Development and optimization of expected cross value for mate selection problems

In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic characteristics are selected to cross in order to maximize the likelihood of the inheritance of desirable genetic materials to the progeny. Unlike approaches that use phenotypic values for parental selection and evaluate individuals separately, we use a criterion that relies on the genetic architecture of traits and evaluates combinations of genomic information of the pairs of individuals. We introduce the expected cross value (ECV) criterion that measures the expected number of desirable alleles for gametes produced by pairs of individuals sampled from a population of potential parents. We use the ECV criterion to develop an integer linear programming formulation for the parental selection problem. The formulation is capable of controlling the inbreeding level between selected mates. We evaluate the approach or two applications: (i) improving multiple target traits simultaneously, and (ii) finding a multi-parental solution to design crossing blocks. We evaluate the performance of the ECV criterion using a simulation study. Finally, we discuss how the ECV criterion and the proposed integer linear programming techniques can be applied to improve breeding efficiency while maintaining genetic diversity in a breeding program.

Genetic Parameters for Maternal Performance Traits in Commercially Farmed New Zealand Beef Cattle

Simple Summary

Enhancing maternal performance in a beef cattle enterprise can increase overall profitability. Knowledge of the degree of genetic variation in relevant traits is required to inform breeding decisions in commercial environments. The objective of this research was to examine the inheritance of maternal performance traits and to evaluate the trait complementarity among reproduction, live weight, hip height, body condition score and maternal weaning weight in 15-month-old heifers, 2-year-old cows and mature cows using data collected on commercial New Zealand hill country farms. Results from this study indicate that almost no genetic variation exists for pregnancy outcomes in 15-month-old heifers and mature cows under New Zealand farming conditions but there is potential to improve reproductive performance in 2-year-old cows through genetic selection. Cows with greater genetic potential for rebreeding performance after their first calving season were more likely to have greater live weight, hip height and body condition score as heifers but were unlikely to become larger cows at maturity. Cows with genetics for greater maternal weaning weight were more likely to carry lower body condition and those animals tended to show greater reproductive performance.

Abstract

Maternal performance is a major driver of profitability in cow-calf beef cattle enterprises. The aim of this research was to evaluate the inheritance of maternal performance traits and examine the intercorrelation among reproduction, live weight, hip height, body condition and maternal contribution to calf weaning weight in 15-month-old heifers, 2-year-old cows and mature cows in New Zealand beef herds. Data were collected on a total of 14,241 cows and their progeny on five commercial New Zealand hill country farms. Heritabilities were low for reproductive traits in heifers and mature cows (0–0.06) but were greater in 2-year-old cows (0.12–0.21). Body condition scores were lowly (0.15–0.26) and live weights (0.42–0.48) and hip heights (0.47–0.65) highly heritable in heifers, 2-year-old cows and mature cows. Results indicate that 2-year-old cows with higher genetic potential for rebreeding ability may have greater genetic merit for live weight, hip height and body condition as heifers (r_g = 0.19–0.54) but are unlikely to be larger cows at maturity (r_g = −0.27–−0.10). The maternal genetic effect on weaning weight had a heritability of 0.20 and was negatively genetically correlated with body condition score in lactating cows (r_g = −0.55–−0.40) but positively genetically correlated with rebreeding performance (r_g = 0.48).

Interrogating the bovine reproductive tract metagenomes using culture-independent approaches: a systematic review

Undesirable microbial infiltration into the female bovine reproductive tracts, for example during calving or mating, is likely to disturb the commensal microflora. Persistent establishment and overgrowth of certain pathogens induce reproductive diseases, render the female bovine reproductive tract unfavourable for pregnancy or can result in transmission to the foetus, leading to death and abortion or birth abnormalities. This review of culture-independent metagenomics studies revealed that normal microflora in the female bovine reproductive tract is reasonably consistently dominated by bacteria from the phyla Bacteroidetes, Firmicutes, Proteobacteria, following by Actinobacteria, Fusobacteria and Tenericutes. Reproductive disease development in the female bovine reproductive tract was demonstrated across multiple studies to be associated with high relative abundances of bacteria from the phyla Bacteroidetes and Fusobacteria. Reduced bacterial diversity in the reproductive tract microbiome in some studies of cows diagnosed with reproductive diseases also indicated an association between dysbiosis and bovine reproductive health. Nonetheless, the bovine genital tract microbiome remains underexplored, and this is especially true for the male genital tract. Future research should focus on the functional aspects of the bovine reproductive tract microbiomes, for example their contributions to cattle fertility and susceptibility towards reproductive diseases.

Genomic evaluation for novel stayability traits in Nellore cattle

Cow stayability plays a major role on the overall profitability of the beef cattle industry, as it is directly related to reproductive efficiency and cow's longevity. Stayability (STAY63) is usually defined as the ability of the cow to calve at least three times until 76 months of age. This is a late-measured and lowly heritable trait, which consequently constrains genetic progress per time unit. Thus, the use of genomic information associated with novel stayability traits measured earlier in life will likely result in higher prediction accuracy and faster genetic progress for cow longevity. In this study, we aimed to compare pedigree-based and single-step GBLUP (ssGBLUP) methods as well as to estimate genetic correlations between the proposed stayability traits: STAY42, STAY53 and STAY64, which are measured at 52, 64 and 76 months of cow's age, considering at least 2, 3 and 4 calving, respectively. ssGBLUP yielded the highest prediction accuracy for all traits. The heritability estimates for STAY42, STAY53, STAY63 and STAY64 were 0.090, 0.151, 0.152 and 0.143, respectively. The genetic correlations between traits ranged from 0.899 (STAY42 and STAY53) to 0.985 (STAY53 and STAY63). The high genetic correlation between STAY42 and STAY53 suggests that besides being related to cow longevity, STAY53 is also associated with the early-stage reproductive efficiency. Thus, STAY53 is recommended as a suitable selection criterion for reproductive efficiency due to its higher heritability, favourable genetic correlation with other traits, and measured earlier in life, compared with the conventional stayability trait, that is STAY63.

Genetic correlations among weight and cumulative productivity of crossbred beef cows

Mature weight of beef cows in the United States has been increasing as a correlated response to selection for calf growth. Unfavorable genetic correlations between cow weight and various measures of female fertility, stayability, and lifetime production suggest declining cow productivity might also be expected as a correlated response to growth selection. National cattle evaluations, however, show increasing trends for stayability and sustained fertility. Random regression (RR) models were employed to further examine genetic relationships among cow weight and productivity, and to assess cumulative productivity traits observed throughout cows' productive lives. Records were from 13,707 females born in the Germplasm Evaluation (GPE) project and mated to calve first as 2-yr olds. Weights observed at pregnancy testing (n = 65,086) and calf production from each exposure to breeding (n = 71,583) were included in uni- and bivariate RR analyses. Production following each breeding season was added to previous production to obtain cumulative production records for each season that the female was exposed to breeding. Zero was added if the cow failed to produce after a breeding season. The number of pregnancies, calves born and calves weaned, as well as age and weight of weaned calves, were accumulated. Projected age-specific heritability (h2) estimates for cumulative production were low (<0.1) at age 2 but increased with age (0.12 to 0.26 at age 6; 0.32 to 0.48 at age 10). Estimated h2 for cow weight were high, fluctuating between 0.6 and 0.7 from ages 2 through 10. Genetic correlations (rg) were positive among all ages within each trait. Between ages 3 and 9, estimated rg were negative between cumulative weaning productivity and cow weight. The correlations were usually weak enough (<-0.2) that small correlated declines from following yearling weight trends might be overcome by culling females after their first reproductive failure. More noticeable increases might be realized by selection among sires with EBV based on productivity of several daughters. The RR EBV for cow weight and cumulative weight weaned represent major sources of variation in cow costs and income, and can be incorporated into economic selection indexes to project differences in cow profitability and value at any age. The RR approach utilizes all available records, enabling later productivity to be projected from observations on young cows.

Economic selection index development for Beefmaster cattle II: General-purpose breeding objective

An economic selection index was developed for Beefmaster cattle in a general-purpose production system in which bulls are mated to a combination of heifers and mature cows, with resulting progeny retained as replacements or sold at weaning. National average prices from 2010 to 2014 were used to establish income and expenses for the system. Genetic parameters were obtained from the literature. Economic values were estimated by simulating 100,000 animals and approximating the partial derivatives of the profit function by perturbing traits 1 at a time, by 1 unit, while holding the other traits constant at their respective means. Relative economic values for the objective traits calving difficultly direct (CDd), calving difficulty maternal (CDm), weaning weight direct (WWd), weaning weight maternal (WWm), mature cow weight (MW), and heifer pregnancy (HP) were -2.11, -1.53, 18.49, 11.28, -33.46, and 1.19, respectively. Consequently, under the scenario assumed herein, the greatest improvements in profitability could be made by decreasing maintenance energy costs associated with MW followed by improvements in weaning weight. The accuracy of the index lies between 0.218 (phenotypic-based index selection) and 0.428 (breeding values known without error). Implementation of this index would facilitate genetic improvement and increase profitability of Beefmaster cattle operations with a general-purpose breeding objective when replacement females are retained and with weaned calves as the sale end point.

Divergent breeding values for fatness or residual feed intake in Angus cattle. 5. Cow genotype affects feed efficiency and maternal productivity

Cow bodyweight gain, calf weaning weight, feed intake and maternal productivity of 500 Angus cows, in 64 replicate groups, were measured over three parities at two locations (Struan and Vasse) as part of the Beef CRC Maternal Productivity Project. The cows were sourced as heifers from the top and bottom 10% of BREEDPLAN Rib Fat EBV (High-Fat and Low-Fat), and from High and Low residual feed intake (RFI) selection lines (High-RFI and Low-RFI). Each of the four genotypes were run under High- and Low-Nutrition (measured as feed on offer) at both sites. The High-Fat cows were 7% more efficient at producing weaner calves under Low-Nutrition than were the Low-Fat cows. This was driven primarily by the 4% difference between the lines in weaning rate. When weaning rate differences were accounted for (as covariate), there was no difference between the Fat lines in the efficiency of weaner weight production. When the weight gain of the cow was included as an output in addition to calf weaning weight, there was also no difference between the Fat lines in efficiency. Low-RFI cows were always more efficient at producing weaner calves than were the High-RFI cows. This was primarily driven through a 7% reduction in annual feed intake (across both nutrition treatments). However, the Low-RFI cows were leaner, had 6.3% lower weaning rate and calved on average 5.4 days later than did the High-RFI cows. Furthermore, the largest differences in feed intake were in spring when feed availability is greatest. In the context of the results herein, a balanced breeding program should include selection for improved reproduction and low RFI.

A review of factors influencing key biological components of maternal productivity in temperate beef cattle

Cow–calf efficiency or maternal productivity is highly correlated with total system efficiency of beef production. Balancing the needs of the cow herd with other production components is a daily challenge beef producers address to maximise the number of calves born and raised to weaning and, in turn, maximise maternal productivity. Pressure to satisfy modern consumer needs has shifted selection emphasis to production traits at the expense of fitness traits allowing adaptability to decline. Balancing the needs of the cow herd with production objectives presents cow–calf producers with the challenge of genetically tailoring their cattle to modern needs, while sustainably managing these cattle and natural resources. This balancing act is highlighted by the debate surrounding the application of residual feed intake to reduce costs associated with provision of feed for beef production. Some uncertainty surrounds the relationships between efficiency, production and maternal productivity traits. This review examines key components and definitions of maternal productivity. Management decisions as well as cow and calf traits have important interacting impacts on maternal productivity. Achieving a calving interval of 365 days represents the single most important production issue affecting maternal productivity and is dependent on heifer development during early life and energy reserves (i.e. body condition score) in subsequent years. Management issues such as calving date and selection decisions interact with environmental factors such as photoperiod and production traits such as feed intake, and previous production levels, to influence heifer development and cow body energy reserves. Some proposed definitions of maternal productivity simply include weaning weight per cow mated which can be averaged over all progeny weaned during a cow’s lifetime. Ideally, a definition should include the inputs and outputs of maternal productivity. Some definitions express maternal productivity over large time scales, e.g. a cow’s productive lifetime. Most definitions focus on the cow–calf unit, while some include progeny growth and feed intake to slaughter. This review recommends a definition that focuses on the cow–calf unit, as follows: (weight of calf weaned and cow weight change)/(metabolisable energy intake per cow and calf unit). This definition has the capacity to be scaled up, to include progeny postweaning production, as well as being applicable over varying time scales (e.g. 1 year to a cow’s whole productive life). Improvements in all facets of maternal productivity using this definition can be expected to improve beef-production efficiency.

Genomic analysis of stayability in Nellore cattle

Stayability, which can be defined as the probability of a cow calving at a certain age when given the opportunity, is an important reproductive trait in beef cattle because it is directly related to herd profitability. The objective of this study was to estimate genetic parameters and to identify possible genomic regions associated with the phenotypic expression of stayability in Nellore cows. The variance components were estimated by Bayesian inference using a threshold animal model that included the systematic effects of contemporary group and sexual precocity and the random effects of animal and residual. The SNP effects were estimated by the single-step genomic BLUP method using information of 2,838 animals (2,020 females and 930 sires) genotyped with the Illumina High-Density BeadChip Array (San Diego, CA, USA). The variance explained by windows formed by 200 consecutive SNPs was used to identify genomic regions of largest effect on the expression of stayability. The heritability was 0.11 ± 0.01 when A matrix (pedigree) was used and 0.14 ± 0.01 when H matrix (relationship matrix that combines pedigree information and SNP data) was used. A total of 147 candidate genes for stayability were identified on chromosomes 1, 2, 5, 6, 9 and 20 and on the X chromosome. New candidate regions for stayability were detected, most of them related to reproductive, immunological and central nervous system functions.

Genetic relationship between purebred and crossbred sow longevity

Background

The overall breeding objective for a nucleus swine selection program is to improve crossbred commercial performance. Most genetic improvement programs are based on an assumed high degree of positive relationship between purebred performance in a nucleus herd and their relatives’ crossbred performance in a commercial herd. The objective of this study was to examine the relationship between purebred and crossbred sow longevity performance. Sow longevity was defined as a binary trait with a success occurring if a sow remained in the herd for a certain number of parities and including the cumulative number born alive as a measure of reproductive success. Heritabilities, genetic correlations, and phenotypic correlations were estimated using THRGIBBS1F90.

Results

Results indicated little to no genetic correlations between crossbred and purebred reproductive traits. This indicates that selection for longevity or lifetime performance at the nucleus level may not result in improved longevity and lifetime performance at the crossbred level. Early parity performance was highly correlated with lifetime performance indicating that an indicator trait at an early parity could be used to predict lifetime performance. This would allow a sow to have her own record for the selection trait before she has been removed from the herd.

Conclusions

Results from this study aid in quantifying the relationship between purebred and crossbred performance and provide information for genetic companies to consider when developing a selection program where the objective is to improve crossbred sow performance. Utilizing crossbred records in a selection program would be the best way to improve crossbred sow productivity.

Correlation between milk suckled and growth of calves of ogaden cattle at one, three and six months of age, east Ethiopia

This study was conducted with the aim to evaluate correlation between milk suckled and growth of calves of Ogaden cattle managed in Beef farm at Harmaya University, eastern Ethiopia. Data was collected by a method of weight-suckle-weight once in a week from 269 calves born from 1994 to 2004. Weight of calves at birth, first, third and sixth months of age were 21.5 ± 3.3, 36.3 ± 4.4, 57.4 ± 11.0 and 91.7 ± 14.7 kg (mean ± SD). The daily weight gain of calves to first, third and six months of age were 0.5 ± 0.1, 0.4 ± 0.1 and 0.4 ± 0.1 kg day^-1, respectively. The amount of milk suckled to first, third and six months of age were 5.0 ± 1.2, 4.6 ± 1.1 and 2.7 ± 0.7 kg day^-1. The milk conversion efficiency to a kg body weight at first and third months of age was 10.2 ± 2.5 and 11.6 ± 2.9, respectively. Correlation between birth weight and daily milk suckled at one, three and six months of age were 0.34 (P< 0.001), 0.22 (P< 0.001) and 0.26 (P<0.05), respectively. The correlation between weight (1 and 3 months) and daily milk suckled at first and third months of age were positive with correlation value of 0.45 (P< 0.001) and 0.43 (P< 0.001), respectively. Correlation between weight change (1 and 3 months) and daily milk suckled at first and third months of age were 0.41 (P< 0.001) and 0.38 (P< 0.001), respectively. Positive association was observed between daily weigh gain and daily milk suckled at first and third months of age with correlation value of 0.44 (P< 0.001) and 0.29 (P< 0.001), respectively. Weight at three months was significantly correlated (P< 0.001) to weight at four, five and six months of age with correlation value of 0.65, 0.63 and 0.53, respectively. The significant correlation between milk suckled and weight at three months; and weight at three months and weight at weaning indicate significant role of milk in determining weaning weight of Ogaden cattle.

Análise bayesiana na estimação de correlações genéticas entre escores visuais e características reprodutivas de bovinos Nelore utilizando modelos linear-limiar

Estimaram-se as correlações genéticas entre os escores visuais e as características reprodutivas, utilizando a estatística bayesiana sob modelo animal linear-limiar, em bovinos da raça Nelore. Foram estudadas características categóricas morfológicas, avaliadas visualmente aos oito, 15 e 22 meses de idade; e características contínuas de perímetro escrotal padronizado aos 365 e 450 dias de idade, além da idade ao primeiro parto. As estimativas de correlações genéticas foram de sentido favorável à seleção, apresentando magnitudes moderadas, sugerindo que a seleção de animais para um biótipo desejável pode levar a animais com maior fertilidade e precocidade sexual. As estimativas de correlação genética para o perímetro escrotal padronizado aos 450 dias e a idade ao primeiro parto com as características morfológicas avaliadas aos 22 meses de idade foram maiores do que as obtidas entre as características de escores visuais avaliadas aos oito e 15 meses de idade. A utilização de escores visuais como critério de seleção trará progresso genético também para as características reprodutivas.

Reducing bias in maintenance energy expected progeny difference by accounting for selection on weaning and yearling weights

Maintenance energy requirements of cattle can be predicted from published equations utilizing metabolic BW and milk production potential. Metabolic BW is a function of BW at a constant fat percentage or BCS. Pedigree and performance records can be used in random regression models to predict genetic merit for metabolic BW and milk production potentials. The purpose of this study was to present a methodology for predicting mature cow maintenance energy EPD using mature cow BW and BCS and accounting for prior selection of replacement females at weaning and yearling ages. Variance components were obtained for direct and maternal effects on weaning weight, direct effects on postweaning BW gain, and direct coefficients for random regression on mature weights (MW) adjusted for BCS. These BW were transformed into metabolic BW by taking BW to the power of 0.75, variance components were estimated for metabolic BW, and were then used to predict breeding values from which cow maintenance energy EPD could be derived. Data used in this analysis were obtained from the Red Angus Association of America and limited to herds with MW and corresponding BCS observations. The data set included 52,338 BW records on 21,103 individuals. Weaning and yearling contemporaries to those with MW observations, but with no MW records themselves, were included to account for selection occurring before maturity. Heritability estimates for weaning weight direct, weaning weight maternal, and postweaning BW gain were 0.18 +/- 0.02, 0.16 +/- 0.02, and 0.18 +/- 0.02, respectively. Mature BW observed at 2, 3, 4, 5, and 6 yr of age had heritability estimates of 0.45 +/- 0.03, 0.44 +/- 0.03, 0.49 +/- 0.03, 0.66 +/- 0.04, and 0.62 +/- 0.05, respectively. Correlations between weaning weight direct and MW ranged from 0.65 +/- 0.07 to 0.82 +/- 0.04, and correlations between MW at different ages ranged from 0.95 +/- 0.03 to 0.99 +/- 0.01. The genetic correlations between postweaning BW gain and MW ranged from 0.48 +/- 0.06 to 0.59 +/- 0.06. The 15-yr genetic increase in metabolic BW was 3.6 kg(0.75), greater than the value of 0.23 kg(0.75) obtained from the same data ignoring weaning and yearling contemporaries with unobserved MW, the approach currently used in the derivation of cow maintenance EPD published by the Red Angus Association of America.

Comparação entre análises para permanência no rebanho de vacas Nelore utilizando modelo linear e modelo de limiar

Foram obtidas estimativas de herdabilidade e preditas diferenças esperadas na progênie para probabilidade de permanência no rebanho (stayability) de 4180 touros com filhas na base de dados do Programa de Melhoramento Genético da Raça Nelore. Modelo de limiar e modelo linear foram utilizados sob análise Bayesiana via software multiple-trait Gibbs sampler for animal models. A implementação adotada considerou tamanho de cadeia de Gibbs de 225 mil, período de descarte amostral de 25 mil e tomada de amostra a cada mil rodadas. As estimativas de herdabilidade foram de menor magnitude para o modelo linear, 0,065, contra 0,158 sob modelo de limiar. Quando transformadas para escala normal subjacente, o valor obtido ficou em 0,13±0,05, bem próximo àquele encontrado sob modelo de limiar. A correlação entre classificações foi de 97%. O modelo de análise considerado para stayability, sob enfoque bayesiano, parece não influenciar a classificação dos animais quanto aos valores genéticos preditos. Análises sob modelo linear, com reduzido tempo de processamento, poderiam ser preferidas bastando transformar a escala da característica para obter a estimativa de herdabilidade.