Livestock Breeding Programs Research Articles

Challenges and opportunities to livestock breeding programmes in India.

Animal breeding in India has a long and chequered history. High pressure on agricultural land and increasing human population opened a new opportunity for the livestock and poultry sector as a promising food industry. Productivity of livestock in India is low due to less coverage of livestock under structured breeding programmes, inadequate nutrition and its entanglement with several socio-economic issues. A bottom-up approach to breeding policy formulation addressing local needs is required with assured flow of investments. Cattle slaughter is banned in India; hence, a legal policy to curb widespread indiscriminate mating is required which may incur substantial financial and infrastructural burdens for castration of stray males and strengthening of cow rehabilitation centres. Genetic evaluation of indigenous cattle with progeny testing (PT) requires substantial financial support, without affecting the already existing PT for exotic cattle breeds used in the local cross-breeding programmes and PT of new genotypes obtained from crosses of exotic and local breeds of cattle and for purebred buffaloes. Small ruminants need special attention due to their socio-economic importance in rural and often highly disadvantaged communities and because they are the second most important meat-producing species after poultry. Genetic improvement of small ruminants should be accompanied by attention to shrinking grazing resources which would require strong political will together with financial support. The outreach of breeding programmes for small ruminants is currently limited; there is also a lack of linkage between the market and producers that discourages farmers from adopting clear breeding objectives like improvement in growth rate, as animals are seldom sold on weight basis. Apart from government agencies, involvement of private sector, non-government organizations, local co-operatives, self-help groups and self-sustainable community-based breeding programmes can strengthen market linkages. Strengthening of the existing infrastructure along with technical input and skilled manpower is essential for achieving the breeding objectives.

Genotyping strategies of selection candidates in livestock breeding programmes.

Benefits of genomic selection (GS) in livestock breeding operations are well known particularly where traits are sex-limited, hard to measure, have a low heritability and/or measured later in life. Sheep and beef breeders have a higher cost:benefit ratio for GS compared to dairy. Therefore, strategies for genotyping selection candidates should be explored to maximize the economic benefit of GS. The aim of the paper was to investigate, via simulation, the additional genetic gain achieved by selecting proportions of male selection candidates to be genotyped via truncation selection. A two-trait selection index was used that contained an easy and early-in-life measurement (such as post-weaning weight) as well as a hard-to-measure trait (such as intra-muscular fat). We also evaluated the optimal proportion of female selection candidates to be genotyped in breeding programmes using natural mating and/or artificial insemination (NatAI), multiple ovulation and embryo transfer (MOET) or juvenile in vitro fertilization and embryo transfer (JIVET). The final aim of the project was to investigate the total dollars spent to increase the genetic merit by one genetic standard deviation (SD) using GS and/or reproductive technologies. For NatAI and MOET breeding programmes, females were selected to have progeny by 2years of age, while 1-month-old females were required for JIVET. Genomic testing the top 20% of male selection candidates achieved 80% of the maximum benefit from GS when selection of male candidates prior to genomic testing had an accuracy of 0.36, while 54% needed to be tested to get the same benefit when the prior selection accuracy was 0.11. To achieve 80% of the maximum benefit in female, selection required 66%, 47% and 56% of female selection candidates to be genotyped in NatAI, MOET and JIVET breeding programmes, respectively. While JIVET and MOET breeding programmes achieved the highest annual genetic gain, genotyping male selection candidates provides the most economical way to increase rates of genetic gain facilitated by genomic testing.

Role of technological innovation in livestock breeding programmes: a case of cereal-sheep system

Farming suffers from a crisis based on lack of profitability. This situation is more relevant in small farms. Farmers have implemented local breeding programmes that have shown good results in terms of biodiversity preservation, increase of technological innovation and improvements in farm’s viability. The objective of this study is to compare technological characteristics among groups of farms, according to their breeding programmes and the viability of dairy sheep system. Furthermore, the role of technologies by means of a canonical discriminant model was analysed. The information from 157 dairy sheep farms in Castilla La Mancha, Spain was used. Technologies were grouped in six technological areas: Management, animal feeding, animal health and biosecurity, land use, milking equipment and dairy, reproduction and genetic. Four canonical discriminant models have been used to classify farms according to technological indicators [Model 1], structural [Model 2], productive [Model 3] and a global model including all the variables (18) [Model 4], by considering the genetic programme and their viability. Afterwards, the relationship among the discriminated groups was analysed using cluster analysis. The canonical model built according to the set of technologies classified a 69.43% of farms [Model 1]. Therefore, the farms that implement a breeding programme (BP) increase the likelihood of viability. First, BP requires higher levels of technological innovation in management and genetics-reproduction. Then, such advances should be implemented in milking equipment and animal health and biosecurity. To conclude, BP is a key factor in the success of technological adoption.HighlightsTechnology adoption plays a strategical role in sheep production systems.Breeding program promotes higher global technological level.Likelihood of viability in dairy sheep farms increases with implementation of a breeding program.

A Strategy To Exploit Surrogate Sire Technology in Livestock Breeding Programs.

In this work, we performed simulations to develop and test a strategy for exploiting surrogate sire technology in animal breeding programs. Surrogate sire technology allows the creation of males that lack their own germline cells, but have transplanted spermatogonial stem cells from donor males. With this technology, a single elite male donor could give rise to huge numbers of progeny, potentially as much as all the production animals in a particular time period. One hundred replicates of various scenarios were performed. Scenarios followed a common overall structure but differed in the strategy used to identify elite donors and how these donors were used in the product development part. The results of this study showed that using surrogate sire technology would significantly increase the genetic merit of commercial sires, by as much as 6.5 to 9.2 years’ worth of genetic gain compared to a conventional breeding program. The simulations suggested that a strategy involving three stages (an initial genomic test followed by two subsequent progeny tests) was the most effective of all the strategies tested. The use of one or a handful of elite donors to generate the production animals would be very different to current practice. While the results demonstrate the great potential of surrogate sire technology there are considerable risks but also other opportunities. Practical implementation of surrogate sire technology would need to account for these.

Physical characteristics of Kosali breed of cattle in its native tract

Kosali, the first breed of cattle from Chhattisgarh, was registered as 36th breed. Characterization is essential to guide decision-making in livestock development and breeding programmes. Hence, a survey was carried out to characterize the Kosali breed of cattle in Central Plain Region of Chhattisgarh state. The coat colour of most animals was red followed by white and black. Mostly muzzles, tail switch, eyelashes, and hooves were black in colour. Body size, hump, dewlap, naval flap, penis sheath flap, udder and teats were small in size. Horns were stumpy, small and slightly inward and ears were horizontal. The estimated average live weight of adult female and male were 168.7±2.82 and 212.5±3.8 kg, respectively. The mean linear measurements of female vs male Kosali cattle were height at wither (99.79±2.76 vs 103.4±2.11 cm), body length (96.56±1.87 vs 99.89±2.32 cm) and chest girth (119.98±1.98 vs 137.12±2.8 cm). Kosali cattle are smaller in size and are well adapted to the existing agroclimatic conditions of the region. Appropriate breeding strategies and conservation models should be designed for overall improvement of this breed.

Genetic and nongenetic profiling of milk pregnancy-associated glycoproteins in Holstein cattle

Pregnancy-associated glycoproteins (PAG) are secreted by the trophoblast and are detectable in maternal circulation around the time of attachment of the fetal placenta, as well as in blood and milk throughout gestation. The understanding of the genetic mechanisms controlling PAG levels can confer advantages for livestock breeding programs given the precocity and the ease of obtaining this phenotype from routine pregnancy diagnosis. The aim of this study was to characterize PAG levels by estimating genetic parameters and correlations with other dairy traits, and to identify genomic regions and candidate genes associated with PAG levels in milk. The PAG data consisted of pregnancy diagnoses using commercial assays from 2012 to 2017, and genotype data consisted of 54,123 SNP markers for 2,352 individuals (embryos and dams). The model included contemporary group (herd, year, and season) and embryo age as fixed effects, and random embryonic (direct) and maternal (indirect) genetic effects. Using genomic data, the estimated heritability for direct and maternal genetic effects (± standard deviations) were 0.23 ± 0.05 and 0.11 ± 0.05, respectively. The genetic correlation between these effects was almost zero (0.001 ± 0.06). A preliminary analysis revealed low correlations between milk PAG levels and other dairy traits. The genome-wide association analysis was performed using 2 approaches: single-marker and single-step using all markers. Four genomic regions with direct genetic effects were detected on Bos taurus autosome (BTA) 6, BTA7, BTA19, and BTA29 of the embryonic genome. The BTA29 locus was within the bovine PAG gene cluster, suggesting a cis-regulatory quantitative trait locus on the PAG expression. However, other associations, without an obvious link to PAG expression, could be related to the transportation of PAG and their concentration in milk. Only 1 region from the maternal genome, on BTA4, had a significant indirect effect, where WNT2 is a candidate gene related to placenta vascularization and gestation health. Collectively, our results suggest a moderate genetic control of milk PAG levels from both maternal and fetal genomes, but larger studies are needed to fully evaluate the usefulness of milk PAG in the genetic evaluation of fetal growth and cow fertility.

35 Software Development for Deterministic Prediction of Selection Response in Livestock Breeding Programs Using Genomic Information.

Theory to predict selection response in traditional livestock breeding programs has been well developed, validated and implemented in software in the past decades, for example in SelAction (Rutten et al. 2002), which has been successful as a tool to predict selection response in traditional livestock breeding programs for a wide range of population structures and selection strategies. This software used standard quantitative genetics theory and selection index theory to develop deterministic recursive equations, which model changes of trait means and variance-covariance structures to predict asymptotic response to multiple trait selection using best linear unbiased prediction (BLUP) estimated breeding values (EBV). Nowadays genetic improvement can further be enhanced by genomic predictions, which provide more accurate estimates of breeding values of animals in their earlier life and can improve the efficiency of breeding programs. While statistical methods to estimate genomic breeding values are now widely available, optimizing the use of genomics in practical livestock breeding programs is limited due to the lack of computer software that implements available theories. We're hereby to present a computer program that extends SelAction. Genomic information is included as the average phenotype of groups of individuals with both genotypic and phenotypic information following Wientjes et al. (2016). The heterogeneity of genomic information is considered in terms of the degree of relationship between selection candidates and the individuals that are both genotyped and phenotyped (van der Werf et al., 2015). This software can be used by breeders to reliably compare alternative breeding programs and for investment decisions for breeding programs that include genomic information.

Genome-wide genotyping uncovers genetic profiles and history of the Russian cattle breeds.

One of the most economically important areas within the Russian agricultural sector is dairy and beef cattle farming contributing about $11 billion to the Russian economy annually. Trade connections, selection and breeding have resulted in the establishment of a number of breeds that are presumably adapted to local climatic conditions. Little however is known about the ancestry and history of Russian native cattle. To address this question, we genotyped 274 individuals from 18 breeds bred in Russia and compared them to 135 additional breeds from around the world that had been genotyped previously. Our results suggest a shared ancestry between most of the Russian cattle and European taurine breeds, apart from a few breeds that shared ancestry with the Asian taurines. The Yakut cattle, belonging to the latter group, was found to be the most diverged breed in the whole combined dataset according to structure results. Haplotype sharing further suggests that the Russian cattle can be divided into four major clusters reflecting ancestral relations with other breeds. Herein, we therefore shed light on to the history of Russian cattle and identified closely related breeds to those from Russia. Our results will facilitate future research on detecting signatures of selection in cattle genomes and eventually inform future genetics-assisted livestock breeding programs in Russia and in other countries.

Vitrification, not cryoprotectant exposure, alters the expression of developmentally important genes in in vitro produced porcine blastocysts

The vitrification of embryos is common practice in advanced livestock breeding programs and in human fertility clinics. Recent studies have revealed that vitrification results in aberrant expression of a number of stress related genes. However, few studies have examined the effect that vitrification has on developmentally important genes, and none have been conducted in porcine embryos. The aim of this study was to determine the effects that different vitrification procedures and cryoprotectant combinations have on the expression of imprinted genes in in vitro produced (IVP) porcine blastocysts. The transcript levels of insulin-like growth factor 2 (IGF2) were lower in all groups of vitrified blastocysts compared to that in non-vitrified control blastocysts (P < 0.05). Expression levels of IGF2 and IGF2 receptor (IGF2R) in blastocysts that had been exposed to cryoprotectants without being vitrified were similar to that in non-vitrified control blastocysts (P > 0.05). Furthermore, blastocysts vitrified using ethylene glycol and propanediol combined, and those vitrified in a closed device, had IGF2R transcript levels similar to that in non-vitrified control blastocysts (P > 0.05). In conclusion, vitrification, but not exposure to cryoprotectants, caused aberrant expression of the imprinted genes IGF2 and IGF2R. Vitrification protocols that incorporated propanediol or a closed device were found to be least disruptive of gene expression in IVP porcine blastocysts.

Peptide biomarkers used for the selective breeding of a complex polygenic trait in honey bees

We present a novel way to select for highly polygenic traits. For millennia, humans have used observable phenotypes to selectively breed stronger or more productive livestock and crops. Selection on genotype, using single-nucleotide polymorphisms (SNPs) and genome profiling, is also now applied broadly in livestock breeding programs; however, selection on protein/peptide or mRNA expression markers has not yet been proven useful. Here we demonstrate the utility of protein markers to select for disease-resistant hygienic behavior in the European honey bee (Apis mellifera L.). Robust, mechanistically-linked protein expression markers, by integrating cis- and trans- effects from many genomic loci, may overcome limitations of genomic markers to allow for selection. After three generations of selection, the resulting marker-selected stock outperformed an unselected benchmark stock in terms of hygienic behavior, and had improved survival when challenged with a bacterial disease or a parasitic mite, similar to bees selected using a phenotype–based assessment for this trait. This is the first demonstration of the efficacy of protein markers for industrial selective breeding in any agricultural species, plant or animal.

Accuracy of genomic breeding values revisited: Assessment of two established approaches and a novel one to determine the accuracy in two-step genomic prediction.

Selection decisions in genomic selection schemes are made based on genomic breeding values (GBV) of candidates. Thus, the accuracy of GBV is a relevant parameter, as it reflects the stability of prediction and the possibility that the GBV might change when more information becomes available. Accuracy of genomic prediction defined as the correlation between GBV and true breeding values (TBV), however, is difficult to assess, considering TBV of the candidates are not available in reality. In previous studies, several methods were proposed to assess the accuracy of GBV including methods using population parameters or parameters inferred from mixed-model equations. In practice, most approaches tended to overestimate the accuracy of genomic prediction. We thus tested approaches used in previous studies in order to assess the magnitude of bias. Analyses were performed based on simulated data under a variety of scenarios mimicking different livestock breeding programmes. Furthermore, we proposed a novel method and tested it both with simulated data and in a real Holstein data set. The new method provided a better prediction for the accuracy of GBV in the simulated scenarios.

The Genetic Architecture of Economically Important Traits Provides Major Challenges for the Implementation of Gene Editing in Livestock

Gene editing has been hyped as a game-changer in many biological fields including medicine and agriculture. This includes the promise to manipulate the DNA of livestock animals at sufficient throughput, both in terms of number of loci and animals, to consider gene editing as a routine component of livestock breeding programmes. In this essay I will argue that the application of gene editing for complex traits in livestock will prove extremely challenging for a number of reasons: 1) our understanding of the genetic control of complex traits remains sketchy; 2) even with cutting edge ‘omics technologies, the identification of functional mutations remains very challenging; 3) before selecting certain mutations for gene editing, we need to capture the pleiotropic effects of the mutation and test whether its effects are truly additive. With the current understanding of complex traits there is a risk that gene editing will revert to a candidate gene approach without knowledge or understanding of where the important mutations reside. This means that it will be some time before we can really benefit from gene editing for truly complex traits in livestock. In the meantime gene editing could deliver quick wins by ‘repairing’ lethal recessive defects that are present in many elite breeding animals. Furthermore I will outline how gene editing can have an important role in the identification of QTN via in-vitro genetics.

Potential of gene drives with genome editing to increase genetic gain in livestock breeding programs

Background This paper uses simulation to explore how gene drives can increase genetic gain in livestock breeding programs. Gene drives are naturally occurring phenomena that cause a mutation on one chromosome to copy itself onto its homologous chromosome.MethodsWe simulated nine different breeding and editing scenarios with a common overall structure. Each scenario began with 21 generations of selection, followed by 20 generations of selection based on true breeding values where the breeder used selection alone, selection in combination with genome editing, or selection with genome editing and gene drives. In the scenarios that used gene drives, we varied the probability of successfully incorporating the gene drive. For each scenario, we evaluated genetic gain, genetic variance (sigma_{A}^{2} ), rate of change in inbreeding (Delta F), number of distinct quantitative trait nucleotides (QTN) edited, rate of increase in favourable allele frequencies of edited QTN and the time to fix favourable alleles.ResultsGene drives enhanced the benefits of genome editing in seven ways: (1) they amplified the increase in genetic gain brought about by genome editing; (2) they amplified the rate of increase in the frequency of favourable alleles and reduced the time it took to fix them; (3) they enabled more rapid targeting of QTN with lesser effect for genome editing; (4) they distributed fixed editing resources across a larger number of distinct QTN across generations; (5) they focussed editing on a smaller number of QTN within a given generation; (6) they reduced the level of inbreeding when editing a subset of the sires; and (7) they increased the efficiency of converting genetic variation into genetic gain.ConclusionsGenome editing in livestock breeding results in short-, medium- and long-term increases in genetic gain. The increase in genetic gain occurs because editing increases the frequency of favourable alleles in the population. Gene drives accelerate the increase in allele frequency caused by editing, which results in even higher genetic gain over a shorter period of time with no impact on inbreeding.

Community based livestock breeding programs in Bangladesh: Present status and challenges

Community based livestock breeding programs in Bangladesh: Present status and challenges

Effect of manipulating recombination rates on response to selection in livestock breeding programs.

BackgroundIn this work, we performed simulations to explore the potential of manipulating recombination rates to increase response to selection in livestock breeding programs.MethodsWe carried out ten replicates of several scenarios that followed a common overall structure but differed in the average rate of recombination along the genome (expressed as the length of a chromosome in Morgan), the genetic architecture of the trait under selection, and the selection intensity under truncation selection (expressed as the proportion of males selected). Recombination rates were defined by simulating nine different chromosome lengths: 0.10, 0.25, 0.50, 1, 2, 5, 10, 15 and 20 Morgan, respectively. One Morgan was considered to be the typical chromosome length for current livestock species. The genetic architecture was defined by the number of quantitative trait variants (QTV) that affected the trait under selection. Either a large (10,000) or a small (1000 or 500) number of QTV was simulated. Finally, the proportions of males selected under truncation selection as sires for the next generation were equal to 1.2, 2.4, 5, or 10 %.ResultsIncreasing recombination rate increased the overall response to selection and decreased the loss of genetic variance. The difference in cumulative response between low and high recombination rates increased over generations. At low recombination rates, cumulative response to selection tended to asymptote sooner and the genetic variance was completely eroded. If the trait under selection was affected by few QTV, differences between low and high recombination rates still existed, but the selection limit was reached at all rates of recombination.ConclusionsHigher recombination rates can enhance the efficiency of breeding programs to turn genetic variation into response to selection. However, to increase response to selection significantly, the recombination rate would need to be increased 10- or 20-fold. The biological feasibility and consequences of such large increases in recombination rates are unknown.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0221-1) contains supplementary material, which is available to authorized users.

Editorial: Improving Animal Welfare through Genetic Selection.

Editorial: Improving Animal Welfare through Genetic Selection.

Accuracy of genomic selection for age at puberty in a multi-breed population of tropically adapted beef cattle.

Genomic selection is becoming a standard tool in livestock breeding programs, particularly for traits that are hard to measure. Accuracy of genomic selection can be improved by increasing the quantity and quality of data and potentially by improving analytical methods. Adding genotypes and phenotypes from additional breeds or crosses often improves the accuracy of genomic predictions but requires specific methodology. A model was developed to incorporate breed composition estimated from genotypes into genomic selection models. This method was applied to age at puberty data in female beef cattle (as estimated from age at first observation of a corpus luteum) from a mix of Brahman and Tropical Composite beef cattle. In this dataset, the new model incorporating breed composition did not increase the accuracy of genomic selection. However, the breeding values exhibited slightly less bias (as assessed by deviation of regression of phenotype on genomic breeding values from the expected value of 1). Adding additional Brahman animals to the Tropical Composite analysis increased the accuracy of genomic predictions and did not affect the accuracy of the Brahman predictions.

Effect of C-type natriuretic peptide on maturation and developmental competence of immature mouse oocytes in vitro.

In vitro maturation (IVM) of oocytes is an important assisted reproductive technology for infertility treatment and livestock breeding programs. Because of asynchronous nuclear and cytoplasmic maturation, the developmental competence of oocytes matured in vitro is compromised. C-Type natriuretic peptide (CNP), which has been proved to be an inhibitor of oocyte maturation, provides a new alternative to optimise synchronisation of nuclear and cytoplasmic maturation and improve developmental capacity of immature oocytes in vitro. To investigate the effect of temporary meiotic arrest mediated by CNP on maturation and subsequent development of immature oocytes, immature mouse oocytes from small antral follicles were temporarily arrested in meiosis by CNP (0, 5, 10 and 50nM) for 24h and then matured for 16h. CNP treatment significantly increased the oocyte maturation rate from less than half to above 80%. After IVF, temporary meiotic arrest mediated by 10 and 50nM CNP significantly improved fertilisation and blastocyst rate of oocytes matured in vitro up to approximately 55% and 30% respectively. Moreover, this positive effect of CNP was attributed, in part, to an increase in the number of mature oocytes with aligned chromosomes and a normal spindle. The present findings indicate the potential to use CNP to improve the efficiency of oocyte IVM.

Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs.

BackgroundGenome editing (GE) is a method that enables specific nucleotides in the genome of an individual to be changed. To date, use of GE in livestock has focussed on simple traits that are controlled by a few quantitative trait nucleotides (QTN) with large effects. The aim of this study was to evaluate the potential of GE to improve quantitative traits that are controlled by many QTN, referred to here as promotion of alleles by genome editing (PAGE).MethodsMultiple scenarios were simulated to test alternative PAGE strategies for a quantitative trait. They differed in (i) the number of edits per sire (0 to 100), (ii) the number of edits per generation (0 to 500), and (iii) the extent of use of PAGE (i.e. editing all sires or only a proportion of them). The base line scenario involved selecting individuals on true breeding values (i.e., genomic selection only (GS only)-genomic selection with perfect accuracy) for several generations. Alternative scenarios complemented this base line scenario with PAGE (GS + PAGE). The effect of different PAGE strategies was quantified by comparing response to selection, changes in allele frequencies, the number of distinct QTN edited, the sum of absolute effects of the edited QTN per generation, and inbreeding.ResultsResponse to selection after 20 generations was between 1.08 and 4.12 times higher with GS + PAGE than with GS only. Increases in response to selection were larger with more edits per sire and more sires edited. When the total resources for PAGE were limited, editing a few sires for many QTN resulted in greater response to selection and inbreeding compared to editing many sires for a few QTN. Between the scenarios GS only and GS + PAGE, there was little difference in the average change in QTN allele frequencies, but there was a major difference for the QTN with the largest effects. The sum of the effects of the edited QTN decreased across generations.ConclusionsThis study showed that PAGE has great potential for application in livestock breeding programs, but inbreeding needs to be managed.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-015-0135-3) contains supplementary material, which is available to authorized users.

Community-based livestock breeding programmes: essentials and examples.

Breeding programmes described as community-based (CBBP) typically relate to low-input systems with farmers having a common interest to improve and share their genetic resources. CBBPs are more frequent with keepers of small ruminants, in particular smallholders of local breeds, than with cattle, pigs or chickens with which farmers may have easier access to alternative programmes. Constraints that limit the adoption of conventional breeding technologies in low-input systems cover a range of organizational and technical aspects. The analysis of 8 CBBPs located in countries of Latin-America, Africa and Asia highlights the importance of bottom-up approaches and involvement of local institutions in the planning and implementation stages. The analysis also reveals a high dependence of these programmes on organizational, technical and financial support. Completely self-sustained CBBPs seem to be difficult to realize. There is a need to implement and document formal socio-economic evaluations of CBBPs to provide governments and other development agencies with the information necessary for creating sustainable CBBPs at larger scales.