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Madeddu M, Zaniboni L, Marelli SP, Tognoli C, Belcredito S, Iaffaldano N, Di Iorio M, Cerolini S. Selection of Male Donors in Local Chicken Breeds to Implement the Italian Semen Cryobank: Variability in Semen Quality, Freezability and Fertility. Vet Sci 2024; 11:148. [PMID: 38668416 PMCID: PMC11054041 DOI: 10.3390/vetsci11040148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/29/2024] [Accepted: 03/21/2024] [Indexed: 04/29/2024] Open
Abstract
Native breed conservation is an important component of poultry biodiversity. The aim of this work is to describe different steps that lead to donor selection for the implementation of the Italian Semen Cryobank of Autochthonous Chicken and Turkey Breeds. The variability within and between breeds was evaluated, and the stored semen reproductive capacity was in vivo tested using artificial insemination. Semen from Bionda Piemontese, Bianca di Saluzzo and Pepoi roosters was collected and processed. Concentration, volume, sperm membrane integrity, total motile sperm, progressive motile sperm and kinetic parameters were analyzed; sperm parameters accounting for bird variability were used to select male donors. Fresh semen quality parameters measured in donor ejaculates showed significant differences between breeds; no differences were found after cryopreservation. Variability in the fertilizing ability of cryopreserved semen was found within a breed (5-16%) and between birds within a breed (BP = 3-7%; BS = 7-31%; PP = 6-22%); only sperm quality parameters measured in fresh ejaculates, not frozen/thawed, may be associated with in vivo fertility results. In conclusion, sperm concentration and progressive motility were successfully used as selection parameters to identify chicken male donors with improved sperm quality for sperm cryobanking. However, new reliable sperm markers to predict cryopreserved semen's fertilizing ability are required.
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Affiliation(s)
- Manuela Madeddu
- Department of Veterinary Medicine and Animal Science, University of Milan, via dell’Università 6, 26900 Lodi, Italy; (M.M.); (S.P.M.); (C.T.); (S.B.); (S.C.)
| | - Luisa Zaniboni
- Department of Veterinary Medicine and Animal Science, University of Milan, via dell’Università 6, 26900 Lodi, Italy; (M.M.); (S.P.M.); (C.T.); (S.B.); (S.C.)
| | - Stefano Paolo Marelli
- Department of Veterinary Medicine and Animal Science, University of Milan, via dell’Università 6, 26900 Lodi, Italy; (M.M.); (S.P.M.); (C.T.); (S.B.); (S.C.)
| | - Cristina Tognoli
- Department of Veterinary Medicine and Animal Science, University of Milan, via dell’Università 6, 26900 Lodi, Italy; (M.M.); (S.P.M.); (C.T.); (S.B.); (S.C.)
| | - Silvia Belcredito
- Department of Veterinary Medicine and Animal Science, University of Milan, via dell’Università 6, 26900 Lodi, Italy; (M.M.); (S.P.M.); (C.T.); (S.B.); (S.C.)
| | - Nicolaia Iaffaldano
- Department of Agricultural, Environmental and Food Science, University of Molise, 86100 Campobasso, Italy; (N.I.); (M.D.I.)
| | - Michele Di Iorio
- Department of Agricultural, Environmental and Food Science, University of Molise, 86100 Campobasso, Italy; (N.I.); (M.D.I.)
| | - Silvia Cerolini
- Department of Veterinary Medicine and Animal Science, University of Milan, via dell’Università 6, 26900 Lodi, Italy; (M.M.); (S.P.M.); (C.T.); (S.B.); (S.C.)
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Rentsch AK, Harlander A, Niel L, Siegford JM, Widowski TM. Raising laying hens: housing complexity and genetic strain affect startle reflex amplitude and behavioural response to fear-inducing stimuli. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231075. [PMID: 38511084 PMCID: PMC10951723 DOI: 10.1098/rsos.231075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 01/12/2024] [Accepted: 02/10/2024] [Indexed: 03/22/2024]
Abstract
Individual variation in fearfulness can be modified during ontogeny, and high levels of fear can affect animal welfare. We asked whether early-life environmental complexity and genetic strain affect fear behaviour in young laying hens (pullets). Four replicates of brown (B) and white (W) genetic strains (breeds) of layers were each raised in four environmental treatments (housing): conventional cages (Conv) and different rearing aviaries with increasing space and complexity (Low < Mid < High). We used a startle reflex test (weeks 4 and 14) to measure startle amplitude and autonomic response (i.e. comb temperature). A combination of novel arena (NA) and novel object (NO) tests was used (week 14) to assess NA exploration and alertness, latency to approach the centre and initial NO avoidance and investigation. Housing × strain affected startle amplitude (B-Conv, B-High < B-Low, B-Mid; B > W; no housing effect in W) but not autonomic response. Fear behaviour was affected by housing (NA exploration, investigation: Conv < Low, Mid, High; NO avoidance: Conv, High < Low, Mid), strain (NA alertness: B > W, NO avoidance: W > B) and their interaction (NA centre approach: B-Conv < all other groups). We present evidence for strain-specific fear responses depending on early experience.
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Affiliation(s)
- Ana K. Rentsch
- Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, OntarioN1G 2W1, Canada
- Campbell Centre for the Study of Animal Welfare, University of Guelph, 50 Stone Road East, Guelph, OntarioN1G 2W1, Canada
| | - Alexandra Harlander
- Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, OntarioN1G 2W1, Canada
- Campbell Centre for the Study of Animal Welfare, University of Guelph, 50 Stone Road East, Guelph, OntarioN1G 2W1, Canada
| | - Lee Niel
- Campbell Centre for the Study of Animal Welfare, University of Guelph, 50 Stone Road East, Guelph, OntarioN1G 2W1, Canada
- Department of Population Medicine, University of Guelph, 50 Stone Road East, Guelph, OntarioN1G 2W1, Canada
| | - Janice M. Siegford
- Department of Animal Science, Michigan State University, 474 South Shaw Lane, East Lansing, MI48824-1225, USA
| | - Tina M. Widowski
- Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, OntarioN1G 2W1, Canada
- Campbell Centre for the Study of Animal Welfare, University of Guelph, 50 Stone Road East, Guelph, OntarioN1G 2W1, Canada
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Dementieva NV, Shcherbakov YS, Ryabova AE, Vakhrameev AB, Makarova AV, Nikolaeva OA, Dysin AP, Azovtseva AI, Reinbah NR, Mitrofanova OV. Comparative peculiarities of genomic diversity in Gallus gallus domesticus chickens with decorative plumage: the muffs and beard phenotype. Vavilovskii Zhurnal Genet Selektsii 2024; 28:108-116. [PMID: 38465249 PMCID: PMC10917671 DOI: 10.18699/vjgb-24-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 03/12/2024] Open
Abstract
Throughout history, humans have been attempting to develop the ornamental features of domestic animals in addition to their productive qualities. Many chicken breeds have developed tufts of elongated feathers that jut out from the sides and bottom of the beak, leading to the phenotype known as muffs and beard. It is an incomplete autosomal dominant phenotype determined by the Mb locus localised on chromosome GGA27. This project aimed to analyse the genetic diversity of chicken breeds using full genomic genotyping with the Chicken 60K BeadChip. A total of 53,313 Single Nucleotide Polymorphisms were analysed. DNA was obtained from breeds with the muffs and beard as a marker phenotype: Faverolles (n = 20), Ukrainian Muffed (n = 18), Orloff (n = 20), Novopavlov White (n = 20), and Novopavlov Coloured (n = 15). The Russian White (n = 20) was selected as an alternative breed without the muffs and beard phenotype. The chickens are owned by the Centre of Collective Use "Genetic Collection of Rare and Endangered Breeds of Chickens" (St. Petersburg region, Pushkin), and are also included in the Core Shared Research Facility (CSRF) and/or Large-Scale Research Facility (LSRF). Multidimensional scaling revealed that the Novopavlov White and the Novopavlov Coloured populations formed a separate group. The Ukrainian Muffed and the Orloff have also been combined into a separate group. Based on cluster analysis, with the cross-validation error and the most probable number of clusters K = 4 taken into account, the Orloff was singled out as a separate group. The Ukrainian Muffed exhibited a notable similarity with the Orloff under the same conditions. At K = 5, the populations of the Novopavlov White and the Novopavlov Coloured diverged. Only at K = 6, a distinct and separate cluster was formed by the Ukrainian Muffed. The Russian White had the greatest number of short (1-2 Mb) homozygous regions. If the HOXB8 gene is located between 3.402 and 3.404 Mb on chromosome GGA27, homozygous regions are rarely found in the chickens with the muffs and beard phenotype. Scanning the chicken genome with the Chicken 60K BeadChip provided enough information about the genetic diversity of the chicken breeds for the peculiarities of the development of the ornamental muffs and beard phenotypes in them to be understood. For example, Phoenix bantams, whose tail feathers grow throughout their lives, require greater consideration of husbandry conditions.
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Affiliation(s)
- N V Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - Y S Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - A E Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - A B Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - A V Makarova
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - O A Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - A P Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - A I Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - N R Reinbah
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
| | - O V Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Tyarlevo, St. Petersburg, Russia
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Meyermans R, Heylen O, Bouhuijzen Wenger J, Martens J, Buys N, Janssens S. The novel IMAGE001 genotyping array as a valuable alternative for genetic diversity screening in chicken: a demonstration in a local chicken breed in Belgium. Poult Sci 2024; 103:103221. [PMID: 37988999 PMCID: PMC10667748 DOI: 10.1016/j.psj.2023.103221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/23/2023] Open
Abstract
Screening for genetic diversity in livestock species breeds is of utmost importance, especially for local, small populations that are at the risk of extinction. Luckily, recent developments in technology increase access to genotyping, also for numerically small breeds. One of these new technologies is the IMAGE001 single nucleotide polymorphism genotyping array that includes markers for 6 different species (cow, pig, sheep, chicken, horse and goat). For our current study, we studied the Turkey-headed Malines chicken, a local chicken breed in Belgium, for the first time. A total of 110 animals were genotyped, together with 29 samples from 4 supposedly related breeds. The genotypes were used to assess the genetic diversity of this local breed. Our analysis revealed an average inbreeding coefficient of 0.20 through runs of homozygosity analysis, and effective population size estimation based on linkage disequilibrium indicated a low genetic diversity (Ne = 34). Moreover, a principal component analysis and a genetic differentiation study (FST) were performed using these marker data to position the Turkey-headed Malines relative to the 4 other indigenous Belgian chicken breeds. Finally, we discussed the practical implications of the overlap between the IMAGE001 array and other existing chicken genotyping arrays. This study is the first use of the novel IMAGE001 array to evaluate a local chicken breed, and demonstrates it as a viable option for genomic characterization a breed. Moreover, with this research, we are able to provide a good basis for further evaluation of the Belgian chicken heritage.
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Affiliation(s)
- Roel Meyermans
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, 3001 Leuven, Belgium.
| | - Olivier Heylen
- OTEAS Consulting & Statistics (Agriculture, Environment & Ecology), 2221 Booischot, Belgium; Steunpunt Levend Erfgoed vzw, 9860 Oosterzele, Belgium
| | | | - Jan Martens
- Steunpunt Levend Erfgoed vzw, 9860 Oosterzele, Belgium
| | - Nadine Buys
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, 3001 Leuven, Belgium
| | - Steven Janssens
- Department of Biosystems, Center for Animal Breeding and Genetics, KU Leuven, 3001 Leuven, Belgium
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Rice ES, Alberdi A, Alfieri J, Athrey G, Balacco JR, Bardou P, Blackmon H, Charles M, Cheng HH, Fedrigo O, Fiddaman SR, Formenti G, Frantz LAF, Gilbert MTP, Hearn CJ, Jarvis ED, Klopp C, Marcos S, Mason AS, Velez-Irizarry D, Xu L, Warren WC. A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biol 2023; 21:267. [PMID: 37993882 PMCID: PMC10664547 DOI: 10.1186/s12915-023-01758-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 11/02/2023] [Indexed: 11/24/2023] Open
Abstract
BACKGROUND The red junglefowl, the wild outgroup 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. METHODS We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. RESULTS 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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Affiliation(s)
- Edward S Rice
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - James Alfieri
- Department of Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, USA
| | - Giridhar Athrey
- Department of Poultry Science, Texas A&M University, College Station, TX, USA
| | - Jennifer R Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Philippe Bardou
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, 31326, France
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Mathieu Charles
- University Paris-Saclay, INRAE, AgroParisTech, GABI, Sigenae, Jouy-en-Josas, France
| | - Hans H Cheng
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Laurent A F Frantz
- Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4DQ, UK
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
| | - Cari J Hearn
- Avian Disease and Oncology Laboratory, USDA, ARS, USNPRC, East Lansing, MI, USA
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
- The Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Christophe Klopp
- Sigenae, Genotoul Bioinfo, MIAT UR875, INRAE, Castanet Tolosan, France
| | - Sofia Marcos
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen (UCPH), Copenhagen, Denmark
- Applied Genomics and Bioinformatics, University of the Basque Country (UPV/EHU), Leioa, Bilbao, Spain
| | | | | | - Luohao Xu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA.
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Rizzi C. A Study on Egg Production and Quality According to the Age of Four Italian Chicken Dual-Purpose Purebred Hens Reared Outdoors. Animals (Basel) 2023; 13:3064. [PMID: 37835671 PMCID: PMC10571830 DOI: 10.3390/ani13193064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/23/2023] [Accepted: 09/06/2023] [Indexed: 10/15/2023] Open
Abstract
The month of hatching and the rearing management, especially temperature and photoperiod, are important factors for pullets and hens reared outdoors. The yield performance and egg quality of dual-purpose chicken breeds from the Veneto region (Italy), Pepoi (PP), Ermellinata di Rovigo (ER), Robusta Maculata (RM) and Robusta Lionata (RL), with different adult body weights (ABW, kg, PP = 1.3; ER = 2.3, RM and RL = 3.1), were studied, using a factorial model (4 × 2), considering breed and age (26-33 weeks, first age, summer-autumn, under decreasing natural photoperiod-on average, 12L:12D, and 42-53 weeks, second age, winter, under implemented photoperiod-14L:10D) as the main effects and interaction. The chicks hatched in spring, and they started laying at the end of summer/beginning of autumn. Significant (p < 0.05) results were shown for many traits. ER showed higher hen-day egg production than that of PP, and RM and RL were the lowest; ER, RM and RL showed medium-size eggs and PP showed small-size eggs. RM produced the most spherical eggs and ER the most ovoid, and they showed the highest and the lowest eggshell thickness, respectively. RM showed the highest yolk to albumen ratio, and RL showed the lowest. The age increased the laying rate and the egg weight in all the groups. At 26-33 weeks, ER and PP showed higher hen-day egg production (on average 24%) than RM and RL (on average, less than 10%). The onset of laying (at least 10% laying rate) was shown, at different ages, according to the % ABW the breeds had reached: PP was the first, followed by ER, then RM, and RL was the last. At 42-53 weeks, the hen-day egg production ranged, on average, from 38 to 52%, according to the breeds; orthogonal contrasts on two-weekly data showed, at first age, increasing linear (ER) and quadratic (other groups) trends, and at second age, positive linear (ER, RM) and cubic (PP, RL) trends. Age (32 vs. 53 weeks) affected almost all the eggshell traits in PP and ER, whereas in RL, and especially RM, fewer traits changed. The age increased the yolk to albumen ratio (unchanged in PP). These results may be useful for the effective management of local purebred chickens, with the purpose to ensure the wellbeing of the hens and for supplying eggs of different quality throughout the year.
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Affiliation(s)
- Chiara Rizzi
- Department of Agronomy, Food, Natural resources, Animals and Environment (DAFNAE), University of Padova, Viale dell'Università, 16, 35020 Legnaro, Italy
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Darrington C, Lin H, Larivière JM, Fulton JE, Zhao X. Discovery of novel MHC-B haplotypes in Chantecler chickens. Poult Sci 2023; 102:102881. [PMID: 37406434 PMCID: PMC10466295 DOI: 10.1016/j.psj.2023.102881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 07/07/2023] Open
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic cluster of genes which contribute to immune response. Located on chromosome 16, the chicken MHC has great influence over disease resistance and susceptibility. Through the use of a high-density SNP panel which encompasses the MHC-B region, haplotypes can be easily identified. This study aims to use an MHC-B SNP panel to evaluate the MHC-B variability in the Chantecler breed. This breed is native to Quebec, Canada, and is a dual-purpose breed known for its strong resistance to extreme cold temperatures. The Chantecler breed faced a near extinction event in the 1970s, which most likely resulted in a genetic bottleneck and loss of diversity. Despite this, SNP haplotype diversity was observed among 4 Chantecler populations. A total of 8 haplotypes were observed. Of these haplotypes, 6 were previously defined in other breeds, and the other 2 were unique to the Chantecler. Within the populations, the number of haplotypes ranged from 4 to 7, with 3 haplotypes, including the novel BSNP-Chant01, being present in all the groups. This study shows existence of reasonable diversity in the MHC-B region of the Chantecler breed and our results further contribute to understanding the variability of this region in chickens.
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Affiliation(s)
| | | | | | | | - Xin Zhao
- McGill University, Montreal, QC, Canada.
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Blackburn HD, Krehbiel BC. A gene bank's collection of genetic diversity among minor chicken breeds. Poult Sci 2023; 102:102827. [PMID: 37343351 PMCID: PMC10404745 DOI: 10.1016/j.psj.2023.102827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/26/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
Genetic differences among heritage or fancier breeds of chickens have not been quantified in the United States. Gene banks collecting germplasm for conserving these breeds need this information as do breeders and companies raising them. Our goal was to evaluate genetic diversity of 10 heritage/fancier chicken breeds that are a component of the national collection and to use this information to establish a baseline of their genetic diversity and future conservation efforts. Breeds could be broadly classified as European, Asian, Mediterranean, and United States (US) in origin. The US breeds were composite breeds developed between the 1849 and 1935. Animals (n = 24-31 per breed) were sampled for DNA analysis from 2 or 3 hatcheries per breed and a total of 8 hatcheries. The hatcheries were assumed to maintain and breed their own populations of the studied breeds. Effective population sizes ranged from 47 to 145 and used to estimate probabilities of extinction for a 50-generation timeline. It was determined that Crevecoeur and Aseel had a probability of extinction that exceeded 40%, the remaining 8 breeds had probabilities of <28%. ADMIXTURE analysis indicated the minimal CV corresponded to 9 populations. In that analysis New Hampshire and Rhode Island Red were classified as the same population, which was not unusual given that New Hampshire was developed as a subpopulation of Rhode Island Red. Crevecoeur and Buttercup were the 2 most genetically divergent breeds based on pairwise Fst among the breeds and principal component analysis, which was supported by the ADMIXTURE results. Inbreeding coefficients computed from genomic information was lowest for Crevecoeur, Rhode Island Red, Buttercup, and Andalusian (0.8-2.6%), while New Hampshire, Buckeye, and Aseel were highest (12.8-14.3%). Within breed Fst among hatcheries supplying animals for sampling generally indicated a genetic structure was present on a breed-by-breed basis. Genetic relationships within hatchery were also computed for each breed. Several of the hatcheries had sent samples that suggested genetic relationships as high as half-sibs while several others had genetic relationships closer to first cousins. We conclude that the chicken breeds evaluated have substantial genetic variability within the in situ populations and the gene bank has captured this diversity for future use.
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Affiliation(s)
- H D Blackburn
- National Animal Germplasm Program, Agricultural Research Service, United States Department of Agriculture, Fort Collins, CO 80521, USA.
| | - B C Krehbiel
- Colorado State University, Fort Collins, CO 80521, USA
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Rentsch AK, Ross E, Harlander A, Niel L, Siegford JM, Widowski TM. The development of laying hen locomotion in 3D space is affected by early environmental complexity and genetic strain. Sci Rep 2023; 13:10084. [PMID: 37344513 DOI: 10.1038/s41598-023-35956-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/26/2023] [Indexed: 06/23/2023] Open
Abstract
Adult laying hens are increasingly housed in spatially complex systems, e.g., non-cage aviaries, where locomotion between elevated structures can be challenging for these gallinaceous birds. This study assessed the effect of early environmental complexity on spatial skills in two genetic strains. Brown (B) and white (W) feathered birds were raised in: Conventional cages with minimal complexity (Conv) or rearing aviaries with low (Low), intermediate (Mid), or high complexity (High). Birds from each housing treatment were challenged at three different time points in three different, age-appropriate vertical spatial tasks. Whites performed better than brown birds in all tests regardless of rearing environment. In chicks, test performance was predominantly explained by variation between replicates and differences in motivation for test participation. Treatment effects were seen in pubertal birds (pullets), with pullets from aviaries performing better than those from Conv. White High pullets performed better than white Mid or Low, an effect that was not found in browns. Pullets preferred to use a ramp to move downwards, but only when ramps had previously been experienced and when the ramp was not too steep. Overall, early environmental complexity affected spatial skills of laying hen pullets with stronger effects in white than brown feathered birds.
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Affiliation(s)
- Ana K Rentsch
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Erin Ross
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | | | - Lee Niel
- Department of Population Medicine, University of Guelph, Guelph, ON, Canada
| | - Janice M Siegford
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Tina M Widowski
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada.
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10
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Pocrnic I, Obšteter J, Gaynor RC, Wolc A, Gorjanc G. Assessment of long-term trends in genetic mean and variance after the introduction of genomic selection in layers: a simulation study. Front Genet 2023; 14:1168212. [PMID: 37234871 PMCID: PMC10206274 DOI: 10.3389/fgene.2023.1168212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Nucleus-based breeding programs are characterized by intense selection that results in high genetic gain, which inevitably means reduction of genetic variation in the breeding population. Therefore, genetic variation in such breeding systems is typically managed systematically, for example, by avoiding mating the closest relatives to limit progeny inbreeding. However, intense selection requires maximum effort to make such breeding programs sustainable in the long-term. The objective of this study was to use simulation to evaluate the long-term impact of genomic selection on genetic mean and variance in an intense layer chicken breeding program. We developed a large-scale stochastic simulation of an intense layer chicken breeding program to compare conventional truncation selection to genomic truncation selection optimized with either minimization of progeny inbreeding or full-scale optimal contribution selection. We compared the programs in terms of genetic mean, genic variance, conversion efficiency, rate of inbreeding, effective population size, and accuracy of selection. Our results confirmed that genomic truncation selection has immediate benefits compared to conventional truncation selection in all specified metrics. A simple minimization of progeny inbreeding after genomic truncation selection did not provide any significant improvements. Optimal contribution selection was successful in having better conversion efficiency and effective population size compared to genomic truncation selection, but it must be fine-tuned for balance between loss of genetic variance and genetic gain. In our simulation, we measured this balance using trigonometric penalty degrees between truncation selection and a balanced solution and concluded that the best results were between 45° and 65°. This balance is specific to the breeding program and depends on how much immediate genetic gain a breeding program may risk vs. save for the future. Furthermore, our results show that the persistence of accuracy is better with optimal contribution selection compared to truncation selection. In general, our results show that optimal contribution selection can ensure long-term success in intensive breeding programs using genomic selection.
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Affiliation(s)
- Ivan Pocrnic
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Jana Obšteter
- Agricultural Institute of Slovenia, Ljubljana, Slovenia
| | - R. Chris Gaynor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
| | - Anna Wolc
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Hy-Line International, Dallas Center, IA, United States
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, United Kingdom
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11
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Tolone M, Sardina MT, Criscione A, Lasagna E, Senczuk G, Rizzuto I, Riggio S, Moscarelli A, Macaluso V, Di Gerlando R, Cassandro M, Portolano B, Mastrangelo S. High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources. Poult Sci 2023; 102:102692. [PMID: 37120867 PMCID: PMC10172703 DOI: 10.1016/j.psj.2023.102692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 05/02/2023] Open
Abstract
Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH hotspots harbored genes related to immune response and adaptation to local hot temperatures. The results on genetic relationship and population structure reported a clear clustering of the populations according to their geographic origin. The COS formed a nonoverlapping genomic cluster and clearly separated from the other populations, but showed evident proximity to the Siciliana breed (SIC). The VPL highlighted intermediate relationships between the COS-SIC group and the rest of the sample, but closer to the other Italian local chickens. Moreover, VPL showed a complex genomic structure, highlighting the presence of 2 subpopulations that match with the different source of the samples. The results obtained from the survey on genetic differentiation underline the hypothesis that Cornuta is a population with a defined genetic structure. The substructure that characterizes the Val Platani chicken is probably the consequence of the combined effects of genetic drift, small population size, reproductive isolation, and inbreeding. These findings contribute to the understanding of genetic diversity and population structure, and represent a starting point for designing programs to monitor and safeguard these local genetic resources, in order to define a possible official recognition program as breeds.
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Affiliation(s)
- Marco Tolone
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Maria Teresa Sardina
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Andrea Criscione
- Department of Agriculture, Food and the Environment, University of Catania, 95131 Catania, Italy
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
| | - Gabriele Senczuk
- Department of Agricultural, Environmental and Food Sciences, University of Molise, 86100 Campobasso, Italy
| | - Ilaria Rizzuto
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Silvia Riggio
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Angelo Moscarelli
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Vito Macaluso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Rosalia Di Gerlando
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, Italy
| | - Baldassare Portolano
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy.
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12
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Tiemann I, Becker S, Fournier J, Damiran D, Büscher W, Hillemacher S. Differences among domestic chicken breeds in tonic immobility responses as a measure of fearfulness. PeerJ 2023; 11:e14703. [PMID: 37033722 PMCID: PMC10081456 DOI: 10.7717/peerj.14703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 12/15/2022] [Indexed: 04/07/2023] Open
Abstract
Background One priority for animal welfare is for animals to experience less fear, especially during human contact. For domestic animals, breeds that are less fearful may provide genetic resources to develop strains with improved welfare due to lower susceptibility to fear. Genetic predispositions inherited in these breeds might reflect the large diversity of chicken breeds. The goal of the present study was to systematically test a diverse group of chicken breeds to search for breeds that experience less fear. Methods Nineteen chicken breeds from commercial hybrid lines, native layer-type, meat-type and dual-purpose breeds, ornamental breeds as well as bantam breeds were tested in a standardized tonic immobility (TI) test. Chickens were manually restrained on their back, and the time to first head movement and first leg movement, the duration of TI, as well as the number of attempts needed to induce TI were measured. Results The TI response differed among chicken breeds (p ≤ 0.001) for naïve, mature hens. The median number of attempts required to induce TI ranged from 1 to 2 and did not differ significantly among breeds. Median durations were much more variable, with Lohmann Brown showing shortest durations (6 s, 12 s, 58 s for time to first head movement, first leg movement and total duration of TI, respectively). In contrast, medians reached the maximum of 600 s for all three measures in German Creepers. Repeated tests on the same individuals did not affect attempts needed to induce TI nor TI durations. Breeds clustered into two main groups, with layer-type native breeds and ornamental breeds having longer TI durations, and bantam, dual-purpose and meat-type native breeds having shorter TI durations. Conclusions Our findings provide evidence for substantial variation of fearfulness among breeds. This variation could be linked to the intended use during the breed's specific history. Knowledge and quantitative measurement of these behavioural responses provide the opportunity to improve welfare through selection and future breeding.
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Affiliation(s)
- Inga Tiemann
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
| | - Senta Becker
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
| | - Jocelyn Fournier
- Department of Animal & Poultry Science, University of Saskatchewan, Saskatoon, Canada
| | - Daalkhaijav Damiran
- Department of Animal & Poultry Science, University of Saskatchewan, Saskatoon, Canada
| | - Wolfgang Büscher
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
| | - Sonja Hillemacher
- Institute of Agricultural Engineering, University of Bonn, Bonn, Germany
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13
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Rentsch AK, Ellis JL, Widowski TM. Fearfulness in Commercial Laying Hens: A Meta-Analysis Comparing Brown and White Egg Layers. Poult Sci 2023; 102:102664. [PMID: 37058921 PMCID: PMC10123257 DOI: 10.1016/j.psj.2023.102664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
High fearfulness in commercial laying hens can negatively affect production parameters and animal welfare. Brown and white egg layers differ in several behavioral characteristics, though reported differences in fearfulness are inconsistent. A meta-analysis was conducted to determine whether there are systematic differences in measures of fearfulness between brown and white layers. Twenty-three studies that examined either 1 or both of 2 behavioral tests were included: tonic immobility (TI) (longer duration = higher fearfulness, 16 studies) and novel object (NO) test (lower approach rate = higher fearfulness, 11 studies). The 2 tests were analyzed separately. TI analyses: A generalized linear mixed effect model (GLMM) with a lognormal distribution was fitted to describe the data with experiment nested in study as a random effect. Explanatory (X) variables were considered through backward selection, where potential X-variables included color (brown vs. white layers), decade (1980s, 2000s, 2020s), age (prelay vs. in lay), genetic stock (hybrid vs. grand-/parent stock), and methodology (back vs. side position). NO test analyses: univariable GLMMs with a beta distribution were fitted with approach rate as the Y-variable and color, decade, age, stock, or 2 methodological factors (test duration, single vs. group testing) as X-variables. Models were evaluated by assessing information criteria, residuals/random effect normality, significance of X-variables and model evaluation statistics (mean square prediction error, concordance correlation coefficient). TI duration was best explained by a color-by-decade interaction (P = 0.0006). Whites in the 1980s had longer TI durations (709.43 ± 143.88 s) than browns in the 1980s (282.90 ± 59.70 s), as well as in comparison to browns (208.80 ± 50.82 s) or whites (204.85 ± 49.60 s) in the 2020s. The NO approach rate was best explained by color (P ≤ 0.05 in 3 models), age (P < 0.05 in 3 models), and decade (P = 0.04). Whites had a higher approach rate (0.7 ± 0.07) than browns (0.5 ± 0.11), birds in lay a higher rate (0.8 ± 0.07) than birds prelay (0.4 ± 0.12), and approach rate for papers published in the 2000s (0.8 ± 0.09) was higher than in the 2020s (0.2 ± 0.12). The phylogenetic difference in the 1980s was no longer detectable after enforcing an upper limit on TI durations (10 min), as became common practice in later studies. Our findings suggest that phylogenetic differences in fearfulness and changes over time are test dependent, and this raises important questions and potential consequences for assessing hen welfare in commercial egg production.
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14
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Gao C, Du W, Tian K, Wang K, Wang C, Sun G, Kang X, Li W. Analysis of Conservation Priorities and Runs of Homozygosity Patterns for Chinese Indigenous Chicken Breeds. Animals (Basel) 2023; 13:ani13040599. [PMID: 36830386 PMCID: PMC9951684 DOI: 10.3390/ani13040599] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
To achieve sustainable development of the poultry industry, the effective conservation of genetic resources has become increasingly important. In the present study, we systematically elucidated the population structure, conservation priority, and runs of homozygosity (ROH) patterns of Chinese native chicken breeds. We used a high-density genotyping dataset of 157 native chickens from eight breeds. The population structure showed different degrees of population stratification among the breeds. Chahua chicken was the most differentiated breed from the other breeds (Nei = 0.0813), and the Wannan three-yellow chicken (WanTy) showed the lowest degree of differentiation (Nei = 0.0438). On the basis of contribution priority, Xiaoshan chicken had the highest contribution to the total gene diversity (1.41%) and the maximum gene diversity of the synthetic population (31.1%). WanTy chicken showed the highest contribution to the total allelic diversity (1.31%) and the maximum allelic diversity of the syntenic population (17.0%). A total of 5242 ROH fragments and 5 ROH island regions were detected. The longest ROH fragment was 41.51 Mb. A comparison of the overlapping genomic regions between the ROH islands and QTLs in the quantitative trait loci (QTL) database showed that the annotated candidate genes were involved in crucial economic traits such as immunity, carcass weight, drumstick and leg muscle development, egg quality and egg production, abdominal fat precipitation, body weight, and feed intake. In conclusion, our findings revealed that Chahua, Xiaoshan, and WanTy should be the priority conservation breeds, which will help optimize the conservation and breeding programs for Chinese indigenous chicken breeds.
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Affiliation(s)
- Chaoqun Gao
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Wenping Du
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Kaiyuan Tian
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Kejun Wang
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Chunxiu Wang
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Guirong Sun
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Xiangtao Kang
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
- Correspondence: (X.K.); (W.L.)
| | - Wenting Li
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
- Correspondence: (X.K.); (W.L.)
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15
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Nash TJ, Morris KM, Mabbott NA, Vervelde L. Temporal transcriptome profiling of floating apical out chicken enteroids suggest stability and reproducibility. Vet Res 2023; 54:12. [PMID: 36793124 PMCID: PMC9933378 DOI: 10.1186/s13567-023-01144-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/26/2023] [Indexed: 02/17/2023] Open
Abstract
Enteroids are miniature self-organising three-dimensional (3D) tissue cultures which replicate much of the complexity of the intestinal epithelium. We recently developed an apical-out leukocyte-containing chicken enteroid model providing a novel physiologically relevant in vitro tool to explore host-pathogen interactions in the avian gut. However, the replicate consistency and culture stability have not yet been fully explored at the transcript level. In addition, causes for the inability to passage apical-out enteroids were not determined. Here we report the transcriptional profiling of chicken embryonic intestinal villi and chicken enteroid cultures using bulk RNA-seq. Comparison of the transcriptomes of biological and technical replicate enteroid cultures confirmed their high level of reproducibility. Detailed analysis of cell subpopulation and function markers revealed that the mature enteroids differentiate from late embryonic intestinal villi to recapitulate many digestive, immune and gut-barrier functions present in the avian intestine. These transcriptomic results demonstrate that the chicken enteroid cultures are highly reproducible, and within the first week of culture they morphologically mature to appear similar to the in vivo intestine, therefore representing a physiologically-relevant in vitro model of the chicken intestine.
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Affiliation(s)
- Tessa J. Nash
- grid.4305.20000 0004 1936 7988Division of Immunology, The Roslin Institute, R(D)SVS, University of Edinburgh, Midlothian Edinburgh, UK
| | - Katrina M. Morris
- grid.4305.20000 0004 1936 7988Division of Immunology, The Roslin Institute, R(D)SVS, University of Edinburgh, Midlothian Edinburgh, UK
| | - Neil A. Mabbott
- grid.4305.20000 0004 1936 7988Division of Immunology, The Roslin Institute, R(D)SVS, University of Edinburgh, Midlothian Edinburgh, UK
| | - Lonneke Vervelde
- Division of Immunology, The Roslin Institute, R(D)SVS, University of Edinburgh, Midlothian, Edinburgh, UK.
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16
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Jia M, Fulton J, Wong E. Temporal expression of avian β defensin 10 and cathelicidins in the yolk sac tissue of broiler and layer embryos. Poult Sci 2022; 102:102334. [PMID: 36481712 PMCID: PMC9723519 DOI: 10.1016/j.psj.2022.102334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022] Open
Abstract
The yolk sac is a multifunctional organ, which not only participates in nutrient absorption, but also plays an important role in immune function. The objective of this study was to compare the mRNA abundance of avian β-defensin 10 (AvBD10) and 3 cathelicidins (CATH1, CATH2, and CATH3) in the yolk sac tissue (YST) of commercial broilers and white egg and brown egg commercial layers. AvBD10 and CATH mRNA abundance was analyzed using two-way ANOVA and Tukey's test, with P < 0.05 being considered significant. AvBD10 and CATH mRNA showed similar temporal expression patterns in the YST of both broiler and layers, with an increase from embryonic day (E) 7 to E9 through E13 followed by a decrease to day of hatch. AvBD10 mRNA showed a breed × age interaction with greater expression in the YST of both layers compared to broilers at E9 and E11. CATH1 mRNA was greater in the YST of brown egg layers than broilers. CATH2 mRNA showed a breed × age interaction, with greater expression in the YST of brown egg layers than broilers at E11. CATH3 mRNA showed no difference in the YST between layers and broilers. Because broilers and brown egg layers are genetically related, these results show that selection for production parameters (broiler vs. layer) and not genetic relatedness (white egg layer vs. brown egg layer and broilers) is the basis for the differences in AvBD10, CATH1, and CATH2 mRNA in the YST of broilers and layers. The yolk-free body weights of broiler embryos were greater than that of both brown and white egg layers from E9 to 17. One possible explanation is that the reduced expression of AvBD10, CATH1 and CATH2 mRNA in the YST of broilers compared to layers at E9 and 11 may be due to faster embryonic growth at the expense of host defense peptide expression in broilers compared to layers.
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Affiliation(s)
- M. Jia
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, USA
| | - J.E. Fulton
- Hy-Line International, Dallas Center, IA 50063, USA
| | - E.A. Wong
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA 24061, USA,Corresponding author:
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17
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Lyu S, Arends D, Nassar MK, Weigend A, Weigend S, Wang E, Brockmann GA. High-density genotyping reveals candidate genomic regions for chicken body size in breeds of Asian origin. Poult Sci 2022; 102:102303. [PMID: 36436378 PMCID: PMC9706647 DOI: 10.1016/j.psj.2022.102303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Body size is one of the main selection indices in chicken breeding. Although often investigated, knowledge of the underlying genetic mechanisms is incomplete. The aim of the current study was to identify genomic regions associated with body size differences between Asian Game and Asian Bantam type chickens. In this study, 94 and 107 chickens from 4 Asian Game and 5 Asian Bantam type breeds, respectively, were genotyped using the chicken 580K single nucleotide polymorphism (SNP) array. A genome-wide association study (GWAS) and principal component analyses (PCA) were performed to identify genomic regions associated with body size related-traits such as wing length, shank length, shank thickness, keel length, and body weight. Hierarchical clustering of genotype data showed a clear genetic difference between the investigated Asian Game and Asian Bantam chicken types. GWAS identified 16 genomic regions associated with wing length (2, FDR ≤ 0.018), shank thickness (6, FDR ≤ 0.008), keel length (5, FDR ≤ 0.023), and body weight (3, FDR ≤ 0.041). PCA showed that the first principal component (PC1) separated the 2 chicken types and significantly correlated with the measured body size related-traits (P ≤ 2.24e-40). SNPs contributing significantly to PC1 were subjected to a more detailed investigation. This analysis identified 11 regions potentially associated with differences in body size related-traits. A region on chromosome 4 (GGA4) (17.3-21.3 Mb) was detected in both analyses GWAS and PCA. This region harbors 60 genes. Among them are myotubularin 1 (MTM1) and secreted frizzled-related protein 2 (SFPR2) which can be considered as potential candidate genes for body size related-traits. Our results clearly show that the investigated Asian Game type chicken breeds are genetically different from the Asian Bantam breeds. A region on GGA4 between 17.3 and 21.3 Mb was identified which contributes to the phenotypic difference, though further validation of candidate genes is necessary.
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Affiliation(s)
- Shijie Lyu
- Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universitt zu Berlin, Berlin 10115, Germany,Institute of Animal Science and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Danny Arends
- Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universitt zu Berlin, Berlin 10115, Germany,Department of Applied Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Mostafa K. Nassar
- Animal Production Department, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee 31535, Germany
| | - Steffen Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee 31535, Germany
| | - Eryao Wang
- Institute of Animal Science and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Gudrun A. Brockmann
- Albrecht Daniel Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universitt zu Berlin, Berlin 10115, Germany,Corresponding author:
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18
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Dementieva NV, Shcherbakov YS, Tyshchenko VI, Terletsky VP, Vakhrameev AB, Nikolaeva OA, Ryabova AE, Azovtseva AI, Mitrofanova OV, Peglivanyan GK, Reinbah NR, Griffin DK, Romanov MN. Comparative Analysis of Molecular RFLP and SNP Markers in Assessing and Understanding the Genetic Diversity of Various Chicken Breeds. Genes (Basel) 2022; 13:genes13101876. [PMID: 36292761 PMCID: PMC9601448 DOI: 10.3390/genes13101876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 11/04/2022] Open
Abstract
Monitoring the genetic diversity of small populations is important with respect to conserving rare and valuable chicken breeds, as well as discovery and innovation in germplasm research and application. Restriction fragment length polymorphisms (RFLPs), the molecular markers that underlie multilocus DNA fingerprinting (MLDF), have historically been employed for this purpose, but over the past two decades, there has been an irreversible shift toward high-throughput single-nucleotide polymorphisms (SNPs). In this study, we conducted a comparative analysis of archived MLDF results and new data from whole-genome SNP genotyping (SNPg) among 18 divergently selected breeds representing a large sample of the world gene pool. As a result, we obtained data that fit the general concept of the phylogenetic distribution of the studied breeds and compared them with RFLP and SNP markers. RFLPs were found to be useful markers for retrospective assessment of changes in the genetic architecture and variability underlying the phenotypic variation in chicken populations, especially when samples from previous generations used for MLDF are unavailable for SNPg. These results can facilitate further research necessary to assess the possibility of extrapolating previous MLDF results to study the long-term dynamics of genetic diversity in various small chicken germplasm populations over time. In general, the whole-genome characterization of populations and breeds by multiple SNP loci will further form the basis for the development and implementation of genomic selection with the aim of effective use of the genetic potential of the domestic gene pool in the poultry industry.
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Affiliation(s)
- Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
- Correspondence: (N.V.D.); (M.N.R.)
| | - Yuri S. Shcherbakov
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Valentina I. Tyshchenko
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | | | - Anatoly B. Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga A. Nikolaeva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Anna E. Ryabova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Anastasiia I. Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Olga V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Grigoriy K. Peglivanyan
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | - Natalia R. Reinbah
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Centre for Animal Husbandry, Pushkin, 196601 St. Petersburg, Russia
| | | | - Michael N. Romanov
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
- Correspondence: (N.V.D.); (M.N.R.)
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19
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Cho E, Cho S, Kim M, Ediriweera TK, Seo D, Lee SS, Cha J, Jin D, Kim YK, Lee JH. Single nucleotide polymorphism marker combinations for classifying Yeonsan Ogye chicken using a machine learning approach. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2022; 64:830-841. [PMID: 36287747 PMCID: PMC9574617 DOI: 10.5187/jast.2022.e64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/15/2022] [Accepted: 08/01/2022] [Indexed: 11/27/2022]
Abstract
Genetic analysis has great potential as a tool to differentiate between different species and breeds of livestock. In this study, the optimal combinations of single nucleotide polymorphism (SNP) markers for discriminating the Yeonsan Ogye chicken (Gallus gallus domesticus) breed were identified using high-density 600K SNP array data. In 3,904 individuals from 198 chicken breeds, SNP markers specific to the target population were discovered through a case-control genome-wide association study (GWAS) and filtered out based on the linkage disequilibrium blocks. Significant SNP markers were selected by feature selection applying two machine learning algorithms: Random Forest (RF) and AdaBoost (AB). Using a machine learning approach, the 38 (RF) and 43 (AB) optimal SNP marker combinations for the Yeonsan Ogye chicken population demonstrated 100% accuracy. Hence, the GWAS and machine learning models used in this study can be efficiently utilized to identify the optimal combination of markers for discriminating target populations using multiple SNP markers.
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Affiliation(s)
- Eunjin Cho
- Department of Bio-AI Convergence, Chungnam
National University, Daejeon 34134, Korea
| | - Sunghyun Cho
- Research and Development Center,
Insilicogen Inc., Yongin 19654, Korea
| | - Minjun Kim
- Division of Animal and Dairy Science,
Chungnam National University, Daejeon 34134, Korea
| | | | - Dongwon Seo
- Department of Bio-AI Convergence, Chungnam
National University, Daejeon 34134, Korea,Research Institute TNT Research
Company, Jeonju 54810, Korea
| | | | - Jihye Cha
- Animal Genome & Bioinformatics,
National Institute of Animal Science, Rural Development
Administration, Wanju 55365, Korea
| | - Daehyeok Jin
- Animal Genetic Resources Research Center,
National Institute of Animal Science, Rural Development
Administration, Hamyang 50000, Korea
| | - Young-Kuk Kim
- Department of Bio-AI Convergence, Chungnam
National University, Daejeon 34134, Korea
| | - Jun Heon Lee
- Department of Bio-AI Convergence, Chungnam
National University, Daejeon 34134, Korea,Division of Animal and Dairy Science,
Chungnam National University, Daejeon 34134, Korea,Corresponding author: Jun Heon Lee,
Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134,
Korea. Tel: +82-42-821-5779, E-mail:
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20
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Unveiling new perspective of phylogeography, genetic diversity, and population dynamics of Southeast Asian and Pacific chickens. Sci Rep 2022; 12:14609. [PMID: 36028749 PMCID: PMC9418149 DOI: 10.1038/s41598-022-18904-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/22/2022] [Indexed: 11/10/2022] Open
Abstract
The complex geographic and temporal origins of chicken domestication have attracted wide interest in molecular phylogeny and phylogeographic studies as they continue to be debated up to this day. In particular, the population dynamics and lineage-specific divergence time estimates of chickens in Southeast Asia (SEA) and the Pacific region are not well studied. Here, we analyzed 519 complete mitochondrial DNA control region sequences and identified 133 haplotypes with 70 variable sites. We documented 82.7% geographically unique haplotypes distributed across major haplogroups except for haplogroup C, suggesting high polymorphism among studied individuals. Mainland SEA (MSEA) chickens have higher overall genetic diversity than island SEA (ISEA) chickens. Phylogenetic trees and median-joining network revealed evidence of a new divergent matrilineage (i.e., haplogroup V) as a sister-clade of haplogroup C. The maximum clade credibility tree estimated the earlier coalescence age of ancestral D-lineage (i.e., sub-haplogroup D2) of continental chickens (3.7 kya; 95% HPD 1985–4835 years) while island populations diverged later at 2.1 kya (95% HPD 1467–2815 years). This evidence of earlier coalescence age of haplogroup D ancestral matriline exemplified dispersal patterns to the ISEA, and thereafter the island clade diversified as a distinct group.
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21
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Miao Y, Zhang X, Chen S, Zhou W, Xu D, Shi X, Li J, Tu J, Yuan X, Lv K, Tian G. Identifying cancer tissue-of-origin by a novel machine learning method based on expression quantitative trait loci. Front Oncol 2022; 12:946552. [PMID: 36016607 PMCID: PMC9396384 DOI: 10.3389/fonc.2022.946552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer of unknown primary (CUP) refers to cancer with primary lesion unidentifiable by regular pathological and clinical diagnostic methods. This kind of cancer is extremely difficult to treat, and patients with CUP usually have a very short survival time. Recent studies have suggested that cancer treatment targeting primary lesion will significantly improve the survival of CUP patients. Thus, it is critical to develop accurate yet fast methods to infer the tissue-of-origin (TOO) of CUP. In the past years, there are a few computational methods to infer TOO based on single omics data like gene expression, methylation, somatic mutation, and so on. However, the metastasis of tumor involves the interaction of multiple levels of biological molecules. In this study, we developed a novel computational method to predict TOO of CUP patients by explicitly integrating expression quantitative trait loci (eQTL) into an XGBoost classification model. We trained our model with The Cancer Genome Atlas (TCGA) data involving over 7,000 samples across 20 types of solid tumors. In the 10-fold cross-validation, the prediction accuracy of the model with eQTL was over 0.96, better than that without eQTL. In addition, we also tested our model in an independent data downloaded from Gene Expression Omnibus (GEO) consisting of 87 samples across 4 cancer types. The model also achieved an f1-score of 0.7-1 depending on different cancer types. In summary, eQTL was an important information in inferring cancer TOO and the model might be applied in clinical routine test for CUP patients in the future.
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Affiliation(s)
- Yongchang Miao
- Gastroenterology Center, The Second People’s Hospital of Lianyungang, Lianyungang, China
- Lianyungang Clinical College of Xuzhou Medical University, Lianyungang, China
- The Second People’s Hospital of Lianyungang, Affiliated to Kangda College of Nanjing Medical University, Lianyungang, China
| | - Xueliang Zhang
- Fifth Division of Cancer, Jiamusi Cancer Hospital, Jiamusi, China
| | - Sijie Chen
- Department of Mathematics, Ocean University of China, Qingdao, China
| | - Wenjing Zhou
- Department of Oncology, Hiser Medical Center of Qingdao, Qingdao, China
| | - Dalai Xu
- Gastrointestinal Surgery, The Second People’s Hospital of Lianyungang, Lianyungang, China
| | - Xiaoli Shi
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
| | - Jian Li
- Department of Mathematics, Ocean University of China, Qingdao, China
| | - Jinhui Tu
- Department of Mathematics, Ocean University of China, Qingdao, China
| | - Xuelian Yuan
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
| | - Kebo Lv
- Department of Mathematics, Ocean University of China, Qingdao, China
| | - Geng Tian
- Department of Science, Geneis Beijing Co., Ltd., Beijing, China
- Qingdao Geneis Institute of Big Data Mining and Precision Medicine, Qingdao, China
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22
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Restoux G, Rognon X, Vieaud A, Guemene D, Petitjean F, Rouger R, Brard-Fudulea S, Lubac-Paye S, Chiron G, Tixier-Boichard M. Managing genetic diversity in breeding programs of small populations: the case of French local chicken breeds. Genet Sel Evol 2022; 54:56. [PMID: 35922745 PMCID: PMC9347113 DOI: 10.1186/s12711-022-00746-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/21/2022] [Indexed: 12/03/2022] Open
Abstract
Background On-going climate change will drastically modify agriculture in the future, with a need for more sustainable systems, in particular regarding animal production. In this context, genetic diversity is a key factor for adaptation to new conditions: local breeds likely harbor unique adaptive features and represent a key component of diversity to reach resilience. However, local breeds often suffer from small population sizes, which puts these valuable resources at risk of extinction. In chickens, population management programs were initiated a few decades ago in France, relying on a particular niche market that aims at promoting and protecting local breeds. We conducted a unique comprehensive study of 22 French local breeds, along with four commercial lines, to evaluate their genetic conservation status and the efficiency of the population management programs. Results Using a 57K single nucleotide polymorphism (SNP) chip, we demonstrated that both the between- and within-breed genetic diversity levels are high in the French local chicken populations. Diversity is mainly structured according to the breeds’ selection and history. Nevertheless, we observed a prominent sub-structuring of breeds according to farmers’ practices in terms of exchange, leading to more or less isolated flocks. By analysing demographic parameters and molecular information, we showed that consistent management programs are efficient in conserving genetic diversity, since breeds that integrated such programs earlier had older inbreeding. Conclusions Management programs of French local chicken breeds have maintained their genetic diversity at a good level. We recommend that future programs sample as many individuals as possible, with emphasis on both males and females from the start, and focus on a quick and strong increase of population size while conserving as many families as possible. We also stress the usefulness of molecular tools to monitor small populations for which pedigrees are not always available. Finally, the breed appears to be an appropriate operational unit for the conservation of genetic diversity, even for local breeds, for which varieties, if present, could also be taken into account. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00746-2.
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Affiliation(s)
- Gwendal Restoux
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| | - Xavier Rognon
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Agathe Vieaud
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Daniel Guemene
- Centre INRAE Val de Loire, UMR-BOA, SYSAAF, 37380, Nouzilly, France.,Centre INRAE Val de Loire, UMR-BOA (UR83), 37380, Nouzilly, France
| | - Florence Petitjean
- Centre de Sélection de Béchanne, Hameau de Béchanne, 01370, Saint-Etienne-Du-Bois, France
| | - Romuald Rouger
- Centre INRAE Val de Loire, UMR-BOA, SYSAAF, 37380, Nouzilly, France
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23
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Shi S, Shao D, Yang L, Liang Q, Han W, Xue Q, Qu L, Leng L, Li Y, Zhao X, Dong P, Walugembe M, Kayang BB, Muhairwa AP, Zhou H, Tong H. Whole Genome Analyses Reveal Novel Genes Associated with Chicken Adaptation to Tropical and Frigid Environments. J Adv Res 2022; 47:13-25. [PMID: 35907630 PMCID: PMC10173185 DOI: 10.1016/j.jare.2022.07.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/01/2022] [Accepted: 07/17/2022] [Indexed: 01/25/2023] Open
Abstract
INTRODUCTION Investigating the genetic footprints of historical temperature selection can get insights to the local adaptation and feasible influences of climate change on long-term population dynamics. OBJECT Chicken is a significative species to study genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties. Yet, few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments. METHOD Here, we generated whole genome resequencing of 119 domesticated chickens in China including the following breeds which are in order of breeding environmental temperature from more tropical to more frigid: Wenchang chicken (WCC), green-shell chicken (GSC), Tibetan chicken (TBC), and Lindian chicken (LDC). RESULTS Our results showed WCC branched off earlier than LDC with an evident genetic admixture between WCC and LDC, suggesting their closer genetic relationship. Further comparative genomic analyses solute carrier family 33 member 1 (SLC33A1) and thyroid stimulating hormone receptor (TSHR) genes exhibited stronger signatures for positive selection in the genome of the more tropical WCC. Furthermore, genotype data from about 3,000 African local ecotypes confirmed that allele frequencies of single nucleotide polymorphisms (SNPs) in these 2 genes appeared strongly associated with tropical environment adaptation. In addition, the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) gene exhibited a strong signature for positive selection in the LDC genome, and SNPs with marked allele frequency differences indicated a significant relationship with frigid environment adaptation. CONCLUSION Our findings partially clarify how selection footprints from environmental temperature stress can lead to advantageous genomic adaptions to tropical and frigid environments in poultry and provide a valuable resource for selective breeding of chickens.
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Affiliation(s)
- Shourong Shi
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Dan Shao
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Lingyun Yang
- Novogene Bioinformatics Institute, Beijing 10089, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 10089, China
| | - Wei Han
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Qian Xue
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Liang Qu
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China
| | - Li Leng
- College of Animal Science and technology, Northeast Agricultural University, Harbin, Heilongjiang, 150038, China
| | - Yishu Li
- Tropical Crop Germplasm Research Institute, Haikou, Hainan, 571101, China
| | - Xiaogang Zhao
- Agriculture and Animal Husbandry Rural and Science and Technology Bureau, Xiangcheng County, Ganzi Tibetan Autonomous Prefecture, Sichuan, 626000, China
| | - Ping Dong
- Agriculture and Animal Husbandry Rural and Science and Technology Bureau, Xiangcheng County, Ganzi Tibetan Autonomous Prefecture, Sichuan, 626000, China
| | - Muhammed Walugembe
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA
| | - Boniface B Kayang
- Department of Animal Science, University of Ghana, Legon, Accra 233, Ghana
| | - Amandus P Muhairwa
- Department of Veterinary Medicine and Public Health, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3000 Chuo Kikuu, Morogoro, Tanzania
| | - Huaijun Zhou
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, CA 95616, USA
| | - Haibing Tong
- Poultry Institute, Chinese Academy of Agriculture Science, Yangzhou, Jiangsu 225125, China.
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24
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Heidaritabar M, Carney V, Groenen MAM, Plastow G. Assessing the genomic diversity and relatedness in 10 Canadian heritage chicken lines using whole-genome sequence data. J Anim Breed Genet 2022; 139:556-573. [PMID: 35579203 DOI: 10.1111/jbg.12720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/01/2022] [Indexed: 11/29/2022]
Abstract
In the past 50 years, there has been a steep increase in the demand for poultry products, met by increasing production along with genetic selection for improved growth, efficiency, health and reproduction. The selection tends to reduce the number and type of genetic resources contributing to the majority of production. The University of Alberta maintains 10 heritage chicken lines (Brown Leghorn (BL), Light Sussex (LS), New Hampshire (NH), Saskatchewan Barred Rock (SaskBR), Shaver Barred Rock (ShaverBR), Shaver Rhode Island Red (RIR), White Leghorn (WL) and three commercial crosses called Alberta Meat Control strains 1957 (AMC-1957), 1978 sire line (AMC-1978-20S) and 1978 dam line (AMC-1978-30D), that played a large role in the evolution of the poultry industry in Canada. Since these lines have not been subjected to the same intensive selection pressures as commercial counterparts, they may contain unique genetic variants lost in commercial lines. Thus, for conservation management of these lines, the first step is to assess their genetic diversity. 71 male samples from across 10 lines were analysed using whole-genome sequencing and patterns of genetic diversity and relatedness among these lines were explored. AMC-1978-30D showed the highest genetic diversity as reflected in observed and expected heterozygosity (0.327 and 0.250), percentage of polymorphic markers (~ 65%) and average recent inbreeding coefficient (-0.039), followed by AMC-1978-20S and AMC-1957. BL showed the lowest genetic diversity as reflected in observed and expected heterozygosity (0.130 and 0.116), percentage of polymorphic markers (~31%) and average recent inbreeding coefficient (0.577), followed by LS, WL and NH. Our findings highlight the need for special attention for the populations of BL, WL, LS and NH, with the largest levels of inbreeding. Our results can be used to develop a breeding strategy to optimize and conserve the genetic variation present in heritage lines.
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Affiliation(s)
- Marzieh Heidaritabar
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
| | - Valerie Carney
- Poultry Innovation Partnership, University of Alberta, Edmonton, Alberta, Canada
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, the Netherlands
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, Alberta, Canada
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25
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Chebo C, Betsha S, Melesse A. Chicken genetic diversity, improvement strategies and impacts on egg productivity in Ethiopia: a review. WORLD POULTRY SCI J 2022. [DOI: 10.1080/00439339.2022.2067020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Chencha Chebo
- Department of Animal Science, Arba Minch University, College of Agricultural Sciences, Arba Minch, Ethiopia
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
| | - Simret Betsha
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
| | - Aberra Melesse
- School of Animal & Range Sciences, Hawassa University, College of Agriculture, Hawassa, Ethiopia
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26
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Marcos S, Parejo M, Estonba A, Alberdi A. Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2100065. [PMID: 36620197 PMCID: PMC9744478 DOI: 10.1002/ggn2.202100065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 03/05/2022] [Indexed: 01/11/2023]
Abstract
Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.
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Affiliation(s)
- Sofia Marcos
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Melanie Parejo
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Andone Estonba
- Applied Genomics and BioinformaticsUniversity of the Basque Country (UPV/EHU)LeioaBilbao48940Spain
| | - Antton Alberdi
- Center for Evolutionary HologenomicsGLOBE InstituteUniversity of CopenhagenCopenhagen1353Denmark
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27
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Freick M, Schreiter R, Weber J, Vahlenkamp TW, Heenemann K. Avian leukosis virus (ALV) is highly prevalent in fancy-chicken flocks in Saxony. Arch Virol 2022; 167:1169-1174. [PMID: 35301570 PMCID: PMC8964621 DOI: 10.1007/s00705-022-05404-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/24/2022] [Indexed: 11/30/2022]
Abstract
The current prevalence of avian leukosis virus (ALV) in fancy chickens in Germany is unknown. Therefore, 537 cloacal swabs from 50 purebred fancy-chicken flocks in Saxony were tested for the presence of the ALV p27 protein using a commercial antigen-capture ELISA. The detection rate was 28.7% at the individual-animal level and 56.0% at the flock level. Phylogenetic analysis of PCR products obtained from 22 different flocks revealed the highest similarity to ALV subtype K. When classifying breeds by their origin, ALV detection rates differed significantly. Evaluation of questionnaire data revealed no significant differences between ALV-positive and negative flocks regarding mortality.
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Affiliation(s)
- Markus Freick
- Faculty Agriculture/Environment/Chemistry, HTW Dresden-University of Applied Sciences, Pillnitzer Platz 2, 01326, Dresden, Germany.
| | - Ruben Schreiter
- ZAFT e.V.-Centre for Applied Research and Technology, Friedrich-List-Platz 1, 01069, Dresden, Germany
| | - Jim Weber
- Veterinary Practice Zettlitz, Straße der Jugend 68, 09306, Zettlitz OT Methau, Germany
| | - Thomas W Vahlenkamp
- Veterinary Faculty, Center for Infectious Diseases, Institute of Virology, University of Leipzig, An den Tierkliniken 29, 04103, Leipzig, Germany
| | - Kristin Heenemann
- Veterinary Faculty, Center for Infectious Diseases, Institute of Virology, University of Leipzig, An den Tierkliniken 29, 04103, Leipzig, Germany
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28
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Assessment of linkage disequilibrium patterns between structural variants and single nucleotide polymorphisms in three commercial chicken populations. BMC Genomics 2022; 23:193. [PMID: 35264116 PMCID: PMC8908679 DOI: 10.1186/s12864-022-08418-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/24/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Structural variants (SV) are causative for some prominent phenotypic traits of livestock as different comb types in chickens or color patterns in pigs. Their effects on production traits are also increasingly studied. Nevertheless, accurately calling SV remains challenging. It is therefore of interest, whether close-by single nucleotide polymorphisms (SNPs) are in strong linkage disequilibrium (LD) with SVs and can serve as markers. Literature comes to different conclusions on whether SVs are in LD to SNPs on the same level as SNPs to other SNPs. The present study aimed to generate a precise SV callset from whole-genome short-read sequencing (WGS) data for three commercial chicken populations and to evaluate LD patterns between the called SVs and surrounding SNPs. It is thereby the first study that assessed LD between SVs and SNPs in chickens. RESULTS The final callset consisted of 12,294,329 bivariate SNPs, 4,301 deletions (DEL), 224 duplications (DUP), 218 inversions (INV) and 117 translocation breakpoints (BND). While average LD between DELs and SNPs was at the same level as between SNPs and SNPs, LD between other SVs and SNPs was strongly reduced (DUP: 40%, INV: 27%, BND: 19% of between-SNP LD). A main factor for the reduced LD was the presence of local minor allele frequency differences, which accounted for 50% of the difference between SNP - SNP and DUP - SNP LD. This was potentially accompanied by lower genotyping accuracies for DUP, INV and BND compared with SNPs and DELs. An evaluation of the presence of tag SNPs (SNP in highest LD to the variant of interest) further revealed DELs to be slightly less tagged by WGS SNPs than WGS SNPs by other SNPs. This difference, however, was no longer present when reducing the pool of potential tag SNPs to SNPs located on four different chicken genotyping arrays. CONCLUSIONS The results implied that genomic variance due to DELs in the chicken populations studied can be captured by different SNP marker sets as good as variance from WGS SNPs, whereas separate SV calling might be advisable for DUP, INV, and BND effects.
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29
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Genome-wide run of homozygosity analysis reveals candidate genomic regions associated with environmental adaptations of Tibetan native chickens. BMC Genomics 2022; 23:91. [PMID: 35100979 PMCID: PMC8805376 DOI: 10.1186/s12864-021-08280-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/23/2021] [Indexed: 01/12/2023] Open
Abstract
Background In Tibet, the two most important breeds are Tibetan chicken and Lhasa white chicken, and the duo exhibit specific adaptations to the high altitude thereby supplying proteins for humans living in the plateau. These breeds are partly included in the conservation plans because they represent important chicken genetic resources. However, the genetic diversity of these chickens is rarely investigated. Based on whole-genome sequencing data of 113 chickens from 4 populations of Tibetan chicken including Shigatse (SH), Nyemo (NM), Dagze (DZ) and Nyingchi (LZ), as well as Lhasa white (LW) chicken breed, we investigated the genetic diversity of these chicken breeds by genetic differentiation, run of homozygosity (ROH), genomic inbreeding and selection signature analyses. Results Our results revealed high genetic diversity across the five chicken populations. The linkage disequilibrium decay was highest in LZ, while subtle genetic differentiation was found between LZ and other populations (Fst ranging from 0.05 to 0.10). Furthermore, the highest ROH-based inbreeding estimate (FROH) of 0.11 was observed in LZ. In other populations, the FROH ranged from 0.04 to 0.06. In total, 74, 111, 62, 42 and 54 ROH islands containing SNPs ranked top 1% for concurrency were identified in SH, NM, DZ, LZ and LW, respectively. Genes common to the ROH islands in the five populations included BDNF, CCDC34, LGR4, LIN7C, GLS, LOC101747789, MYO1B, STAT1 and STAT4. This suggested their essential roles in adaptation of the chickens. We also identified a common candidate genomic region harboring AMY2A, NTNG1 and VAV3 genes in all populations. These genes had been implicated in digestion, neurite growth and high-altitude adaptation. Conclusions High genetic diversity is observed in Tibetan native chickens. Inbreeding is more intense in the Nyingchi population which is also genetically distant from other chicken populations. Candidate genes in ROH islands are likely to be the drivers of adaptation to high altitude exhibited by the five Tibetan native chicken populations. Our findings contribute to the understanding of genetic diversity offer valuable insights for the genetic mechanism of adaptation, and provide veritable tools that can help in the design and implementation of breeding and conservation strategies for Tibetan native chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08280-z.
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30
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Pook T, Nemri A, Gonzalez Segovia EG, Valle Torres D, Simianer H, Schoen CC. Increasing calling accuracy, coverage, and read-depth in sequence data by the use of haplotype blocks. PLoS Genet 2021; 17:e1009944. [PMID: 34941872 PMCID: PMC8699914 DOI: 10.1371/journal.pgen.1009944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 11/13/2021] [Indexed: 01/16/2023] Open
Abstract
High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics, requiring geneticists and breeders to find a balance between data quality and the number of genotyped lines under a variety of different existing genotyping technologies when resources are limited. In this work, we are proposing a new imputation pipeline (“HBimpute”) that can be used to generate high-quality genomic data from low read-depth whole-genome-sequence data. The key idea of the pipeline is the use of haplotype blocks from the software HaploBlocker to identify locally similar lines and subsequently use the reads of all locally similar lines in the variant calling for a specific line. The effectiveness of the pipeline is showcased on a dataset of 321 doubled haploid lines of a European maize landrace, which were sequenced at 0.5X read-depth. The overall imputing error rates are cut in half compared to state-of-the-art software like BEAGLE and STITCH, while the average read-depth is increased to 83X, thus enabling the calling of copy number variation. The usefulness of the obtained imputed data panel is further evaluated by comparing the performance of sequence data in common breeding applications to that of genomic data generated with a genotyping array. For both genome-wide association studies and genomic prediction, results are on par or even slightly better than results obtained with high-density array data (600k). In particular for genomic prediction, we observe slightly higher data quality for the sequence data compared to the 600k array in the form of higher prediction accuracies. This occurred specifically when reducing the data panel to the set of overlapping markers between sequence and array, indicating that sequencing data can benefit from the same marker ascertainment as used in the array process to increase the quality and usability of genomic data. High-throughput genotyping of large numbers of lines remains a key challenge in plant genetics and breeding. Cost, precision, and throughput must be balanced to achieve optimal efficiency given available technologies and finite resources. Although genotyping arrays are still considered the gold standard in high-throughput quantitative genetics, recent advances in sequencing provide new opportunities. Both the quality and cost of genomic data generated based on sequencing are highly dependent on the used read-depth. In this work, we propose a new imputation pipeline (“HBimpute”) that uses haplotype blocks to detect individuals of the same genetic origin and subsequently uses all reads of those individuals in the variant calling. Thus, the obtained virtual read-depth is artificially increased, leading to higher calling accuracy, coverage, and the ability to call copy number variation based on low read-depth sequencing data. To conclude, our approach makes sequencing a cost-competitive alternative to genotyping arrays with the added benefit of allowing the calling of structural variation.
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Affiliation(s)
- Torsten Pook
- Center for Integrated Breeding Research, Animal Breeding and Genetics Group, University of Goettingen, Goettingen, Germany
- * E-mail:
| | | | | | - Daniel Valle Torres
- Plant Breeding, Technical University of Munich, TUM School of Life Sciences Weihenstephan, Freising, Germany
| | - Henner Simianer
- Center for Integrated Breeding Research, Animal Breeding and Genetics Group, University of Goettingen, Goettingen, Germany
| | - Chris-Carolin Schoen
- Plant Breeding, Technical University of Munich, TUM School of Life Sciences Weihenstephan, Freising, Germany
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31
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Soglia D, Sartore S, Lasagna E, Castellini C, Cendron F, Perini F, Cassandro M, Marzoni M, Iaffaldano N, Buccioni A, Dabbou S, Castillo A, Maione S, Bianchi C, Profiti M, Sacchi P, Cerolini S, Schiavone A. Genetic Diversity of 17 Autochthonous Italian Chicken Breeds and Their Extinction Risk Status. Front Genet 2021; 12:715656. [PMID: 34594362 PMCID: PMC8477013 DOI: 10.3389/fgene.2021.715656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/26/2021] [Indexed: 11/29/2022] Open
Abstract
The preservation of genetic variability of autochthonous poultry breeds is crucial in global biodiversity. A recent report revealed small breed size and potential risk of extinction of all native Italian poultry breeds; therefore, a correct assessment of their genetic diversity is necessary for a suitable management of their preservation. In this work, we provided an overview of the contribution to poultry biodiversity of some Italian autochthonous breeds reared in conservation centers devoted to local biodiversity preservation. The level of genetic diversity, molecular kinship, inbreeding, contribution to overall genetic diversity, and rate of extinction of each breed were analyzed with a set of 14 microsatellite loci in 17 autochthonous chicken breeds. To evaluate genetic variability, total number (Na), and effective number (Ne) of alleles, observed (Ho) and expected (He) heterozygosity, and F (Wright’s inbreeding coefficient) index were surveyed. The contribution of each analyzed breed to genetic diversity of the whole dataset was assessed using MolKin3.0; global genetic diversity and allelic richness contributions were evaluated. All the investigated loci were polymorphic; 209 alleles were identified (94 of which private alleles). The average number of alleles per locus was 3.62, and the effective number of alleles was 2.27. The Ne resulted lower in all breeds due to the presence of low-frequency alleles that can be easily lost by genetic drift, thus reducing the genetic variability of the breeds, and increasing their risk of extinction. The global molecular kinship was 27%, the average breed molecular kinship was 53%, and the mean inbreeding rate 43%, with a self-coancestry of 78%. Wright’s statistical analysis showed a 41% excess of homozygous due to breed genetic differences (34%) and to inbreeding within the breed (9%). Genetic variability analysis showed that 11 breeds were in endangered status. The contribution to Italian poultry genetic diversity, estimated as global genetic diversity, and ranged from 30.2 to 98.5%. In conclusion, the investigated breeds maintain a unique genetic pattern and play an important role in global Italian poultry biodiversity, providing a remarkable contribution to genetic variability.
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Affiliation(s)
- Dominga Soglia
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Turin, Italy
| | - Stefano Sartore
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Turin, Italy
| | - Emiliano Lasagna
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Cesare Castellini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università di Padova, Viale dell'Università, Legnaro, Italy
| | - Francesco Perini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Perugia, Italy
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Università di Padova, Viale dell'Università, Legnaro, Italy
| | | | - Nicolaia Iaffaldano
- Dipartimento Agricoltura, Ambiente e Alimenti, Università degli Studi del Molise, Campobasso, Italy
| | - Arianna Buccioni
- Dipartimento di Scienze e Tecnologie Agrarie, Alimentari, Ambientali e Forestali, Università di Firenze, Florence, Italy
| | - Sihem Dabbou
- Center Agriculture Food Environment (C3A), University of Trento, Trento, Italy.,Research and Innovation Center, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Annelisse Castillo
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Turin, Italy
| | - Sandra Maione
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Turin, Italy
| | - Chiara Bianchi
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Turin, Italy
| | - Margherita Profiti
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Turin, Italy
| | - Paola Sacchi
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Turin, Italy
| | - Silvia Cerolini
- Dipartimento di Medicina Veterinaria, Università degli Studi di Milano, Lodi, Italy
| | - Achille Schiavone
- Dipartimento di Scienze Veterinarie, Università degli Studi di Torino, Turin, Italy
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32
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Manjula P, Fulton JE, Seo D, Lee JH. Comparison of major histocompatibility complex-B variability in Sri Lankan indigenous chickens with five global chicken populations using MHC-B SNP panel. Anim Genet 2021; 52:824-833. [PMID: 34523150 DOI: 10.1111/age.13137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2021] [Indexed: 11/29/2022]
Abstract
In the present study, we investigated the major histocompatibility complex (MHC)-B haplotypes diversity of Sri Lankan indigenous chickens from three different geographical sites consisting of highly mixed populations using 90 SNPs in the MHC-B region. A total of 48 haplotypes were identified. Those included 37 novel haplotypes and 11 previously identified 'standard' haplotypes. The MHC-linked marker, LEI0258, had 23 alleles showing less diversity than defined by MHC-B SNP haplotypes. Among those identified haplotypes, five standard haplotypes-BSNP-O02, BSNP-M01, BSNP-A04, BSNP-K03, BSNP-T04-were most commonly observed, suggesting past introgression of imported breeds. Comparison of the MHC-B haplotypes of Sri Lankan and four other global populations with previously defined haplotypes indicated the sharing of 23 standard haplotypes with common origins. Novel haplotypes are population-specific and not shared among the geographical boundaries. Backyard indigenous chickens are unselected, highly crossbred, and generally thrive under dynamic environmental conditions. Hence free-range production systems may be responsible for maintaining high diversity in the MHC-B region with novel haplotypes.
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Affiliation(s)
- P Manjula
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - J E Fulton
- Hy-Line International, Dallas Center, IA, 50063, USA
| | - D Seo
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, 34134, Korea
| | - J H Lee
- Division of Animal and Dairy Sciences, Chungnam National University, Daejeon, 34134, Korea
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33
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Fallahshahroudi A, Johnsson M, Sorato E, Ubhayasekera SJKA, Bergquist J, Altimiras J, Jensen P. Effects of the domestic thyroid stimulating hormone receptor (TSHR) variant on the hypothalamic-pituitary-thyroid axis and behavior in chicken. Genetics 2021; 217:1-9. [PMID: 33683367 DOI: 10.1093/genetics/iyaa050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 12/21/2020] [Indexed: 12/18/2022] Open
Abstract
Domestic chickens are less fearful, have a faster sexual development, grow bigger, and lay more eggs than their primary ancestor, the red junglefowl. Several candidate genetic variants selected during domestication have been identified, but only a few studies have directly linked them with distinct phenotypic traits. Notably, a variant of the thyroid stimulating hormone receptor (TSHR) gene has been under strong positive selection over the past millennium, but it's function and mechanisms of action are still largely unresolved. We therefore assessed the abundance of the domestic TSHR variant and possible genomic selection signatures in an extensive data set comprising multiple commercial and village chicken populations as well as wild-living extant members of the genus Gallus. Furthermore, by mean of extensive backcrossing we introgressed the wild-type TSHR variant from red junglefowl into domestic White Leghorn chickens and investigated gene expression, hormone levels, cold adaptation, and behavior in chickens possessing either the wild-type or domestic TSHR variant. While the domestic TSHR was the most common variant in all studied domestic populations and in one of two red junglefowl population, it was not detected in the other Gallus species. Functionally, the individuals with the domestic TSHR variant had a lower expression of the TSHR in the hypothalamus and marginally higher in the thyroid gland than wild-type TSHR individuals. Expression of TSHB and DIO2, two regulators of sexual maturity and reproduction in birds, was higher in the pituitary gland of the domestic-variant chickens. Furthermore, the domestic variant was associated with higher activity in the open field test. Our findings confirm that the spread of the domestic TSHR variant is limited to domesticated chickens, and to a lesser extent, their wild counterpart, the red junglefowl. Furthermore, we showed that effects of genetic variability in TSHR mirror key differences in gene expression and behavior previously described between the red junglefowl and domestic chicken.
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Affiliation(s)
- Amir Fallahshahroudi
- Department of Medical Biochemistry and Microbiology, Biomedical Center (BMC), Uppsala University, Uppsala 752 37, Sweden
| | - Martin Johnsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Enrico Sorato
- Reneco International Wildlife Consultants, Abu Dhabi, UAE
| | | | - Jonas Bergquist
- Department of Chemistry, Biomedical Center (BMC), Uppsala University, Uppsala 75124, Sweden
| | - Jordi Altimiras
- AVIAN Behavioural Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping 58183, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, Department of Physics, Chemistry and Biology (IFM), Linköping University, Linköping 58183, Sweden
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34
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Lundberg R, Scharch C, Sandvang D. The link between broiler flock heterogeneity and cecal microbiome composition. Anim Microbiome 2021; 3:54. [PMID: 34332648 PMCID: PMC8325257 DOI: 10.1186/s42523-021-00110-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 07/06/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Despite low genetic variation of broilers and deployment of considerate management practices, there still exists considerable body weight (BW) heterogeneity within broiler flocks which adversely affects the commercial value. The purpose of this study was to investigate the role of the cecal microbiome in weight differences between animals. Understanding how the gut microbiome may contribute to flock heterogeneity helps to pave the road for identifying methods to improve flock uniformity and performance. RESULTS Two hundred eighteen male broiler chicks were housed in the same pen, reared for 37 days, and at study end the 25 birds with highest BW (Big) and the 25 birds with lowest BW (Small) were selected for microbiome analysis. Cecal contents were analyzed by a hybrid metagenomic sequencing approach combining long and short read sequencing. We found that Big birds displayed higher microbial alpha diversity, higher microbiome uniformity (i.e. lower beta diversity within the group of Big birds), higher levels of SCFA-producing and health-associated bacterial taxa such as Lachnospiraceae, Faecalibacterium, Butyricicoccus and Christensenellales, and lower levels of Akkermansia muciniphila and Escherichia coli as compared to Small birds. CONCLUSION Cecal microbiome characteristics could be linked to the size of broiler chickens. Differences in alpha diversity, beta diversity and taxa abundances all seem to be directly associated with growth differences observed in an otherwise similar broiler flock.
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Affiliation(s)
- Randi Lundberg
- Chr. Hansen A/S, Boege Allé 10-12, 2970, Hoersholm, Denmark.
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35
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Wang K, Hu H, Tian Y, Li J, Scheben A, Zhang C, Li Y, Wu J, Yang L, Fan X, Sun G, Li D, Zhang Y, Han R, Jiang R, Huang H, Yan F, Wang Y, Li Z, Li G, Liu X, Li W, Edwards D, Kang X. The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size. Mol Biol Evol 2021; 38:5066-5081. [PMID: 34329477 PMCID: PMC8557422 DOI: 10.1093/molbev/msab231] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional ∼66.5 Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression level are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based GWAS identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size QTL located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.
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Affiliation(s)
- Kejun Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Haifei Hu
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, 6009 WA, Australia
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Jingyi Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, 430070 Wuhan, Hubei, China
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Chenxi Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Yiyi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Junfeng Wu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Lan Yang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Xuewei Fan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Hetian Huang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Fengbin Yan
- Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Yanbin Wang
- Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Crawley, 6009 WA, Australia
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources,Zhengzhou, 450046, China
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36
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Lawal RA, Hanotte O. Domestic chicken diversity: Origin, distribution, and adaptation. Anim Genet 2021; 52:385-394. [PMID: 34060099 DOI: 10.1111/age.13091] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 12/13/2022]
Abstract
Chicken is the most numerous among the domesticated livestock species. Across cultures, religions, and societies, chicken is widely accepted with little or no taboo compared to other domestic animals. Its adaptability to diverse environmental conditions and demonstrated potential for breeding improvement provide a unique genetic resource for addressing the challenges of food security in a world impacted by climatic change and human population growth. Recent studies, shedding new knowledge on the chicken genomes, have helped reconstruct its past evolutionary history. Here, we review the literature concerning the origin, dispersion, and adaptation of domestic chicken. We highlight the role of human and natural selection in shaping the diversity of the species and provide a few examples of knowledge gaps that may be the focus of future research.
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Affiliation(s)
- R A Lawal
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, 04609, USA
| | - O Hanotte
- Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.,Centre for Tropical Livestock Genetics and Health, The Roslin Institute, Edinburgh, EH25 9RG, UK.,LiveGene, International Livestock Research Institute (ILRI), P.O. 5689, Addis Ababa, Ethiopia
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37
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Mehlhorn J, Caspers S. The Effects of Domestication on the Brain and Behavior of the Chicken in the Light of Evolution. BRAIN, BEHAVIOR AND EVOLUTION 2021; 95:287-301. [PMID: 34044402 DOI: 10.1159/000516787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/16/2021] [Indexed: 11/19/2022]
Abstract
The avian class is characterized by particularly strong variability in their domesticated species. With more than 250 breeds and highly efficient commercial lines, domestic chickens represent the outcome of a really long period of artificial selection. One characteristic of domestication is the alterations in brain size and brain composition. The influence of domestication on brain morphology has been reviewed in the past, but mostly with a focus on mammals. Studies on avian species have seldom been taken into account. In this review, we would like to give an overview about the changes and variations in (brain) morphology and behavior in the domestic chicken, taking into consideration the constraints of evolutionary theory and the sense or nonsense of excessive artificial selection.
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Affiliation(s)
- Julia Mehlhorn
- Institute for Anatomy I, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Svenja Caspers
- Institute for Anatomy I, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.,Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Jülich, Germany
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38
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Keel Bone Damage in Laying Hens-Its Relation to Bone Mineral Density, Body Growth Rate and Laying Performance. Animals (Basel) 2021; 11:ani11061546. [PMID: 34070496 PMCID: PMC8228274 DOI: 10.3390/ani11061546] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 02/04/2023] Open
Abstract
Simple Summary Keel bone damage is an important welfare issue for laying hens. Four lines of laying hens, differing in phylogenetic origin and laying rate kept in single cages or a floor housing system were weighed and deformities of the keel bone were evaluated regularly between 15 and 69 weeks of age. Deformities, fractures and the bone mineral density of the keels were assessed after hens were euthanized. We analyzed the relationship between bone mineral density and total egg number as well as body growth. Hens kept in cages showed more deformities, but fewer fractures and a lower bone mineral density of the keel bone than did floor-housed hens. Keel bones of white-egg layers had a lower mineral density and were more often deformed compared with brown-egg layers. Keel bones were more often broken in hens of the layer lines with a high laying rate compared to the lines with a moderate laying rate. Laying rate and adult body weight had an effect on the keel bone mineral density. The study contributes to the understanding of factors causing keel bone damage in laying hens. It showed that the bone mineral density greatly affects keel bone deformities. Abstract Keel bone damage is an important animal welfare problem in laying hens. Two generations of four layer lines, differing in phylogenetic background and performance level and kept in single cages or floor pens were weighed and scored for keel bone deformities (KBD) during the laying period. KBD, keel bone fractures (KBF) and the bone mineral density (BMD) of the keels were assessed post mortem. For BMD, relationships to laying performance and body growth were estimated. Caged hens showed more deformities, but fewer fractures and a lower BMD of the keel bone than floor-housed hens. White-egg layers had a lower BMD (0.140–0.165 g/cm2) and more KBD than brown-egg layers (0.179–0.184 g/cm2). KBF occurred more often in the high-performing lines than the moderate-performing ones. However, in the high-performing lines, BMD was positively related to total egg number from 18 to 29 weeks of age. The adult body weight derived from fitted growth curves (Gompertz function) had a significant effect (p < 0.001) on keels’ BMD. The study contributes to the understanding of predisposing factors for keel bone damage in laying hens. It showed that the growth rate has a rather subordinate effect on keels’ BMD, while the BMD itself greatly affects KBD.
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39
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Geibel J, Reimer C, Pook T, Weigend S, Weigend A, Simianer H. How imputation can mitigate SNP ascertainment Bias. BMC Genomics 2021; 22:340. [PMID: 33980139 PMCID: PMC8114708 DOI: 10.1186/s12864-021-07663-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/30/2022] Open
Abstract
Background Population genetic studies based on genotyped single nucleotide polymorphisms (SNPs) are influenced by a non-random selection of the SNPs included in the used genotyping arrays. The resulting bias in the estimation of allele frequency spectra and population genetics parameters like heterozygosity and genetic distances relative to whole genome sequencing (WGS) data is known as SNP ascertainment bias. Full correction for this bias requires detailed knowledge of the array design process, which is often not available in practice. This study suggests an alternative approach to mitigate ascertainment bias of a large set of genotyped individuals by using information of a small set of sequenced individuals via imputation without the need for prior knowledge on the array design. Results The strategy was first tested by simulating additional ascertainment bias with a set of 1566 chickens from 74 populations that were genotyped for the positions of the Affymetrix Axiom™ 580 k Genome-Wide Chicken Array. Imputation accuracy was shown to be consistently higher for populations used for SNP discovery during the simulated array design process. Reference sets of at least one individual per population in the study set led to a strong correction of ascertainment bias for estimates of expected and observed heterozygosity, Wright’s Fixation Index and Nei’s Standard Genetic Distance. In contrast, unbalanced reference sets (overrepresentation of populations compared to the study set) introduced a new bias towards the reference populations. Finally, the array genotypes were imputed to WGS by utilization of reference sets of 74 individuals (one per population) to 98 individuals (additional commercial chickens) and compared with a mixture of individually and pooled sequenced populations. The imputation reduced the slope between heterozygosity estimates of array data and WGS data from 1.94 to 1.26 when using the smaller balanced reference panel and to 1.44 when using the larger but unbalanced reference panel. This generally supported the results from simulation but was less favorable, advocating for a larger reference panel when imputing to WGS. Conclusions The results highlight the potential of using imputation for mitigation of SNP ascertainment bias but also underline the need for unbiased reference sets. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07663-6.
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Affiliation(s)
- Johannes Geibel
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany. .,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.
| | - Christian Reimer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Torsten Pook
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
| | - Steffen Weigend
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.,Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Höltystrasse 10, 31535, Neustadt-Mariensee, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Höltystrasse 10, 31535, Neustadt-Mariensee, Germany
| | - Henner Simianer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany.,Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
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Guo Y, Ou J, Zan Y, Wang Y, Li H, Zhu C, Chen K, Zhou X, Hu X, Carlborg Ö. Researching on the fine structure and admixture of the worldwide chicken population reveal connections between populations and important events in breeding history. Evol Appl 2021; 15:553-564. [PMID: 35505888 PMCID: PMC9046761 DOI: 10.1111/eva.13241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/10/2021] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
Here, we have evaluated the general genomic structure and diversity and studied the divergence resulting from selection and historical admixture events for a collection of worldwide chicken breeds. In total, 636 genomes (43 populations) were sequenced from chickens of American, Chinese, Indonesian, and European origin. Evaluated populations included wild junglefowl, rural indigenous chickens, breeds that have been widely used to improve modern western poultry populations and current commercial stocks bred for efficient meat and egg production. In‐depth characterizations of the genome structure and genomic relationships among these populations were performed, and population admixture events were investigated. In addition, the genomic architectures of several domestication traits and central documented events in the recent breeding history were explored. Our results provide detailed insights into the contributions from population admixture events described in the historical literature to the genomic variation in the domestic chicken. In particular, we find that the genomes of modern chicken stocks used for meat production both in eastern (Asia) and western (Europe/US) agriculture are dominated by contributions from heavy Asian breeds. Further, by exploring the link between genomic selective divergence and pigmentation, connections to functional genes feather coloring were confirmed.
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Affiliation(s)
- Ying Guo
- State Key Laboratory for Agro‐Biotechnology China Agricultural University Beijing China
- Beijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing China
- Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden
| | - Jen‐Hsiang Ou
- Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden
| | - Yanjun Zan
- Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden
| | - Yuzhe Wang
- State Key Laboratory for Agro‐Biotechnology China Agricultural University Beijing China
| | - Huifang Li
- Jiangsu Institute of Poultry Science Yangzhou China
| | - Chunhong Zhu
- Jiangsu Institute of Poultry Science Yangzhou China
| | - Kuanwei Chen
- Jiangsu Institute of Poultry Science Yangzhou China
| | - Xin Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health China Agricultural University Beijing China
| | - Xiaoxiang Hu
- State Key Laboratory for Agro‐Biotechnology China Agricultural University Beijing China
- National Engineering Laboratory for Animal Breeding China Agricultural University Beijing China
| | - Örjan Carlborg
- Department of Medical Biochemistry and Microbiology Uppsala University Uppsala Sweden
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Habig C, Weigend A, Baulain U, Petow S, Weigend S. Influence of Age and Phylogenetic Background on Blood Parameters Associated With Bone Metabolism in Laying Hens. Front Physiol 2021; 12:678054. [PMID: 33995131 PMCID: PMC8117343 DOI: 10.3389/fphys.2021.678054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 04/09/2021] [Indexed: 11/13/2022] Open
Abstract
The high laying performance of today’s laying hens places enormous demands on their mineral metabolism. While up-to-date data are rare, the present study aimed to describe blood parameters associated with egg laying and bone metabolism during the pre-laying period, in the course of the laying period and the daily egg laying cycle. Ten to 15 laying hens of two high-performing, phylogenetically divergent lines (BLA: brown-egg layer; WLA: white-egg layer), kept in single cages were blood sampled at 17, 25, 29, 49, and 69 weeks of age. Sampling was made at 6 a.m., 10 a.m., 2 p.m. and, with the exception of week 17, 6 p.m. Blood samples were analyzed for concentrations of total and ionized calcium, inorganic phosphate (PO4), markers of bone formation (osteocalcin) and resorption [carboxyterminal crosslinked telopeptide of type I collagen (CTX-I)], 25-hydroxycholecalciferol (25(OH)D3) and estradiol-17β. In the pre-laying period (17 week), the estradiol-17β level calculated for WLA was more than twice as high as the level calculated for BLA, while no significant difference could be observed in the laying period (25 to 69 weeks). BLA hens had significantly higher total calcium concentrations at 49 weeks of age as well as up to twice as high levels of osteocalcin and 25(OH)D3 than WLA at any time of the day from 25 to 69 weeks of age. While osteocalcin, CTX-I and 25(OH)D3 concentrations were significantly higher before the onset of lay, total calcium and estradiol-17β levels significantly increased from 17 to 69 weeks of age. In contrast, PO4 values varied only slightly during the experimental period and ionized calcium was highest at 17 and 49 weeks of age and lowest around peak production (29 week). In the course of the daily egg laying cycle blood concentrations clearly reflected the stage of egg formation. Our results provide up-to-date data of bone- and egg laying-associated blood parameters of two contemporary purebred layer lines over the course of the pre- and egg-laying period and the daily egg laying cycle. Differences between brown- and white-egg layers raise questions, whether phylogenetic background determines their efficiency to cope with high calcium demands relating to egg production.
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Affiliation(s)
- Christin Habig
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Ulrich Baulain
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Stefanie Petow
- Institute of Animal Welfare and Animal Husbandry, Friedrich-Loeffler-Institut, Celle, Germany
| | - Steffen Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
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42
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Malomane DK, Weigend S, Schmitt AO, Weigend A, Reimer C, Simianer H. Genetic diversity in global chicken breeds in relation to their genetic distances to wild populations. Genet Sel Evol 2021; 53:36. [PMID: 33853523 PMCID: PMC8048360 DOI: 10.1186/s12711-021-00628-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 03/30/2021] [Indexed: 12/03/2022] Open
Abstract
Background Migration of a population from its founder population is expected to cause a reduction of its genetic diversity and facilitates differentiation between the population and its founder population, as predicted by the theory of genetic isolation by distance. Consistent with that theory, a model of expansion from a single founder predicts that patterns of genetic diversity in populations can be explained well by their geographic expansion from their founders, which is correlated with genetic differentiation. Methods To investigate this in chicken, we estimated the relationship between the genetic diversity of 160 domesticated chicken populations and their genetic distances to wild chicken populations. Results Our results show a strong inverse relationship, i.e. 88.6% of the variation in the overall genetic diversity of domesticated chicken populations was explained by their genetic distance to the wild populations. We also investigated whether the patterns of genetic diversity of different types of single nucleotide polymorphisms (SNPs) and genes are similar to that of the overall genome. Among the SNP classes, the non-synonymous SNPs deviated most from the overall genome. However, genetic distance to the wild chicken still explained more variation in domesticated chicken diversity across all SNP classes, which ranged from 83.0 to 89.3%. Conclusions Genetic distance between domesticated chicken populations and their wild relatives can predict the genetic diversity of the domesticated populations. On the one hand, genes with little genetic variation across populations, regardless of the genetic distance to the wild population, are associated with major functions such as brain development. Changes in such genes may be detrimental to the species. On the other hand, genetic diversity seems to change at a faster rate within genes that are associated with e.g. protein transport and protein and lipid metabolic processes. In general, such genes may be flexible to changes according to the populations’ needs. These results contribute to the knowledge of the evolutionary patterns of different functional genomic regions in the chicken. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00628-z.
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Affiliation(s)
- Dorcus Kholofelo Malomane
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany. .,Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.
| | - Steffen Weigend
- Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Armin Otto Schmitt
- Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Breeding Informatics Group, Department of Animal Sciences, Georg August-Universität Goettingen, Goettingen, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt, Germany
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Center for Integrated Breeding Research, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
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43
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Geibel J, Reimer C, Weigend S, Weigend A, Pook T, Simianer H. How array design creates SNP ascertainment bias. PLoS One 2021; 16:e0245178. [PMID: 33784304 PMCID: PMC8009414 DOI: 10.1371/journal.pone.0245178] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/22/2020] [Indexed: 12/30/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs), genotyped with arrays, have become a widely used marker type in population genetic analyses over the last 10 years. However, compared to whole genome re-sequencing data, arrays are known to lack a substantial proportion of globally rare variants and tend to be biased towards variants present in populations involved in the development process of the respective array. This affects population genetic estimators and is known as SNP ascertainment bias. We investigated factors contributing to ascertainment bias in array development by redesigning the Axiom™ Genome-Wide Chicken Array in silico and evaluating changes in allele frequency spectra and heterozygosity estimates in a stepwise manner. A sequential reduction of rare alleles during the development process was shown. This was mainly caused by the identification of SNPs in a limited set of populations and a within-population selection of common SNPs when aiming for equidistant spacing. These effects were shown to be less severe with a larger discovery panel. Additionally, a generally massive overestimation of expected heterozygosity for the ascertained SNP sets was shown. This overestimation was 24% higher for populations involved in the discovery process than not involved populations in case of the original array. The same was observed after the SNP discovery step in the redesign. However, an unequal contribution of populations during the SNP selection can mask this effect but also adds uncertainty. Finally, we make suggestions for the design of specialized arrays for large scale projects where whole genome re-sequencing techniques are still too expensive.
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Affiliation(s)
- Johannes Geibel
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
- * E-mail:
| | - Christian Reimer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
| | - Steffen Weigend
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| | - Annett Weigend
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Neustadt-Mariensee, Germany
| | - Torsten Pook
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
| | - Henner Simianer
- Department of Animal Sciences, Animal Breeding and Genetics Group, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Göttingen, Germany
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44
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Manjula P, Kim M, Cho S, Seo D, Lee JH. High Levels of Genetic Variation in MHC-Linked Microsatellite Markers from Native Chicken Breeds. Genes (Basel) 2021; 12:240. [PMID: 33567601 PMCID: PMC7915948 DOI: 10.3390/genes12020240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/01/2021] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
The major histocompatibility complex (MHC) is a highly polymorphic gene region that regulates cellular communication in all specific immune responses. In this study, we investigated 11 microsatellite (MS) markers in the MHC-B region of chicken populations from four countries: Sri Lanka, Bangladesh, South Korea, and Nigeria. The MS markers were divided into two sets. Set 1 included five novel MS markers, which we assessed using 192 samples from 21 populations. Set 2 included six previously reported markers, which we assessed using 881 samples from 29 populations. The Set 1 MS markers had lower polymorphism (polymorphic information content (PIC) < 0.5) than the Set 2 markers (PIC = 0.4-0.9). In all populations, the LEI0258 marker was the most polymorphic, with a total of 38 alleles (PIC = 0.912, expected heterozygosity (He) = 0.918). Local populations from Sri Lanka, Bangladesh, and Nigeria had higher allele diversity and more haplotypes for Set 2 MS markers than Korean and commercial populations. The Sri Lankan Karuwalagaswewa village population had the highest MHC diversity (mean allele number = 8.17, He = 0.657), whereas the white leghorn population had the lowest (mean allele number = 2.33, He = 0.342). A total of 409 haplotypes (89 shared and 320 unique), with a range of 4 (Rhode Island red) to 46 (Karuwalagaswewa village (TA)), were identified. Among the shared haplotypes, the B21-like haplotype was identified in 15 populations. The genetic relationship observed in a neighbour-joining tree based on the DA distance agreed with the breeding histories and geographic separations. The results indicated high MHC diversity in the local chicken populations. The difference in the allelic pattern among populations presumably reflects the effects of different genotypes, environments, geographic variation, and breeding policies in each country. The selection of MHC allele in domestic poultry can vary due to intensification of poultry production. Preserved MHC diversity in local chicken provides a great opportunity for future studies that address the relationships between MHC polymorphisms and differential immune responses.
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Affiliation(s)
| | | | | | | | - Jun Heon Lee
- Division of Animal and Dairy Science, Chungnam National University, Daejeon 34134, Korea; (P.M.); (M.K.); (S.C.); (D.S.)
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Cendron F, Mastrangelo S, Tolone M, Perini F, Lasagna E, Cassandro M. Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds. Poult Sci 2021; 100:441-451. [PMID: 33518095 PMCID: PMC7858015 DOI: 10.1016/j.psj.2020.10.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 10/16/2020] [Accepted: 10/22/2020] [Indexed: 12/25/2022] Open
Abstract
The aim of this study was to conduct a genome-wide comparative analysis of 8 local Italian chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo [PML], Polverara Bianca, Polverara Nera, Padovana, Pepoi [PPP], Robusta Lionata, and Robusta Maculata), all under a conservation plan, to understand their genetic diversity and population structure. A total of 152 animals were analyzed using the Affymetrix Axiom 600 K Chicken Genotyping Array. The levels of genetic diversity were highest and lowest in PML and PPP, respectively. The results of genomic inbreeding based on runs of homozygosity (ROH; FROH) showed marked differences among breeds and ranged from 0.161 (PML) to 0.478 (PPP). Furthermore, in all breeds, short ROH (<4 Mb in length) were more frequent than long segments. Patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed nonoverlapping clusters and were clearly separate populations. The 2 Polverara breeds shared a similar genetic background and showed the lowest genetic differentiation in comparison with purebred lines; the local populations showed separated groups. PPP and PML were closer to the group of the purebred broiler lines (BRSA, BRSB, BRDA, and BRDB). Six genomic regions are presented as hotspots of autozygosity among the Italian chicken breeds, with candidate genes involved in multiple morphological phenotypes as breast muscle, muscle dry matter content, and body weight. This study is the first exhaustive genome-wide analysis of the diversity of these Italian local chickens from Veneto region. We conclude that breeds have conserved authentic genetic patterns. The results are of significant importance because they will help design and implement conservation strategies. In fact, the conservation of these breeds may also have positive impacts on the local economy, niche traditional markets, and offering a source of high-quality products to consumers. In this context, genomic information may play a crucial role in the management of local breeds.
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Affiliation(s)
- F Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, PD, Italy.
| | - S Mastrangelo
- Department of Agricultural, Food and Forest Sciences, University of Palermo 90128 Palermo, PA, Italy
| | - M Tolone
- Department of Agricultural, Food and Forest Sciences, University of Palermo 90128 Palermo, PA, Italy
| | - F Perini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia 06121 Perugia, PG, Italy
| | - E Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia 06121 Perugia, PG, Italy
| | - M Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Legnaro, PD, Italy
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Mariadassou M, Suez M, Sathyakumar S, Vignal A, Arca M, Nicolas P, Faraut T, Esquerré D, Nishibori M, Vieaud A, Chen CF, Manh Pham H, Roman Y, Hospital F, Zerjal T, Rognon X, Tixier-Boichard M. Unraveling the history of the genus Gallus through whole genome sequencing. Mol Phylogenet Evol 2020; 158:107044. [PMID: 33346111 DOI: 10.1016/j.ympev.2020.107044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/23/2020] [Accepted: 12/14/2020] [Indexed: 12/16/2022]
Abstract
The genus Gallus is distributed across a large part of Southeast Asia and has received special interest because the domestic chicken, Gallus gallus domesticus, has spread all over the world and is a major protein source for humans. There are four species: the red junglefowl (G. gallus), the green junglefowl (G. varius), the Lafayette's junglefowl (G. lafayettii) and the grey junglefowl (G. sonneratii). The aim of this study is to reconstruct the history of these species by a whole genome sequencing approach and resolve inconsistencies between well supported topologies inferred using different data and methods. Using deep sequencing, we identified over 35 million SNPs and reconstructed the phylogeny of the Gallus genus using both distance (BioNJ) and maximum likelihood (ML) methods. We observed discrepancies according to reconstruction methods and genomic components. The two most supported topologies were previously reported and were discriminated by using phylogenetic and gene flow analyses, based on ABBA statistics. Terminology fix requested by the deputy editor led to support a scenario with G. gallus as the earliest branching lineage of the Gallus genus, instead of G. varius. We discuss the probable causes for the discrepancy. A likely one is that G. sonneratii samples from parks or private collections are all recent hybrids, with roughly 10% of their autosomal genome originating from G. gallus. The removal of those regions is needed to provide reliable data, which was not done in previous studies. We took care of this and additionally included two wild G. sonneratii samples from India, showing no trace of introgression. This reinforces the importance of carefully selecting and validating samples and genomic components in phylogenomics.
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Affiliation(s)
| | - Marie Suez
- Université Paris Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France
| | | | - Alain Vignal
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France
| | - Mariangela Arca
- Université Paris Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France
| | - Pierre Nicolas
- Université Paris Saclay, INRAE, MaIAGE, 78350 Jouy-en-Josas, France
| | - Thomas Faraut
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France
| | - Diane Esquerré
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France; Get-PlaGe, INRAE, 31326 Castanet Tolosan, France
| | - Masahide Nishibori
- Lab. of Animal Genetics, Department of Animal Life Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8528, Japan
| | - Agathe Vieaud
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Chih-Feng Chen
- Department of Animal Science, iEGG and Animal Biotechnology Center, National Chung-Hsing University, Taichung 40227, Taiwan
| | - Hung Manh Pham
- Faculty of Animal Science, Vietnam National University of Agriculture, Trau Quy Town, Gia Lam District, Ha Noi City, Viet Nam
| | | | - Frédéric Hospital
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Tatiana Zerjal
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Xavier Rognon
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
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Zhang J, Nie C, Li X, Ning Z, Chen Y, Jia Y, Han J, Wang L, Lv X, Yang W, Qu L. Genome-Wide Population Genetic Analysis of Commercial, Indigenous, Game, and Wild Chickens Using 600K SNP Microarray Data. Front Genet 2020; 11:543294. [PMID: 33101376 PMCID: PMC7545075 DOI: 10.3389/fgene.2020.543294] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 09/02/2020] [Indexed: 12/13/2022] Open
Abstract
Following chicken domestication, diversified chicken breeds were developed by both natural and artificial selection, which led to the accumulation of abundant genetic and phenotypic variations, making chickens an ideal genetic research model. To better understand the genetic structure of chicken breeds under different selection pressures, we genotyped various chicken populations with specific selection targets, including indigenous, commercial, gamecock, and wild ancestral chickens, using the 600K SNP array. We analyzed the population structure, genetic relationships, run of homozygosity (ROH), effective population number (Ne), and other genetic parameters. The wild ancestral population, red junglefowl (RJF), possessed the highest diversity, in comparison with all other domesticated populations, which was supported by linkage disequilibrium decay (LD), effective population number, and ROH analyses. The gamecock breeds, which were subjected to stronger male-biased selection for fighting-related traits, also presented higher variation than the commercial and indigenous breeds. Admixture analysis also indicated that game breed is a relatively independent branch of Chinese local breeds. Following intense selection for reproductive and productive traits, the commercial lines showed the least diversity. We also observed that the European local chickens had lower genetic variation than the Chinese local breeds, which could be attributed to the shorter history of the European breed. ROH were present in a breed specific manner and 191 ROH island were detected on four groups (commercial, local, game and wild chickens). These ROH islands were involved in egg production, growth and silky feathers and other traits. Moreover, we estimated the effective sex ratio of these breeds to demonstrate the change in the ratio of the two sexes. We found that commercial chickens had a greater sex imbalance between females and males. The commercial lines showed the highest female-to-male ratios. Interestingly, RJF comprised a greater proportion of males than females. Our results show the population genetics of chickens under selection pressures, and can aid in the development of better conservation strategies for different chicken breeds.
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Affiliation(s)
- Jinxin Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Changsheng Nie
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xinghua Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Yaxiong Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianlin Han
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Bone Health or Performance? Adaptation Response of Genetically Divergent Chicken Layer Lines to a Nutritive Calcium Depletion. Animals (Basel) 2020; 10:ani10091645. [PMID: 32937747 PMCID: PMC7552123 DOI: 10.3390/ani10091645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/05/2020] [Accepted: 09/10/2020] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Selection for high egg production in laying hens has led to an increased calcium requirement and consequently to an intensified calcium mobilization from the bones. However, excessive demineralization can lead to osteoporosis, which is manifested by a high incidence of bone-damaged hens. In this study, we characterized the adaptation response of laying hens to a repeated dietary calcium restriction (1.09% instead of 4.26% calcium) by means of egg production, eggshell quality, body weight and bone stability. The animal model included four layer lines differing in performance level (high vs. moderately performing lines) and phylogenetic origin (white-egg vs. brown-egg layers). We assumed that the high performing lines would respond by maintaining egg production level at the expense of eggshell quality and bone health. Egg production and eggshell quality declined considerably and bone demineralization occurred in all lines. Contrary to our hypothesis, there was evidence that phylogeny rather than performance level influenced the hens′ response. The brown-egg lines appeared to be more tolerant to the calcium depletion, while the white-egg lines were more sensitive. Our findings demonstrate the influence of genetics on the adaptive capacity of chickens and underline the importance of preserving genetic variability to cope with potential future environmental challenges. Abstract In modern laying hybrids, calcium (Ca) homeostasis is immensely challenged by daily eggshell calcification. However, excessive mobilization of Ca from bones may lead to osteoporosis, which then manifests in a high incidence of poor bone quality. The aim of this study was to characterize the hens’ adaptation response to an alternating dietary Ca restriction. The animal model consisted of four purebred layer lines, differing in laying performance (high vs. moderately performing lines) and phylogenetic origin (white- vs. brown-egg lines). According to the resource allocation theory, hens selected for high egg production were assumed to show a different response pattern to cope with this nutritive challenge compared to moderately performing lines. Data collected included egg number, egg quality traits, body weight and bone characteristics. The Ca depletion led to a temporary drop in egg production and shell quality and a loss of bone stability due to Ca mobilization. The white-egg lines response was more pronounced, whereas the brown-egg lines were less sensitive towards reduced Ca supply. Our study shows that the hens’ responsiveness to coping with a nutritive Ca depletion is not ultimately linked to genetic selection for increased egg production but rather to phylogenetic origin.
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Cendron F, Perini F, Mastrangelo S, Tolone M, Criscione A, Bordonaro S, Iaffaldano N, Castellini C, Marzoni M, Buccioni A, Soglia D, Schiavone A, Cerolini S, Lasagna E, Cassandro M. Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds. Animals (Basel) 2020; 10:E1441. [PMID: 32824706 PMCID: PMC7460279 DOI: 10.3390/ani10081441] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 01/06/2023] Open
Abstract
The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.
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Affiliation(s)
- Filippo Cendron
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro, Italy; (F.C.); (M.C.)
| | - Francesco Perini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.P.); (C.C.)
| | - Salvatore Mastrangelo
- Department of Agricultural, Food and Forest sciences, University of Palermo, Viale delle Scienze, Ed. 4, 90128 Palermo, Italy; (S.M.); (M.T.)
| | - Marco Tolone
- Department of Agricultural, Food and Forest sciences, University of Palermo, Viale delle Scienze, Ed. 4, 90128 Palermo, Italy; (S.M.); (M.T.)
| | - Andrea Criscione
- Department of Agronomy, Food, and Environment, University of Catania, Via Valdisavoia, 5, 95100 Catania, Italy; (A.C.); (S.B.)
| | - Salvatore Bordonaro
- Department of Agronomy, Food, and Environment, University of Catania, Via Valdisavoia, 5, 95100 Catania, Italy; (A.C.); (S.B.)
| | - Nicolaia Iaffaldano
- Department of Agricultural, Environment and Food, University of Molise, Via De Sanctis s/n, 86100 Campobasso, Italy;
| | - Cesare Castellini
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.P.); (C.C.)
| | - Margherita Marzoni
- Department of Veterinary Science, University of Pisa, Viale delle Piagge 2, 56124 Pisa, Italy;
| | - Arianna Buccioni
- Department of Agriculture, Food, Environment and Forestry, University of Firenze, Via di San Bonaventura, 50145 Firenze, Italy;
| | - Dominga Soglia
- Department of Veterinary Science, University of Torino, Largo Paolo Braccini, 2, 10095 Grugliasco, Italy; (D.S.); (A.S.)
| | - Achille Schiavone
- Department of Veterinary Science, University of Torino, Largo Paolo Braccini, 2, 10095 Grugliasco, Italy; (D.S.); (A.S.)
| | - Silvia Cerolini
- Department of Veterinary Science, University of Milano, Via Trentacoste, 2, 20134 Milano, Italy;
| | - Emiliano Lasagna
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 74, 06121 Perugia, Italy; (F.P.); (C.C.)
| | - Martino Cassandro
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Viale dell’Università, 16, 35020 Legnaro, Italy; (F.C.); (M.C.)
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50
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Chickens in motion: Effects of egg production level and pen size on the motor abilities and bone stability of laying hens (Gallus gallus forma domestica). Appl Anim Behav Sci 2020. [DOI: 10.1016/j.applanim.2020.104998] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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