross between L. sativa cv. Salinas and L. serriola accession UC96US23. This revealed several candidate genes that are located in the genomic regions containing quantitative trait loci (QTLs) associated with temperature and light requirements for germination. In particular, LsNCED4, a temperature-regulated gene in the biosynthetic pathway for abscisic acid (ABA), a germination inhibitor, mapped to the center of a previously detected QTL for high temperature germination (Htg6.1) from UC96US23. Three sets of sister BC3S2 near-isogenic lines (NILs) that were homozygous for the UC96US23 allele of LsNCED4 at Htg6.1 were developed by backcrossing to cv. Salinas and marker-assisted selection followed by selfing. The maximum temperature for germination of NIL seed lots with the UC96US23 allele at LsNCED4 was increased by 2–3°C when compared with sister NIL seed lots lacking the introgression. In addition, the expression of LsNCED4 was two- to threefold lower in the former NIL lines as compared to expression in the latter. Together, these data strongly implicate LsNCED4 as the candidate gene responsible for the Htg6.1 phenotype and indicate that decreased ABA biosynthesis at high imbibition temperatures is a major factor responsible for the increased germination thermotolerance of UC96US23 seeds.

Genbank and The Compositae Genome Project database, containing over 42,000 lettuce unigenes from Lactuca sativa cv. Salinas and L. serriola accession UC96US23 were mined to identify 702 candidate genes involved in pathogen recognition ( RGC s), resistance signal transduction, defense responses, and disease susceptibility. In addition, to identify sequences representing additional sub-families of nucleotide binding site (NBS)-leucine-rich repeat encoding genes; the major classes of resistance genes ( R- genes), NBS-encoding sequences were amplified by PCR using degenerate oligonucleotides designed to NBS sub-families specific to the subclass Asteridae, which includes the Compositae family. These products were cloned and sequenced resulting in 18 novel NBS sequences from cv. Salinas and 15 novel NBS sequences from UC96US23. Using a variety of marker technologies, 294 of the 735 candidate disease resistance genes were mapped in our primary mapping population, which consisted of 119 F 7 recombinant inbred lines derived from an interspecific cross between cv. Salinas and UC96US23. Using markers shared across multiple genetic maps, 36 resistance phenotypic loci, including two new loci for resistance to downy mildew and two quantitative trait loci for resistance to anthracnose were positioned onto the reference map to provide a global view of the genomic architecture of disease resistance in lettuce and to identify candidate genes for resistance phenotypes. The majority but not all of the resistance phenotypes were genetically associated with RGC s.

Bacterial plant pathogens manipulate their hosts by injection of numerous effector proteins into host cells via type III secretion systems. Recognition of these effectors by the host plant leads to the induction of a defense reaction that often culminates in a hypersensitive response manifested as cell death. Genes encoding effector proteins can be exchanged between different strains of bacteria via horizontal transfer, and often individual strains are capable of infecting multiple hosts. Host plant species express diverse repertoires of resistance proteins that mediate direct or indirect recognition of bacterial effectors. As a result, plants and their bacterial pathogens should be considered as two extensive coevolving groups rather than as individual host species coevolving with single pathovars. To dissect the complexity of this coevolution, we cloned 171 effector-encoding genes from several pathovars of Pseudomonas and Ralstonia. We used Agrobacterium tumefaciens-mediated transient assays to test the ability of each effector to induce a necrotic phenotype on 59 plant genotypes belonging to four plant families, including numerous diverse accessions of lettuce (Lactuca sativa) and tomato (Solanum lycopersicum). Known defense-inducing effectors (avirulence factors) and their homologs commonly induced extensive necrosis in many different plant species. Nonhost species reacted to multiple effector proteins from an individual pathovar more frequently and more intensely than host species. Both homologous and sequence-unrelated effectors could elicit necrosis in a similar spectrum of plants, suggesting common effector targets or targeting of the same pathways in the plant cell.

Lettuce (Lactuca saliva L.) is susceptible to dieback, a soilborne disease caused by two viruses from the family Tombusviridae. Susceptibility to dieback is widespread in romaine and leaf-type lettuce, while modern iceberg cultivars are resistant to this disease. Resistance in iceberg cultivars is conferred by Tvr1 - a single, dominant gene that provides durable resistance. This study describes fine mapping of the resistance gene, analysis of nucleotide polymorphism and linkage disequilibrium in the Tvr1 region, and development of molecular markers for marker-assisted selection.

Chapter 12 Bremia lactucae and Lettuce Downy Mildew Richard Michelmore, Richard Michelmore The Genome Center and Department of Plant Sciences, University of California, Davis, California, USASearch for more papers by this authorOswaldo Ochoa, Oswaldo Ochoa The Genome Center and Department of Plant Sciences, University of California, Davis, California, USASearch for more papers by this authorJoan Wong, Joan Wong The Genome Center and Department of Plant Sciences, University of California, Davis, California, USASearch for more papers by this author Richard Michelmore, Richard Michelmore The Genome Center and Department of Plant Sciences, University of California, Davis, California, USASearch for more papers by this authorOswaldo Ochoa, Oswaldo Ochoa The Genome Center and Department of Plant Sciences, University of California, Davis, California, USASearch for more papers by this authorJoan Wong, Joan Wong The Genome Center and Department of Plant Sciences, University of California, Davis, California, USASearch for more papers by this author Book Editor(s):Kurt Lamour, Kurt Lamour Department of Entomology and Plant Pathology, University of Tennessee, Institute of Agriculture, Knoxville, TN, USASearch for more papers by this authorSophien Kamoun, Sophien Kamoun Sainsbury Laboratory, Colney Lane, Norwich, NR4 7UH, UKSearch for more papers by this author First published: 10 November 2008 https://doi.org/10.1002/9780470475898.ch12Citations: 6 AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Summary This chapter contains sections titled: Introduction Taxonomy, Host Range, and Importance Culture Host-Pathogen Interactions Classic and Molecular Genetics of Host Resistance Mating System Somatic Variation Genetics of Avirulence Genetic Mapping Karyotype and Chromosomal Assignment of Markers Epidemiology Genome Size and Composition Transformation Molecular Genetics and Genomics Future Directions Acknowledgments References Citing Literature Oomycete Genetics and Genomics: Diversity, Interactions, and Research Tools RelatedInformation

Seed thermoinhibition (inhibition of germination at warm temperatures) can reduce seedling emergence and stand establishment of cultivated lettuce (Lactuca sativa L.) when soil temperatures are warm (>25 degrees C) at planting. Genetic variation for high temperature germination tolerance exists among accessions of lettuce and related wild species. Seeds of a L. serriola accession (UC96US23) germinated 100% up to 37 degrees C, while seeds of L. sativa 'Salinas' were completely inhibited from germinating at temperatures above 31 degrees C. A recombinant inbred line population, developed from a cross between 'Salinas' and UC96US23, was analyzed for germination capacity at high temperatures. A major quantitative trait loci (QTL) for high temperature germination (Htg6.1) and additional QTL having smaller effects were identified. Near-isogenic lines confirmed the effect of Htg6.1 and are being utilized for further fine-mapping of the locus. Candidate genes associated with seed dormancy have been mapped to test for co-localization with thermoinhibition QTL. Expression patterns of candidate genes, particularly those associated with gibberellin and abscisic acid synthesis and metabolism, have also been analyzed in relation to genotype and germination temperature. Combined genetic and molecular analyses hold promise for elucidating the physiological regulation of thermoinhibition and for developing lettuce cultivars with enhanced stand establishment of warm temperature plantings.

The RGC2 gene cluster in lettuce (Lactuca sativa) is one of the largest known families of genes encoding nucleotide binding site-leucine-rich repeat (NBS-LRR) proteins. One of its members, RGC2B, encodes Dm3 which determines resistance to downy mildew caused by the oomycete Bremia lactucae carrying the cognate avirulence gene, Avr3. We developed an efficient strategy for analysis of this large family of low expressed genes using post-transcriptional gene silencing (PTGS). We transformed lettuce cv. Diana (carrying Dm3) using chimeric gene constructs designed to simultaneously silence RGC2B and the GUS reporter gene via the production of interfering hairpin RNA (ihpRNA). Transient assays of GUS expression in leaves accurately predicted silencing of both genes and were subsequently used to assay silencing in transgenic T(1) plants and their offspring. Levels of mRNA were reduced not only for RGC2B but also for all seven diverse RGC2 family members tested. We then used the same strategy to show that the resistance specificity encoded by the genetically defined Dm18 locus in lettuce cv. Mariska is the result of two resistance specificities, only one of which was silenced by ihpRNA derived from RGC2B. Analysis of progeny from crosses between transgenic, silenced tester stocks and lettuce accessions carrying other resistance genes previously mapped to the RGC2 locus indicated that two additional resistance specificities to B. lactucae, Dm14 and Dm16, as well as resistance to lettuce root aphid (Pemphigus bursarius L.), Ra, are encoded by RGC2 family members.

Renewed interest in the identification of alternative sources of natural rubber to Hevea brasiliensis has focused on the Compositae family. In our search for Compositae models for rubber synthesis, we extracted latex from stems of two lettuce species: Lactuca serriola, prickly lettuce, and Lactuca sativa cv. Salinas, crisphead lettuce. Both species contained cis-1,4-polyisoprene rubber in the dichloromethane-soluble portions of their latex, and sesquiterpene lactones in their acetone-soluble portions. The rubber from both species and their progeny had molecular weights in excess of 1,000,000g/mol, and polydispersity values of 1.1. Rubber transferase activity was detected across a range of farnesyl diphosphate initiator concentrations, with decreased activity as initiator concentrations exceeded putative saturation. These results add lettuce to the short list of plant species that produce high molecular weight rubber in their latex. Due to the genomic and agronomic resources available in lettuce species, they provide the opportunity for further dissection of natural rubber biosynthesis in plants.

Resistance genes can exhibit heterogeneous patterns of variation. However, there are few data on their frequency and variation in natural populations. We analysed the frequency and variation of the resistance gene Dm3, which confers resistance to Bremia lactucae (downy mildew) in 1033 accessions of Lactuca serriola (prickly lettuce) from 49 natural populations. Inoculations with an isolate of Bremia lactucae carrying avirulence gene Avr3 indicated that the frequency of Dm3 in natural populations of L. serriola was very low. Molecular analysis demonstrated that Dm3 was present in only one of the 1033 wild accessions analysed. The sequence of the 5' region of Dm3 was either highly conserved among accessions, or absent. In contrast, frequent chimeras were detected in the 3' leucine-rich repeat-encoding region. Therefore low frequency of the Dm3 specificity in natural populations was due to either the recent evolution of Dm3 specificity, or deletions of the whole gene as well as variation in 3' region caused by frequent gene conversions. This is the most extensive analysis of the prevalence of a known disease resistance gene to date, and indicates that the total number of resistance genes in a species may be very high. This has implications for the scales of germplasm conservation and exploitation of sources of resistance.

Downy mildew on lettuce is currently controlled using host resistance genes (Dm genes) that confer race-specific resistance in seedlings. Field resistance (FR) that is active in adult plants but not seedlings was identified in the cvs. Grand Rapids and Iceberg. The goal of our study was to evaluate the utility of Grand Rapids as a source of novel Bremia resistance alleles, particularly in comparison with Iceberg. To measure FR, downy mildew symptoms were evaluated following natural infection in field experiments. The responses of Grand Rapids and Iceberg were similar in many respects. Although both cultivars had a small percentage of plants exhibiting disease symptoms, the average disease ratings were as low as for cultivars with effective Dm genes. We observed no evidence for race specificity. FR was effective over 3 years of our study, despite documented variation within pathogen populations. Both cultivars lacked all known seedling resistance genes except Dm13, which was not responsible for the resistance observed in field experiments. Similar segregation of FR was observed in F2 populations for both Grand Rapids and Iceberg. The presence of highly susceptible families within Grand Rapids × Iceberg populations suggested the presence of at least one unique resistance allele in each cultivar. Preliminary genetic analysis of FR from Grand Rapids revealed a high estimate of narrow-sense heritability that suggested simple inheritance, but single gene models did not fit the observed data. Our results suggest that Grand Rapids may represent an underutilized resource for controlling downy mildew in lettuce.

To demonstrate the applicability of the target region amplification polymorphism (TRAP) marker technique to lettuce genotyping, we fingerprinted 53 lettuce (Lactuca sativa L.) cultivars and six wild accessions (three from each of the two wild species, L. saligna L. and L. serriola L.). Seven hundred and sixty-nine fragments from 50 to 900 bp in length were amplified in 10 PCR reactions using 10 fixed primers in combination with four fluorescent labeled arbitrary primers. Three hundred and eighty-eight of these fragments were polymorphic among the 59 Lactuca entries and 107 fragments were polymorphic among the 53 lettuce cultivars and the six wild accessions; 251 fragments were present only in the wild species. These markers not only discriminated all cultivars, but also revealed the evolutionary relationship among the three species: L. sativa, the cultivated species, is more closely related to L. serriola than to L. saligna. Cluster analysis grouped the cultivars by horticultural types with a few exceptions. These results are consistent with previous findings using RFLP, AFLP, and SAMPL markers. The TRAP markers revealed significant differences in genetic variability among horticultural types, measured by the average genetic similarity among the cultivars of the same type. Within the sample set, the leaf type and butterhead types possessed relatively high genetic variability, the iceberg types had moderate variability and the romaine types had the lowest variability. The genetic behavior of TRAP markers was assessed with a mapping population of 45 recombinant inbred lines (RILs) derived from an interspecific cross between L. serriola and L. sativa. Almost all the markers segregated in the expected 1:1 Mendelian ratio and are being incorporated into the existing lettuce linkage maps. Our results indicate that the TRAP markers can provide a powerful technique for fingerprinting lettuce cultivars.

Seed and seedling traits related to germination and stand establishment are important in the production of cultivated lettuce (Lactuca sativa L.). Six seed and seedling traits segregating in a L. sativa cv. Salinas x L. serriola recombinant inbred line population consisting of 103 F8 families revealed a total of 17 significant quantitative trait loci (QTL) resulting from three seed production environments. Significant QTL were identified for germination in darkness, germination at 25 and 35 degrees C, median maximum temperature of germination, hypocotyl length at 72 h post-imbibition, and plant (seedling) quality. Some QTL for germination and early seedling growth characteristics were co-located, suggestive of pleiotropic loci regulating these traits. A single QTL (Htg6.1) described 25 and 23% of the total phenotypic variation for high temperature germination in California- and Netherlands-grown populations, respectively, and was significant between 33 and 37 degrees C. Additionally, Htg6.1 showed significant epistatic interactions with other Htg QTL and a consistent effect across all the three seed production environments. L. serriola alleles increased germination at these QTL. The estimate of narrow-sense heritability (h2) of Htg6.1 was 0.84, indicating potential for L. serriola as a source of germination thermotolerance for lettuce introgression programs.