Agriaquaculture Nutritional Genomic Center

Temuco, Chile

Agriaquaculture Nutritional Genomic Center

Temuco, Chile
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Soto-Cerda B.J.,Agriaquaculture Nutritional Genomic Center | Soto-Cerda B.J.,Agriculture and Agri Food Canada | Maureira-Butler I.,Agriaquaculture Nutritional Genomic Center | Munoz G.,Andrés Bello University | And 2 more authors.
Molecular Breeding | Year: 2012

Flax seed mucilage (SM) presents specific biological activities useful for the food and pharmaceutical industries. Understanding the population structure, genetic diversity and linkage disequilibrium (LD) of germplasm varying for mucilage content is pivotal for the identification of genes and quantitative trait loci underlying mucilage variation by association mapping (AM). In this study, 150 microsatellite loci were used to assess the population structure, genetic diversity and LD of a set of 60 flax cultivars/accessions capturing the breadth of SM variation in flax germplasm. STRUCTURE analysis and similarity-based methods revealed the presence of three populations reflecting mainly their geographic origins (South Asia, South America and North America), and the impact of germplasm exchange within and between North American flax breeding programs. Analysis of molecular variance showed that 78. 32% of the genetic variation resided within populations and 21. 68% among populations. The phi-statistic (Φ st) value of 0. 22 confirmed the presence of a strong population structure. A total of 408 alleles were detected, with the South American population capturing the highest overall diversity. However, the genetic diversity was narrow, as indicated by the small number of alleles per locus (2. 72) and gene diversity (mean = 0. 34). LD was significant between 3. 9% (r 2) and 36. 2% (D′) of the loci pairs (FDR < 0. 05). The mean r 2 and D′ were 0. 26 and 0. 53, respectively. The results suggest that the collection could be useful in AM studies aimed at the discovery of genes/alleles involved in SM; however a greater diversity may be required to improve the AM resolution. © 2011 Crown Copyright.

Ramadugu C.,University of California at Riverside | Pfeil B.E.,CSIRO | Pfeil B.E.,Gothenburg University | Keremane M.L.,Agricultural Research Service National Clonal Germplasm Repository for Citrus and Dates | And 3 more authors.
PLoS ONE | Year: 2013

Background:Genus Citrus (Rutaceae) comprises many important cultivated species that generally hybridize easily. Phylogenetic study of a group showing extensive hybridization is challenging. Since the genus Citrus has diverged recently (4-12 Ma), incomplete lineage sorting of ancestral polymorphisms is also likely to cause discrepancies among genes in phylogenetic inferences. Incongruence of gene trees is observed and it is essential to unravel the processes that cause inconsistencies in order to understand the phylogenetic relationships among the species.Methodology and Principal Findings:(1) We generated phylogenetic trees using haplotype sequences of six low copy nuclear genes. (2) Published simple sequence repeat data were re-analyzed to study population structure and the results were compared with the phylogenetic trees constructed using sequence data and coalescence simulations. (3) To distinguish between hybridization and incomplete lineage sorting, we developed and utilized a coalescence simulation approach. In other studies, species trees have been inferred despite the possibility of hybridization having occurred and used to generate null distributions of the effect of lineage sorting alone (by coalescent simulation). Since this is problematic, we instead generate these distributions directly from observed gene trees. Of the six trees generated, we used the most resolved three to detect hybrids. We found that 11 of 33 samples appear to be affected by historical hybridization. Analysis of the remaining three genes supported the conclusions from the hybrid detection test.Conclusions:We have identified or confirmed probable hybrid origins for several Citrus cultivars using three different approaches-gene phylogenies, population structure analysis and coalescence simulation. Hybridization and incomplete lineage sorting were identified primarily based on differences among gene phylogenies with reference to null expectations via coalescence simulations. We conclude that identifying hybridization as a frequent cause of incongruence among gene trees is critical to correctly infer the phylogeny among species of Citrus.

Parra-Gonzalez L.B.,Agriaquaculture Nutritional Genomic Center | Aravena-Abarzua G.A.,Agriaquaculture Nutritional Genomic Center | Navarro-Navarro C.S.,Agriaquaculture Nutritional Genomic Center | Udall J.,Brigham Young University | And 5 more authors.
BMC Genomics | Year: 2012

Background: Yellow lupin (Lupinus luteus L.) is a minor legume crop characterized by its high seed protein content. Although grown in several temperate countries, its orphan condition has limited the generation of genomic tools to aid breeding efforts to improve yield and nutritional quality. In this study, we report the construction of 454-expresed sequence tag (EST) libraries, carried out comparative studies between L. luteus and model legume species, developed a comprehensive set of EST-simple sequence repeat (SSR) markers, and validated their utility on diversity studies and transferability to related species.Results: Two runs of 454 pyrosequencing yielded 205 Mb and 530 Mb of sequence data for L1 (young leaves, buds and flowers) and L2 (immature seeds) EST- libraries. A combined assembly (L1L2) yielded 71,655 contigs with an average contig length of 632 nucleotides. L1L2 contigs were clustered into 55,309 isotigs. 38,200 isotigs translated into proteins and 8,741 of them were full length. Around 57% of L. luteus sequences had significant similarity with at least one sequence of Medicago, Lotus, Arabidopsis, or Glycine, and 40.17% showed positive matches with all of these species. L. luteus isotigs were also screened for the presence of SSR sequences. A total of 2,572 isotigs contained at least one EST-SSR, with a frequency of one SSR per 17.75 kbp. Empirical evaluation of the EST-SSR candidate markers resulted in 222 polymorphic EST-SSRs. Two hundred and fifty four (65.7%) and 113 (30%) SSR primer pairs were able to amplify fragments from L. hispanicus and L. mutabilis DNA, respectively. Fifty polymorphic EST-SSRs were used to genotype a sample of 64 L. luteus accessions. Neighbor-joining distance analysis detected the existence of several clusters among L. luteus accessions, strongly suggesting the existence of population subdivisions. However, no clear clustering patterns followed the accession's origin.Conclusion: L. luteus deep transcriptome sequencing will facilitate the further development of genomic tools and lupin germplasm. Massive sequencing of cDNA libraries will continue to produce raw materials for gene discovery, identification of polymorphisms (SNPs, EST-SSRs, INDELs, etc.) for marker development, anchoring sequences for genome comparisons and putative gene candidates for QTL detection. © 2012 Parra-González et al.; licensee BioMed Central Ltd.

Millao S.,University of the Frontier | Uquiche E.,University of the Frontier | Uquiche E.,Agriaquaculture Nutritional Genomic Center
Journal of Supercritical Fluids | Year: 2016

Nannochloropsis gaditana is a microalga characterized by its high content of lipids and as an important source of carotenoids, which are recognized to be potent natural antioxidants. A central composite design using response surface methodology was used to study the effects of temperature (36–64 °C) and CO2 density (914–956 kg/m3, in a pressure range between 31.7 and 54.3 MPa) on the recovery of oil and carotenoids from pelletized N. gaditana by supercritical CO2. Extraction yields of oil and carotenoids varied between 110.1 and 152.9 g/kg dry substrate and between 393.0 and 773.7 mg/kg.d.s., respectively. The recovery of oil and carotenoids increased with the temperature and CO2 density, reaching the highest recovery at 64 °C and 956 kg/m3 (59.3 MPa). Temperature had a greater effect on response variables than CO2 density. Antioxidant activity (DPPH assay and bleaching β-carotene assay) and anti-inflammatory activity (lipoxygenase inhibition) were measured in selected supercritical extract, and important antioxidant properties were demonstrated. © 2016 Elsevier B.V.

Soto-Cerda B.J.,University of Manitoba | Soto-Cerda B.J.,Agriculture and Agri Food Canada | Soto-Cerda B.J.,Agriaquaculture Nutritional Genomic Center | Diederichsen A.,Agriculture and Agri Food Canada | And 4 more authors.
BMC Plant Biology | Year: 2013

Background: Flax is valued for its fiber, seed oil and nutraceuticals. Recently, the fiber industry has invested in the development of products made from linseed stems, making it a dual purpose crop. Simultaneous targeting of genomic regions controlling stem fiber and seed quality traits could enable the development of dual purpose cultivars. However, the genetic diversity, population structure and linkage disequilibrium (LD) patterns necessary for association mapping (AM) have not yet been assessed in flax because genomic resources have only recently been developed. We characterized 407 globally distributed flax accessions using 448 microsatellite markers. The data was analyzed to assess the suitability of this core collection for AM. Genomic scans to identify candidate genes selected during the divergent breeding process of fiber flax and linseed were conducted using the whole genome shotgun sequence of flax.Results: Combined genetic structure analysis assigned all accessions to two major groups with six sub-groups. Population differentiation was weak between the major groups (FST = 0.094) and for most of the pairwise comparisons among sub-groups. The molecular coancestry analysis indicated weak relatedness (mean = 0.287) for most individual pairs. Abundant genetic diversity was observed in the total panel (5.32 alleles per locus), and some sub-groups showed a high proportion of private alleles. The average genome-wide LD (r2) was 0.036, with a relatively fast decay of 1.5 cM. Genomic scans between fiber flax and linseed identified candidate genes involved in cell-wall biogenesis/modification, xylem identity and fatty acid biosynthesis congruent with genes previously identified in flax and other plant species.Conclusions: Based on the abundant genetic diversity, weak population structure and relatedness and relatively fast LD decay, we concluded that this core collection is suitable for AM studies targeting multiple agronomic and quality traits aiming at the improvement of flax as a true dual purpose crop. Our genomic scans provide the first insights into candidate regions affected by divergent selection in flax. In combination with AM, genomic scans have the ability to increase the power to detect loci influencing complex traits. © 2013 Soto-Cerda et al.; licensee BioMed Central Ltd.

Soto-Cerda B.J.,Agriculture and Agri Food Canada | Soto-Cerda B.J.,Agriaquaculture Nutritional Genomic Center | Cloutier S.,Agriculture and Agri Food Canada
Plant Molecular Biology Reporter | Year: 2013

Genomic microsatellites (gSSRs) and expressed sequence tag-derived SSRs (EST-SSRs) have gained wide application for elucidating genetic diversity and population structure in plants. Both marker systems are assumed to be selectively neutral when making demographic inferences, but this assumption is rarely tested. In this study, three neutrality tests were assessed for identifying outlier loci among 150 SSRs (85 gSSRs and 65 EST-SSRs) that likely influence estimates of population structure in three differentiated flax sub-populations (F ST = 0.19). Moreover, the utility of gSSRs, EST-SSRs, and the combined sets of SSRs was also evaluated in assessing genetic diversity and population structure in flax. Six outlier loci were identified by at least two neutrality tests showing footprints of balancing selection. After removing the outlier loci, the STRUCTURE analysis and the dendrogram topology of EST-SSRs improved. Conversely, gSSRs and combined SSRs results did not change significantly, possibly as a consequence of the higher number of neutral loci assessed. Taken together, the genetic structure analyses established the superiority of gSSRs to determine the genetic relationships among flax accessions, although the combined SSRs produced the best results. Genetic diversity parameters did not differ statistically (P > 0.05) between gSSRs and EST-SSRs, an observation partially explained by the similar number of repeat motifs. Our study provides new insights into the ability of gSSRs and EST-SSRs to measure genetic diversity and structure in flax and confirms the importance of testing for the occurrence of outlier loci to properly assess natural and breeding populations, particularly in studies considering only few loci. © 2013 The Author(s).

Uquiche E.,University of the Frontier | Uquiche E.,Agriaquaculture Nutritional Genomic Center | Cirano N.,University of the Frontier | Millao S.,University of the Frontier
Industrial Crops and Products | Year: 2015

Supercritical CO2 extraction was applied to recover bioactive extract from L. rivularis leaves. A response surface design was applied to study the effects of temperature (38-52°C) and pressure (10.8-19.2MPa) on extraction yield, which varied from 2.91 to 5.05g/100g d.s. Extraction yield was affected positively by the temperature (p<0.01) and negatively by the pressure (p<0.05). The negative effect of the pressure was attributed by a reflection of the increased repulsive solute-solvent interactions, or by effect of the pressure in decreasing the mass transfer parameters. Based on the response surface analysis, two pressures were selected at 52°C: 10.8 and 19.2MPa. The extract obtained at 19.2MPa (0.61mmolTE/kg) showed higher antioxidant activity than that at 10.8MPa (0.35mmolTE/kg). Quantitative analysis by GC-FID showed that the extract with higher antioxidant activity contained all three target terpenoids: α-thujone (5.36mg/g), β-caryophyllene (3.43mg/g) and caryophyllene oxide (5.72mg/g), while only caryophyllene oxide (11.02mg/g) was found in the low pressure extracts. The yield with supercritical extraction (at 52°C and 19.2MPa) was 2.2 times higher than with hydrodistillation (2.11g/100g d.s.). Furthermore, supercritical extracts displayed higher antioxidant activity than hydrodistilled extract, compared by DPPH assay (0.60 and 0.46mmol TE/kg, respectively) and bleaching β-carotene assay (IC50 values of 1.99 and 10.10mg/mL, respectively). © 2015 Elsevier B.V.

Millao S.,University of the Frontier | Uquiche E.,University of the Frontier | Uquiche E.,Agriaquaculture Nutritional Genomic Center
Journal of Supercritical Fluids | Year: 2016

Nannochloropsis gaditana is a microalga characterized by its high lipid content and as an important source of carotenoids, recognized as potent natural antioxidants. The objective of this work was to study the effects of temperature (36-64°C) and CO2 density (914-956 kg/m3) on the content of carotenoids and tocopherols (minor lipids), and the antioxidant activity of oil extracted from N. gaditana using supercritical CO2. Antioxidant activity was measured by the DPPH assay, FRAP assay and β-carotene bleaching assay. A process development unit was used for extraction experiments, performed under a central composite rotatable design. The experimental data were analyzed by means of the response surface methodology. Content of carotenoids and tocopherols showed differences of 1.5- and 2.3-fold, respectively. The minor lipid content and the antioxidant activity increased with the increase of the temperature and CO2 density, reaching the highest values at 64°C and 956 kg/m3 for all responses studied. Important antioxidant properties in the oil showed a positive correlation with the content of minor lipids. © 2016 Elsevier B.V. All rights reserved.

Uquiche E.,University of the Frontier | Uquiche E.,Agriaquaculture Nutritional Genomic Center | Garces F.,University of the Frontier
Journal of Supercritical Fluids | Year: 2016

We studied the effects of temperature (40, 50, and 60 °C) and pressure (9, 12, and 15 MPa) on the recovery and antioxidant activity of the essential oil from Leptocarpha rivularis leaves by supercritical CO2 using a 32 factorial design. Experimental data were analyzed with the response surface methodology. Extraction yield varied from 23.5 to 42.6 g/kg d.s., and the resultant antioxidant activity (DPPH assay) varied from 0.60 to 1.84 mmol TE/kg. The highest extraction yield and antioxidant activity in the supercritical extract at 40 °C and 15 MPa, respectively 2.5 and 5 times higher than in hydrodistilled extract. However, the extraction yield and antioxidant activity of a hydroethanolic extract were higher than those of supercritical extracts. Three target terpenoids of L. rivularis (α-thujone, β-caryophyllene and caryophyllene oxide) were quantified in the supercritical extract using GC/FID; they were not detected in the hydroethanolic extract. © 2015 Elsevier B.V. All rights reserved.

Demmig-Adams B.,University of Colorado at Boulder | Cohu C.M.,University of Colorado at Boulder | Amiard V.,Agriaquaculture Nutritional Genomic Center | van Zadelhoff G.,University Utrecht | And 3 more authors.
New Phytologist | Year: 2013

This review summarizes evidence for a mechanistic link between plant photoprotection and the synthesis of oxylipin hormones as regulators of development and defense. Knockout mutants of Arabidopsis, deficient in various key components of the chloroplast photoprotection system, consistently produced greater concentrations of the hormone jasmonic acid or its precursor 12-oxo-phytodienoic acid (OPDA), both members of the oxylipin messenger family. Characterized plants include several mutants deficient in PsbS (an intrinsic chlorophyll-binding protein of photosystem II) or pigments (zeaxanthin and/or lutein) required for photoprotective thermal dissipation of excess excitation energy in the chloroplast and a mutant deficient in reactive oxygen detoxification via the antioxidant vitamin E (tocopherol). Evidence is also presented that certain plant defenses against herbivores or pathogens are elevated for these mutants. This evidence furthermore indicates that wild-type Arabidopsis plants possess less than maximal defenses against herbivores or pathogens, and suggest that plant lines with superior defenses against abiotic stress may have lower biotic defenses. The implications of this apparent trade-off between abiotic and biotic plant defenses for plant ecology as well as for plant breeding/engineering are explored, and the need for research further addressing this important issue is highlighted. © 2013 New Phytologist Trust.

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