Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach

Background: Meat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal's life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality.Results: The set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism.Conclusions: These results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle. © 2013 Mokry et al.; licensee BioMed Central Ltd.

Evaluation of Rice Bran Extract as a Nitrogen Source for Improved Hemicellulosic Ethanol Production from Sugarcane Bagasse by New Xylose-Fermenting Yeast Strains Isolated from Brazilian Forests

Xylose is the main sugar in hemicellulosic hydrolysates and its fermentation into ethanol by microorganisms is influenced by nutritional factors, such as nitrogen source, vitamins and other elements. Rice bran extract (RBE) is an inexpensive nitrogen source primarily consisting of high amount of protein. This study evaluates the potential of RBE as a nitrogen source for the hemicellulosic ethanol production from sugarcane bagasse dilute acid hydrolysate by novel yeast strains Scheffersomyces shehatae (syn. Candida shehatae) CG8-8BY and Spathaspora arborariae UFMG-HM19.1A, isolated from Brazilian forests. Two different media formulations were used for inoculum preparation and production medium, using yeast extract and RBE as nitrogen sources. S. shehatae CG8-8BY showed ethanol production of 17.0 g/l with the ethanol yield (0.33 g/g) and fermentation efficiency (64 %) from medium supplemented with RBE. On the other hand, S. arborariae presented 5.4 g/l of ethanol production with ethanol yield (0.14 g/g) and fermentation efficiency (21 %) in a fermentation medium supplemented with RBE. Appropriate media formulation is an important parameter to increase the productivity of bioconversion process and RBE proved to be an efficient and inexpensive nitrogen source to supplement sugarcane bagasse hemicellulosic hydrolysate for second generation ethanol production. © 2013 Society for Sugar Research & Promotion.

Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height

Background: Birth weight (BW) is an economically important trait in beef cattle, and is associated with growth- and stature-related traits and calving difficulty. One region of the cattle genome, located on Bos primigenius taurus chromosome 14 (BTA14), has been previously shown to be associated with stature by multiple independent studies, and contains orthologous genes affecting human height. A genome-wide association study (GWAS) for BW in Brazilian Nellore cattle (Bos primigenius indicus) was performed using estimated breeding values (EBVs) of 654 progeny-tested bulls genotyped for over 777,000 single nucleotide polymorphisms (SNPs).Results: The most significant SNP (rs133012258, PGC = 1.34 × 10-9), located at BTA14:25376827, explained 4.62% of the variance in BW EBVs. The surrounding 1 Mb region presented high identity with human, pig and mouse autosomes 8, 4 and 4, respectively, and contains the orthologous height genes PLAG1, CHCHD7, MOS, RPS20, LYN, RDHE2 (SDR16C5) and PENK. The region also overlapped 28 quantitative trait loci (QTLs) previously reported in literature by linkage mapping studies in cattle, including QTLs for birth weight, mature height, carcass weight, stature, pre-weaning average daily gain, calving ease, and gestation length.Conclusions: This study presents the first GWAS applying a high-density SNP panel to identify putative chromosome regions affecting birth weight in Nellore cattle. These results suggest that the QTLs on BTA14 associated with body size in taurine cattle (Bos primigenius taurus) also affect birth weight and size in zebu cattle (Bos primigenius indicus). © 2013 Utsunomiya et al.; licensee BioMed Central Ltd.

The Genome of Anopheles darlingi, the main neotropical malaria vector

Anopheles darlingi is the principal neotropical malaria vector, responsible for more than a million cases of malaria per year on the American continent. Anopheles darlingi diverged from the African and Asian malaria vectors ∼100 million years ago (mya) and successfully adapted to the New World environment. Here we present an annotated reference A. darlingi genome, sequenced from a wild population of males and females collected in the Brazilian Amazon. A total of 10 481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species. In spite of a long period of divergent evolution, conserved gene synteny was observed between A. darlingi and A. gambiae. More than 10 million single nucleotide polymorphisms and short indels with potential use as genetic markers were identified. Transposable elements correspond to 2.3% of the A. darlingi genome. Genes associated with hematophagy, immunity and insecticide resistance, directly involved in vectorhuman and vectorparasite interactions, were identified and discussed. This study represents the first effort to sequence the genome of a neotropical malaria vector, and opens a new window through which we can contemplate the evolutionary history of anopheline mosquitoes. It also provides valuable information that may lead to novel strategies to reduce malaria transmission on the South American continent. The A. darlingi genome is accessible at www.labinfo.lncc.br/index.php/anopheles- darlingi. © 2013 The Author(s).

Chromosomal organization of repetitive DNA sequences in Astyanax bockmanni (Teleostei, Characiformes): dispersive location, association and co-localization in the genome

Repetitive DNA sequences constitute a great portion of the genome of eukaryotes and are considered key components to comprehend evolutionary mechanisms and karyotypic differentiation. Aiming to contribute to the knowledge of chromosome structure and organization of some repetitive DNA classes in the fish genome, chromosomes of two allopatric populations of Astyanax bockmanni were analyzed using classic cytogenetics techniques and fluorescent in situ hybridization, with probes for ribosomal DNA sequences, histone DNA and transposable elements. These Astyanax populations showed the same diploid number (2n = 50), however with differences in chromosome morphology, distribution of constitutive heterochromatin, and location of 18S rDNA and retroelement Rex3 sites. In contrast, sites for 5S rDNA and H1, H3 and H4 histones showed to be co-located and highly conserved. Our results indicate that dispersion and variability of 18S rDNA and heterochromatin sites are not associated with macro rearrangements in the chromosome structure of these populations. Similarly, distinct evolutionary mechanisms would act upon histone genes and 5S rDNA, contributing to chromosomal association and co-location of these sequences. Data obtained indicate that distinct mechanisms drive the spreading of repetitive DNAs in the genome of A. bockmanni. Also, mobile elements may account for the polymorphism of the major rDNA sites and heterochromatin in this genus. © 2013 Springer Science+Business Media Dordrecht.

Cover crop termination timing on rice crop production in a no-till system

Measuring shikimic acid accumulation in response to glyphosate applications can be a rapid and accurate way to quantify and predict glyphosate-induced damage to sensitive plants. The objective of this paper was to evaluate the effect of cover crop termination timing by glyphosate application on rice (Oryza sativa L.) yield in a no-till system. A factorial experiment, arranged in a split-plot design, was conducted for 2 yr. Treatments consisted of cover crops (main plots) and timed herbicide applications (subplots) to these cover crops (30, 20, 10, and 0 d before rice planting). There was a decrease in rice yield from 2866 kg ha-1 to 2322 kg ha-1 when the herbicide was applied closer to the rice planting day. Glyphosate application on cover crops increased shikimate concentrations in rice seedlings cultivated under palisade grass (Brachiaria brizantha), signal grass (B. ruziziensis), guinea grass (Panicum maximum), and weedy fallow (spontaneous vegetation) but not under millet (Pennisetum glaucum), which behaved similarly to the control (clean fallow, no glyphosate application). Glyphosate applications in the timing intervals used were associated with stress in the rice plants, and this association increased if cover crops took longer to completely dry and if higher amounts of biomass were produced. Millet, as a cover crop, allowed the highest seedling dry matter for upland rice and the highest rice yield. Our results suggest that using millet as a cover crop, with glyphosate application far from upland rice planting day (10 d or more), was the best option for upland rice under a no-tillage system. © Crop Science Society of America.

Research on sugar-cane and rice

Analiza la estructura de la industria azucarera en Trinidad y Tabago, sus politicas y funciones, sus programas de investigacion y objetivos. Presenta un sumario de los proyectos en curso para 1983- 84 y los efectos de los proyectos de investigacion sobre la productividad de cultivos distintos de los del azucar de cana.

Report of Workshop on Co-operation in Rice Research between the Governments of the Caribbean Development and Co-operation Committee

Includes bibliography

Trade patterns and policies of CDCC countries in rice, legumes, ground provisions, fresh vegetables and citrus products and identification of areas for joint action

Includes bibliography

Genome-wide scans to uncover loci underlying bovine reproductive biology

Pós-graduação em Medicina Veterinária - FCAV

Isolamento e caracterização de promotores órgão-específicos a partir de informações do Banco FORESTs (Eucalyptus Genome Sequencing Project Consortium)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Mitochondrial DNA-like sequence in the nuclear genome of Saguinus (Callitrichinae, Primates): transfer estimation

Seqüências tipo mitocondriais têm comumente sido encontradas no genoma nuclear de diversos organismos. Quando acidentalmente incluídas em estudos de seqüências mitocondriais, diversas conclusões errôneas podem ser obtidas. No entanto, estes pseudogenes nucleares tipo mitocondriais podem ser usados para a estimativa da taxa relativa de evolução de genes mitocondriais e também como grupo externo em análises filogenéticas. No presente trabalho, seqüências mitocondriais com características do tipo de pseudogene, tais como deleções e/ou inserções e códons de parada, foram encontradas em tamarins (Saguinus spp., Callitrichinae, Primates). A análise filogenética permitiu a estimativa do tempo da migração da seqüência mitocondrial para o genoma nuclear e algumas inferências filogenéticas. A escolha de um grupo externo não adequado (Aotus infulatus) não permitiu uma reconstrução filogenética confiável da subfamília Callitrichinae. A divergência bastante antiga de Cebidae (Callitrichinae, Aotinae e Cebinae) pode ter favorecido o aparecimento de homoplasias, obscurecendo a análise.

Processing and characterization of extruded breakfast meal formulated with broken rice and bean flour

O objetivo deste trabalho foi elaborar um produto matinal extrusado de quirera de arroz e bandinha de feijão, além de verificar a influência do processo de extrusão nas suas características físico-químicas, nutricionais, tecnológicas e sensoriais. O produto final apresentou teor considerável de proteínas (9,9 g.100 g^-1), podendo ser considerado uma boa fonte desse nutriente para crianças e adolescentes. Para a fibra alimentar, observou-se teor de 3,71 g.100 g^-1 do produto pronto para o consumo. Dessa forma, o floco matinal de arroz e feijão pode receber a alegação de alimento fonte de fibras, de acordo com a legislação brasileira. Com relação às propriedades tecnológicas, o extrusado estudado apresentou índice de expansão de 8,89 e densidade aparente de 0,25 g.cm^-3. Quanto à análise sensorial, o floco matinal avaliado obteve notas médias de aceitação, situadas no intervalo de 6,8 a 7,7, que corresponde às categorias "gostei ligeiramente" e "gostei muito". Para a intenção de compra, 79% dos provadores opinaram que certamente ou possivelmente comprariam o produto. O emprego de quirera de arroz e bandinha de feijão é uma interessante alternativa para a elaboração de produto matinal extrusado, apresentando boas qualidades de ordem nutricional, tecnológica e sensorial.

Impact strength and abrasion resistance of high strength concrete with rice husk ash and rubber tires

The paper discusses the application of High Strength Concrete (HSC) technology for concrete production with the incorporation of Rice Husk Ash (RHA) residues by replacing a bulk of the material caking and rubber tires with partial aggregate volume, assessing their influence on the mechanical properties and durability. For concrete with RHA and rubber, it was possible to reduce the brittleness by increasing the energy absorbing capacity. With respect to abrasion, the RHA and rubber concretes showed lower mass loss than the concrete without residues, indicating that this material is attractive to be used in paving. It is thus hoped that these residues may represent a technological and ecological alternative for the production of concrete in construction works.

The Buffalo Genome and the Application of Genomics in Animal Management and Improvement

The publication of the human genome sequence in 2001 was a major step forward in knowledge necessary to understand the variations between individuals. For farmed species, genomic sequence information will facilitate the selection of animals optimised to live, and be productive, in particular environments. The availability of cattle genome sequence has allowed the breeding industry to take the first steps towards predicting phenotypes from genotypes by estimating a genomic breeding value (gEBV) for bulls using genome-wide DNA markers. The sequencing of the buffalo genome and creation of a panel of DNA markers has created the opportunity to apply molecular selection approaches for this species.The genomes of several buffalo of different breeds were sequenced and aligned with the bovine genome, which facilitated the identification of millions of sequence variants in the buffalo genomes. Based on frequencies of variants within and among buffalo breeds, and their distribution across the genome compared with the bovine genome, 90,000 putative single nucleotide polymorphisms (SNP) were selected to create an Axiom (R) Buffalo Genotyping Array 90K. This SNP Chip was tested in buffalo populations from Italy and Brazil and found to have at least 75% high quality and polymorphic markers in these populations. The 90K SNP chip was then used to investigate the structure of buffalo populations, and to localise the variations having a major effect on milk production.