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Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

ABSTRACT: BACKGROUND: Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. RESULTS: Testing of newly developed markers on a set of 36 Lactuca accession (33?L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe?=?0.56) and the number of loci per SSR (Na?=?5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe?=?0.32, Na?=?3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. CONCLUSIONS: The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.

SUBMITTER: Rauscher G

PROVIDER: S-EPMC3557189 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature

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Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

Rauscher Gilda G Simko Ivan I

BMC plant biology 20130122

<h4>Background</h4>Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers.<h4>Results</h4>Testing of newly developed markers on a set of 36 Lactuca accession (33 L. s ...[more]

PMID: 23339733

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Project description:A diet rich in phytonutrients from fruit and vegetables has been acknowledged to afford protection against a range of human diseases, but many of the most popular vegetables are low in phytonutrients. Wild relatives of crops may contain allelic variation for genes determining the concentrations of these beneficial phytonutrients, and therefore understanding the genetic basis of this variation is important for breeding efforts to enhance nutritional quality. In this study, lettuce recombinant inbred lines, generated from a cross between wild and cultivated lettuce (Lactuca serriola and Lactuca sativa, respectively), were analysed for antioxidant (AO) potential and important phytonutrients including carotenoids, chlorophyll and phenolic compounds. When grown in two environments, 96 quantitative trait loci (QTL) were identified for these nutritional traits: 4 for AO potential, 2 for carotenoid content, 3 for total chlorophyll content and 87 for individual phenolic compounds (two per compound on average). Most often, the L. serriola alleles conferred an increase in total AOs and metabolites. Candidate genes underlying these QTL were identified by BLASTn searches; in several cases, these had functions suggesting involvement in phytonutrient biosynthetic pathways. Analysis of a QTL on linkage group 3, which accounted for >30% of the variation in AO potential, revealed several candidate genes encoding multiple MYB transcription factors which regulate flavonoid biosynthesis and flavanone 3-hydroxylase, an enzyme involved in the biosynthesis of the flavonoids quercetin and kaempferol, which are known to have powerful AO activity. Follow-up quantitative RT-PCR of these candidates revealed that 5 out of 10 genes investigated were significantly differentially expressed between the wild and cultivated parents, providing further evidence of their potential involvement in determining the contrasting phenotypes. These results offer exciting opportunities to improve the nutritional content and health benefits of lettuce through marker-assisted breeding.

Project description:BackgroundIdentification and screening of cultivars rich in bioactive phytoconstituents can be potentially useful to make nutrient-dense dishes and in medicinal formulations. In this study, we have identified, characterized and quantified caffeoylquinic acids, dicaffeoylquinic acid, dicaffeoyltartaric acid, kaempferol conjugates, quercetin malonylglucoside, sesquiterpene lactones, and cyanidin in 22 lettuce cultivars at mature and bolting stages using UPLC-PDA-Q-TOF-HDMS, UPLC, and HPLC.ResultsThe composition and contents of the studied metabolites and antioxidant activity varied significantly and depend on leaf color, cultivar type and stage of maturity. The main phenolic acid components of lettuce were quinic and tartaric acid derivatives, whereas kaempferol derivatives were the dominant flavonoids. The sum of the content of phenolic acids ranged from 18.3 to 54.6 mg/100 g DW and 15.5 to 54.6 mg/100 g DW, whereas the sum of the contents of flavonoids ranged from 9.2 to 25.9 mg/100 g DW and 14.9 to 83.0 mg/100 g DW in mature and bolting stage cultivars, respectively. The content of cyanidin, lactucin, lactucopicrin, and ABTS radical antioxidant activity were in the range of 0.3 to 9.7 (mature stage) and 0.5 to 10.2 mg/g DW (bolting stage), 1.8 to 41.9 (mature stage) and 9.7 to 213.0 (bolting stage) µg/g DW, 9.9 to 344.8 (mature stage) and 169.2 to 3888.2 (bolting stage) µg/g DW, and 12.1 to 29.0 (mature stage) and 15.7 to 30.3 (bolting stage) mg TE/g DW, respectively. The principal component analysis (PCA) showed that the green and red pigmented lettuce cultivars were grouped to the negative and positive sides of PC1, respectively, while the green/red pigmented cultivars were distributed throughout the four quadrants of the PCA plots with no prominent grouping. The loading plot showed that phenolic acids, flavonoids, and cyanidin are the most potent contributors to the radical scavenging activity of lettuce extracts.ConclusionsLettuce at the bolting stage accumulate relatively high amount of sesquiterpene lactones (SLs), quercetin malonylglucoside (QMG), methylkaempferol glucuronide (MKGR), kaempferol malonylglucoside (KMG), and 3-O-caffeoylquinic acid (3-CQA) compared to the mature stage. Higher amount of phytoconstituents were found to be accumulated in the red pigmented lettuce leaves compared to the green lettuce leaves. In addition, the contents of most of the metabolites in lettuce seem to increase with age of the leaves. The presence of the two bitter SLs, lactucin and lactucopicrin, in significantly high amount in lettuce leaves at bolting stage could diminish consumer acceptance. However, alternatively, these leaves could be utilized by nutraceutical companies working to recover these compounds.

Dataset Information

Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

Publications

Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

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