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Investigation of molecular marker effects on production traits is essential to define marker assisted selection strategies in beef cattle. We looked for a possible association of molecular markers and backfat thickness (BFT) and rib eye area (REA) in Canchim (5/8 Charolais + 3/8 Zebu) and MA (offspring of Charolais bulls and 1/2 Canchim + 1/2 Zebu cows) animals raised exclusively on pasture. Traits were measured on 987 individuals from seven herds from two Brazilian States (São Paulo and Goiás), in March and April from 2005 to 2007, when animals were, on average, 19 months of age. Five microsatellite markers lying in QTL regions for BFT and REA (BMS490 and ETH10 on chromosome 5, INRA133 and ILSTS090 on chromosome 6, and BMS2142 on chromosome 19) were genotyped and association analyses were performed under an animal model using the restricted Candidate gene region for control of rib eye area maximum likelihood method. After correction for multiple tests, a significant effect of microsatellite BMS490 on REA was observed, suggesting that at least one QTL affecting carcass traits in this region of the BTA5. No significant effect on BFT was observed for these markers. Made available in DSpace on 2022-07-28T18:35:59Z (GMT). No. of bitstreams: 1 gmr1175.pdf: 387982 bytes, checksum: 01ffb00d40063ac120206b31ab919f13 (MD5) Previous issue date: 2011

Background Meat and egg-type chickens have been selected for several generations for different traits. Artificial and natural selection for different phenotypes can change frequency of genetic variants, leaving particular genomic footprints throghtout the genome. Thus, the aims of this study were to sequence 28 chickens from two Brazilian lines (meat and white egg-type) and use this information to characterize genome-wide genetic variations, identify putative regions under selection using Fst method, and find putative pathways under selection. Results A total of 13.93 million SNPs and 1.36 million INDELs were identified, with more variants detected from the broiler (meat-type) line. Although most were located in non-coding regions, we identified 7255 intolerant non-synonymous SNPs, 512 stopgain/loss SNPs, 1381 frameshift and 1094 non-frameshift INDELs that may alter protein functions. Genes harboring intolerant non-synonymous SNPs affected metabolic pathways related mainly to reproduction and endocrine systems in the white-egg layer line, and lipid metabolism and metabolic diseases in the broiler line. Fst analysis in sliding windows, using SNPs and INDELs separately, identified over 300 putative regions of selection overlapping with more than 250 genes. For the first time in chicken, INDEL variants were considered for selection signature analysis, showing high level of correlation in results between SNP and INDEL data. The putative regions of selection signatures revealed interesting candidate genes and pathways related to important phenotypic traits in chicken, such as lipid metabolism, growth, reproduction, and cardiac development. Conclusions In this study, Fst method was applied to identify high confidence putative regions under selection, providing novel insights into selection footprints that can help elucidate the functional mechanisms underlying different phenotypic traits relevant to meat and egg-type chicken lines. In addition, we generated a large catalog of line-specific and common genetic variants from a Brazilian broiler and a white egg layer line that can be used for genomic studies involving association analysis with phenotypes of economic interest to the poultry industry. Electronic supplementary material The online version of this article (10.1186/s12864-018-4444-0) contains supplementary material, which is available to authorized users.

In contrast to the Mendelian inheritance model, parental alleles can contribute unequally to gene expression, which may result in phenotypic variance among individuals and bias in the predicted additive effect of molecular markers associated with production traits. Given the need to understand the effects of allelic variation and parent-of-origin effects on the expression of genes with a commercial interest in cattle, we analyzed the expression of KCNJ11 (potassium inwardly rectifying channel, subfamily J, member 11), which was previously described as a functional candidate gene for meat tenderness. Allele-specific and parent-of-origin-dependent expression of this gene were assessed in bovine muscle using the rs379610823 single nucleotide polymorphism as a reference. Biallelic expression was observed; however, the T allele was expressed at significantly higher levels than the C allele. Furthermore, increased expression of KCNJ11 was found in animals harboring the maternal T allele. This study is the first to describe the differential allelic expression of bovine KCNJ11. Our findings are important for understanding the mechanisms that underlie the pattern of KCNJ11 expression and its potential impact on the phenotypic variation of meat tenderness in Nelore beef cattle. This reinforces the need for further investigation of allelic- and parent-of-origin expression deviation in genetic markers eligible for the selection of target traits.

Canchim is a composite cattle breed developed in Brazil for beef production. One of the breeding objectives is to increase fat deposition. QTLs for fat thickness and/or marbling have been reported on BTA4 and BTA14. The IGFBP3 and DDEF1 genes, mapped to BTA4 and BTA14, respectively, affect adipogenesis. We looked for SNPs in the IGFBP3 and DDEF1 genes that could be associated with backfat thickness in Canchim beef cattle. For SNP identification, sires with the highest accuracy were ranked according to expected breeding value for fat thickness; the 12 extremes (six sires with the highest and six with the lowest expected breeding value for the trait) were chosen. Six regions of the IGFBP3 and 14 regions of the DDEF1 were sequenced using the Sanger method. Nine SNPs were identified in IGFBP3 and 76 in the DDEF1. After an initial analysis, two SNPs were selected to be genotyped for the whole population; these were DDEF1g.279401A>G and IGFBP3c.4394T>C(Trp>Arg). We found a significant effect (P ≤ 0.05) of allele substitution on backfat thickness; however, the IGFBP3 SNP did not significantly affect this trait.

The potassium inwardly rectifying channel, subfamily J, member 11 ( KCNJ11) gene was investigated as a candidate for meat tenderness based on the effects reported on muscle for KCNJ11 gene knockout in rat models and its position in a quantitative trait locus (QTL) for meat tenderness in the bovine genome. Sequence variations in the KCNJ11 gene were described by sequencing six amplified fragments, covering almost the entire gene. We identified single nucleotide polymorphisms (SNP) and validated them by different approaches, taking advantage of simultaneous projects that are being developed with the same Nelore population. By sequencing the KCNJ11 in Nelore steers representing extreme phenotypes for Warner-Bratzler shear force (WBSF), it was possible to identify 22 SNPs. We validated two of the identified markers by genotyping the whole population ( n = 460). Analysis of association between genotypes and WBSF values revealed a significant additive effect of a SNP at different meat aging times ( P ≤ 0.05). In addition, an association between the expression levels of KCNJ11 and WBSF was found, with lower expression levels of KCNJ11 associated with more tender meat ( P ≤ 0.05). The results showed that the KCNJ11 gene is a candidate mapped to a QTL for meat tenderness previously identified on BTA15 and may be useful to identify animals with genetic potential to produce tender meat. The effect of KCNJ11 observed on muscle is potentially due to changes in activity of KATP channels, which in turn influence the flow of potassium in the intracellular space, allowing establishment of the membrane potential necessary for muscle contraction.

Genetic differences in susceptibility to ticks (Rhipicephalus (Boophilus) microplus) are considerable in bovines. Here, mapping, association and gene expression approaches were employed to further advance our understanding of the molecular basis of tick resistance. A B. taurus x B. indicus F 2 population was developed by Embrapa and 382 individuals were measured for parasitic load. Scanning of all chromosomes is in progress. Quantitative trait loci (QTL) for tick load were mapped to chromosomes 4, 5, 7, 10, 14, 18 and 23 out of the 20 chromosomes scanned and were dependent on the season in which the phenotype was scored. In the candidate gene approach, females from the genetic groups Nelore (NE - 184), Canchim x Nelore (CN - 153), Aberdeen Angus x Nelore (AN - 123) and Simmental x Nelore (SN - 120) were evaluated under natural infestation. Microsatellite markers close to the genes for interleukin 2 (1L2), interleukin 4 (1L4) and interferon gamma (IFNG) were analysed. Tick counts were associated with the marker for interleukin 4 (P

Intramuscular fat (IMF) content is related to insulin resistance, which is an important prediction factor for disorders, such as cardiovascular disease, obesity and type 2 diabetes in human. At the same time, it is an economically important trait, which influences the sensorial and nutritional value of meat. The deposition of IMF is influenced by many factors such as sex, age, nutrition, and genetics. In this study Nellore steers (Bos taurus indicus subspecies) were used to better understand the molecular mechanisms involved in IMF content. This was accomplished by identifying differentially expressed genes (DEG), biological pathways and putative regulatory factors. Animals included in this study had extreme genomic estimated breeding value (GEBV) for IMF. RNA-seq analysis, gene set enrichment analysis (GSEA) and co-expression network methods, such as partial correlation coefficient with information theory (PCIT), regulatory impact factor (RIF) and phenotypic impact factor (PIF) were utilized to better understand intramuscular adipogenesis. A total of 16,101 genes were analyzed in both groups (high (H) and low (L) GEBV) and 77 DEG (FDR 10%) were identified between the two groups. Pathway Studio software identified 13 significantly over-represented pathways, functional classes and small molecule signaling pathways within the DEG list. PCIT analyses identified genes with a difference in the number of gene-gene correlations between H and L group and detected putative regulatory factors involved in IMF content. Candidate genes identified by PCIT include: ANKRD26, HOXC5 and PPAPDC2. RIF and PIF analyses identified several candidate genes: GLI2 and IGF2 (RIF1), MPC1 and UBL5 (RIF2) and a host of small RNAs, including miR-1281 (PIF). These findings contribute to a better understanding of the molecular mechanisms that underlie fat content and energy balance in muscle and provide important information for the production of healthier beef for human consumption.

Background In tropical countries, losses caused by bovine tick Rhipicephalus (Boophilus) microplus infestation have a tremendous economic impact on cattle production systems. Genetic variation between Bos taurus and Bos indicus to tick resistance and molecular biology tools might allow for the identification of molecular markers linked to resistance traits that could be used as an auxiliary tool in selection programs. The objective of this work was to identify QTL associated with tick resistance/susceptibility in a bovine F2 population derived from the Gyr (Bos indicus) × Holstein (Bos taurus) cross. Results Through a whole genome scan with microsatellite markers, we were able to map six genomic regions associated with bovine tick resistance. For most QTL, we have found that depending on the tick evaluation season (dry and rainy) different sets of genes could be involved in the resistance mechanism. We identified dry season specific QTL on BTA 2 and 10, rainy season specific QTL on BTA 5, 11 and 27. We also found a highly significant genome wide QTL for both dry and rainy seasons in the central region of BTA 23. Conclusions The experimental F2 population derived from Gyr × Holstein cross successfully allowed the identification of six highly significant QTL associated with tick resistance in cattle. QTL located on BTA 23 might be related with the bovine histocompatibility complex. Further investigation of these QTL will help to isolate candidate genes involved with tick resistance in cattle.

Submitted by Guilherme Lemeszenski (guilherme@nead.unesp.br) on 2013-08-22T19:01:17Z No. of bitstreams: 1 S0103-90162012000100001.pdf: 195226 bytes, checksum: 4ac5347d14b45e3c4ce3a5ba5ed0e95c (MD5) Made available in DSpace on 2013-08-22T19:01:17Z (GMT). No. of bitstreams: 1 S0103-90162012000100001.pdf: 195226 bytes, checksum: 4ac5347d14b45e3c4ce3a5ba5ed0e95c (MD5) Previous issue date: 2012-02-01 Made available in DSpace on 2013-09-30T20:01:09Z (GMT). No. of bitstreams: 2 S0103-90162012000100001.pdf: 195226 bytes, checksum: 4ac5347d14b45e3c4ce3a5ba5ed0e95c (MD5) S0103-90162012000100001.pdf.txt: 25514 bytes, checksum: 1bf717b7c8de97d8f5c3059e6a3e6867 (MD5) Previous issue date: 2012-02-01 Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T15:15:39Z No. of bitstreams: 2 S0103-90162012000100001.pdf: 195226 bytes, checksum: 4ac5347d14b45e3c4ce3a5ba5ed0e95c (MD5) S0103-90162012000100001.pdf.txt: 25514 bytes, checksum: 1bf717b7c8de97d8f5c3059e6a3e6867 (MD5) Made available in DSpace on 2014-05-20T15:15:39Z (GMT). No. of bitstreams: 2 S0103-90162012000100001.pdf: 195226 bytes, checksum: 4ac5347d14b45e3c4ce3a5ba5ed0e95c (MD5) S0103-90162012000100001.pdf.txt: 25514 bytes, checksum: 1bf717b7c8de97d8f5c3059e6a3e6867 (MD5) Previous issue date: 2012-02-01 Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Canchim, a synthetic breed of cattle derived from the Charolais and Zebu group has been used in the beef-cattle industry in Brazil as an alternative for intensifying production. One of the main concerns with this breed is its poor fat deposition and consequently, there is an effort to increase the performance for this trait. The thyroglobulin gene is located in a QTL region for fat deposition, and reports describe the influence of a polymorphism in the 5´ leader sequence of that gene on marbling and subcutaneous fat thickness. This study analyzed the association of this polymorphism in the thyroglobulin gene, as well as of two flanking microsatellite markers, CSSM066 and ILSTS011, with backfat thickness in 987 Canchim beef cattle. The CSSM066 and ILSTS011 microsatellite markers have a effect on fat thickness in the studied populations. However, this trait did not have association with the polymorphism of the thyroglobulin gene, which suggests that other genes of bovine chromosome 14 may be responsible for the variation in this trait. UFSCar Depto. de Genética e Evolução UNESP FCAV Depto. de Genética e Melhoramento Animal Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Pecuária Sudeste UNIVASF Colegiado Acadêmico de Zootecnia UNESP FCAV Depto. de Genética e Melhoramento Animal