Genomic structure and marker-derived gene networks for growth and meat quality traits of Brazilian Nelore beef cattle

Abstract\ud \ud Background\ud Nelore is the major beef cattle breed in Brazil with more than 130 million heads. Genome-wide association studies (GWAS) are often used to associate markers and genomic regions to growth and meat quality traits that can be used to assist selection programs. An alternative methodology to traditional GWAS that involves the construction of gene network interactions, derived from results of several GWAS is the AWM (Association Weight Matrices)/PCIT (Partial Correlation and Information Theory). With the aim of evaluating the genetic architecture of Brazilian Nelore cattle, we used high-density SNP genotyping data (~770,000 SNP) from 780 Nelore animals comprising 34 half-sibling families derived from highly disseminated and unrelated sires from across Brazil. The AWM/PCIT methodology was employed to evaluate the genes that participate in a series of eight phenotypes related to growth and meat quality obtained from this Nelore sample.\ud \ud \ud Results\ud Our results indicate a lack of structuring between the individuals studied since principal component analyses were not able to differentiate families by its sires or by its ancestral lineages. The application of the AWM/PCIT methodology revealed a trio of transcription factors (comprising VDR, LHX9 and ZEB1) which in combination connected 66 genes through 359 edges and whose biological functions were inspected, some revealing to participate in biological growth processes in literature searches.\ud \ud \ud Conclusions\ud The diversity of the Nelore sample studied is not high enough to differentiate among families neither by sires nor by using the available ancestral lineage information. The gene networks constructed from the AWM/PCIT methodology were a useful alternative in characterizing genes and gene networks that were allegedly influential in growth and meat quality traits in Nelore cattle.This study was conducted with funding from EMBRAPA (Macroprograma1,\ud 01/2005) and FAPESP (process number 2012/23638-8). GBM, LLC, LCAR and\ud MMA were granted CNPq fellowships. We thank Sean McWilliam, Marina R. S.\ud Fortes, Edilson Guimaraes, Robson Rodrigues Santiago, Roselito F. da Silva,\ud Fernando F. Cardoso, Flavia Aline Bressani, Wilson Malago Jr., Avelardo U. C.\ud Ferreira, Michel E. B. Yamaguishi and Fabio D. Vieira for the help and\ud technical assistance. The authors would like to acknowledge the\ud collaborative efforts among EMBRAPA, University of Sao Paulo and CSIRO

Vegetação arbórea em remanescentes florestais urbanos: Bosque do Lago da Paz, Dois Vizinhos, PR

Esse estudo teve por objetivo analisar a florística, estrutura e diversidade da vegetação arbórea e da regeneração de um fragmento florestal situado na área urbana de Dois Vizinhos, PR, por meio do método de censo. Foram utilizados os descritores fitossociológicos tradicionais como parâmetros de análise, dando indicações sobre o valor ecológico do fragmento. Evidenciou-se a ocorrência de 231 indivíduos em 2.500 m² de área, distribuídos em 35 espécies de 22 famílias botânicas. As famílias com maior número de espécies foram Lauraceae e Myrtaceae, com três espécies cada, seguida por Boraginaceae, Euphorbiaceae, Fabaceae, Meliaceae, Myrsinaceae, Rosaceae e Sapindaceae, com duas espécies cada, ficando as demais famílias com uma espécie cada. Entre as oito espécies exóticas, quatro são invasoras potenciais, tais como Ligustrum lucidum (34,04%) e Dyospyrus kaki (13,59%), destacando-se pelo alto valor de cobertura (VC) e pela dominância, com mais de 50% dos indivíduos. A maioria das espécies encontradas pertence a estágios iniciais de sucessão. Na regeneração, foram encontradas 20 espécies, com apenas três exóticas e, dentre estas, uma invasora (L. lucidum). A ocorrência de espécies exóticas invasoras em fragmentos florestais urbanos demanda a atenção dos gestores públicos quanto à necessidade de intervenções silviculturais, visando à recuperação da florística e estrutura original

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

Additional file 1: of Selection signatures in Canchim beef cattle

Candidate regions identified for piHS = 4 (P < 0.0001). (DOC 61 kb

Additional file 4: Fig. S1. of Candidate genes for male and female reproductive traits in Canchim beef cattle

Linkage disequilibrium for scrotal circumference at 420 d of age on chromosome 5. Fig. S2. Linkage disequilibrium for scrotal circumference at 420 d of age on chromosome 9. Fig. S3. Linkage disequilibrium for scrotal circumference at 420 d of age on chromosome 13. Fig. S4. Linkage disequilibrium for scrotal circumference at 420 d of age on chromosome 14. Fig. S5. Linkage disequilibrium for scrotal circumference at 420 d of age on chromosome 18. Fig. S6. Linkage disequilibrium for scrotal circumference at 420 d of age on chromosome 21. (ZIP 1985 kb

Additional file 1: of Candidate genes for male and female reproductive traits in Canchim beef cattle

Significantly associated single nucleotide polymorphism (SNP) with scrotal circumference at 420 days of age (SC420) after Bonferroni (B) and false discovery rate (FDR) correction at a chromosome-wise (CW) and genome-wide (GW) level. (DOCX 95 kb

Additional file 2: of Candidate genes for male and female reproductive traits in Canchim beef cattle

Genome-wide (in bold) and chromosome-wise associations for scrotal circumference at 420 days of age. Gene symbols, SNP reference number, and chromosomes (Chr) and positions (Pos, in megabase) were obtained from NCBI website. Distances to gene (kilobase) are presented from 5′ to gene and 3′ to gene directions. If distance equals zero (0.00), the SNP is on intragenic region. P-values are presented as the minimum (Min) and maximum (Max) significance obtained from the generalized quasi-likelihood method. (DOCX 34 kb

Manhattan plots of p-values for birth weight (BW), weaning weight (WW), and long-yearling weight (LYW).

<p>Significance levels were determined by false discovery rate (FDR) correction at levels of 1% (red line), 5% (blue line), and 10% (black line). Positions were presented in megabase pair (Mbp). Associations were observed in autosome (BTA) 4, 6, 7, 9, 11, 22, 25, and 27.</p

Significantly associated SNPs for birth weight (BW), weaning weight (WW), and long-yearling weight (LYW) obtained by the Generalized Quasi-Likelihood Score method (GQLS).

<p>Single locus regression was carried out to estimate allele substitution effects for significant SNPs.</p><p>*Coefficient of regression (P<0.001); FDR  =  False discovery rate; MAF  =  Minor allele frequency; bp  =  base pairs; BTA  =  <i>Bos taurus</i> autosome.</p