Genetic diversity in Mexican wild populations of the Great Curassow (Crax rubra) / Diversidad genética en poblaciones silvestres mexicanas del hocofaisán (Crax rubra)

Abstract The Great Curassow (Crax rubra) is a Neotropical bird with a wide distribution; it is classified under different threat categories and is listed as a vulnerable species by the IUCN. The Official Mexican Standard, the NOM-059-SEMARNAT-2010, indicates that the Great Curassow is a threatened species, and the subspecies Crax rubra griscomi, which is restricted to the island of Cozumel, is classified as critically endangered. Habitat loss and fragmentation, hunting, overexploitation, and illegal trade are among the main factors that have placed the bird at an endangered status. The objective of the present study was to determine the genetic structure and variation of the species within the Mexican populations of Crax rubra by using three mitochondrial markers, and one nuclear marker (COI, ND2, Cyt b, and MUSK). We used 47 samples obtained by noninvasive collection (feathers) including the two different color phases of the female plumage: dark brown and barred (rare in Mexico). Gene flow between the remaining populations is recent and extensive, even between the continental and the island population (C. r. griscomi). The results indicate that the subspecies C. r. rubra and C. r. griscomi do not present a marked genetic differentiation because the second exhibits an exclusive haplotype and a shared haplotype. With this study, we provide the first genetic-geographic approximation of the curassow in Mexico, where a gradual geographic differentiation is observed between the western and eastern populations of the Isthmus of Tehuantepec, and we provide a baseline for future studies. Finally, the information obtained indicates that important genetic diversity persists in the Mexican populations of the Great Curassow and that sufficient conservation within the ecosystems of these subspecies can be obtained by protecting them from overexploitation and by conserving and restoring their habitat.

Resumen El hocofaisán (Crax rubra) es un ave de la región Neotropical con amplia distribución, que se encuentra en diferentes categorías de riesgo, por la IUCN está catalogada como una especie Vulnerable. A nivel nacional, dentro de la NOM-059-SEMARNAT-2010 está considerada como una especie amenazada, y la subespecie Crax rubra griscomi restringida a la isla de Cozumel, está categorizada como en peligro de extinción. Entre los factores principales por los que se encuentra en grave riesgo, destacan la pérdida y fragmentación del hábitat, la cacería, la sobreexplotación, la extracción y el comercio ilegal. El objetivo del presente estudio es conocer la estructura y variación genética de la especie dentro de las poblaciones silvestres mexicanas de Crax rubra, mediante el uso de tres marcadores mitocondriales y uno nuclear (COI, ND2, Cyt b y MUSK). A partir de 47 muestras obtenidas mediante colecta no invasiva (plumas) que incluyen las dos fases de plumaje de la hembra: café oscura y barrada (rara en México). Se observó que el flujo génico entre las poblaciones remanentes es reciente y extenso, incluso entre las poblaciones continentales y la isleña (C. r. griscomi). Los resultados indican que las subespecies C. r. rubra y C. r. griscomi no presentan una marcada diferenciación genética dado que la segunda presentó un haplotipo exclusivo y uno compartido. Con el presente estudio brindamos la primera aproximación genético-geográfica del hocofaisán en México y una línea de base para futuros estudios, en el que se observa una diferenciación geográfica gradual entre las poblaciones del oeste y del este del Istmo de Tehuantepec. Finalmente, la información obtenida indica que en las poblaciones mexicanas del hocofaisán persiste una diversidad genética importante y que su conservación en los ecosistemas puede ser suficiente mediante la protección a la sobreexplotación, la conservación y restauración de su hábitat.

Mapping QTLs for drought tolerance in a SEA 5 x AND 277 common bean cross with SSRs and SNP markers

Abstract The common bean is characterized by high sensitivity to drought and low productivity. Breeding for drought resistance in this species involves genes of different genetic groups. In this work, we used a SEA 5 x AND 277 cross to map quantitative trait loci associated with drought tolerance in order to assess the factors that determine the magnitude of drought response in common beans. A total of 438 polymorphic markers were used to genotype the F8 mapping population. Phenotyping was done in two greenhouses, one used to simulate drought and the other to simulate irrigated conditions. Fourteen traits associated with drought tolerance were measured to identify the quantitative trait loci (QTLs). The map was constructed with 331 markers that covered all 11 chromosomes and had a total length of 1515 cM. Twenty-two QTLs were discovered for chlorophyll, leaf and stem fresh biomass, leaf biomass dry weight, leaf temperature, number of pods per plant, number of seeds per plant, seed weight, days to flowering, dry pod weight and total yield under well-watered and drought (stress) conditions. All the QTLs detected under drought conditions showed positive effects of the SEA 5 allele. This study provides a better understanding of the genetic inheritance of drought tolerance in common bean.

Associations between DRDs and schizophrenia in a Korean population: multi-stage association analyses

The dysregulation of the dopaminergic system has been implicated in the pathophysiology of major psychosis, including schizophrenia, with dopamine receptor genes (DRDs) presently targeted as the most promising candidate genes. We investigated DRD1-5 for association with schizophrenia using a multi-stage approach in a Korean sample. One hundred forty-two SNPs in DRD1-5 were selected from the dbSNP, and the associations of each SNP were then screened and typed by MALDI-TOF mass spectrometry using pooled DNA samples from 150 patients with major psychosis and 150 controls. Each of the suggested SNPs was then genotyped and tested for an association within the individual samples comprising each pool. Finally, the positively associated SNPs were genotyped in an extended sample of 270 patients with schizophrenia and 350 controls. Among the 142 SNPs, 88 (62%) SNPs in our Korean population were polymorphic. At the pooling stage, 10 SNPs (DRD1: 2, DRD2: 3, and DRD4: 5) were identified (P < 0.05). SNPs rs1799914 of DRD1 (P = 0.046) and rs752306 of DRD4 (P = 0.017) had significantly different allele frequencies in the individually genotyped samples comprising the pool. In the final stage, with the extended sample, the suggestive association of DRD4 with rs752306 was lost, but the association of DRD1 with rs1799914 gained greater significance (P = 0.017). In these large-scale multi-stage analyses, we were able to find a possible association between DRD1 and schizophrenia. These findings suggested the potential contribution of a multi-step strategy for finding genes related to schizophrenia.

Genetic diversity within and between broodstocks of the white shrimp Litopenaeus vannamei (Boone, 1931) (Decapoda, Penaeidae) and its implication for the gene pool conservation

Genetic variation within and between fifteen closed broodstock lines of the Pacific white shrimp Litopenaeus vannamei, reared at different hatcheries in the Brazilian coast, was assessed by RAPD analysis. Fifty two polymorphic loci were identified when a set of five decamer primers was used in PCR. The genetic diversity analysis within lines evidenced genetic variation loss probably related to bottleneck effects and inbreeding. In addition, the genetic divergence values between the different samples appear to reflect the initial founder composition of such stocks, in some cases, sharing a common origin, suggesting a putative importance of interbreeding for the establishment of genetic improvement programs for these broodstocks. The genetic variation monitoring appears to be helpful to the gene pool conservation of this aquaculture species, mainly if considered its exotic status in Brazil and the current impossibility of new introduction of wild individuals.

A variação genética existente dentro e entre quinze linhagens fechadas de reprodutores do camarão branco Litopenaeus vannamei, mantidas em diferentes laboratórios de larvicultura na costa brasileira, foi estudada utilizando análises RAPD. Através de um conjunto de cinco iniciadores decâmeros em PCR, foram identificados 52 locos polimórficos. A análise da diversidade genética dentro de cada linhagem evidenciou perda da variação genética provavelmente devida a efeitos de bottleneck e endocruzamento. Em adição, os valores de divergência genética entre as diferentes linhagens parecem refletir a composição inicial de fundação desses estoques, em alguns casos, compartilhando uma origem comum, sugerindo uma importância potencial do exo-cruzamento para estabelecer programas de melhoramento genético baseado nessas linhagens reprodutoras. O monitoramento da variação genética será muito útil para a conservação do conjunto gênico desta espécie de aquacultura, especialmente se for considerado seu status exótico no Brasil e que atualmente é impossível a realização de novas introduções de indivíduos selvagens.

Genetic diversity within and between broodstocks of the white shrimp Litopenaeus vannamei (Boone, 1931) (Decapoda, Penaeidae) and its implication for the gene pool conservation

Genetic variation within and between fifteen closed broodstock lines of the Pacific white shrimp Litopenaeus vannamei, reared at different hatcheries in the Brazilian coast, was assessed by RAPD analysis. Fifty two polymorphic loci were identified when a set of five decamer primers was used in PCR. The genetic diversity analysis within lines evidenced genetic variation loss probably related to bottleneck effects and inbreeding. In addition, the genetic divergence values between the different samples appear to reflect the initial founder composition of such stocks, in some cases, sharing a common origin, suggesting a putative importance of interbreeding for the establishment of genetic improvement programs for these broodstocks. The genetic variation monitoring appears to be helpful to the gene pool conservation of this aquaculture species, mainly if considered its exotic status in Brazil and the current impossibility of new introduction of wild individuals.

A variação genética existente dentro e entre quinze linhagens fechadas de reprodutores do camarão branco Litopenaeus vannamei, mantidas em diferentes laboratórios de larvicultura na costa brasileira, foi estudada utilizando análises RAPD. Através de um conjunto de cinco iniciadores decâmeros em PCR, foram identificados 52 locos polimórficos. A análise da diversidade genética dentro de cada linhagem evidenciou perda da variação genética provavelmente devida a efeitos de bottleneck e endocruzamento. Em adição, os valores de divergência genética entre as diferentes linhagens parecem refletir a composição inicial de fundação desses estoques, em alguns casos, compartilhando uma origem comum, sugerindo uma importância potencial do exo-cruzamento para estabelecer programas de melhoramento genético baseado nessas linhagens reprodutoras. O monitoramento da variação genética será muito útil para a conservação do conjunto gênico desta espécie de aquacultura, especialmente se for considerado seu status exótico no Brasil e que atualmente é impossível a realização de novas introduções de indivíduos selvagens.

Allelic relationships of anthracnose (Colletotrichum lindemuthianum) resistance in the common bean (Phaseolus vulgaris L.) cultivar Michelite and the proposal of a new anthracnose resistance gene, Co-11

The genetic resistance of Phaseolus vulgaris L. cultivar Michelite to races 8 and 64 of Colletotrichum lindemuthianum, causal agent of bean anthracnose, was characterized. Crosses were made between Michelite and Mexico 222 cultivars and the F2 population was inoculated with race 64 in order to study the inheritance of resistance to anthracnose in Michelite. The segregation of F2 population fitted in a ratio of 3R:1S, showing the presence of a dominant gene in Michelite gene conditioning resistance to race 64. Allelism tests were conducted with F2 populations derived from crosses between Michelite and AB 136, AND 277, BAT 93, Cornell 49-242, G 2333, Kaboon, Mexico 222, Michigan Dark Red Kidney (MRDK), Ouro Negro, Perry Marrow, PI 207262, TO, TU, and Widusa. All the cultivars (except Mexico 222) were resistant to race 64. While F2 derived from the Michelite x Mexico 222 was inoculated with race 8. Additionally, allelism tests indicated that the gene present in Michelite is independent from Co-1, Co-2, Co-3, Co-4, Co-5, Co-6, Co-7, Co-9 and Co-10 genes. The monogenic inheritance observed in Michelite and the independence of this gene from those previously characterized allow the authors to propose that the anthracnose resistant gene in Michelite should be named Co-11.

Immunoscreening and Identification of Chinese HCV Genomic cDNA ? gt11 Library / 第二军医大学学报

Hepatitis C virus (HCV) is a major causative agent for sporadic and post-transfusion hepatitis, which frequently progresses into chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. In order to clarify the genomic variations and the structural characteristics of Chinese HCV isolate, we extracted HCV genomic RNA from plasma specimens of Chinese hepatitis C (HC) patients, reverse-transcribed to HCV cDNA with random primers and constructed successfully an HCV cDNA R gt11 library of Chinese type. Two positive clones (Q349 and Q653) were selected by immunoscreening from the library and subcloned into plasmid vector pUC18. Sequence analyses indicated that Q349 was derived from core region (positions 554-902) of HCV genome while Q653 was from NS3 region (positions 4175-4827) corresponding with the prototype HCV nucleotide sequence. The homologies of Q349 and Q653 with the equivalent sequences of HCV prototype were 86.8% and 80.2% at the nucleotide level, and 97.3% and 93.1% at the amino acid level, respectively. It was found that Chinese HCV clones had higher homologies with Japanese HCV isolates, and should belong to HCV group II. Specificity test proved that the encoded peptides of the 2 Chinese HCV cDNA clones reacted specifically with sera from HC patients and had no reaction with sera from healthy individuals. More importantly, clone Q653 showed higher positive reaction rates with Chinese HC sera (95.8%) than those with Japanese ones (85.7%), which strongly suggests that the sequences from Chinese HCV genome (especially from NS regions) would be more suitable for primer designing or peptide synthesis for the use in the detection of HCV infection among Chinese people.