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Selection for milk production later in lactation (changing the shape of the lactation curve) also may provide an opportunity to increase milk production during a time in an animal's life when energy allocation is possible. Keywords: Genetic Selection; Estimated Breeding Value; Milk Composition EN Genetic Selection Estimated Breeding Value Milk Composition 55 63 9 06/20/23 20230601 NES 230601 Implications Genetic selection to increase milk yield has been very successful. Milk production of domesticated dairy cows can reach 30-50 L per day or 6,000 to 12,000 Lover a lactation compared to 8-10 L per day and <1,000 L over lactation in feral cows ([85]). Milk production in cows follow a dynamic curve starting with an initial rapid increase in milk yield in early lactation (approx. 0-45 days-in-milk, [DIM]), followed by a peak (approx. 46-55 DIM), and then a slow decline in milk yield during late lactation (approx. 56-340 DIM) ([76]). Flow of data between different components of a national milk recording system, including DNA and test-day milk samples collected on farms, milk composition information produced by milk testing laboratories, standardized records computed by dairy records processing centers, and breeding values calculated by the genetic evaluation center. [Extracted from the article]

Atlantic herring (Clupea harengus) and Pacific herring (C. pallasii) are sister species that split from a common ancestor about 2 million years ago. Balsfjord, a subarctic fjord in Northern Norway, harbors an outpost population of Pacific herring within the range of the Atlantic herring. We used whole genome sequencing to show that gene flow from Atlantic herring into the Balsfjord population has generated a stable hybrid population that has persisted for thousands of generations. The Atlantic herring ancestry in Balsfjord was estimated in the range 25–26%. The old age and large proportion of introgressed regions suggest there are no obvious genetic incompatibilities between species. Introgressed regions were widespread in the genome and large, with some in excess of 1 Mb, and they were overrepresented in low-recombination regions. We show that the distribution of introgressed material is non-random; introgressed sequence blocks in different individuals are shared more often than expected by chance. Furthermore, introgressed regions tend to show elevated divergence (F ST) between Atlantic and Pacific herring. Together, our results suggest that introgression of genetic material has facilitated adaptation in the Balsfjord population. The Balsfjord population provides a rare example of a stable interspecies hybrid population that has persisted over thousands of years. [ABSTRACT FROM AUTHOR]

Abstract: Our objective was to detect single nucleotide polymorphisms (SNPs) associated with resistance to the salmon louse in the Saint John River aquacultural population of North American Atlantic salmon using estimated breeding values (EBVs) and 6K genotypes from the parent‐generation and lice count phenotypes from the challenged, but ungenotyped, offspring‐generation. In 2011 and 2012, we challenged recent smolts with approximately 100 copepodids each. Fish were euthanized once the lice reached the chalimus stages and lice count, sex, tank and salt water weight were recorded. We used a multiple trait model to estimate breeding values for the parent‐generation using their own fresh water weights and the salt water weights and lice counts of the offspring‐generation. Salmon lice count heritability for untransformed and transformed data was 0.17 and 0.29 respectively. Two different genome‐wide association study methods were compared: (i) forward multiple linear regression and (ii) a mixed linear model using principal components to correct for population stratification as implemented in the egscore function of GenABEL. The two methods detected different SNPs located on different chromosomes. The multiple regression method incorporated 70 SNPs found on chromosomes 2, 7, 9, 12, 14, 15, 21, 22, 1p/23, 24. Many SNPs entered into the forward multiple regression are likely to be false positives from not correcting for the observed population stratification and cryptic relatedness. In contrast, the mixed linear model identified only two SNPs, one on chromosome 1p/23 (6.9%) and one on chromosome 1q (6.1%) consistent with louse‐resistance being a quantitative trait. [ABSTRACT FROM AUTHOR]

Background: Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep. Results: Three datasets were analysed: pedigree information of the whole population, pedigree information for 100 animals of the population, and microsatellite genotypes for 94 of the 100 animals. The average inbreeding coefficient for lambs born during a six year time period (2007-2012) did not increase during that time period. The inbreeding calculated from the entire pedigree (0.038) and for a sample of the population (0.018) was very low. Sheep were more heterozygous at the microsatellite markers than expected (average multilocus heterozygosity and Ritland inbreeding estimates 1.01845 and -0.03931) and five of seven microsatellite markers were not in Hardy Weinberg equilibrium due to heterozygosity excess. The total effective population size estimated from the pedigree information was 155.4 and the average harmonic mean effective population size estimated from microsatellites was 88.3. Pedigree and microsatellite genotype estimations of inbreeding were consistent with a breeding program with the purpose of reducing inbreeding. Conclusion: Our results showed that current breeding programs of the Swedish Gute sheep are consistent with efforts of keeping this breed viable and these breeding programs are an example for other small local breeds in conserving breeds for the future. [ABSTRACT FROM AUTHOR]

The Canadian dairy industry implemented genomic selection in 2009 to improve breeding in Holstein cattle and has been applied to several other dairy cattle breeds since then. Genomic selection is an effective breeding tool that can increase the accuracy of prediction and help to select young animals using genotypic information. As well as shortening generation intervals, genomic selection has also increased the genetic gain per generation and the profitability of the industry. However, genomic selection tends to increase inbreeding, reduce the effective population size and cause a loss in genetic variation. These consequences could lead to future challenges like lower selection response. To evaluate the sustainability of current breeding practices, investigation is warranted to observe the effects of genomic selection. Therefore, the objective of this study is to compare the population structure of Canadian Holstein cattle before and after the implementation of genomic selection in 2009. Using pedigree information to identify the number of sires used for breeding at three different time points (2000, 2010 and 2020), the number of daughters per sire, and length of time sires were used were investigated. Results show that the average number of offspring per top sire (top 10%) has decreased by 50%, however the average relatedness of available sires has increased considerably. This information will add to our knowledge of the effects genomic selection has had on the Canadian dairy industry and will inform future recommendations for sustainable breeding strategies that facilitate continual genetic progress. [ABSTRACT FROM AUTHOR]

Animal breeders have exploited many technological advances for increasing genetic gain in economically and functionally important traits. The implementation of such technologies in routine breeding programs has permitted genetic gains in traditional milk, meat and egg production traits as well as, more recently, in low-heritability traits like health, fertility, and even behavior. As global demand for animal products increases, animal breeders must ensure the technologies, methods and strategies employed are sustainable, to consider the many emerging technologies that are currently being investigated in various fields, and to ensure a social license to continue producing animal products. Here we discuss the societal, ethical, environmental, and economical aspects of sustainability in the context of livestock breeding. We review a number of technologies that have helped shape livestock breeding programs in the past and present, along with those potentially forthcoming. These tools have materialized in the areas of reproduction, genotyping and sequencing, genetic modification, epigenetics, and other areas of "omics" technologies. Although many of these technologies bring encouraging opportunities for genetic improvement of livestock populations, their applications and benefits need to be weighed with their impacts on sustainability. [ABSTRACT FROM AUTHOR]

The Atlantic herring is a model species for exploring the genetic basis for ecological adaptation, due to its huge population size and extremely low genetic differentiation at selectively neutral loci. However, such studies have so far been hampered because of a highly fragmented genome assembly. Here, we deliver a chromosome-level genome assembly based on a hybrid approach combining a de novo Pacific Biosciences (PacBio) assembly with Hi-C-supported scaffolding. The assembly comprises 26 autosomes with sizes ranging from 12.4 to 33.1 Mb and a total size, in chromosomes, of 726 Mb, which has been corroborated by a high-resolution linkage map. A comparison between the herring genome assembly with other high-quality assemblies from bony fishes revealed few inter-chromosomal but frequent intra-chromosomal rearrangements. The improved assembly facilitates analysis of previously intractable large-scale structural variation, allowing, for example, the detection of a 7.8-Mb inversion on Chromosome 12 underlying ecological adaptation. This supergene shows strong genetic differentiation between populations. The chromosome-based assembly also markedly improves the interpretation of previously detected signals of selection, allowing us to reveal hundreds of independent loci associated with ecological adaptation., (© 2019 Pettersson et al.; Published by Cold Spring Harbor Laboratory Press.)