Leveraging barrel medic genome sequence for the development and use of genomic resources for genetic analysis and breeding in legumes

BACKGROUND: A total of 62,591 cowpea expressed sequence tags (ESTs) were BLAST aligned to the whole-genome sequence of barrel medic (Medicago truncatula) to develop conserved intron scanning primers (CISPs). The efficacy of the primers was tested across 10 different legumes and on different varieties of cowpea, chickpea, and pigeon pea. Genetic diversity was assessed using the same primers on different cowpea genotypes. Singlenucleotide polymorphisms (SNPs) were detected, which were later converted to length polymorphism markers for easy genotyping. CISPs developed in this study were used in tagging resistance to bacterial leaf blight disease in cowpea. RESULTS: A total of 1262 CISPs were designed. The single-copy amplification success rates using these primers on 10 different legumes and on different varieties of cowpea, chickpea, and pigeon pea were approximately 60% in most of the legumes except soybean (47%) and peanut (37%). Genetic diversity analysis of 35 cowpea genotypes using 179 CISPs revealed 123 polymorphic markers with PIC values ranging from 0.05 to 0.59. Potential SNPs identified in cowpea, chickpea, and pigeon pea were converted to PCR primers of various sizes for easy genotyping. Using the markers developed in this study, a genetic linkage map was constructed with 11 linkage groups in cowpea. QTL mapping with 194 F3 progeny families derived from the cross C-152 × V-16 resulted in the identification of three QTLs for resistance to bacterial leaf blight disease. Conclusions: CISPs were proved to be efficient markers to identify various other marker classes like SNPs through comparative genomic studies in lesser studied crops and to aid in systematic sampling of the entire genome for well-distributed markers at low cost

Genetic variants associated with fetal hemoglobin levels show the diverse ethnic origin in Colombian patients with sickle cell anemia / Las variantes genéticas asociadas con niveles de hemoglobina fetal señalan diversos orígenes étnicos en pacientes colombianos con anemia falciforme.

Introduction: Fetal hemoglobin is an important factor in modulating the severity of sickle cell anemia. Its level in peripheral blood underlies strong genetic determination. Associated loci with increased levels of fetal hemoglobin display population-specific allele frequencies. Objective: We investigated the presence and effect of known common genetic variants promoting fetal hemoglobin persistence (rs11886868, rs9399137, rs4895441, and rs7482144) in 60 Colombian patients with sickle cell anemia. Materials and methods: Four single nucleotide polymorphisms (SNP) were genotyped by restriction fragment length polymorphisms (RFLP) and the use of the TaqMan procedure. Fetal hemoglobin (HbF) from these patients was quantified using the oxyhemoglobin alkaline denaturation technique. Genotype frequencies were compared with frequencies reported in global reference populations. Results: We detected genetic variants in the four SNPs, reported to be associated with higher HbF levels for all four SNPs in the Colombian patients. Genetic association between SNPs and HbF levels did not reach statistical significance. The frequency of these variants reflected the specific ethnic make-up of our patient population: A high prevalence of rs7482144-'A' reflects the West-African origin of the sickle cell mutation, while high frequencies of rs4895441-'G' and rs11886868-'C' point to a significant influence of an Amerindian ethnic background in the Colombian sickle cell disease population. Conclusion: These results showed that in the sickle cell disease population in Colombia there is not a unique genetic background, but two (African and Amerindian). This unique genetic situation will provide opportunities for a further study of these loci, such as fine-mapping and molecular-biological investigation. Colombian patients are expected to yield a distinctive insight into the effect of modifier loci in sickle cell disease.

Introducción. La hemoglobina fetal es un importante factor modulador de la gravedad de la anemia falciforme, cuya expresión está muy condicionada por el factor genético. Los loci asociados con el incremento de la hemoglobina fetal pueden presentar frecuencias alélicas específicas para cada población. Objetivo. Investigar la presencia y el efecto de las variantes genéticas rs11886868, rs9399137, rs4895441 y rs7482144 asociadas con la persistencia de hemoglobina fetal, en 60 pacientes colombianos con anemia falciforme. Materiales y métodos. Se hizo la genotipificación de los polimorfismos de nucleótido simple ( Single Nucleotide Polymorphisms, SNP) mediante la técnica de polimorfismos de longitud de fragmentos de restricción ( Restriction Fragment Length Polymorphisms, RFLP) y el procedimiento TaqMan. La hemoglobina fetal (HbF) se cuantificó utilizando la técnica de desnaturalización alcalina de la oxihemoglobina. Las frecuencias genotípicas se compararon con las reportadas en poblaciones de referencia global. Resultados. Se observaron variantes genéticas ya reportadas para aumento de HbF en los cuatro SNP. La asociación genética entre los SNP y el incremento de la HbF no alcanzó significancia estadística. La frecuencia de estos alelos reflejó la siguiente composición específica en esta muestra de pacientes colombianos: una gran prevalencia de rs7482144-'A', lo que indica que el origen de la mutación para la anemia falciforme es África occidental, y una gran frecuencia de rs4895441-'G' y rs11886868-'C', lo que denota la influencia significativa del origen genético amerindio. Conclusión. Los resultados evidenciaron que la población con anemia falciforme de Colombia no tiene un único origen genético, sino que existen dos (africano y amerindio). Esta situación genética única ofrece la oportunidad de llevar a cabo un estudio más amplio de estos loci a nivel molecular. Se espera que el estudio de pacientes colombianos permita una visión diferente del efecto de los loci modificadores en esta enfermedad.

Reverse Cardiac Remodeling: A Marker of Better Prognosis in Heart Failure / Reversão da Remodelação Cardíaca: um Marcador de Melhor Prognóstico na Insuficiência Cardíaca

In heart failure syndrome, myocardial dysfunction causes an increase in neurohormonal activity, which is an adaptive and compensatory mechanism in response to the reduction in cardiac output. Neurohormonal activity is initially stimulated in an attempt to maintain compensation; however, when it remains increased, it contributes to the intensification of clinical manifestations and myocardial damage. Cardiac remodeling comprises changes in ventricular volume as well as the thickness and shape of the myocardial wall. With optimized treatment, such remodeling can be reversed, causing gradual improvement in cardiac function and consequently improved prognosis.

Na síndrome da insuficiência cardíaca, a disfunção do miocárdio gera um aumento da atividade neuro-hormonal, que é um mecanismo adaptativo e compensatório em resposta à redução do débito cardíaco. A atividade neuro-hormonal é estimulada inicialmente na tentativa de manter o paciente compensado, mas quando permanece aumentada, contribui para a intensificação das manifestações clínicas e do dano miocárdico. A remodelação cardíaca consiste nas alterações no volume do ventrículo bem como na espessura e forma da parede do miocárdio. Com o tratamento otimizado, pode ocorrer a reversão da remodelação, com melhora gradual da função cardíaca e consequente melhora do prognóstico.

Analysis of monotherapy prostate brachytherapy in patients with prostate cancer. Initial PSA and Gleason are important for recurrence?

Purpose To evaluate the clinical outcome of a cohort of localized prostate cancer patients treate with 125-I permanent brachytherapy at the São José Hospital – CHLC, Lisbon. Materials and Methods A retrospective analysis was carried out on 429 patients with low and intermediate-risk of prostate adenocarcinoma, according to the recommendations of the EORTC, who underwent 125I brachytherapies in intraoperative dosimetry “real-time” system between September 2003 and September 2013. Results The mean follow-up was 71.98 months. Biochemical relapse of disease by rising PSA (Phoenix criterion) was observed in 18 patients (4.2%). Through the application of Kaplan-Meier survival curves in this sample, the rate of survival at 6 years without biochemical relapse was higher than 95%. By Iog rank test comparing biochemical relapse with initial PSA (15-10 and <10) and Gleason values (7 and <7), there was no statistical difference (P=0.830) of the initial PSA in the probability of developing biochemical relapse. In relation to Gleason score, it was noted a statistical difference (P<0.05), demonstrating that patients with Gleason 7 are more likely to develop biochemical relapse. Conclusions Brachytherapy as monotherapy is at present an effective choice in the treatment of localized prostate adenocarcinoma. Biochemical relapses are minimal. The initial PSA showed no statistically difference in the rate of relapses, unlike the value Gleason, where it was demonstrated that patients with Gleason 7 have a higher probability of biochemical relapse. Cases with PSA bounce should be controlled before starting a salvage treatment. .

Identification of groundnut (Arachis hypogaea) SSR markers suitable for multiple resistance traits QTL mapping in African germplasm

Background This study aimed to identify and select informative Simple Sequence Repeat (SSR) markers that may be linked to resistance to important groundnut diseases such as Early Leaf Spot, Groundnut Rosette Disease, rust and aflatoxin contamination. To this end, 799 markers were screened across 16 farmer preferred and other cultivated African groundnut varieties that are routinely used in groundnut improvement, some with known resistance traits. Results The SSR markers amplified 817 loci and were graded on a scale of 1 to 4 according to successful amplification and ease of scoring of amplified alleles. Of these, 376 markers exhibited Polymorphic Information Content (PIC) values ranging from 0.06 to 0.86, with 1476 alleles detected at an average of 3.7 alleles per locus. The remaining 423 markers were either monomorphic or did not work well. The best performing polymorphic markers were subsequently used to construct a dissimilarity matrix that indicated the relatedness of the varieties in order to aid selection of appropriately diverse parents for groundnut improvement. The closest related varieties were MGV5 and ICGV-SM 90704 and most distant were Chalimbana and 47-10. The mean dissimilarity value was 0.51, ranging from 0.34 to 0.66. Discussion Of the 376 informative markers identified in this study, 139 (37%) have previously been mapped to the Arachis genome and can now be employed in Quantitative Trait Loci (QTL) mapping and the additional 237 markers identified can be used to improve the efficiency of introgression of resistance to multiple important biotic constraints into farmer-preferred varieties of Sub-Saharan Africa.

Pleiotropic effects of the sdw1 locus in barley populations representing different rounds of recombination

Background In the present study populations, representing different rounds of recombination were used for the analysis of phenotypic effects associated with the sdw1/denso locus. Other studies have mostly focused only on one type of population. Many different QTLs mapped at the same position as the sdw1/denso locus may indicate a pleiotropy of this gene or a tight linkage between genes conditioning quantitative traits. To date, results of studies have not unequivocally proven either of these two phenomena. Results Both breeding and molecular mapping experiments were undertaken to examine 200 single seed descent (SSD) and 60 doubled haploid (DH) lines obtained from the Maresi (with a semi-dwarfing gene) and Pomo cross combination. They were evaluated for the type of juvenile growth habit and certain agronomic traits were measured after harvesting. The estimates of mean values, standard errors and significance of effects were analyzed. In terms of the analyzed characteristics, the greatest variability was obtained for genotypes with the prostrate growth habit. Microsatellite markers (SSR) were also used to identify co-segregation with the sdw1/denso locus and Bmag0013, Bmag0877, Bmag0306b markers were linked the closest. A partial linkage map of chromosome 3H with the sdw1/denso semi-dwarfing gene was constructed and QTLs were identified. Conclusions Our experiments confirmed the impact of the semi-dwarfing gene on plant height, heading and flowering date both in SSD and DH populations, which may indicate pleiotropy. Moreover, a partial linkage between sdw1/denso locus and grain weight per spike and 1000-grain weight was found in the SSD population.

Caracterização molecular da resistência a inseticidas químicos em populações de Aedes aegypti / Molecular characterization of chemical insecticide resistance in Aedes aegypti

A resistência a inseticidas químicos representa uma das maiores limitações em programas de controle de insetos. Dentre os diferentes mecanismos que levam o inseto à resistência, os principais são as alterações do sítio-alvo e a via metabólica. Essa última é representada por enzimas de detoxificação, como esterases, glutationas S-tranferases e oxidases. Mais de 200 genes de detoxificação foram identificados em Ae. aegypti, o que torna complexa a identificação mutações pontuais envolvidas neste mecanismo. Sendo assim, o presente estudo teve como objetivo identificar e caracterizar genes envolvidos na resistência a inseticidas em Ae. aegypti. Para o mapeamento de loci de herança quantitativa (QTL), microssatélites foram utilizados para genotipar indivíduos das gerações F0 e F2, provenientes dos cruzamentos entre a linhagem resistente ao temephos RecR, e as susceptíveis Red e MoyoD. Um QTL foi mapeada no cromossomo II, respondendo a aproximadamente 97 por cento da variação da resistência ao temephos. Diferentes genes de esterase foram identificados na região de QTL, demonstrando o envolvimento de outros genes de resistência na RecR, além daqueles identificados em trabalho prévio, com um chip de microarranjos. O presente trabalho estudou a região 5' UTR do gene da oxidase CYP6N12, identificado previamente como superexpresso na linhagem RecR. A análise da região revelou na RecR a presença de um alelo (R), com 14 pb a mais, que encontrava-se associado com a resistência ao temephos (fR= 0,625). Enquanto que, o mesmo alelo foi encontrado em menor frequência na RecRev (fR = 0,12). A presença desse alelo induziu a uma expressão do gene em 10 vezes na RecR e 4 vezes na RecRev. O sequenciamento de parte do gene da acetilcolinesterase de mosquitos da RecR e da linhagem susceptível Rockefeller, demonstrou a ausência de mutações nas duas colônia. Por fim, mutações no gene do canal de sódio foram avaliadas em populações de Ae. aegypti do Ceará, resistentes à cipermetrina. A mutação Ile1011Met foi encontrada em associação com a resistência em indivíduos do Crato, enquanto que o alelo mutante 1016Ile foi detectado pela primeira vez no Crato e Juazeiro do Norte. A identificação e mapeamento dos genes de resistência a inseticidas químicos em Ae. aegypti poderão contribuir para o desenvolvimento de novos métodos de diagnóstico e manejo da resistência.

QTL mapping for physiology, yield and plant architecture traits in cotton (Gossypium hirsutum L. ) grown under well-watered versus water-stress conditions

Increasing scarcity of irrigation water is a major threat to sustainable production of cotton (Gossypium hirsutum L.). Identifying genomic regions contributing to abiotic stress tolerance will help develop cotton cultivars suitable for water-limited regions through molecular marker-assisted breeding. A molecular mapping F2 population was derived from an intraspecific cross of the drought sensitive G. hirsutum cv. FH-901 and drought tolerant G. hirsutum cv. RH-510. Field data were recorded on physiological traits (osmotic potential and osmotic adjustment); yield and its component traits (seedcotton yield, number of bolls/plant and boll weight); and plant architecture traits (plant height and number of nodes per plant) for F2, F2:3 and F2:4 generations under well-watered versus water-limited growth conditions. The two parents were surveyed for polymorphism using 6500 SSR primer pairs. Joinmap3.0 software was used to construct linkage map with 64 polymorphic markers and it resulted into 35 markers mapped on 12 linkage groups. QTL analysis was performed by composite interval mapping (CIM) using QTL Cartographer2.5 software. In total, 7 QTLs (osmotic potential 2, osmotic adjustment 1, seedcotton yield 1, number of bolls/plant 1, boll weight 1 and plant height 1) were identified. There were three QTLs (qtlOP-2, qtlOA-1, and qtlPH-1) detected only in water-limited conditions. Two QTLs (qtlSC-1 and qtlBW-1) were detected for relative values. Two QTLs (qtlOP-1 and qtlBN-1) were detected for well-watered treatment. Significant QTLs detected in this study can be employed in MAS for molecular breeding programs aiming at developing drought tolerant cotton cultivars.

Detection of single copy sequences using BAC-FISH and C-PRINS techniques in sunflower chromosomes

Bacterial artificial chromosome-fluorescence in situ hybridization (BAC-FISH) and cycling-primed in situ labeling (C-PRINS) techniques were evaluated for integration of physical and genetic maps of sunflower (Helianthus annuus L.). Single-site SSR markers were selected from three linkage groups of a high-density sunflower genetic map. This selection was based on previously identified QTL associated to S. sclerotiorum. These markers were used to select BACs contaning single copy sequences for BAC-FISH aplication. Blocking of highly dispersed repetitive sunflower sequences reduced unspecific hybridization, and allowed the detection of specific signals for BACs containing SSR markers HA4222 and HA2600, anchored to LG 16 and LG 10, respectively. Single-site FISH signal detection was optimized by adjusting the relative quantity and quality of unlabelled repetitive sequences present in the blocking DNA. The SSR marker ORS1247 anchored to the LG 17 was detected by C-PRINS, which yielded fluorescence signals that were specific and intense. This progress in localizing single-copy sequences using BAC-FISH and indirect C-PRINS strategies in sunflower will facilitate the integration of genetic and physical maps, allowing the identification of chromosomes containing key genes and/or QTL associated to agronomic important traits in sunflower.

Zero-inflated Poisson regression models for QTL mapping applied to tick-resistance in a Gyr x Holstein F2 population

Nowadays, an important and interesting alternative in the control of tick-infestation in cattle is to select resistant animals, and identify the respective quantitative trait loci (QTLs) and DNA markers, for posterior use in breeding programs. The number of ticks/animal is characterized as a discrete-counting trait, which could potentially follow Poisson distribution. However, in the case of an excess of zeros, due to the occurrence of several noninfected animals, zero-inflated Poisson and generalized zero-inflated distribution (GZIP) may provide a better description of the data. Thus, the objective here was to compare through simulation, Poisson and ZIP models (simple and generalized) with classical approaches, for QTL mapping with counting phenotypes under different scenarios, and to apply these approaches to a QTL study of tick resistance in an F2 cattle (Gyr x Holstein) population. It was concluded that, when working with zero-inflated data, it is recommendable to use the generalized and simple ZIP model for analysis. On the other hand, when working with data with zeros, but not zero-inflated, the Poisson model or a data-transformation-approach, such as square-root or Box-Cox transformation, are applicable.

The genetic dissection of quantitative traits in crops

Most traits of interest in plant breeding show quantitative inheritance, which complicate the breeding process since phenotypic performances only partially reflects the genetic values of individuals. The genetic variation of a quantitative trait is assumed to be controlled by the collective effects of quantitative trait loci (QTLs), epistasis (interaction between QTLs), the environment, and interaction between QTL and environment. Exploiting molecular markers in breeding involve finding a subset of markers associated with one or more QTLs that regulate the expression of complex traits. Many QTL mapping studies conducted in the last two decades identified QTLs that generally explained a significant proportion of the phenotypic variance, and therefore, gave rise to an optimistic assessment of the prospects of markers assisted selection. Linkage analysis and association mapping are the two most commonly used methods for QTL mapping. This review provides an overview of the two QTL mapping methods, including mapping population type and size, phenotypic evaluation of the population, molecular profiling of either the entire or a subset of the population, marker-trait association analysis using different statistical methods and software as well as the future prospects of using markers in crop improvement.

Desempenho fenotípico ao utilizar diferentes densidades de marcadores moleculares no mapeamento genômico / Phenotypic performance using different molecular markers density in genomic mapping

Objetivou-se avaliar, através do programa de simulação genética GENESYS, a densidade de marcadores moleculares (MM) no mapeamento de QTL (Quantitative Trait Loci). Foram considerados mapeamentos de alta, média e baixa resolução, em que os marcadores foram dispostos regulamente a cada 5 cM (192 MM), 10 cM (95 MM) e 20 cM (47 MM), respectivamente. Para cada intervalo, o mesmo número de marcadores utilizados foi reconsiderado, contudo, admitindo espaçamento aleatório. Os mapas foram comparados aos pares, com o mesmo número de marcadores distribuídos em intervalos regulares e de forma aleatória. A seleção assistida por marcadores foi utilizada para avaliar o desempenho fenotípico em cada cenário. Em todos os casos, os mapas que admitiram marcadores dispersosem intervalos fixos foram superiores em relação aos ganhos fenotípicos, em especial para o mapeamento de baixaresolução. Infere-se que a disposição estratégica de marcadores moleculares no mapeamento genômico é tanto maisrelevante quanto menor for o número de marcadores considerados na análise.

The objective of this study was to evaluate, through the program of genetic simulation GENESYS, the density of molecular markers (MM) in the mapping of QTL (Quantitative Trait Loci). High, medium and low resolution mapping were considered, in which markers were arranged regularly every 5 cM (192 MM), 10 cM (95 MM) and 20 cM (47 MM), respectively. For each gap, the same number of markers used was reconsidered, however, assuming random spacing. The maps were compared in pairs, with the same number of markers distributed at regularintervals and at random. The selection assisted by markers was used to assess the phenotypic performance in eachscenario. In all cases, the maps which admitted sparse markers at fixed intervals were superior in relation to phenotypic gains, especially for the mapping of low resolution. We conclude that the strategic distribution of molecular markers in genomic mapping is more relevant as the lower is the number of markers considered in the analysis.

Mapping aluminum tolerance loci in cereals: a tool available for crop breeding

Aluminum (Al) toxicity is the main factor limiting crop productivity in acidic soils around the world. In cereals, this problem reduces crop yields by 30-40 percent. The use of DNA-based markers linked to phenotypic traits is an interesting alternative approach. Strategies such as molecular marker-assisted selection (MAS) in conjunction with bioinformatics-based tools such as graphical genotypes (GGT) have been important for confirming introgression of genes or genomic regions in cereals but also to reduce the time and cost of identifying them through genetic selection. These biotechnologies also make it possible to identify target genes or quantitative trait loci (QTL) that can be potentially used in similar crops to increase their productivity. This review presents the main advances in the genetic improvement of cereals for Al-tolerance.

Programa de mejoramiento genético para características económicas en razas cebuinas lecheras / Breeding programs for the main economically important traits of zebu dairy cattle

En regiones tropicales, las razas bovinas Gyr y Guzerat, pertenecientes a la subespecie Bos indicus, son las más exploradas en la industria lechera, entre otras razones, porque están más adaptadas al clima tropical. Gyr y Guzerat son razas cebuinas comunes en Brasil, y son utilizadas para generar las razas sintéticas Gyrolando (5/8 Holstein: 3/8 Gyr) y Guzolando (5/8 Holstein: 3/8 Guzerat), en orden a combinar una buena producción y tolerancia al calor y los parásitos en el trópico. Programas de mejoramiento para las características de importancia económica en cebú lechero, han sido introducidos recientemente en Brasil, basados en el uso de reproductores genéticamente superiores de los diferentes rebaños. El principal objetivo de QTL (loci de características cuantitativas) y genes candidatos, es encontrar genes y marcadores que puedan ser implementados en programas de mejoramiento a través de la selección asistida por marcadores (MAS). En cebuinos lecheros, la selección asistida por marcadores puede ser usada para preseleccionar toros candidatos jóvenes para pruebas de progenie, incrementando así, el diferencial de selección, reducción del intervalo generacional e incrementando el mérito genético...

Analysis of the association between spawning time QTL markers and the biannual spawning behavior in rainbow trout (Oncorhynchus mykiss)

The rainbow trout is a salmonid fish that occasionally exhibits broodstocks with biannual spawning behavior, a phenomenon known as a double annual reproductive cycle (DARC). Spawning time quantitative trait loci (SPT-QTLs) affect the time of the year that female rainbow trout spawn and may influence expression of the DARC trait. In this study, microsatellite markers linked and unlinked to SPT-QTLs were genotyped to investigate the underlying genetics of this trait. SPT-QTLs influenced the DARC trait since in two case-control comparisons three linked markers (OmyFGT12TUF, One3ASC and One19ASC) had significant levels of allelic frequency differentiation and marker-character association. Furthermore, alleles of One3ASC and One19ASC had significantly higher frequencies in populations that carried the DARC trait.

Comparison of Phenotypic and Genetic Performance of Local Silkworm Groups and Two Commercial Lines

Five Iranian native silkworm groups: Baghdad, Khorasan Orange, Guilan Orange, Khorasan Pink, Khorasan Lemon, and 107 and 110 commercial lines (12 families from each breed) were randomly selected and reared during 2003-2005 (five generations in spring and autumn). In each family, 30 male and 30 female cocoons were individually recorded for weight, shell weight and shell ratio. From among the native groups, the highest average in all three traits belonged to Baghdad and Khorasan Pink, and the lowest to Khorasan Orange and Khorasan Lemon. From among the commercial lines, the highest average in all three traits belonged to 107. In comparing heritabihty for cocoon weight in native groups, the highest heritabihty belonged to Guilan Orange (0.5147) and Khorasan Orange (0.5036) and the lowest heritabihty belonged to Khorasan Pink (0.0967). In the two other traits, the highest heritabihty belonged to Khorasan Orange and Baghdad and the lowest to Khorasan Pink. In the commercial lines, linellO had higher heritabihty than linel07 for cocoon weight and cocoon shell weight. In all the groups, genetic correlations between cocoon weight and cocoon shell weight were high, expect for the Baghdad group. There was médium or low genetic correlation among cocoon weight, cocoon shell weight and cocoon shell ratio.

Polymorphisms on SSC15q21-q26 Containing QTL for reproduction in Swine and its association with litter size

Several quantitative trait loci (QTL) for important reproductive traits (ovulation rate) have been identified on the porcine chromosome 15 (SSC15). To assist in the selection of positional candidate swine genes for these QTL on SSC15, twenty-one genes had already been assigned to SSC15 in a previous study in our lab, by using the radiation hybrid panel IMpRH. Further polymorphism studies were carried out on these positional candidate genes with four breeds of pigs (Duroc, Erhualian, Dahuabai and Landrace) harboring significant differences in reproduction traits. A total of nineteen polymorphisms were found in 21 genes. Among these, seven in six genes were used for association studies, whereby NRP2 polymorphism was found to be significantly (p < 0.05) associated with litter-size traits. NRP2 might be a candidate gene for pig-litter size based on its chromosome location (Du et al., 2006), significant association with litter-size traits and relationships with Sema and the VEGF super families.

Endogamia e limite de seleção em populações sob seleção assistida por marcadores moleculares / Endogamy and its selection limit in populations under assisted selection by molecular markers

Foram utilizados diferentes níveis de significância genômica na seleção assistida por marcadores para estimar a endogamia média e o limite de seleção, assim como os valores fenotípicos, em características quantitativas de baixa, média e alta herdabilidade. Uma comparação entre os níveis de 1 por cento, 5 por cento, 10 por cento e 20 por cento foi realizada por meio do sistema computacional de simulação genética (GENESYS), utilizado para a simulação de três genomas (cada qual constituído de um único caráter de baixa, média ou alta herdabilidade), e das populações base e inicial. Os resultados indicaram superioridade dos níveis de significância de maior magnitude (10 por cento e 20 por cento) com relação aos valores fenotípicos, resultante de menor média endogâmica, além de menor limite de seleção ao longo das gerações sob seleção para estes níveis. Estes resultados foram observados para todas as três características, embora de forma mais expressiva para o caráter de baixa herdabilidade. Assim, apesar de os níveis de 1 por cento e 5 por cento apresentarem maior precisão na detecção de marcadores ligados a quantitative trait loci (QTL), eles conduzem a maiores médias endogâmicas e limite de seleção, propiciando ganhos fenotípicos menores.

Different levels of genomic significance were used in the selection assisted by molecular markers to estimate the medium endogamy and the selection limit, as well as the phenotypic value, for quantitative traits of low, medium, and high heritability. A comparison among the levels of genomic significance of 1 percent, 5 percent, 10 percent, and 20 percent was accomplished by a computer system of genetic simulation (GENESYS), used to simulate three genomes, each of them constituted by only one character of low, medium and high heritability, and to simulate the base and the initial populations. The results suggest superiority of higher significance levels (10 percent and 20 percent) for all phenotypic values, as a consequence of lower endogamy, and lower selection limit for low, medium, and high heritability traits, but in more expressive way for low heritability trait. Although the significant levels of 1 percent and 5 percent for molecular marker assisted selection showed a high precision in detecting markers related to a quantitative trait loci (QTLs), they lead to higher endogamy and selection limits, resulting in low phenotypic gains.

Association of a locus on rat chromosome 4 with anxiety-related behaviors in two selectively bred rat lines

The Floripa H and L rat lines, selected for high and low locomotion in the central aversive area of an open field, a widely used emotionality test, were proposed as a model for studying the genetic basis of anxiety. The present study aimed to verify if the QTL Ofil1, mapped to rat chromosome 4 and previously identified as being related to emotionality in another population of rats, contributes to the behavioral variability observed in the Floripa rat lines. To this purpose, rats of five generations of selective breeding were genotyped for two polymorphic markers, D4RAT59 and D4MGH27, flanking Ofil1. Changes in genotype and allele frequencies throughout generations were evaluated in both H and L lines, in order to assess if the bidirectional selection based on behavioral scores induced divergent changes in the genotype of this genome region. There were significant changes in genotype frequencies for both molecular markers, however, only the genotype variations of the D4RAT59 marker were significantly correlated with the variations in the selected phenotype. This result suggests that the region of the genome near D4RAT59 contains one or more genes contributing to the interindividual variation in central locomotion in the open field test.

Quantitative trait loci for carcass, internal organ and meat quality traits on porcine chromosomes 16, 17 and 18

The objective of this study was to map quantitative trait loci (QTL) on porcine chromosomes 16, 17 and 18 and to determine their association with carcass, organ and meat quality traits. An F2 population was produced by crossing two boars of the naturalized Brazilian Piau breed with 18 commercial females (Landrace x Large White x Pietrain). The population was genotyped for 11 microsatellite markers distributed over the three chromosomes and the results were used to construct a marker-specific linkage map for the population. Analysis of the polymorphic information content showed that the microsatellite markers were adequate for the study of quantitative traits. QTL were identified by regression interval mapping using QTL Express software. QTL not previously described in the literature were detected on chromosome 16, whereas QTL described in other populations were detected on chromosomes 17 and 18. The information from the significant QTL identified here will be useful for future fine-mapping studies and should provide a better understanding of productive phenotypes in pigs.