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Animal population genetics

Section edited by Anna Malacrida, Li Ma and Pim van Hooft

This section incorporates all aspects of the genetics of animal populations including but not limited to: analysis of evolutionary, ecological and conservation genetics of animal populations.

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  1. Content type: Research article

    The Chinese grass shrimp, Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration of germplasm...

    Authors: Yingying Zhao, Xiaochen Zhu, Zhi Li, Weibin Xu, Jing Dong, Hua Wei, Yingdong Li and Xiaodong Li

    Citation: BMC Genetics 2019 20:75

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  2. Content type: Research article

    Rhodeus sinensis is a bitterling species occurring throughout the numerous freshwater systems on the East Asia. Here, we analyzed the diversity of the MHC class IIB (DAB) genes from this species, which may offer ...

    Authors: Hyung-Bae Jeon, Hari Won and Ho Young Suk

    Citation: BMC Genetics 2019 20:74

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  3. Content type: Research article

    Myogenic Differentiation 1 (MyoD) is a crucial master switch in regulating muscle-specific gene transcription. Forced expression of myoD is equipped to induce several cell lineages into myoblast, which then diffe...

    Authors: Suying Ding, Yaping Nie, Xumeng Zhang, Xiaohong Liu, Chen Wang, Renqiang Yuan, Keren Chen, Qi Zhu, Shufang Cai, Ying Fang, Yaosheng Chen and Delin Mo

    Citation: BMC Genetics 2019 20:72

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  4. Content type: Research article

    Our initial genome-wide association study (GWAS) identified 20 promising candidate genes for milk fatty acid (FA) traits in a Chinese Holstein population, including PRLR, MOGAT1, MINPP1 and CHUK genes. In this st...

    Authors: Lijun Shi, Lin Liu, Xiaoqing Lv, Zhu Ma, Yuze Yang, Yanhua Li, Feng Zhao, Dongxiao Sun and Bo Han

    Citation: BMC Genetics 2019 20:69

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  5. Content type: Research article

    Egg production is the most economically-important trait in layers as it directly influences benefits of the poultry industry. To better understand the genetic architecture of egg production, we measured traits...

    Authors: Zhuang Liu, Ning Yang, Yiyuan Yan, Guangqi Li, Aiqiao Liu, Guiqin Wu and Congjiao Sun

    Citation: BMC Genetics 2019 20:67

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  6. Content type: Research article

    The Sapsaree is a breed of dog (Canis familiaris) native to Korea, which became perilously close to extinction in the mid-1980s. However, with systematic genetic conservation and restoration efforts, this breed w...

    Authors: Chandima Gajaweera, Ji Min Kang, Doo Ho Lee, Soo Hyun Lee, Yeong Kuk Kim, Hasini I. Wijayananda, Jong Joo Kim, Ji Hong Ha, Bong Hwan Choi and Seung Hwan Lee

    Citation: BMC Genetics 2019 20:66

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  7. Content type: Research article

    Ketosis in dairy cattle has been shown to cause a high morbidity in the farm and substantial financial losses to dairy farmers. Ketosis symptoms, however, are difficult to identify, therefore, the amount of ke...

    Authors: S. Nayeri, F. Schenkel, A. Fleming, V. Kroezen, M. Sargolzaei, C. Baes, A. Cánovas, J. Squires and F. Miglior

    Citation: BMC Genetics 2019 20:58

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  8. Content type: Research article

    Ticks are a problem for cattle production mainly in tropical and subtropical regions, because they generate great economic losses. Acaricides and vaccines have been used to try to keep tick populations under c...

    Authors: S. G. Martínez-Arzate, J. C. Sánchez-Bermúdez, S. Sotelo-Gómez, H. M. Diaz-Albiter, W. Hegazy-Hassan, E. Tenorio-Borroto, A. Barbabosa-Pliego and J. C. Vázquez-Chagoyán

    Citation: BMC Genetics 2019 20:56

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  9. Content type: Research article

    We previously conducted a genome-wide association study (GWAS) strategy for milk fatty acids in Chinese Holstein, and identified 83 genome-wide significant single nucleotide polymorphisms (SNPs) and 314 sugges...

    Authors: Lijun Shi, Xiaoqing Lv, Lin Liu, Yuze Yang, Zhu Ma, Bo Han and Dongxiao Sun

    Citation: BMC Genetics 2019 20:53

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  10. Content type: Research article

    Microsatellite loci have been used extensively over the past two decades to study the genetic characteristics of non-model species. The ease of microsatellite development and ability to adapt markers from rela...

    Authors: William L. Miller, Jessie Edson, Peter Pietrandrea, Cassandra Miller-Butterworth and W. David Walter

    Citation: BMC Genetics 2019 20:49

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  11. Content type: Research article

    In Atlantic salmon in the wild, age at maturity is strongly influenced by the vgll3 locus. Under farming conditions, light, temperature and feeding regimes are known significantly advance or delay age at maturity...

    Authors: Fernando Ayllon, Monica F. Solberg, Kevin A. Glover, Faezeh Mohammadi, Erik Kjærner-Semb, Per Gunnar Fjelldal, Eva Andersson, Tom Hansen, Rolf B. Edvardsen and Anna Wargelius

    Citation: BMC Genetics 2019 20:44

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  12. Content type: Research article

    The inheritance of different coat colours in the Cane Corso Italiano dog has not been described thus far. We analysed data from 23,271 dogs and bitches using the Cane Corso Italiano Pedigree Database. We are d...

    Authors: Evžen Korec, Matyáš Hančl, Marie Bydžovská, Ondřej Chalupa and Jana Korcová

    Citation: BMC Genetics 2019 20:24

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  13. Content type: Research article

    The collection and analysis of fecal DNA is a common practice, especially when dealing with wildlife species that are difficult to track or capture. While fecal DNA is known to be lower quality than traditiona...

    Authors: David Forgacs, Rick L. Wallen, Amy L. Boedeker and James N. Derr

    Citation: BMC Genetics 2019 20:22

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  14. Content type: Research article

    Arapaima gigas (Schinz, 1822) is the largest freshwater scaled fish in the world, and an emerging species for tropical aquaculture development. Conservation of the species, and the expansion of aquaculture requir...

    Authors: Lucas Simon Torati, John Bernard Taggart, Eduardo Sousa Varela, Juliana Araripe, Stefanie Wehner and Hervé Migaud

    Citation: BMC Genetics 2019 20:13

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  15. Content type: Research article

    Rattus tanezumi is a common commensal rat and an important host animal of bubonic plague in South China and Southeast Asia. The northward dispersal of this species in mainland China has been reported in recent de...

    Authors: Song Guo, Guichang Li, Jinli Liu, Jun Wang, Liang Lu and Qiyong Liu

    Citation: BMC Genetics 2019 20:11

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  16. Content type: Research article

    Grass carp (Ctenopharyngodon idellus, GC), as the highest-output fish in China, is economically important. The production of gynogenetic grass carp (GGC) will provide important germplasm resource for producing im...

    Authors: Zhuangwen Mao, Yeqing Fu, Yude Wang, Shi Wang, Minghe Zhang, Xin Gao, Kaikun Luo, Qinbo Qin, Chun Zhang, Min Tao, Zhanzhou Yao and Shaojun Liu

    Citation: BMC Genetics 2019 20:3

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  17. Content type: Research article

    China exhibits a great diversity of ecosystems and abundant cattle resources, with nearly 30 million cattle from 53 indigenous breeds reared in specific geographic regions. To explore the genetic diversity and...

    Authors: Wengang Zhang, Xue Gao, Yang Zhang, Yumin Zhao, Jiabao Zhang, Yutang Jia, Bo Zhu, Lingyang Xu, Lupei Zhang, Huijiang Gao, Junya Li and Yan Chen

    Citation: BMC Genetics 2018 19:114

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  18. Content type: Research article

    The whole repeat unit of 5S rDNA and the internal transcribed spacer (ITS) of four European Donax species were analysed. After amplifying, cloning and sequencing several 5S and ITS units, their basic features and...

    Authors: Jenyfer Fernández-Pérez, Ana Nantón and Josefina Méndez

    Citation: BMC Genetics 2018 19:97

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  19. Content type: Research article

    Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals’ phenotypic variation. ...

    Authors: Artur Gurgul, Igor Jasielczuk, Katarzyna Ropka-Molik, Ewelina Semik-Gurgul, Klaudia Pawlina-Tyszko, Tomasz Szmatoła, Magdalena Szyndler-Nędza, Monika Bugno-Poniewierska, Tadeusz Blicharski, Karolina Szulc, Ewa Skrzypczak and Jędrzej Krupiński

    Citation: BMC Genetics 2018 19:95

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  20. Content type: Research article

    Previous studies on linkage disequilibrium have investigated second order linkage disequilibrium in animal and plant populations. The objective of this paper was to investigate the genome-wide levels of third ...

    Authors: Luis Gomez-Raya, Luis Silio, Wendy M. Rauw, Luis Alberto Gracia-Cortés and Carmen Rodríguez

    Citation: BMC Genetics 2018 19:60

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  21. Content type: Research article

    Atlantic cod (Gadus morhua L.) has formed the basis of many economically significant fisheries in the North Atlantic, and is one of the best studied marine fishes, but a legacy of overexploitation has depleted po...

    Authors: Geir Dahle, María Quintela, Torild Johansen, Jon-Ivar Westgaard, François Besnier, Asgeir Aglen, Knut E. Jørstad and Kevin A. Glover

    Citation: BMC Genetics 2018 19:42

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  22. Content type: Research article

    Identification of genetic mechanisms and idiosyncrasies at the breed-level can provide valuable information for potential use in evolutionary studies, medical applications, and breeding of selective traits. He...

    Authors: Kelsey Caetano-Anolles, Kwondo Kim, Woori Kwak, Samsun Sung, Heebal Kim, Bong-Hwan Choi and Dajeong Lim

    Citation: BMC Genetics 2018 19:37

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  23. Content type: Research article

    Bovine leukocyte antigens (BoLAs) are used extensively as markers of disease and immunological traits in cattle. However, until now, characterization of BoLA gene polymorphisms in Zebu breeds using high resolu...

    Authors: Shin-nosuke Takeshima, Claudia Corbi-Botto, Guillermo Giovambattista and Yoko Aida

    Citation: BMC Genetics 2018 19:33

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  24. Content type: Research article

    Defining hidden genetic diversity within species is of great significance when attempting to maintain the evolutionary potential of natural populations and conduct appropriate management. Our hypothesis is tha...

    Authors: Samer Angelone, Michael J. Jowers, Anna Rita Molinar Min, Paulino Fandos, Paloma Prieto, Mario Pasquetti, Francisco Javier Cano-Manuel, Gregorio Mentaberre, Jorge Ramón López Olvera, Arián Ráez-Bravo, José Espinosa, Jesús M. Pérez, Ramón C. Soriguer, Luca Rossi and José Enrique Granados

    Citation: BMC Genetics 2018 19:28

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  25. Content type: Research article

    Female lions generally do not disperse far beyond their natal range, while males can disperse distances of over 200 km. However, in bush-like ecosystems dispersal distances less than 25 km are reported. Here, ...

    Authors: Pim van Hooft, Dewald F. Keet, Diana K. Brebner and Armanda D. S. Bastos

    Citation: BMC Genetics 2018 19:21

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  26. Content type: Methodology article

    Accurate imputation plays a major role in genomic studies of livestock industries, where the number of genotyped or sequenced animals is limited by costs. This study explored methods to create an ideal referen...

    Authors: Steven G. Larmer, Mehdi Sargolzaei, Luiz F. Brito, Ricardo V. Ventura and Flávio S. Schenkel

    Citation: BMC Genetics 2017 18:120

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  27. Content type: Research article

    Populations of the earthworm, Lumbricus rubellus, are commonly found across highly contaminated former mine sites and are considered to have under-gone selection for mitigating metal toxicity. Comparison of adapt...

    Authors: Craig Anderson, Luis Cunha, Pierfrancesco Sechi, Peter Kille and David Spurgeon

    Citation: BMC Genetics 2017 18:97

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  28. Content type: Research article

    Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the gene...

    Authors: Siham A. Rahmatalla, Danny Arends, Monika Reissmann, Ammar Said Ahmed, Klaus Wimmers, Henry Reyer and Gudrun A. Brockmann

    Citation: BMC Genetics 2017 18:92

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  29. Content type: Research article

    Previous studies in the Norwegian pig breeds Landrace and Duroc have revealed a QTL for levels of skatole located in the region 74.7–80.5 Mb on SSC7. Skatole is one of the main components causing boar taint, w...

    Authors: Maren van Son, Matthew P. Kent, Harald Grove, Rahul Agarwal, Hanne Hamland, Sigbjørn Lien and Eli Grindflek

    Citation: BMC Genetics 2017 18:85

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  30. Content type: Research article

    The allotetraploid hybrid fish (4nAT) that was created in a previous study through an intergeneric cross between red crucian carp (Carassius auratus red var., ♀) and common carp (Cyprinus carpio L., ♂) provided a...

    Authors: Lihai Ye, Chun Zhang, Xiaojun Tang, Yiyi Chen and Shaojun Liu

    Citation: BMC Genetics 2017 18:75

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  31. Content type: Research article

    Investments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Selection may erode genetic diversity, which is a crucial factor for the success of breeding program...

    Authors: Vincent Prieur, Shannon M. Clarke, Luiz F. Brito, John C. McEwan, Michael A. Lee, Rudiger Brauning, Ken G. Dodds and Benoît Auvray

    Citation: BMC Genetics 2017 18:68

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  32. Content type: Research article

    Genome-wide investigation of molecular mechanisms for high-altitude adaptation has attracted great attention in the last few years. In order to understand the contribution of gene expression level variations t...

    Authors: Weizhao Yang, Yin Qi, Bin Lu, Liang Qiao, Yayong Wu and Jinzhong Fu

    Citation: BMC Genetics 2017 18:62

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  33. Content type: Research article

    Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability ...

    Authors: E. Gorla, M. C. Cozzi, S. I. Román-Ponce, F. J. Ruiz López, V. E. Vega-Murillo, S. Cerolini, A. Bagnato and M. G. Strillacci

    Citation: BMC Genetics 2017 18:61

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  34. Content type: Research article

    Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually conside...

    Authors: Kanokwan Srirattana, Kieren McCosker, Tim Schatz and Justin C. St. John

    Citation: BMC Genetics 2017 18:59

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  35. Content type: Research article

    Correlated genetic response in survival to selection for high growth has not been reported in giant freshwater prawn (GFP) (Macrobrachium rosenbergii). The main aim of this study was to measure genetic changes an...

    Authors: Nguyen Thanh Vu, Trinh Quoc Trong and Nguyen Hong Nguyen

    Citation: BMC Genetics 2017 18:56

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  36. Content type: Research article

    The South West Indian Ocean (SWIO) archipelagos and Madagascar constitute a hotspot of biodiversity with a high rate of endemism. In this area, the endemic subspecies A. m. unicolor has been described in Madagasc...

    Authors: Maéva Angélique Techer, Johanna Clémencet, Christophe Simiand, Sookar Preeaduth, Hamza Abdou Azali, Bernard Reynaud and Delatte Hélène

    Citation: BMC Genetics 2017 18:53

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  37. Content type: Research article

    Genotyping-by-sequencing (GBS) has emerged as a powerful and cost-effective approach for discovering and genotyping single-nucleotide polymorphisms. The GBS technique was largely used in crop species where its...

    Authors: Jean-Simon Brouard, Brian Boyle, Eveline M. Ibeagha-Awemu and Nathalie Bissonnette

    Citation: BMC Genetics 2017 18:32

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  38. Content type: Research article

    Knowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establ...

    Authors: Luiz F. Brito, John C. McEwan, Stephen P. Miller, Natalie K. Pickering, Wendy E. Bain, Ken G. Dodds, Flávio S. Schenkel and Shannon M. Clarke

    Citation: BMC Genetics 2017 18:25

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  39. Content type: Research article

    The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC rem...

    Authors: Melinda J. Hofmann, Seraina E. Bracamonte, Christophe Eizaguirre and Marta Barluenga

    Citation: BMC Genetics 2017 18:15

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  40. Content type: Research article

    Africa is home to numerous cattle breeds whose diversity has been shaped by subtle combinations of human and natural selection. African Sanga cattle are an intermediate type of cattle resulting from interbreed...

    Authors: Mengistie Taye, Jaemin Kim, Sook Hee Yoon, Wonseok Lee, Olivier Hanotte, Tadelle Dessie, Stephen Kemp, Okeyo Ally Mwai, Kelsey Caetano-Anolles, Seoae Cho, Sung Jong Oh, Hak-Kyo Lee and Heebal Kim

    Citation: BMC Genetics 2017 18:11

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  41. Content type: Research article

    New Zealand has some unique Terminal Sire composite sheep breeds, which were developed in the last three decades to meet commercial needs. These composite breeds were developed based on crossing various Termin...

    Authors: Luiz F. Brito, Shannon M. Clarke, John C. McEwan, Stephen P. Miller, Natalie K. Pickering, Wendy E. Bain, Ken G. Dodds, Mehdi Sargolzaei and Flávio S. Schenkel

    Citation: BMC Genetics 2017 18:7

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  42. Content type: Research article

    Knowledge on the levels of linkage disequilibrium (LD) across the genome, persistence of gametic phase between breed pairs, genetic diversity and population structure are important parameters for the successfu...

    Authors: Daniela A. Grossi, Mohsen Jafarikia, Luiz F. Brito, Marcos E. Buzanskas, Mehdi Sargolzaei and Flávio S. Schenkel

    Citation: BMC Genetics 2017 18:6

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  43. Content type: Research article

    Genomic selection (GS) has played an important role in cattle breeding programs. However, genotyping prices are still a challenge for implementation of GS in beef cattle and there is still a lack of informatio...

    Authors: Mario L. Piccoli, Luiz F. Brito, José Braccini, Fernando F. Cardoso, Mehdi Sargolzaei and Flávio S. Schenkel

    Citation: BMC Genetics 2017 18:2

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  44. Content type: Research article

    Nucleolar dominance is an epigenetic phenomenon that occurs in interspecific hybrids and involves the expression of 45S rRNA genes inherited from one progenitor due to the silencing of the other progenitor’s r...

    Authors: Jun Xiao, Fangzhou Hu, Kaikun Luo, Wuhui Li and Shaojun Liu

    Citation: BMC Genetics 2016 17:150

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  45. Content type: Research article

    The widespread use of individual sires for artificial insemination promotes the propagation of recessive conditions. Inadvertent matings between unnoticed carriers of deleterious alleles may result in the mani...

    Authors: Hubert Pausch, Simon Ammermüller, Christine Wurmser, Henning Hamann, Jens Tetens, Cord Drögemüller and Ruedi Fries

    Citation: BMC Genetics 2016 17:149

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  46. Content type: Research article

    Colour polymorphisms are common among animal species. When combined with genetic and ecological data, these polymorphisms can be excellent systems in which to understand adaptation and the molecular changes un...

    Authors: Ana S. B. Rodrigues, Sara E. Silva, Francisco Pina-Martins, João Loureiro, Mariana Castro, Karim Gharbi, Kevin P. Johnson, Christopher H. Dietrich, Paulo A. V. Borges, José A. Quartau, Chris D. Jiggins, Octávio S. Paulo and Sofia G. Seabra

    Citation: BMC Genetics 2016 17:144

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