| Species name: Lettuce (Lactuca sativa L)|
Lettuce (Lactuca sativa L.) is an annual plant in the daisy family, Compositae (Asteraceae), tribe Lactuceae of subfamily Cichorioideae (K?ístková et al., 2008). L. sativa is diploid with 2n=2x=18 chromosomes. The genome size has been estimated by flow cytometry to be ~2.3 pg (Koopman & De Jong, 1996) or 2.5 Gb by (Michaelson et al., 1991). This has been corroborated by whole genome sequencing and assembly of L. sativa cv. Salinas at ~2.7 Gb. It is inbreeding with limited genetic diversity within cultivated types (Hill et al., 1996). There are four well-established major species within the subsection Lactuca, cultivated L. sativa and three wild species, L. serriola, L. saligna, and L. virosa, as well as several less well characterized species (Feráková, 1977). Wild species, particularly L. serriola, have been sources of disease resistance genes (Crute, 1988 & 1992); however, they remain a rich potential source of variation that has not been accessed systematically (Sicard et al. , 1999; Lebeda & Zinkernagel, 2003; Beharav et al. , 2006; Kuang et al. , 2008).
The name of the genus is derived from lac, Latin for milk, due to the plant’s milky latex that exudes from the stem when cut. The earliest description of lettuce is in carvings at the temple of Senusret I at Karnak in Egypt. Lettuce was considered an aphrodisiac food in ancient Egypt. Lactucarium (or "Lettuce Opium") is a mild opiate-like substance in the latex of all types of lettuce. Ancient Greek physicians recognized that lettuce could act as a sleep-inducing agent. Both Romans and Egyptians took advantage of this by eating lettuce at the end of a meal to induce sleep (http://en.wikipedia.org/wiki/Lactuca_sativa). Lettuce was introduced to the New World by Christopher Columbus. It is now used worldwide as a leaf vegetable. It is eaten either raw in salads, sandwiches, hamburgers, tacos, and many other dishes, or cooked, as in Chinese cuisine, in which the stem is as important as the leaf. Lettuce is a low calorie food and is a source of vitamin A and folic acid. Because of the volume eaten, it is significant part of the American diet.
Cultivated lettuce was likely domesticated from the successful weed L. serriola (Lindvist, 1960; Kesseli et al. , 1991; de Vries et al., 1997). L. sativa and L. serriola can be readily crossed and there are no major barriers to gene flow between these species (Lindqvist, 1960). Cultivated lettuce initially has a short stem (rosette stage), but when it flowers (bolts), the stem and branches lengthen and produce many flower heads (Figures 1 & 2). Domestication has resulted in slower bolting, exaggeration of the leaves at the rosette stage, a variety of leaf shapes and colors, lower latex content, and a non-shattering involucre.
Lettuce is an important vegetable crop species and ranks as one of the top ten most valuable crops in the U.S. with an annual value of over $2 billion (Anon., 2011). The United States is the second largest lettuce-producing country behind China (http://usda.mannlib.cornell.edu/usda/current/lettuce/lettuce-01-14-2009.pdf). There are five commonly recognized types of lettuce that are consumed as leaves (Figures 3 & 4) plus the stem and oil seed types.
Lettuce is amenable to classical and molecular genetic analyses. The generation time is usually three to five months depending on the genotype and environment, allowing multiple generations each year. Lettuce can be routinely transformed using Agrobacterium tumefaciens; transgenic seed can be generated within 3 to 5 months depending on the genotype (Michelmore et al., 1987). Agrobacterium-mediated transient assays and RNAi are routine (Wroblewski et al., 2005 & 2007). Extensive genetic and genomic tools including the transcriptome genome sequences are now available that are ready to be exploited for lettuce improvement (Matvienko et al., 2013).
- Crisphead or Iceberg: Large tightly wrapped heads of thick, crisp leaves. Popular in the US because it ships and stores well; ~80% of production occurs in California and Arizona and is then shipped throughout the US. Lowest nutritional value of all the lettuce types.
- Cos or Romaine: Tall, upright heads with dark green leaves. Increasingly popular in the US.
- Leafy or looseleaf: Open heads with loosely bunched leaves of a variety of shapes and colors.
- Butterhead or bibb: Heads with a loose arrangement of leaves with sweet flavor and tender texture.
- Batavian or French Crisp: Intermediate between the crisphead and leaf types.
- Stem. The seed stalk rather than its leaves is eaten. Primarily used in China in stewed and creamed dishes.
- Oilseed. Very minor type grown for the oil in its large seeds.
Multiple genetic maps have been generated using several intra-specific (Landry et al., 1987; Kesseli et al., 1994; Waycott et al., 1999; Hayashi et al., 2008) and inter-specific populations (Johnson et al., 2000; Jeuken et al., 2001; Syed et al., 2006; McHale et al., 2009) using a variety of molecular markers to provide increasingly dense maps as different technologies became available. Particular markers often only segregated in one or a few of these populations which hampered the transfer of genetic and phenotypic information among the different maps. A single integrated map of lettuce with 2,744 loci was therefore constructed that combined seven separate maps into nine chromosomal linkage groups (Truco et al., 2007). The majority of these maps rely on anonymous RFLP, RAPD, and AFLP markers.
One of the populations used to produce the integrated map was a RIL (Recombinant Inbred Line) population resulting from an inter-specific cross between L. sativa cv. Salinas x L. serriola acc. US96UC23. This has emerged as a core reference mapping population and now comprises 356 F7:8 RILs. Sets of these RILs have been distributed to researchers worldwide for diverse studies. This population has also been genotyped for genes involved in disease resistance (McHale et al., 2009) and candidate genes for horticultural and domestication traits (Lavelle, 2009) as well as phenotyped for multiple traits (Argyris et al., 2005 & 2008; Zhang et al., 2007; Hartman et al., 2012). An ultra-high density, transcript-based genetic map has been generated from this reference mapping population; this consists of 12,842 unigenes mapped in 3,696 genetic bins distributed over nine chromosomal linkage groups (Truco et al., 2013). A large amount of genotypic and phenotypic information for this RIL population is available in the Compositae Genome Project database (http://compgenomics.ucdavis.edu).
We collaborated with BGI, Shenzhen to sequence the lettuce genome (L. sativa cv. Salinas) with funding from an international consortium of ten breeding companies. The sequencing has been completed and the draft genome assembled into 15,471 scaffolds comprising 2.5 Gb of the 2.7 Gb genome with a contig N50 of 11.7 kb and a scaffold N50 of 461 kb. Of the scaffolds that contained multiple mapped unigenes (over 60% of the assembled genome), 95% are genetically consistent with our ultra-dense transcript-based map; most of the remaining mapped scaffolds analyzed were simple chimeras. We have placed these validated scaffolds into chromosomal linkage groups relative to numerous phenotypes including disease resistance genes. Additional scaffolds have been placed into the chromosomal linkage groups based on sequencing of the gene-space of the core mapping population. The genome has been annotated using the BGI and MAKER pipelines to provide ca. 45,000 gene models. These data are publicly available as of August 2012 (http://lgr.genomecenter.ucdavis.edu; http://www.ncbi.nlm.nih.gov/bioproject/173551).
Lettuce is grown as extensive monocultures, often with several crops per year. Such intensive production makes the crop susceptible to major epidemics and lettuce suffers from several economically important pests and diseases ( http://michelmorelab.ucdavis.edu/index.php?link=disease) (Davis et al., 1997). These are currently controlled by a combination of genetic resistance, cultural practices, and chemical protection including the application of over 1.6 million pounds of insecticides and fungicides (USDA-NASS, 2007). When genetic sources of disease resistance are available, breeding is the cheapest, cleanest, safest, and most dependable method of crop protection available. Breeding efforts have consequently emphasized disease resistance and resistance to physiological disorders.
Lettuce downy mildew (http://bremia.ucdavis.edu/), caused by Bremia lactucae, is the most important disease affecting lettuce worldwide. Several other diseases ( http://michelmorelab.ucdavis.edu/index.php?link=disease) are problematic in lettuce (Davis et al., 1997). These include bacterial corky root caused by Sphingomonas suberifaciens, and fungal diseases such as lettuce drop caused by Sclerotinia minor and S. sclerotiorum, lettuce anthracnose caused by Microdochium panattonianum, grey mold (Botrytis cinerea), and wilts caused by Fusarium oxysporum and Verticillium dahliae. There are also several viral diseases of varying importance such as lettuce mosaic, lettuce dieback, lettuce big vein, beet western yellows, and tomato bushy stunt. Other pathogens, such as powdery mildew (Erysiphe cichoracearum), bacterial spot (Xanthomonas campestris pv. vitians), lettuce infectious yellows, turnip mosaic virus, and tomato spotted wilt virus are present but currently rarely cause significant losses.
Resistance is known for most but not all lettuce diseases. Over 52 phenotypically characterized resistance genes have been identified in lettuce (McHale et al., 2009; Truco & Michelmore, unpublished). Although major genes for downy mildew resistance (Dm genes) are highly effective and have been widely used, they have had limited lifespans because they have been rendered ineffective by changes in the pathogen (Ilott et al., 1987; Michelmore & Wong, 2008). The interaction between lettuce and Bremia lactucae, the causal agent of lettuce downy mildew, is one of the most extensively characterized gene-for-gene plant-pathogen relationships (Crute & Johnson, 1976; Farrara et al., 1987; Hulbert & Michelmore, 1985; Michelmore et al., 1984; Norwood & Crute, 1984; Norwood et al., 1983; Ilott et al., 1987 & 1989). At least 25 major Dm genes are now known that provide resistance against specific isolates of B. lactucae in a gene-for-gene manner (Farrara et al., 1987; Bonnier et al., 1994; Maisonneuve et al., 1994; Jeuken & Lindhout, 2002). The known Dm genes are located in five clusters in the genome (Hulbert & Michelmore, 1985; Farrara et al., 1987; Bonnier et al., 1994). The major cluster contains over nine genetically separable Dm specificities, as well as resistance to root aphid. Another large cluster contains several Dm genes, resistance to the root-infecting downy mildew Plasmopara lactucae-radicis, and the hypersensitive reaction to Turnip Mosaic Virus (Witsenboer et al., 1995).
The Dm3 and Dm7 downy mildew resistance genes have been cloned through combinations of map-based cloning, candidate gene, RNAi, and mutant analysis approaches (Shen et al., 1998 & 2002; Christopoulou et al., unpublished). Both encode nucleotide-binding-site and leucine-rich-repeat (NBS-LRR) proteins, similar to genes cloned from other species for resistance to downy mildews and other pathogens (McHale et al., 2006). Dm3 is a member of the large RGC2 (Resistance Gene Candidate2) multigene family (Meyers et al., 1998a & b). The RGC2 cluster is not highly recombinagenic; it exhibits a recombination frequency 18 times lower than the genome-wide average (Chin et al., 2001). Numerous haplotypes and homologs at the RGC2 cluster of resistance genes have been identified. Fifty-one different haplotypes were identified in 74 accessions studied using molecular markers diagnostic of the RGC2 cluster (Sicard et al., 1999). The copy number of RGC2 paralogs at a locus varies from 12 to over 30 (Kuang et al., 2004). The large number of different haplotypes is consistent with there being a minimum of several hundred distinct Dm genes in Lactuca species and indicates that wild germplasm will be a rich source of new resistance genes that can be introgressed and pyramided using molecular markers.
Supplemental information is available at: http://cgpdb.ucdavis.edu/supplemental_data/lmh_2008/ and http://michelmorelab.ucdavis.edu.
- Numerous genetic linkage maps based on thousands of genetic markers and a variety of crosses (Truco et al., 2007 & 2013).
- Recombinant Inbred Line (RIL) mapping populations. L. sativa cv. Salinas x L. serriola accession “UC96US23” = core mapping population (Truco et al. 2013).
- Germplasm: breeding lines, mutants, and USDA, CGN, and other foreign collections
- Lactuca sativa cDNA clones (http://genome.arizona.edu/
- CGP(Compositae Genome Project) resources at NCBI:
- Lactuca sativa nucleotide sequences in GenBank: http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4236
- Lactuca sativa ESTs in GenBank http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=4236
- Lactuca sativa Illumina data at NCBI Sequence Read Archive (SRA) http://www.ncbi.nlm.nih.gov/sra/?term=txid4236[Organism:exp]
- Illumina genomic reads (400+ million reads of high quality). (Accession: SRX099365, SRX099215, SRX099223, SRX098725)
- Illumina mRNA-Seq reads (90+ million reads of high quality). (Accession: SRX034873, SRX033326)
- Illumina reads (295 Gb) of genomic libraries from BGI http://trace.ncbi.nlm.nih.gov/Traces/sra/?study=SRP015354
- Lactuca sativa transcriptome assemblies (51482 total). http://www.ncbi.nlm.nih.gov/nuccore?term=lactuca sativa transcriptome assembly
- Lactuca sativa gene-spece shotgun sequencing and assembly project http://www.ncbi.nlm.nih.gov/nuccore/AFSA00000000.1
- Morohodb, phenotypic information for a RILs and diversity panel accessions http://compgenomics.ucdavis.edu/morphodb_index.php
- Affy GeneChip for 213 RIL population and diversity panel: http://chiplett.ucdavis.edu/public/Data/data.php
- lettuce genome resource https://lgr.genomecenter.ucdavis.edu/
| Images of Lactuca sativa|
| Figure 1: Five lettuce types. Photo by Oswaldo Ochoa||
| Figure 2: Field planting of different breeding lines. Photo by Oswaldo Ochoa||
| Figure 3: Flowering plants and details of lettuce flowers. Photo by Oswaldo Ochoa||
| Figure 4: Domestication traits in lettuce. Photo by Oswaldo Ochoa||
| Figure 5: Lettuce Seeds. Photo by Alex Kozik.||
Anonymous. 2011 http://usda.mannlib.cornell.edu/MannUsda/viewDocumentInfo.do?documentID=1576
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