Poultry genetics and breeding

Athrey, Giridhar

doi:10.1016/b978-0-12-817052-6.00018-5

Cited by 7 publications

(3 citation statements)

References 104 publications

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“…Poultry breeding is a highly specialized process. Modern meat and egg production are characterized by the use of high-performance hybrid breeds (Cheng 2010;Athrey 2020;Scanes et al 2020). Thereby, specialized genetics are used both in egg and in meat production (Scanes et al 2020).…”

Section: Breeding-rating 3 (High Relevance)mentioning

confidence: 99%

Hotspot analysis for organic laying hen husbandry—identification of sustainability problems as potential risk points to lose consumers’ trust

2023

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Over the last decade, there has been growing societal concern about the welfare of farmed animals. Although organic agriculture provides higher living standards, there are still critical points which can damage consumers’ trust in organic livestock farming. That is a risk, as especially organic farming relies on consumer trust. A hotspot analysis was conducted to identify critical points within the organic laying hen husbandry in Germany. This methodology aims to examine the sustainability of a product along its whole life cycle. Based on literature reviews, the life phases breeding, keeping, feeding, animal health, transport, and slaughter were assessed with ecological, social, and animal welfare criteria. Finally, the results were triangulated with various experts, and the critical points were classified in terms of their potential to diverge from consumers’ expectations. Our results show a high dependency of the organic sector on the conventional breeding process and its specialized breeds. This fact involves critical points which contradict the ideology of organic farming. The loopholes in the organic EU regulations in transport and slaughter were identified as additional threats to consumer trust in the organic system. The overall not better animal health compared to the conventional poultry system and the high numbers of poultry kept on some organic farms are also possible causes of disappointment in consumers’ vision of organic livestock farming. Therefore, we recommend an adjustment of some organic EU regulations regarding these points. Further, a linkage of the organic certification of a slaughterhouse to higher animal welfare standards during slaughter should be considered.

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Section: Breeding-rating 3 (High Relevance)mentioning

confidence: 99%

Hotspot analysis for organic laying hen husbandry—identification of sustainability problems as potential risk points to lose consumers’ trust

2023

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“…Accurately detecting sequence variation associated with traits of economic importance in the domestic chicken is a major goal of genetic research into this globally widespread dietary protein source [1]. Many groups are now genotyping chicken genomes to discover the underlying molecular basis of specific traits [2][3][4][5][6], but current methods, both sequence-and array-based, have unquantified limitations in assessing the underlying variation that connects many loci to studied traits.…”

Section: Introductionmentioning

confidence: 99%

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Rice¹,

Alberdi²,

Alfieri³

et al. 2023

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Background. The red junglefowl, the wild progenitor of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. Results. We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K ‘feathering’ locus using short reads, which would not be possible using a linear reference. Conclusions. We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.

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“…Given the widespread popularity of chicken meat in the global diet, finding a suitable substitute is challenging. The primary objective of genetic projects is to identify sequence variations associated with key economic traits in chickens (1). This review explores the efficacy of Candidate Genes (CGs) and various molecular markers in relation to economic traits in chickens.…”

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confidence: 99%

Determining the Relationships Between Genotype and Phenotype Using Molecular Genetic Tools in Chickens

Hajibarat,

Saidi,

Zeinalabedini

et al. 2024

Jentashapir J Cell Mol Biol

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Context: Chicken meat is one of the rich sources of protein and is considered one of the most commonly consumed meats in the world. Enhancing poultry production and its products is achievable through chicken breeding. Effective breeding projects for future genetic improvement require an understanding of the genetic potential of a given population. Evidence Acquisition: Articles were selected based on novel molecular markers related to economic traits of chicken in Animal quantitative trait loci (QTL) database, Ensemble genome browser, CorrDB, ChickVD, Galbase, and Google Scholar. These databases contain QTLs, markers, and reference genomes of chicken. Galbase provides research communities with updated possibilities to conduct thorough functional genomics research on chickens. ChickVD manages high-quality sequence variation data, variation analysis in relation to chicken genes, cDNAs, genetic markers, and QTLs. CorrDB compiles all available chicken genetic and phenotypic trait correlation data to aid in the analysis of genetic networks and facilitate systems biology research. Animal Quantitative Trait Loci Database (Animal QTLdb) gathers and compiles all existing data on trait mapping, including QTL (phenotype/expression, eQTL), candidate gene, association data (GWAS), and copy number variations (CNV) for livestock animal genomes. This comprehensive database facilitates the easier identification and comparison of discoveries within and across species. Ensemble genome browser is a powerful tool for analyzing vertebrate genomes, offering valuable insights into comparative genomics, evolutionary processes, sequence variations, and transcriptional regulation. Results: valuating the relatedness of the studied broilers and layers is important for maintaining and improving the genetic reserves of the same population. Candidate genes (CGs) are used to determine genes related to economic traits in chickens. Molecular genetic techniques such as whole-genome re-sequencing (WGRS) can identify single nucleotide polymorphisms (SNPs), insertion/deletion polymorphisms (indels), structural variations (SV), CNV, and simple sequence repeats (SSRs) and their chromosomal regions in terms of QTL. Recently, the pan-genome (PG) has become one of the most important tools to study genome variation and changes in important traits. The use of molecular markers and CGs can aid in evaluating the genetic relationships between phenotype and genotype of broilers and layers. Conclusions: This review introduces molecular genetic methods and new approaches to identify novel genes related to important biological pathways and significant production and reproductive traits.

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Poultry genetics and breeding

Cited by 7 publications

References 104 publications

Hotspot analysis for organic laying hen husbandry—identification of sustainability problems as potential risk points to lose consumers’ trust

Hotspot analysis for organic laying hen husbandry—identification of sustainability problems as potential risk points to lose consumers’ trust

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Determining the Relationships Between Genotype and Phenotype Using Molecular Genetic Tools in Chickens

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