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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. Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestri...

    Authors: Eeva Jansson, Francois Besnier, Ketil Malde, Carl André, Geir Dahle and Kevin A. Glover

    Citation: BMC Genetics 2020 21:118

    Content type: Research article

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  2. Brachygnathia, cardiomegaly and renal hypoplasia syndrome (BCRHS, OMIA 001595–9940) is a previously reported recessively inherited disorder in Australian Poll Merino/Merino sheep. Affected lambs are stillborn ...

    Authors: S. A. Woolley, S. E. Hayes, M. R. Shariflou, F. W. Nicholas, C. E. Willet, B. A. O’Rourke and I. Tammen

    Citation: BMC Genetics 2020 21:106

    Content type: Research article

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  3. Canine progressive retinal atrophies are a group of hereditary retinal degenerations in dogs characterised by depletion of photoreceptor cells in the retina, which ultimately leads to blindness. PRA in the Lha...

    Authors: Rebekkah J. Hitti-Malin, Louise M. Burmeister, Sally L. Ricketts, Thomas W. Lewis, Louise Pettitt, Mike Boursnell, Ellen C. Schofield, David Sargan and Cathryn S. Mellersh

    Citation: BMC Genetics 2020 21:100

    Content type: Research article

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  4. Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly...

    Authors: Guillermo Giovambattista, Kyaw Kyaw Moe, Meripet Polat, Liushiqi Borjigin, Si Thu Hein, Hla Hla Moe, Shin-Nosuke Takeshima and Yoko Aida

    Citation: BMC Genetics 2020 21:95

    Content type: Research article

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  5. Triatoma brasiliensis Neiva, 1911 is the main vector of Trypanosoma cruzi in the caatinga of Northeastern Brazil. Despite of its epidemiological relevance, there are few studies on its genetic variability. Using ...

    Authors: Claudia Mendonça Bezerra, Carlota Josefovicz Belisário, Grasielle Caldas D’Ávilla Pessoa, Aline Cristine Luiz Rosa, Carla Patrícia Barezani, Flávio Campos Ferreira, Alberto Novaes Ramos Jr, Ricardo Esteban Gürtler and Liléia Diotaiuti

    Citation: BMC Genetics 2020 21:92

    Content type: Research article

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  6. The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian s...

    Authors: Natascha M. D. Ivy-Israel, Carolyn E. Moore, Tonia S. Schwartz and Stephen S. Ditchkoff

    Citation: BMC Genetics 2020 21:83

    Content type: Research article

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  7. Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyo...

    Authors: Matthew L. Workentine, Rebecca Chen, Shawna Zhu, Stefan Gavriliuc, Nicolette Shaw, Jill de Rijke, Elizabeth M. Redman, Russell W. Avramenko, Janneke Wit, Jocelyn Poissant and John S. Gilleard

    Citation: BMC Genetics 2020 21:74

    Content type: Database

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  8. In several fish species homozygous and heterozygous clonal lines have been produced using gynogenetic and androgenetic techniques. These lines are standardized and can be reproduced over generations. In rainbo...

    Authors: Tom Johnny Hansen, David Penman, Kevin Alan Glover, Thomas William Kenneth Fraser, Tone Vågseth, Anders Thorsen, Anne Grete Eide Sørvik and Per Gunnar Fjelldal

    Citation: BMC Genetics 2020 21:71

    Content type: Research article

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  9. Munchkin cats were founded on a naturally occurring mutation segregating into long-legged and short-legged types. Short-legged cats showed disproportionate dwarfism (chondrodysplasia) in which all four legs ar...

    Authors: Ann-Kathrin Struck, Marina Braun, Kim Aline Detering, Peter Dziallas, Jasmin Neßler, Michael Fehr, Julia Metzger and Ottmar Distl

    Citation: BMC Genetics 2020 21:67

    Content type: Research article

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  10. African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat prod...

    Authors: Archile Paguem, Babette Abanda, Mbunkah Daniel Achukwi, Praveen Baskaran, Stefan Czemmel, Alfons Renz and Albert Eisenbarth

    Citation: BMC Genetics 2020 21:64

    Content type: Research article

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  11. Triploid organisms have three sets of chromosomes. In Atlantic salmon, hydrostatic pressure treatment of newly fertilized eggs has been extensively used to produce triploids which are functionally sterile due ...

    Authors: K. A. Glover, A. C. Harvey, T. J. Hansen, P. G. Fjelldal, F. N. Besnier, J. B. Bos, F. Ayllon, J. B. Taggart and M. F. Solberg

    Citation: BMC Genetics 2020 21:59

    Content type: Research article

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  12. Domestication is the process by which organisms become adapted to the human-controlled environment. Since the selection pressures that act upon cultured and natural populations differ, adaptations that favour ...

    Authors: Beatrix Bicskei, John B. Taggart, James E. Bron and Kevin A. Glover

    Citation: BMC Genetics 2020 21:57

    Content type: Research article

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  13. Caudata species such as salamanders are easily affected by environmental changes, which can drastically reduce their population. The effects of acute X-rays and chronic γ-irradiation on Hynobius lichenatus, the J...

    Authors: Toshiki Kamada, Yumi Une, Kumi Matsui, Shoichi Fuma, Teruo Ikeda and Mariko Okamoto

    Citation: BMC Genetics 2020 21:53

    Content type: Research article

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  14. Due to the advent of SNP array technology, a genome-wide analysis of genetic differences between populations and breeds has become possible at a previously unattainable level. The Wright’s fixation index (Fst) an...

    Authors: M. G. Smaragdov and A. A. Kudinov

    Citation: BMC Genetics 2020 21:47

    Content type: Research article

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  15. Heat stress adversely affects pig growth and reproduction performance by reducing feed intake, weight gain, farrowing rate, and litter size. Heat tolerance is an important characteristic in pigs, allowing them...

    Authors: Yuqing He, Christian Maltecca, Francesco Tiezzi, Emmanuel Lozada Soto and William L. Flowers

    Citation: BMC Genetics 2020 21:44

    Content type: Research article

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  16. Constraints in migratory capabilities, such as the disruption of gene flow and genetic connectivity caused by habitat fragmentation, are known to affect genetic diversity and the long-term persistence of popul...

    Authors: Jennifer Brunke, Isa-Rita M. Russo, Pablo Orozco-terWengel, Elke Zimmermann, Michael W. Bruford, Benoit Goossens and Ute Radespiel

    Citation: BMC Genetics 2020 21:43

    Content type: Research article

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  17. Horses produce only one foal from an eleven-month gestation period, making the maintenance of high reproductive rates essential. Genetic bottlenecks and inbreeding can increase the frequency of deleterious var...

    Authors: Evelyn T. Todd, Natasha A. Hamilton, Brandon D. Velie and Peter C. Thomson

    Citation: BMC Genetics 2020 21:41

    Content type: Research article

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  18. Long non-coding RNAs (lncRNAs) can play important roles in uterine and ovarian functions. However, little researches have been done on the role of lncRNAs in the adrenal gland of sheep. Herein, RNA sequencing ...

    Authors: Qing Xia, Qiuling Li, Shangquan Gan, Xiaofei Guo, Xiaosheng Zhang, Jinlong Zhang and Mingxing Chu

    Citation: BMC Genetics 2020 21:39

    Content type: Research article

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  19. While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released...

    Authors: Maria Cortázar-Chinarro, Yvonne Meyer-Lucht, Tom Van der Valk, Alex Richter-Boix, Anssi Laurila and Jacob Höglund

    Citation: BMC Genetics 2020 21:38

    Content type: Research article

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  20. Autotetraploid Carassius auratus (4nRCC, 4n = 200, RRRR) was derived from the whole genome duplication of diploid red crucian carp (Carassius auratus red var.) (2nRCC, 2n = 100, RR). To investigate the genetic ef...

    Authors: Xu Huang, Qinbo Qin, Kaijun Gong, Chang Wu, Yuwei Zhou, Qian Chen, Wenjing Feng, Yiying Xing, Chongqing Wang, Yude Wang, Liu Cao, Min Tao and Shaojun Liu

    Citation: BMC Genetics 2020 21:35

    Content type: Research article

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  21. Indigenous domestic chicken represents a major source of protein for agricultural communities around the world. In the Middle East and Africa, they are adapted to hot dry and semi-dry areas, in contrast to the...

    Authors: Ahmed S. Al-Jumaili, Selma Farah Boudali, Adebabay Kebede, Sahar A. Al-Bayatti, Abdulamir A. Essa, Abulgasim Ahbara, Riyadh S. Aljumaah, Raed M. Alatiyat, Joram M. Mwacharo, Gro Bjørnstad, Arifa N. Naqvi, Semir Bechir Suheil Gaouar and Olivier Hanotte

    Citation: BMC Genetics 2020 21:30

    Content type: Research article

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  22. Native Swedish sheep breeds are part of the North European short-tailed sheep group; characterized in part by their genetic uniqueness. Our objective was to study the population structure of native Swedish she...

    Authors: Christina Marie Rochus, Elisabeth Jonas and Anna M. Johansson

    Citation: BMC Genetics 2020 21:27

    Content type: Research article

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  23. Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regio...

    Authors: Seyed Mohammad Ghoreishifar, Hossein Moradi-Shahrbabak, Mohammad Hossein Fallahi, Ali Jalil Sarghale, Mohammad Moradi-Shahrbabak, Rostam Abdollahi-Arpanahi and Majid Khansefid

    Citation: BMC Genetics 2020 21:16

    Content type: Research article

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    The Correction to this article has been published in BMC Genetics 2020 21:42

  24. Modern breeding in the poultry industry mainly aims to produce high-performance poultry lines and breeds in two main directions of productivity, meat and eggs. To understand more about the productive potential...

    Authors: Jing-Jing Li, Long Zhang, Peng Ren, Ye Wang, Ling-Qian Yin, Jin-Shan Ran, Xian-Xian Zhang and Yi-Ping Liu

    Citation: BMC Genetics 2020 21:12

    Content type: Research article

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  25. Connectivity among jaguar (Panthera onca) populations will ensure natural gene flow and the long-term survival of the species throughout its range. Jaguar conservation efforts have focused primarily on connecting...

    Authors: Angelica Menchaca, Natalia A. Rossi, Jeremy Froidevaux, Isabela Dias-Freedman, Anthony Caragiulo, Claudia Wultsch, Bart Harmsen, Rebecca Foster, J. Antonio de la Torre, Rodrigo A. Medellin, Salisa Rabinowitz and George Amato

    Citation: BMC Genetics 2019 20:100

    Content type: Research article

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  26. Drip loss is a key aspect of meat quality. Transcriptome profiles of muscle with divergent drip loss would offer important insight into the genetic factors responsible for the trait. In this study, drip loss a...

    Authors: Xueyan Zhao, Cheng Wang, Yanping Wang, Haichao Lin, Huaizhong Wang, Hongmei Hu and Jiying Wang

    Citation: BMC Genetics 2019 20:89

    Content type: Research article

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  27. Distant hybridization can generate changes in phenotypes and genotypes that lead to the formation of new hybrid lineages with genetic variation. In this study, the establishment of two bisexual fertile carp li...

    Authors: Kaikun Luo, Shi Wang, Yeqing Fu, Pei Zhou, Xuexue Huang, Qianhong Gu, Wuhui Li, Yude Wang, Fangzhou Hu and Shaojun Liu

    Citation: BMC Genetics 2019 20:87

    Content type: Research article

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  28. The freshwater species on Taiwan Island have been documented to have originated from mainland China and the Japanese islands from multiple events and by multiple colonization routes. Moreover, the sequences fr...

    Authors: Chiao-Chuan Han, Kui-Ching Hsu, Lee-Shing Fang, I-Ming Cheng and Hung-Du Lin

    Citation: BMC Genetics 2019 20:86

    Content type: Research article

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  29. Genetic improvement of honey bees is more difficult compared to other livestock, due to the very different reproductive behavior. Estimation of breeding values requires specific adjustment and the use of sires...

    Authors: Sreten Andonov, Cecilia Costa, Aleksandar Uzunov, Patrizia Bergomi, Daniela Lourenco and Ignacy Misztal

    Citation: BMC Genetics 2019 20:78

    Content type: Research article

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  30. 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

    Content type: Research article

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  31. 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

    Content type: Research article

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  32. 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

    Content type: Research article

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  33. 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

    Content type: Research article

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  34. 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

    Content type: Research article

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  35. 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

    Content type: Research article

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  36. 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

    Content type: Research article

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  37. 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

    Content type: Research article

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  38. 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

    Content type: Research article

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  39. 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

    Content type: Research article

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  40. 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

    Content type: Research article

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  41. 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

    Content type: Research article

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  42. 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

    Content type: Research article

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  43. 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

    Content type: Research article

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  44. 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

    Content type: Research article

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  45. 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

    Content type: Research article

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    The Correction to this article has been published in BMC Genetics 2020 21:56

  46. 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

    Content type: Research article

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  47. 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

    Content type: Research article

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  48. 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

    Content type: Research article

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