Genetic (co-)variation of methane emissions, efficiency, and production traits in Danish Holstein cattle along and across lactations

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Selecting for Feed Efficient Cows Will Help to Reduce Methane Gas Emissions

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Ingresos corrientes, empobrecimiento y problemas socioeconómicos en la península de Yucatán (2016-2022)

La península de Yucatán está integrada por los estados mexicanos de Campeche, Quintana Roo y Yucatán, región rica en flora, fauna y bellezas naturales. Esto ha sido el atractivo para que sea visitada por turistas nacionales y extranjeros. De igual modo, la inversión en infraestructura ha sido creciente y por tanto, se han creado empleos, ya sea directos o indirectos. Los trabajadores reciben salarios para poder satisfacer sus necesidades básicas como la alimentación, ente otros. Sin embargo, la pandemia COVID-19 y la más reciente guerra entre Rusia y Ucrania en 2022 han traído una crisis económica y social grave, y esto no es solo para la península de Yucatán, ya que, al estar en un mundo globalizado, lo que sucede fuera del país tiene su afectación en la nación mexicana y sus regiones. En este sentido, esta investigación tiene como objetivo analizar las condiciones socioeconómicas de los estados que forman la península de Yucatán, en específico la evolución de los salarios pagados y cómo han impactado en la pobreza, marginación y desigualdad social. Para cumplir con este objetivo, se consultan fuentes de información secundarias de instituciones oficiales como el Instituto Nacional de Estadística y Geografía (INEGI) y, en ciertos casos, se construyen indicadores para conocer los cambios en las variables consideradas. Entre los principales resultados, se menciona que considerando el periodo 2018-2022, se han perdido empleos de altos ingresos para incrementarse los salarios bajos. Esto, sin duda ha repercutido en el incremento de la pobreza multidimensional, específicamente en la pobreza extrema y la pobreza laboral. De igual modo, los índices de marginación y desigualdad social se han incrementado, especialmente, durante y después de la pandemia. Se observa que las transferencias que incluyen la ayuda social han contribuido a que los indicadores de pobreza no se eleven significativamente. También las remesas recibidas y la inversión extranjera directa han mitigado esta problemática. Entre las principales conclusiones se puede mencionar que a pesar de que el gobierno federal ha dado más ayuda social a la región, las problemáticas socioeconómicas se han incrementado. Si la crisis económica mundial provocada por la guerra Rusia-Ucrania no se resuelve pronto, las expectativas económicas a futuro no serán favorables para la población; en pocas palabras, más empobrecimiento y desigualdad. Entre las principales recomendaciones está garantizar que el salario no pierda su poder adquisitivo ya que ayuda a disminuir la pobreza multidimensional y pobreza laboral. De igual manera, la ayuda social por parte del gobierno, no debe interrumpirse pues ha contribuido a que el empobrecimiento no sea mayor

Estimación de parámetros genéticos para características de crecimiento en borregos Katahdin usando diferentes modelos

Genetic parameters for growth traits of Katahdin lambs were estimated using six variants of the animal model. Data on birth weight (BW; n= 13,099), weaning weight adjusted to 75 d (WW; n=11,509) and postweaning weight adjusted to 120 d (AW; n=6,886) were collected for seven years (2004-2010) in 20 states across Mexico. Analyses were carried out by ignoring or including maternal effects. The simplest model included the direct additive genetic effect as the only random effect. The most complete model included direct and maternal genetic effects, their covariance, and the maternal permanent environmental effect. Selection of the best model was based on likelihood-ratio test. When maternal effects were not taken into account, estimates of direct heritability and direct genetic variance were overestimated for all traits. Direct heritability estimates for the best model were 0.18 ± 0.03, 0.30 ± 0.04, and 0.20 ± 0.05 for BW, WW and AW, respectively. Maternal heritability estimates also varied depending on the model; estimates ranged from 0.05 to 0.23, 0.00 to 0.12, and 0.09 to 0.25 for BW, WW and AW. Ignoring maternal effects in the model would result in inaccurate genetic evaluation for growth traits in Katahdin sheep.Se estimaron parámetros genéticos para características de crecimiento en corderos Katahdin, usando seis variantes del modelo animal. Se usó información de pesos al nacimiento (BW; n= 13,099), al destete ajustado a 75 d (WW; n= 11,509) y posdestete ajustado a 120 d (AW; n= 6,886) tomada durante 7 años (2004-2010) en 20 estados de la República Mexicana. Los análisis se hicieron ignorando o incluyendo efectos maternos. El modelo más sencillo incluyó el efecto genético aditivo directo como el único efecto aleatorio. El modelo más completo incluyó los efectos genéticos directo y materno, la covarianza entre ellos, y el efecto del ambiente permanente materno. Para seleccionar el mejor modelo se usó la prueba de razón de verosimilitud. Cuando los efectos maternos no fueron incluidos en el modelo, los estimadores de la heredabilidad directa y de la varianza genética directa resultaron sobreestimados. Las heredabilidades directas con el mejor modelo fueron 0.18 ± 0.03, 0.30 ± 0.04 y 0.20 ± 0.05 para BW, WW y AW, respectivamente. Las heredabilidades maternas también variaron dependiendo del modelo, de 0.05 a 0.23, 0.00 a 0.12, y 0.09 a 0.25 para BW, WW y AW. El ignorar los efectos maternos en el modelo resultaría en una evaluación genética equivocada para las características de crecimiento en borregos Katahdin

Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency.

BACKGROUND Sharing individual phenotype and genotype data between countries is complex and fraught with potential errors, while sharing summary statistics of genome-wide association studies (GWAS) is relatively straightforward, and thus would be especially useful for traits that are expensive or difficult-to-measure, such as feed efficiency. Here we examined: (1) the sharing of individual cow data from international partners; and (2) the use of sequence variants selected from GWAS of international cow data to evaluate the accuracy of genomic estimated breeding values (GEBV) for residual feed intake (RFI) in Australian cows. RESULTS GEBV for RFI were estimated using genomic best linear unbiased prediction (GBLUP) with 50k or high-density single nucleotide polymorphisms (SNPs), from a training population of 3797 individuals in univariate to trivariate analyses where the three traits were RFI phenotypes calculated using 584 Australian lactating cows (AUSc), 824 growing heifers (AUSh), and 2526 international lactating cows (OVE). Accuracies of GEBV in AUSc were evaluated by either cohort-by-birth-year or fourfold random cross-validations. GEBV of AUSc were also predicted using only the AUS training population with a weighted genomic relationship matrix constructed with SNPs from the 50k array and sequence variants selected from a meta-GWAS that included only international datasets. The genomic heritabilities estimated using the AUSc, OVE and AUSh datasets were moderate, ranging from 0.20 to 0.36. The genetic correlations (rg) of traits between heifers and cows ranged from 0.30 to 0.95 but were associated with large standard errors. The mean accuracies of GEBV in Australian cows were up to 0.32 and almost doubled when either overseas cows, or both overseas cows and AUS heifers were included in the training population. They also increased when selected sequence variants were combined with 50k SNPs, but with a smaller relative increase. CONCLUSIONS The accuracy of RFI GEBV increased when international data were used or when selected sequence variants were combined with 50k SNP array data. This suggests that if direct sharing of data is not feasible, a meta-analysis of summary GWAS statistics could provide selected SNPs for custom panels to use in genomic selection programs. However, since this finding is based on a small cross-validation study, confirmation through a larger study is recommended

Novel genetic parameters for genetic residual feed intake in dairy cattle using time series data from multiple parities and countries in North America and Europe.

Residual feed intake is viewed as an important trait in breeding programs that could be used to enhance genetic progress in feed efficiency. In particular, improving feed efficiency could improve both economic and environmental sustainability in the dairy cattle industry. However, data remain sparse, limiting the development of reliable genomic evaluations across lactation and parity for residual feed intake. Here, we estimated novel genetic parameters for genetic residual feed intake (gRFI) across the first, second, and third parity, using a random regression model. Research data on the measured feed intake, milk production, and body weight of 7,379 cows (271,080 records) from 6 countries in 2 continents were shared through the Horizon 2020 project GenTORE and Resilient Dairy Genome Project. The countries included Canada (1,053 cows with 47,130 weekly records), Denmark (1,045 cows with 72,760 weekly records), France (329 cows with 16,888 weekly records), Germany (938 cows with 32,614 weekly records), the Netherlands (2,051 cows with 57,830 weekly records), and United States (1,963 cows with 43,858 weekly records). Each trait had variance components estimated from first to third parity, using a random regression model across countries. Genetic residual feed intake was found to be heritable in all 3 parities, with first parity being predominant (range: 22-34%). Genetic residual feed intake was highly correlated across parities for mid- to late lactation; however, genetic correlation across parities was lower during early lactation, especially when comparing first and third parity. We estimated a genetic correlation of 0.77 ± 0.37 between North America and Europe for dry matter intake at first parity. Published literature on genetic correlations between high input countries/continents for dry matter intake support a high genetic correlation for dry matter intake. In conclusion, our results demonstrate the feasibility of estimating variance components for gRFI across parities, and the value of sharing data on scarce phenotypes across countries. These results can potentially be implemented in genetic evaluations for gRFI in dairy cattle

The Resilient Dairy Genome Project - a general overview of methods and objectives related to feed efficiency and methane emissions.

The Resilient Dairy Genome Project (RDGP) is an international large-scale applied research project that aims to generate genomic tools to breed more resilient dairy cows. In this context, improving feed efficiency and reducing greenhouse gases from dairy is a high priority. The inclusion of traits related to feed efficiency (e.g., dry matter intake [DMI]) or greenhouse gases (e.g., methane emissions [CH4]) relies on available genotypes as well as high quality phenotypes. Currently, 7 countries, i.e., Australia [AUS], Canada [CAN], Denmark [DNK], Germany [DEU], Spain [ESP], Switzerland [CHE], and United States of America [USA] contribute with genotypes and phenotypes including DMI and CH4. However, combining data is challenging due to differences in recording protocols, measurement technology, genotyping, and animal management across sources. In this study, we provide an overview of how the RDGP partners address these issues to advance international collaboration to generate genomic tools for resilient dairy. Specifically, we describe the current state of the RDGP database, data collection protocols in each country, and the strategies used for managing the shared data. As of February 2022, the database contains 1,289,593 DMI records from 12,687 cows and 17,403 CH4 records from 3,093 cows and continues to grow as countries upload new data over the coming years. No strong genomic differentiation between the populations was identified in this study, which may be beneficial for eventual across-country genomic predictions. Moreover, our results reinforce the need to account for the heterogeneity in the DMI and CH4 phenotypes in genomic analysis

Supplemental Figure S1

Supplemental Figure S1. Manuscript "Genome-wide association study for methane emission traits in Danish Holstein cattle" Journal of Dairy Science. In pressTHIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV