Selective signatures in composite MONTANA TROPICAL beef cattle reveal potential genomic regions for tropical adaptation.

Genomic regions related to tropical adaptability are of paramount importance for animal breeding nowadays, especially in the context of global climate change. Moreover, understanding the genomic architecture of these regions may be very relevant for aiding breeding programs in choosing the best selection scheme for tropical adaptation and/or implementing a crossbreeding scheme. The composite MONTANA TROPICAL® population was developed by crossing cattle of four different biological types to improve production in harsh environments. Pedigree and genotype data (51962 SNPs) from 3215 MONTANA TROPICAL® cattle were used to i) characterize the population structure; ii) identify signatures of selection with complementary approaches, i.e. Integrated Haplotype Score (iHS) and Runs of Homozygosity (ROH); and iii) understand genes and traits related to each selected region. The population structure based on principal components had a weak relationship with the genetic contribution of the different biological types. Clustering analyses (ADMIXTURE) showed different clusters according to the number of generations within the composite population. Considering results of both selection signatures approaches, we identified only one consensus region on chromosome 20 (35399405-40329703 bp). Genes in this region are related to immune function, regulation of epithelial cell differentiation, and cell response to ionizing radiation. This region harbors the slick locus which is related to slick hair and epidermis anatomy, both of which are related to heat stress adaptation. Also, QTLs in this region were related to feed intake, milk yield, mastitis, reproduction, and slick hair coat. The signatures of selection detected here arose in a few generations after crossbreeding between contrasting breeds. Therefore, it shows how important this genomic region may be for these animals to thrive in tropical conditions. Further investigations on sequencing this region can identify candidate genes for animal breeding and/or gene editing to tackle the challenges of climate change.

Nucleocapsid (N) gene mutations of SARS-CoV-2 can affect real-time RT-PCR diagnostic and impact false-negative results

The current COVID-19 pandemic demands massive testing by Real-time RT-PCR (Reverse Transcription Polymerase Chain Reaction), which is considered the gold standard diagnostic test for the detection of the SARS-CoV-2 virus. However, the virus continues to evolve with mutations that lead to phenotypic alterations as higher transmissibility, pathogenicity or vaccine evasion. Another big issue are mutations in the annealing sites of primers and probes of RT-PCR diagnostic kits leading to false-negative results. Therefore, here we identify mutations in the N (Nucleocapsid) gene that affects the use of the GeneFinder COVID-19 Plus RealAmp Kit. We sequenced SARS-CoV-2 genomes from 17 positive samples with no N gene detection but with RDRP (RNA-dependent RNA polymerase) and E (Envelope) genes detection, and observed a set of three different mutations affecting the N detection: a deletion of 18 nucleotides (Del28877-28894), a substitution of GGG to AAC (28881-28883) and a frameshift mutation caused by deletion (Del28877-28878). The last one cause a deletion of six AAs (amino acids) located in the central intrinsic disorder region at protein level. We also found this mutation in 99 of the 14,346 sequenced samples by the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants, demonstrating the circulation of the mutation in Sao Paulo, Brazil. Continuous monitoring and characterization of mutations affecting the annealing sites of primers and probes by genomic surveillance programs are necessary to maintain the effectiveness of the diagnosis of COVID-19.

Características de carcaça e qualidade de carne em linhagens da raça Nelore / Carcass and meat quality traits in lineages of Nellore breed

O objetivo deste estudo foi avaliar diferenças entre linhagens da raça Nelore para características de carcaça e qualidade de carne. Foram avaliadas treze linhagens da raça Nelore para as características de peso de carcaça quente, área de olho de lombo, espessura de gordura subcutânea, marmoreio e força de cisalhamento aos 7,14 e 21 dias de maturação. Para isso, foram utilizadas informações fenotípicas de 516 animais da raça Nelore e estimadas as diferenças esperadas na progênie para comparação entre as linhagens. Dentre os genearcas estudados, Golias obteve os melhores valores das diferenças esperadas na progênie para peso de carcaça quente (+1,20kg), área de olho de lombo (+0,88cm), marmoreio (+3,47un) e força de cisalhamento média (-0,09kg) e Akasamu para espessura de gordura subcutânea (+0,05mm). As diferenças entre linhagens da raça Nelore encontradas neste estudo podem ser utilizadas na escolha de touros para melhoria genética de características de carcaça e carne em rebanhos de gado de corte brasileiros.

The aim of this study was to evaluate the differences between lineages of Nellore breed for carcass and meat quality traits. Thirteen lineages of Nellore breed were evaluated from data of carcass and meat quality of 516 animals for estimating the expected progeny difference for hot carcass weight, rib eye area, fat thickness, marbling and shear force values at 7, 14 and 21 days of ageing. The founder Golias reached the better values of expected progeny difference for hot carcass weight (+1.20kg), rib eye area (+0.88cm), marbling (+3.47un) and average shear force (-0,09kg), and Akasamu the better value for fat thickness (+0.05mm). The differences between lineages of Nellore breed found in this study couldbe used to select sires for genetic improvement of carcass and meat quality traits in Brazilian beef cattle herds.