A Past Genetic Bottleneck from Argentine Beans and a Selective Sweep Led to the Race Chile of the Common Bean (Phaseolus vulgaris L.).

The domestication process of the common bean gave rise to six different races which come from the two ancestral genetic pools, the Mesoamerican (Durango, Jalisco, and Mesoamerica races) and the Andean (New Granada, Peru, and Chile races). In this study, a collection of 281 common bean landraces from Chile was analyzed using a 12K-SNP microarray. Additionally, 401 accessions representing the rest of the five common bean races were analyzed. A total of 2543 SNPs allowed us to differentiate a genetic group of 165 accessions that corresponds to the race Chile, 90 of which were classified as pure accessions, such as the bean types 'Tórtola', 'Sapito', 'Coscorrón', and 'Frutilla'. Our genetic analysis indicates that the race Chile has a close relationship with accessions from Argentina, suggesting that nomadic ancestral peoples introduced the bean seed to Chile. Previous archaeological and genetic studies support this hypothesis. Additionally, the low genetic diversity (π = 0.053; uHe = 0.53) and the negative value of Tajima' D (D = -1.371) indicate that the race Chile suffered a bottleneck and a selective sweep after its introduction, supporting the hypothesis that a small group of Argentine bean genotypes led to the race Chile. A total of 235 genes were identified within haplotype blocks detected exclusively in the race Chile, most of them involved in signal transduction, supporting the hypothesis that intracellular signaling pathways play a fundamental role in the adaptation of organisms to changes in the environment. To date, our findings are the most complete investigation associated with the origin of the race Chile of common bean.

Nutritional Characterization of Chilean Landraces of Common Bean.

Common bean (Phaseolus vulgaris L.) is the primary grain legume cultivated worldwide for direct human consumption due to the high nutritional value of its seeds and pods. The high protein content of common beans highlights it as the most promising source of plant-based protein for the food industry. Additionally, landraces of common bean have great variability in nutritional traits, which is necessary to increase the nutritional quality of elite varieties. Therefore, the main objective of this study was to nutritionally characterize 23 Chilean landraces and 5 commercial varieties of common bean to identify genotypes with high nutritional value that are promising for the food industry and for genetic improvement programs. The landrace Phv23 ('Palo') was the most outstanding with high concentrations of minerals such as P (7.53 g/kg), K (19.8 g/kg), Mg (2.43 g/kg), Zn (52.67 mg/kg), and Cu (13.67 mg/kg); essential amino acids (364.8 mg/g protein); and total proteins (30.35 g/100 g seed). Additionally, the landraces Phv9 ('Cimarrón'), Phv17 ('Juanita'), Phv3 ('Araucano'), Phv8 ('Cabrita/Señorita'), and Phv4 ('Arroz') had a high protein content. The landrace Phv24 ('Peumo') stood out for its phenolic compounds (TPC = 218.1 mg GA/100 g seed) and antioxidant activity (ORAC = 22,167.9 µmol eq trolox/100 g extract), but it has moderate to low mineral and protein concentrations. In general, the concentration of nutritional compounds in some Chilean landraces was significantly different from the commercial varieties, highlighting their high nutritional value and their potential use for the food industry and for genetic improvement purposes.

Draft genome data of Prunus avium cv 'Stella'.

Prunus avium cv. 'Stella' total cellular DNA was isolated from emerging leaf tissue and sequenced using Roche 454 GS FLX Titanium, and Illumina HiSeq 2000 High Throughput Sequencing (HTS) technologies. Sequence data were filtered and trimmed to retain nucleotides corresponding to Phred score 30, and assembled with CLC Genomics Workbench v.6.0.1. A total of 107,531 contigs were assembled with 185 scaffolds with a maximum length of 132,753 nucleotides and an N50 value of 4,601. The average depth of coverage was 135.87 nucleotides with a median depth of coverage equal to 31.50 nucleotides. The draft 'Stella' genome presented here covers 77.8% of the estimated 352.9Mb P. avium genome and is expected to facilitate genetics and genomics research focused on identifying genes and quantitative trait loci (QTL) underlying important agronomic and consumer traits.

Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools.

A genotyping by sequencing (GBS) approach was used to analyze the organization of genetic diversity in V. pubescens and V. chilensis. GBS identified 4675 and 4451 SNPs/INDELs in two papaya species. The cultivated orchards of V. pubescens exhibited scarce genetic diversity and low but significant genetic differentiation. The neutrality test yielded a negative and significant result, suggesting that V. pubescens suffered a selective sweep or a rapid expansion after a bottleneck during domestication. In contrast, V. chilensis exhibited a high level of genetic diversity. The genetic differentiation among the populations was slight, but it was possible to distinguish the two genetic groups. The neutrality test indicated no evidence that natural selection and genetic drift affect the natural population of V. chilensis. Using the Carica papaya genome as a reference, we identified critical SNPs/INDELs associated with putative genes. Most of the identified genes are related to stress responses (salt and nematode) and vegetative and reproductive development. These results will be helpful for future breeding and conservation programs of the Caricaceae family.

An Upgraded, Highly Saturated Linkage Map of Japanese Plum (Prunus salicina Lindl.), and Identification of a New Major Locus Controlling the Flavan-3-ol Composition in Fruits.

Japanese plum fruits are rich in phenolic compounds, such as anthocyanins and flavan-3-ols, whose contents vary significantly among cultivars. Catechin (C) and epicatechin (EC) are flavan-3-ol monomers described in the fruits of this species and are associated with bitterness, astringency, antioxidant capacity, and susceptibility to enzymatic mesocarp browning. In this study, we aimed to identify quantitative trait loci (QTL) associated with the content of flavan-3-ol in Japanese plum fruits. We evaluated the content of C and EC in the mesocarp and exocarp of samples from 79 and 64 seedlings of an F1 progeny (<'98-99' × 'Angeleno'>) in the first and second seasons, respectively. We also constructed improved versions of linkage maps from '98-99' and 'Angeleno,' presently called single-nucleotide polymorphisms (SNPs) after mapping the already available GBS reads to Prunus salicina Lindl. cv. 'Sanyueli' v2.0 reference genome. These data allowed for describing a cluster of QTLs in the cultivar, 'Angeleno,' associated with the flavan-3-ol composition of mesocarp and exocarp, which explain up to 100% of the C/EC ratio. Additionally, we developed a C/EC metabolic marker, which was mapped between the markers with the highest log of odds (LOD) scores detected by the QTL analysis. The C/EC locus was located in the LG1, at an interval spanning 0.70 cM at 108.30-108.90 cM. Our results suggest the presence of a novel major gene controlling the preferential synthesis of C or EC in the Japanese plum fruits. This study is a significant advance in understanding the regulation of synthesizing compounds associated with fruit quality, postharvest, and human health promotion.

A de novo transcriptome analysis revealed that photomorphogenic genes are required for carotenoid synthesis in the dark-grown carrot taproot.

Carotenoids are terpenoid pigments synthesized by all photosynthetic and some non-photosynthetic organisms. In plants, these lipophilic compounds are involved in photosynthesis, photoprotection, and phytohormone synthesis. In plants, carotenoid biosynthesis is induced by several environmental factors such as light including photoreceptors, such as phytochromes (PHYs) and negatively regulated by phytochrome interacting factors (PIFs). Daucus carota (carrot) is one of the few plant species that synthesize and accumulate carotenoids in the storage root that grows in darkness. Contrary to other plants, light inhibits secondary root growth and carotenoid accumulation suggesting the existence of new mechanisms repressed by light that regulate both processes. To identify genes induced by dark and repressed by light that regulate carotenoid synthesis and carrot root development, in this work an RNA-Seq analysis was performed from dark- and light-grown carrot roots. Using this high-throughput sequencing methodology, a de novo transcriptome model with 63,164 contigs was obtained, from which 18,488 were differentially expressed (DEG) between the two experimental conditions. Interestingly, light-regulated genes are preferably expressed in dark-grown roots. Enrichment analysis of GO terms with DEGs genes, validation of the transcriptome model and DEG analysis through qPCR allow us to hypothesize that genes involved in photomorphogenesis and light perception such as PHYA, PHYB, PIF3, PAR1, CRY2, FYH3, FAR1 and COP1 participate in the synthesis of carotenoids and carrot storage root development.

Transcriptome datasets from leaves and fruits of the sweet cherry cultivars 'Bing', 'Lapins' and 'Rainier'.

Sweet cherry fruits from different cultivars have different pre- and post-harvest qualities. Here we present the transcriptome profile datasets of leaves and mature fruits of three sweet cherry cultivars ('Bing', 'Lapin' and 'Rainier'). Using 454 GS-FLX technology (454 Life Sciences, Roche), transcriptomes of leaves and mature fruits were obtained from these cultivars. These transcriptome data sets are reported here.

RNA-seq Analysis of Salt-Stressed Versus Non Salt-Stressed Transcriptomes of Chenopodium quinoa Landrace R49.

Quinoa (Chenopodium quinoa Willd.), a model halophytic crop species, was used to shed light on salt tolerance mechanisms at the transcriptomic level. An RNA-sequencing analysis of genotype R49 at an early vegetative stage was performed by Illumina paired-ends method comparing high salinity and control conditions in a time-course pot experiment. Genome-wide transcriptional salt-induced changes and expression profiling of relevant salt-responsive genes in plants treated or not with 300 mM NaCl were analyzed after 1 h and 5 days. We obtained up to 49 million pairs of short reads with an average length of 101 bp, identifying a total of 2416 differentially expressed genes (DEGs) based on the treatment and time of sampling. In salt-treated vs. control plants, the total number of up-regulated and down-regulated genes was 945 and 1471, respectively. The number of DEGs was higher at 5 days than at 1 h after salt treatment, as reflected in the number of transcription factors, which increased with time. We report a strong transcriptional reprogramming of genes involved in biological processes like oxidation-reduction, response to stress and response to abscisic acid (ABA), and cell wall organization. Transcript analyses by real-time RT- qPCR supported the RNA-seq results and shed light on the contribution of roots and shoots to the overall transcriptional response. In addition, it revealed a time-dependent response in the expression of the analyzed DEGs, including a quick (within 1 h) response for some genes, suggesting a "stress-anticipatory preparedness" in this highly salt-tolerant genotype.

Nitrogen physiology of contrasting genotypes of Chenopodium quinoa Willd. (Amaranthaceae).

Quinoa has been highlighted as a promising crop to sustain food security. The selection of physiological traits that allow identification genotypes with high Nitrogen use efficiency (NUE) is a key factor to increase Quinoa cultivation. In order to unveil the underpinning mechanisms for N-stress tolerance in Quinoa, three genotypes with similar phenology, but different NUE were developed under high (HN) or low (LN) nitrogen conditions. N metabolism processes and photosynthetic performance were studied after anthesis and in correlation with productivity to identify principal traits related to NUE. We found that protein content, net photosynthesis and leaf dry-mass were determinant attributes for yield at both HN and LN conditions. Contrastingly, the enhancement of N related metabolites ([Formula: see text], proline, betacyanins) and processes related with re-assimilation of [Formula: see text], including an increment of glutamine synthetase activity and up-regulation of CqAMT1,1 transporter expression in leaves, were negatively correlated with grain yield at both N conditions. Biochemical aspects of photosynthesis and root biomass were traits exclusively associated with grain yield at LN. The impact of N supply on seed quality is discussed. These results provide new insights towards the understanding the N metabolism of Quinoa.

Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling.

This study reports the construction of high density linkage maps of Japanese plum (Prunus salicina Lindl.) using single nucleotide polymorphism markers (SNPs), obtained with a GBS strategy. The mapping population (An x Au) was obtained by crossing cv. "Angeleno" (An) as maternal line and cv. "Aurora" (Au) as the pollen donor. A total of 49,826 SNPs were identified using the peach genome V2.1 as a reference. Then a stringent filtering was carried out, which revealed 1,441 high quality SNPs in 137 An x Au offspring, which were mapped in eight linkage groups. Finally, the consensus map was built using 732 SNPs which spanned 617 cM with an average of 0.96 cM between adjacent markers. The majority of the SNPs were distributed in the intragenic region in all the linkage groups. Considering all linkage groups together, 85.6% of the SNPs were located in intragenic regions and only 14.4% were located in intergenic regions. The genetic linkage analysis was able to co-localize two to three SNPs over 37 putative orthologous genes in eight linkage groups in the Japanese plum map. These results indicate a high level of synteny and collinearity between Japanese plum and peach genomes.

Regeneration of highland papaya (Vasconcellea pubescens) from anther culture.

PREMISE OF THE STUDY: Vasconcellea pubescens is an important Caricaceae species cultivated in several countries of South America. The objective of this study was to investigate different media compositions and plant growth regulators to induce plant regeneration. METHODS: Anthers were cultured in Murashige and Skoog medium with varying concentrations of naphthalene acetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D) plus a cytokinin (N-(2-chloro-4-pyridyl)-N'-phenylurea). The effect of the basal medium supplemented with auxins and cytokinins on shoot regeneration from the induced calli was also evaluated. Addition of maltose to the basal medium was also tested. RESULTS: The combination of 0.54 µM NAA and 22.66 µM 2,4-D induced the highest rate of calli formation. Regeneration via organogenesis was obtained in Murashige and Skoog and Woody Plant Medium supplemented with maltose and containing 8.88 µM 6-benzylaminopurine, 5.71 µM indoleacetic acid, and 2.28 µM zeatin. DISCUSSION: The plant regeneration protocol reported here permits the development of haploid and double haploid plants that can be useful for propagation purposes, allow a better molecular understanding of the species, and facilitate the production of new cultivars.

Effect of sowing date and water availability on growth of plants of chia (Salvia hispanica L) established in Chile.

From 2010 to 2014 two trials were performed to assess the effect of sowing date (SD1, SD2) and irrigation treatments (IT1, IT2) on the growth of chia in central Chile, measuring leaf area (LA) and dry matter (DM) as primary parameters and relative growth rate (RGR), net assimilation rate (NAR), leaf weight ratio (LWR), crop growth rate (CGR) and specific leaf weight (SLW) as secondary parameters. Both LA and DM reached maximum values between 640 and 1150 accumulated degree days (ADD). However, LA and DM were 25% greater for sowing dates than for available water. Flowering date was also not affected by sowing date or water availability; plants flowered at 1140 and 942 ADD in SD1 and SD2 respectively, and at 499 ADD in the water availability trial. Sowing date had a significant effect on RGR 0.15 g g-1 d-1 for SD1 and 0.12 g g-1 d-1 for SD2 at 410 ADD. Greater water availability increased RGR by 60% compared to stressed plants, however NAR was similar between sowing dates with a tendency to greater values in SD2 plants; maximum values were recorded at 514 ADD in IT1 and IT2, with a tendency toward higher values in IT1. Thus, the primary growth variables LA, DM and flowering are genetically determined. However, the derived growth variables RGR, LWR, NAR, CGR and SLW were affected by sowing date and water availability, with significant differences at p≤ 0.05. The results showed that the sowing date and water availability influence significantly the growth parameters. The physiological component (NAR) show a strong influence on the growth rate of the chia (RGR), above the morphological component (SLW and LAR).

Evaluation of Morpho-Physiological Traits Adjustment of Prosopis tamarugo Under Long-Term Groundwater Depletion in the Hyper-Arid Atacama Desert.

Water extraction from the underground aquifers of the Pampa del Tamarugal (Atacama Desert, Chile) reduced the growing area of Prosopis tamarugo, a strict phreatic species endemic to northern Chile. The objective of this work was to evaluate the effect of various architectural and morpho-physiological traits adjustment of P. tamarugo subjected to three groundwater depletion intervals (GWDr): <1 m (control), 1-4 m and 6-9 m. The traits were evaluated at three levels, plant [height, trunk cross-section area, leaf fraction (fGCC), and crown size], organ [length of internodes, leaf mass per unit area (LMA), leaflet mass and area], and tissue level [wood density (WD), leaf 13C, 18O isotope composition (δ), and intrinsic water use efficiency (iWUE)]. In addition, soil water content (VWC) to 1.3 m soil depth, pre-dawn and midday water potential difference (ΔΨ), and stomatal conductance (gs) were evaluated. At the deeper GWDr, P. tamarugo experienced significant growth restriction and reduced fGCC, the remaining canopy had a significantly higher LMA associated with smaller leaflets. No differences in internode length and WD were observed. Values for δ13C and δ18O indicated that as GWDr increased, iWUE increased as a result of partial stomata closure with no significant effect on net assimilation over time. The morpho-physiological changes experienced by P. tamarugo allowed it to acclimate and survive in a condition of groundwater depletion, keeping a functional but diminished canopy. These adjustments allowed maintenance of a relatively high gs; ΔΨ was not different among GWDrs despite smaller VWC at greater GWDr. Although current conservation initiatives of this species are promising, forest deterioration is expected continue as groundwater depth increases.

RNA-seq analysis of the head-kidney transcriptome response to handling-stress in the red cusk-eel (Genypterus chilensis).

Stress is a primary contributing factor of fish disease and mortality in aquaculture. We have previously reported that the red cusk-eel (Genypterus chilensis), an important farmed marine fish, demonstrates a handling-stress response that results in increased juvenile mortality, which is mainly associated with skeletal muscle atrophy and liver steatosis. To better understand the systemic effects of stress on red cusk-eel immune-related gene expression, the present study assessed the transcriptomic head-kidney response to handling-stress. The RNA sequencing generated a total of 61,655,525 paired-end reads from control and stressed conditions. De novo assembly using the CLC Genomic Workbench produced 86,840 transcripts and created a reference transcriptome with a N50 of 1426bp. Reads mapped onto the assembled reference transcriptome resulted in the identification of 569 up-regulated and 513 down-regulated transcripts. Gene ontology enrichment analysis revealed a significant up-regulation of the biological processes, like response to stress, response to biotic stimulus, and immune response. Conversely, a significant down-regulation of biological processes is associated with metabolic processes. These results were validated by RT-qPCR analysis for nine candidate genes involved in the immune response. The present data demonstrated that short term stress promotes the immune innate response in the marine teleost G. chilensis. This study is an important step towards understanding the immune adaptive response to stress in non-model teleost species.

Transcriptomic analysis of the hepatic response to stress in the red cusk-eel (Genypterus chilensis): Insights into lipid metabolism, oxidative stress and liver steatosis.

Teleosts exhibit a broad divergence in their adaptive response to stress, depending on the magnitude, duration, and frequency of stressors and the species receiving the stimulus. We have previously reported that the red cusk-eel (Genypterus chilensis), an important marine farmed fish, shows a physiological response to stress that results in increased skeletal muscle atrophy mediated by over-expression of components of the ubiquitin proteasome and autophagy-lysosomal systems. To better understand the systemic effects of stress on the red cusk-eel metabolism, the present study assessed the transcriptomic hepatic response to repetitive handling-stress. Using high-throughput RNA-seq, 259 up-regulated transcripts were found, mostly associated with angiogenesis, gluconeogenesis, and triacylglyceride catabolism. Conversely, 293 transcripts were down-regulated, associated to cholesterol biosynthesis, PPARα signaling, fatty acid biosynthesis, and glycolysis. This gene signature was concordant with hepatic metabolite levels and hepatic oxidative damage. Moreover, the increased plasmatic levels of AST (aspartate aminotransferase), ALT (alanine aminotransferase) and AP (alkaline phosphatase), as well as liver histology suggest stress-induced liver steatosis. This study offers an integrative molecular and biochemical analysis of the hepatic response to handling-stress, and reveals unknown aspects of lipid metabolism in a non-model teleost.

Transcriptional Responses of Chilean Quinoa (Chenopodium quinoa Willd.) Under Water Deficit Conditions Uncovers ABA-Independent Expression Patterns.

HIGHLIGHTS R49 genotype displayed best performance on selected physiological parameters and highest tolerance to drought.R49 drought over-represented transcripts has exhibited 19% of genes (306 contigs) that presented no homology to published databases.Expression pattern for canonical responses to drought such as ABA biosynthesis and other genes induced in response to drought were assessed by qPCR. Global freshwater shortage is one of the biggest challenges of our time, often associated to misuse, increased consumption demands and the effects of climate change, paralleled with the desertification of vast areas. Chenopodium quinoa (Willd.) represents a very promising species, due to both nutritional content and cultivation under water constraint. We characterized drought tolerance of three Chilean genotypes and selected Genotype R49 (Salares ecotype) based upon Relative Water Content (RWC), Electrolyte Leakage (EL) and maximum efficiency of photosystem II (Fv/Fm) after drought treatment, when compared to another two genotypes. Exploratory RNA-Seq of R49 was generated by Illumina paired-ends method comparing drought and control irrigation conditions. We obtained 104.8 million reads, with 54 million reads for control condition and 51 million reads for drought condition. Reads were assembled in 150,952 contigs, were 31,523 contigs have a reading frame of at least 300 nucleotides (100 aminoacids). BLAST2GO annotation showed a 15% of genes without homology to NCBI proteins, but increased to 19% (306 contigs) when focused into drought-induced genes. Expression pattern for canonical drought responses such as ABA biosynthesis and other genes induced were assessed by qPCR, suggesting novelty of R49 drought responses.

De novo transcriptome assembly of 'Angeleno' and 'Lamoon' Japanese plum cultivars (Prunus salicina).

Japanese plum (Prunus salicina L.) is a fruit tree of the Rosaceae family, which is an economically important stone fruit around the world. Currently, Japanese plum breeding programs combine traditional breeding and plant physiology strategies with genetic and genomic analysis. In order to understand the flavonoid pathway regulation and to develop molecular markers associated to the fuit skin color (EST-SSRs), we performed a next generation sequencing based on Illumina Hiseq2000 platform. A total of 22.4 GB and 21 GB raw data were obtained from 'Lamoon' and 'Angeleno' respectively, corresponding to 85,404,726 raw reads to 'Lamoon' and 79,781,666 to 'Angeleno'. A total of 139,775,975 reads were filtered after removing low-quality reads and trimming the adapter sequences. De novo transcriptome assembly was performed using CLC Genome Workbench software and a total of 54,584 unique contigs were generated, with an N50 of 1343 base pair (bp) and a mean length of 829 bp. This work contributed with a specific Japanese plum skin transcriptome, providing two libraries of contrasting fruit skin color phenotype (yellow and red) and increasing substantially the GB of raw data available until now for this specie.

Salares versus coastal ecotypes of quinoa: Salinity responses in Chilean landraces from contrasting habitats.

Quinoa (Chenopodium quinoa Willd.) is a highly salt-tolerant species subdivided into five ecotypes and exhibiting broad intra-specific differences in tolerance levels. In a greenhouse study, Chilean landraces belonging either to the salares (R49) or coastal lowlands (VI-1, Villarrica) ecotype with contrasting agro-ecological origins were investigated for their responses to high salinity. The effects of two levels of salinity, 100 (T1) and 300 (T2) mM NaCl, on plant growth and on some physiological parameters were measured. Leaf and root Na(+) accumulation differed among landraces. T2 reduced growth and seed yield in all landraces with maximum inhibition relative to controls in R49. Salinity negatively affected chlorophyll and total polyphenol content (TPC) in VI-1 and Villarrica but not R49. Germination on saline or control media of seeds harvested from plants treated or not with NaCl was sometimes different; the best performing landrace was R49 insofar as 45-65% of seeds germinated on 500 mM NaCl-containing medium. In all landraces, average seedling root length declined strongly with increasing NaCl concentration, but roots of R49 were significantly longer than those of VI-1 and Villarrica up to 300 mM NaCl. Salt caused increases in seed TPC relative to controls, but radical scavenging capacity was higher only in seeds from T2 plants of R49. Total SDS-extractable seed proteins were resolved into distinct bands (10-70 kDa) with some evident differences between landraces. Salt-induced changes in protein patterns were landrace-specific. The responses to salinity of the salares landrace are discussed in relation to its better adaptation to an extreme environment.

mRNA-seq reveals skeletal muscle atrophy in response to handling stress in a marine teleost, the red cusk-eel (Genypterus chilensis).

BACKGROUND: Fish reared under intensive conditions are repeatedly exposed to stress, which negatively impacts growth. Although most fish follow a conserved pattern of stress response, with increased concentrations of cortisol, each species presents specificities in the cell response and stress tolerance. Therefore, culturing new species requires a detailed knowledge of these specific responses. The red cusk-eel (Genypterus chilensis) is a new economically important marine species for the Chilean aquaculture industry. However, there is no information on the stress- and cortisol-induced mechanisms that decrease skeletal muscle growth in this teleost. RESULTS: Using Illumina RNA-seq technology, skeletal muscle sequence reads for G. chilensis were generated under control and handling stress conditions. Reads were mapped onto a reference transcriptome, resulting in the in silico identification of 785 up-regulated and 167 down-regulated transcripts. Gene ontology enrichment analysis revealed a significant up-regulation of catabolic genes associated with skeletal muscle atrophy. These results were validated by RT-qPCR analysis for ten candidates genes involved in ubiquitin-mediated proteolysis, autophagy and skeletal muscle growth. Additionally, using a primary culture of fish skeletal muscle cells, the effect of cortisol was evaluated in relation to red cusk-eel skeletal muscle atrophy. CONCLUSIONS: The present data demonstrated that handling stress promotes skeletal muscle atrophy in the marine teleost G. chilensis through the expression of components of the ubiquitin-proteasome and autophagy-lysosome systems. Furthermore, cortisol was a powerful inductor of skeletal muscle atrophy in fish myotubes. This study is an important step towards understanding the atrophy system in non-model teleost species and provides novel insights on the cellular and molecular mechanisms that control skeletal muscle growth in early vertebrates.

Characterization of the acetohydroxyacid synthase multigene family in the tetraploide plant Chenopodium quinoa

Background Currently, the technology called Clearfield® is used in the development of crops resistant to herbicides that inhibit the enzyme acetohydroxy acid synthase (AHAS, EC 2.2.1.6). AHAS is the first enzyme of the biosynthetic pathway that produces the branched-chain of the essential amino acids valine, leucine, and isoleucine. Therefore, multiple copies of the AHAS gene might be of interest for breeding programs targeting herbicide resistance. In this work, the characterization of the AHAS gene was accomplished for the Chenopodium quinoa Regalona-Baer cultivar. Cloning, sequencing, and Southern blotting were conducted to determine the number of gene copies. Results The presence of multiple copies of the AHAS gene as has been shown previously in several other species is described. Six copies of the AHAS gene were confirmed with Southern blot analyses. CqHAS1 and CqAHAS2 variants showed the highest homology with AHAS mRNA sequences found in the NR Database. A third copy, CqAHAS3, shared similar fragments with both CqAHAS1 and CqAHAS2, suggesting duplication through homeologous chromosomes pairing. Conclusions The presence of multiple copies of the gene AHAS shows that gene duplication is a common feature in polyploid species during evolution. In addition, to our knowledge, this is the first report of the interaction of sub-genomes in quinoa.