2,078 results match your criteria BMC genetics[Journal]


An IL17RA frameshift variant in a Holstein cattle family with psoriasis-like skin alterations and immunodeficiency.

BMC Genet 2020 May 24;21(1):55. Epub 2020 May 24.

Institute of Animal Breeding and Genetics, Faculty of Agricultural Sciences, Nutritional Sciences and Environmental Management, Justus-Liebig University Giessen, 35390, Giessen, Germany.

Background: Skin lesions and dermatoses in cattle are often associated with infections due to bacteria, fungi or environmental risk factors. Dermatoses with genetic etiology have been described in cattle. Among these rare disorders, there are primary congenital dermatoses that are associated with inherited nutritional deficiencies, such as bovine hereditary zinc deficiency or zinc deficiency-like syndrome. Read More

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http://dx.doi.org/10.1186/s12863-020-00860-4DOI Listing

Cloning of Hynobius lichenatus (Tohoku hynobiid salamander) p53 and analysis of its expression in response to radiation.

BMC Genet 2020 May 20;21(1):53. Epub 2020 May 20.

Laboratory of Veterinary Immunology, Department of Veterinary Medicine, School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa, 252-5201, Japan.

Background: 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 Japanese Tohoku hynobiid salamander, are known. However, the expression of radiation-inducible genes, such as the DNA-damage checkpoint response gene p53, has not been analyzed in H. Read More

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http://dx.doi.org/10.1186/s12863-020-00856-0DOI Listing

Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

BMC Genet 2020 May 20;21(1):54. Epub 2020 May 20.

Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, 72701, USA.

Background: Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. Read More

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http://dx.doi.org/10.1186/s12863-020-00859-xDOI Listing

Knock-out of TERMINAL FLOWER 1 genes altered flowering time and plant architecture in Brassica napus.

BMC Genet 2020 May 19;21(1):52. Epub 2020 May 19.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.

Background: TERMINAL FLOWER 1 (TFL1) is a member of phosphatidylethanolamine-binding protein (PEBP) family, which plays an important role in the determination of floral meristem identity and regulates flowering time in higher plants.

Results: Five BnaTFL1 gene copies were identified in the genome of Brassica napus. The phylogenetic analysis indicated that all five BnaTFL1 gene copies were clustered with their corresponding homologous copies in the ancestral species, B. Read More

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http://dx.doi.org/10.1186/s12863-020-00857-zDOI Listing

A method for obtaining flexible broccoli varieties for sustainable agriculture.

BMC Genet 2020 May 7;21(1):51. Epub 2020 May 7.

Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Borgo XX Giugno 74, 06121, Perugia, Italy.

Background: The use of high inputs in agriculture resulted in few varieties (hybrids and pure lines) used in all agricultural systems. Also varieties of vegetables, including broccoli, for organic and low-input agriculture, are almost exclusively hybrids, since there are very few specific breeding programs and varieties for sustainable agriculture systems. A strategy to overcome this issue is the adoption of specific breeding programs for developing heterogeneous varieties (i. Read More

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http://dx.doi.org/10.1186/s12863-020-00846-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203864PMC

Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23.

BMC Genet 2020 Apr 29;21(1):49. Epub 2020 Apr 29.

Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK.

Background: Tilapias (Family Cichlidae) are the second most important group of aquaculture species in the world. They have been the subject of much research on sex determination due to problems caused by early maturation in culture and their complex sex-determining systems. Different sex-determining loci (linkage group 1, 20 and 23) have been detected in various tilapia stocks. Read More

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http://dx.doi.org/10.1186/s12863-020-00853-3DOI Listing

Genetic dissection of stem WSC accumulation and remobilization in wheat (Triticum aestivum L.) under terminal drought stress.

BMC Genet 2020 Apr 29;21(1):50. Epub 2020 Apr 29.

Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou, 730070, Gansu, China.

Background: The accumulation and remobilization of stem water soluble carbohydrates (WSC) are determinant physiological traits highly influencing yield potential in wheat against drought stress. However, knowledge gains of the genetic control are still limited. A hexaploid wheat population of 120 recombinant inbred lines were developed to identify quantitative trait loci (QTLs) and to dissect the genetic basis underlying eight traits related to stem WSC under drought stress (DS) and well-watered (WW) conditions across three environments. Read More

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http://dx.doi.org/10.1186/s12863-020-00855-1DOI Listing

Assessing the power of principal components and wright's fixation index analyzes applied to reveal the genome-wide genetic differences between herds of Holstein cows.

BMC Genet 2020 Apr 28;21(1):47. Epub 2020 Apr 28.

Russian Research Institute of Farm Animal Genetics and Breeding - Branch of the l.K. Ernst Federal Science Center for Animal Husbandry, St. Petersburg, Pushkin, Russia.

Background: 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 (F) and the principal component analysis (PCA) are widely used methods in animal genetics studies. In paper we compared the power of these methods, their complementing each other and which of them is the most powerful. Read More

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http://dx.doi.org/10.1186/s12863-020-00848-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189535PMC

Puccinia triticina pathotypes THTT and THTS display complex transcript profiles on wheat cultivar Thatcher.

BMC Genet 2020 Apr 28;21(1):48. Epub 2020 Apr 28.

Department of Plant Pathology, Hebei Agricultural University/Technological Innovation Center for Biological Control of Plant Diseases and Insect Pests of Hebei Province/National Engineering Research Center for Agriculture in Northern Mountainous Areas, Baoding, 071001, China.

Background: Wheat leaf rust is an important disease worldwide. Understanding the pathogenic molecular mechanism of Puccinia triticina Eriks. (Pt) and the inconstant toxic region is critical for managing the disease. Read More

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http://dx.doi.org/10.1186/s12863-020-00851-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7189582PMC

Transcriptome profiling of developing testes and spermatogenesis in the Mongolian horse.

BMC Genet 2020 Apr 28;21(1):46. Epub 2020 Apr 28.

College of Animal Science, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, 010018, China.

Background: Horse testis development and spermatogenesis are complex physiological processes.

Methods: To study these processes, three immature and three mature testes were collected from the Mongolian horse, and six libraries were established using high-throughput RNA sequencing technology (RNA-Seq) to screen for genes related to testis development and spermatogenesis.

Results: A total of 16,237 upregulated genes and 8,641 downregulated genes were detected in the testis of the Mongolian horse. Read More

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http://dx.doi.org/10.1186/s12863-020-00843-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7187496PMC

Molecular marker assisted gene stacking for disease resistance and quality genes in the dwarf mutant of an elite common wheat cultivar Xiaoyan22.

BMC Genet 2020 Apr 23;21(1):45. Epub 2020 Apr 23.

State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, China.

Background: Development of wheat cultivars with multiple disease resistance and high quality are major objectives in modern wheat breeding programs. Gene stacking is an efficient approach to achieve this target. In this study, we pyramided yellow rust resistance gene (Yr26), powdery mildew resistance gene (ML91260) and high-molecular-weight glutenin subunits Dx5 + Dy10 into the dwarf mutant of an elite wheat cultivar, Xiaoyan22. Read More

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http://dx.doi.org/10.1186/s12863-020-00854-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178591PMC

Transcriptome analysis identifies genes and co-expression networks underlying heat tolerance in pigs.

BMC Genet 2020 Apr 21;21(1):44. Epub 2020 Apr 21.

Department of Animal Science, North Carolina State University, Raleigh, NC, 27695-7621, USA.

Background: 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 to mitigate the negative effects of heat stress on their physiological activities. Yet, genetic variation and signaling pathways associated with the biological processes of heat-tolerant pigs are currently not fully understood. Read More

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http://dx.doi.org/10.1186/s12863-020-00852-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171765PMC

Dispersal and genetic structure in a tropical small mammal, the Bornean tree shrew (Tupaia longipes), in a fragmented landscape along the Kinabatangan River, Sabah, Malaysia.

BMC Genet 2020 04 17;21(1):43. Epub 2020 Apr 17.

University of Veterinary Medicine Hannover, Institute of Zoology, Buenteweg 17, 30559, Hannover, Germany.

Background: 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 populations. Although negative population trends due to ongoing forest loss are widespread, the consequence of habitat fragmentation on genetic diversity, gene flow and genetic structure has rarely been investigated in Bornean small mammals. To fill this gap in knowledge, we used nuclear and mitochondrial DNA markers to assess genetic diversity, gene flow and the genetic structure in the Bornean tree shrew, Tupaia longipes, that inhabits forest fragments of the Lower Kinabatangan Wildlife Sanctuary, Sabah. Read More

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http://dx.doi.org/10.1186/s12863-020-00849-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7164274PMC

Correction to: Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis.

BMC Genet 2020 Apr 8;21(1):42. Epub 2020 Apr 8.

AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia.

Following publication of the original article [1], the authors flagged that the article had published with the author 'Ali Jalil Sarghale' erroneously omitted from the author list. Read More

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http://dx.doi.org/10.1186/s12863-020-00841-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140384PMC

The effects of inbreeding on covering success, gestation length and foal sex ratio in Australian thoroughbred horses.

BMC Genet 2020 04 8;21(1):41. Epub 2020 Apr 8.

School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.

Background: 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 variants, resulting in reduced reproductive levels in a population. In this study we examined the influence of inbreeding levels on foaling rate, gestation length and secondary sex ratio in Australian Thoroughbred mares. Read More

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http://dx.doi.org/10.1186/s12863-020-00847-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140579PMC

Putting RFMix and ADMIXTURE to the test in a complex admixed population.

BMC Genet 2020 04 7;21(1):40. Epub 2020 Apr 7.

DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Room 4036, 4th Floor Education Building, Francie van Zijl Drive, Cape Town, 8000, South Africa.

Background: Global and local ancestry inference in admixed human populations can be performed using computational tools implementing distinct algorithms. The development and resulting accuracy of these tools has been tested largely on populations with relatively straightforward admixture histories but little is known about how well they perform in more complex admixture scenarios.

Results: Using simulations, we show that RFMix outperforms ADMIXTURE in determining global ancestry proportions even in a complex 5-way admixed population, in addition to assigning local ancestry with an accuracy of 89%. Read More

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http://dx.doi.org/10.1186/s12863-020-00845-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7140372PMC

Exploring the roles of fecundity-related long non-coding RNAs and mRNAs in the adrenal glands of small-tailed Han Sheep.

BMC Genet 2020 04 6;21(1):39. Epub 2020 Apr 6.

Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China.

Background: 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 was used to compare and analyze gene expressions in adrenal tissues between follicular phases and luteal phases in FecB (MM) and FecB (WW) sheep, respectively, and differentially expressed lncRNAs and genes associated with reproduction were identified. Read More

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http://dx.doi.org/10.1186/s12863-020-00850-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7137433PMC

Characterization of TMC-1 in C. elegans sodium chemotaxis and sodium conditioned aversion.

BMC Genet 2020 03 30;21(1):37. Epub 2020 Mar 30.

Department of Human Science, Georgetown University Medical Center, Washington, DC, 20057, USA.

Background: While sodium is attractive at low and aversive at high concentrations in most studied species, including Caenorhabditis elegans, the molecular mechanisms behind transduction remain poorly understood. Additionally, past studies with C. elegans provide evidence that the nematode's innate behavior can be altered by previous experiences. Read More

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http://dx.doi.org/10.1186/s12863-020-00844-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106803PMC

Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans.

BMC Genet 2020 03 30;21(1):38. Epub 2020 Mar 30.

Animal Ecology/Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden.

Background: 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 from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. Read More

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http://dx.doi.org/10.1186/s12863-020-00839-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7106915PMC

Correction to: Assessing genotype-phenotype associations in three dorsal colour morphs in the meadow spittlebug Philaenus spumarius (L.) (Hemiptera: Aphrophoridae) using genomic and transcriptomic resources.

BMC Genet 2020 Mar 24;21(1):36. Epub 2020 Mar 24.

Computational Biology and Population Genomics Group, cE3c - Centre for Ecology, Evolution and Environmental Changes, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, P-1749-016, Lisbon, Portugal.

Following publication of the original article [1], it has been brought to the authors' attention that in their paper (Rodrigues et al. 2016) they reported the genome size based on 2C values (diploid genome) when it is more common to present it as 1C value. Read More

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http://dx.doi.org/10.1186/s12863-020-00842-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092421PMC

Comparative analyses of the Sox9a-Amh-Cyp19a1a regulatory Cascade in Autotetraploid fish and its diploid parent.

BMC Genet 2020 03 21;21(1):35. Epub 2020 Mar 21.

State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, PR China.

Background: 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 effects of tetraploidization, we analyzed DNA variation, epigenetic modification and gene expression changes in the Sox9a-Amh-Cyp19a1a regulatory cascade between 4nRCC and 2nRCC. Read More

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http://dx.doi.org/10.1186/s12863-020-00840-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7085200PMC

On rare variants in principal component analysis of population stratification.

BMC Genet 2020 03 17;21(1):34. Epub 2020 Mar 17.

State Key Laboratory of Integrated Services Networks, Xidian University, 2 South Taibai Road, Xi'an, 710071, Shaanxi, China.

Background: Population stratification is a known confounder of genome-wide association studies, as it can lead to false positive results. Principal component analysis (PCA) method is widely applied in the analysis of population structure with common variants. However, it is still unclear about the analysis performance when rare variants are used. Read More

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http://dx.doi.org/10.1186/s12863-020-0833-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7077175PMC

The maternal origin of indigenous domestic chicken from the Middle East, the north and the horn of Africa.

BMC Genet 2020 03 14;21(1):30. Epub 2020 Mar 14.

School of Life Sciences, the University of Nottingham, University Park, Nottingham, NG7 2RD, UK.

Background: 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 their wild ancestor, the Red junglefowl, which lives in humid and sub-humid tropical areas. Indigenous populations are declining following increased demand for poultry meat and eggs, favouring the more productive exotic commercial breeds. Read More

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http://dx.doi.org/10.1186/s12863-020-0830-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7071775PMC

Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle.

BMC Genet 2020 03 14;21(1):32. Epub 2020 Mar 14.

Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, China.

Background: Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, single-trait GWAS, multi-trait GWAS and LONG-GWAS. Read More

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http://dx.doi.org/10.1186/s12863-020-0837-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7071762PMC

Selected neuropeptide genes show genetic differentiation between Africans and non-Africans.

BMC Genet 2020 03 14;21(1):31. Epub 2020 Mar 14.

Monash University Malaysia Genomics Facility, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.

Background: Publicly available genome data provides valuable information on the genetic variation patterns across different modern human populations. Neuropeptide genes are crucial to the nervous, immune, endocrine system, and physiological homeostasis as they play an essential role in communicating information in neuronal functions. It remains unclear how evolutionary forces, such as natural selection and random genetic drift, have affected neuropeptide genes among human populations. Read More

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http://dx.doi.org/10.1186/s12863-020-0835-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7071772PMC

miR-34a regulates adipogenesis in porcine intramuscular adipocytes by targeting ACSL4.

BMC Genet 2020 03 14;21(1):33. Epub 2020 Mar 14.

Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, No. 61, Daizong Street, Tai'an City, 271018, Shandong Province, China.

Background: Intramuscular fat (IMF) content is an important factor in porcine meat quality. Previously, we showed that miR-34a was less abundant in liver tissue from pigs with higher backfat thickness, compared to pigs with lower backfat thickness. The purpose of this present study was to explore the role of miR-34a in adipogenesis. Read More

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http://dx.doi.org/10.1186/s12863-020-0836-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073017PMC

The genetic control of leaf allometry in the common bean, Phaseolus vulgaris.

BMC Genet 2020 03 14;21(1):29. Epub 2020 Mar 14.

Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.

Background: To maximize photosynthetic efficiency, plants have evolved a capacity by which leaf area scales allometrically with leaf mass through interactions with the environment. However, our understanding of genetic control of this allometric relationship remains limited.

Results: We integrated allometric scaling laws expressed at static and ontogenetic levels into genetic mapping to identify the quantitative trait loci (QTLs) that mediate how leaf area scales with leaf mass and how such leaf allometry, under the control of these QTLs, varies as a response to environment change. Read More

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http://dx.doi.org/10.1186/s12863-020-00838-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7071654PMC

Genetic and genomic characterization of vulva size traits in Yorkshire and Landrace gilts.

BMC Genet 2020 03 12;21(1):28. Epub 2020 Mar 12.

Department of Animal Science, Iowa State University, IA50010, Ames, USA.

Background: Reproductive performance is critical for efficient swine production. Recent results indicated that vulva size (VS) may be predictive of reproductive performance in sows. Study objectives were to estimate genetic parameters, identify genomic regions associated, and estimate genomic prediction accuracies (GPA) for VS traits. Read More

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http://dx.doi.org/10.1186/s12863-020-0834-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7068987PMC

Population structure of five native sheep breeds of Sweden estimated with high density SNP genotypes.

BMC Genet 2020 03 6;21(1):27. Epub 2020 Mar 6.

Department of Animal Breeding and Genetics; Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7023, SE75007, Uppsala, Sweden.

Background: 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 sheep. Five breeds were genotyped using the 600 K SNP array. Read More

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http://dx.doi.org/10.1186/s12863-020-0827-8DOI Listing

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon.

BMC Genet 2020 03 6;21(1):25. Epub 2020 Mar 6.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

Background: POLG, located on nuclear chromosome 15, encodes the DNA polymerase γ(Pol γ). Pol γ is responsible for the replication and repair of mitochondrial DNA (mtDNA). Pol γ is the only DNA polymerase found in mitochondria for most animal cells. Read More

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http://dx.doi.org/10.1186/s12863-020-0828-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059407PMC

Genome-wide identification of Diacylglycerol Acyltransferases (DGAT) family genes influencing Milk production in Buffalo.

BMC Genet 2020 03 6;21(1):26. Epub 2020 Mar 6.

Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agriculture University, Wuhan, China.

Background: The diacylglycerol acyltransferases (DGAT) are a vital group of enzymes in catalyzing triacylglycerol biosynthesis. DGAT genes like DGAT1 and DGAT2, have been identified as two functional candidate genes affecting milk production traits, especially for fat content in milk. Buffalo milk is famous for its excellent quality, which is rich in fat and protein content. Read More

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http://dx.doi.org/10.1186/s12863-020-0832-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7059399PMC
March 2020
2.397 Impact Factor

Hox genes reveal variations in the genomic DNA of allotetraploid hybrids derived from Carassius auratus red var. (female) × Cyprinus carpio L. (male).

BMC Genet 2020 03 4;21(1):24. Epub 2020 Mar 4.

State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.

Background: Hox transcription factors are master regulators of animal development. Although highly conserved, they can contribute to the formation of novel biological characteristics when modified, such as during the generation of hybrid species, thus potentially serving as species-specific molecular markers. Here, we systematically studied the evolution of genomic sequences of Hox loci in an artificial allotetraploid lineage (4nAT, 4n = 200) derived from a red crucian carp (♀, RCC, 2n = 100) × common carp (♂, CC, 2n = 100) cross and its parents (RCC and CC). Read More

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http://dx.doi.org/10.1186/s12863-020-0823-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7057633PMC

Fatty acid biosynthesis and transcriptional regulation of Stearoyl-CoA Desaturase 1 (SCD1) in buffalo milk.

BMC Genet 2020 03 2;21(1):23. Epub 2020 Mar 2.

Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China.

Background: Buffalo milk is considered as a highly nutritious food owing to its higher contents of fatty acids (FA) and rich nutrient profile. Higher fat contents of buffalo milk make it suitable for processing to develop various healthy and nutritious products. Moreover, buffalo milk contains more unsaturated FAs (UFA) such as oleic and linolenic acid, which are important from the human health point of view owing to their desirable physiological effects. Read More

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http://dx.doi.org/10.1186/s12863-020-0829-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7053061PMC

Detection of CNV in the SH3RF2 gene and its effects on growth and carcass traits in chickens.

BMC Genet 2020 02 28;21(1):22. Epub 2020 Feb 28.

Department of Animal genetics and breeding, College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450046, Henan, China.

Background: The SH3RF2 gene is a protein-coding gene located in a quantitative trait locus associated with body weight, and its deletion has been shown to be positively associated with body weight in chickens.

Results: In the present study, CNV in the SH3RF2 gene was detected in 4079 individuals from 17 populations, including the "Gushi ×Anka" F2 resource population and populations of Chinese native chickens, commercial layers, and commercial broilers. The F2 resource population was then used to investigate the genetic effects of the chicken SH3RF2 gene. Read More

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http://dx.doi.org/10.1186/s12863-020-0831-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7048116PMC
February 2020

Estimating linkage disequilibrium from genotypes under Hardy-Weinberg equilibrium.

BMC Genet 2020 02 26;21(1):21. Epub 2020 Feb 26.

Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, SL5 7PY, UK.

Background: Measures of linkage disequilibrium (LD) play a key role in a wide range of applications from disease association to demographic history estimation. The true population LD cannot be measured directly and instead can only be inferred from genetic samples, which are unavoidably subject to measurement error. Previous studies of r (a measure of LD), such as the bias due to finite sample size and its variance, were based on the special case that the true population-wise LD is zero. Read More

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http://dx.doi.org/10.1186/s12863-020-0818-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7045472PMC
February 2020

Molecular cloning of SLC35D3 and analysis of its role during porcine intramuscular preadipocyte differentiation.

BMC Genet 2020 02 22;21(1):20. Epub 2020 Feb 22.

Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, 61 Daizong Street, Tai'an, 271018, People's Republic of China.

Background: Solute carrier family 35 (SLC35) is one of a large number of membrane transporter protein families. Member D3 of this family is thought to be involved in adipose deposition and metabolic control.

Results: We obtained 2238 bp cDNA of porcine SLC35D3, it contains a 1272 bp ORF, encoding a 423 amino acid polypeptide, and a 966 bp 3' UTR. Read More

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http://dx.doi.org/10.1186/s12863-020-0822-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7036214PMC
February 2020

Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats.

BMC Genet 2020 02 21;21(1):19. Epub 2020 Feb 21.

GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France.

Background: Goats were domesticated 10,500 years ago to supply humans with useful resources. Since then, specialized breeds that are adapted to their local environment have been developed and display specific genetic profiles. The VarGoats project is a 1000 genomes resequencing program designed to cover the genetic diversity of the Capra genus. Read More

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http://dx.doi.org/10.1186/s12863-020-0826-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7035711PMC
February 2020

Genetic diversity and population structure analysis based on the high density SNP markers in Ethiopian durum wheat (Triticum turgidum ssp. durum).

BMC Genet 2020 02 12;21(1):18. Epub 2020 Feb 12.

International Maize and Wheat Improvement Center (CIMMYT), Addis Ababa, Ethiopia.

Background: Ethiopia has been considered as a center of diversity and the second possible center of domestication of durum wheat. Genetic diversity and population structure analysis in the existing Ethiopian durum wheat germplasm have enormous importance in enhancing breeding effort and for sustainable conservation. Hence, 192 Ethiopian durum wheat accessions comprising 167 landraces collected from major wheat-growing areas of the country and 25 improved varieties released from Debre Zeit and Sinana Agricultural Research Centers, Ethiopia in different years (1994-2010) were assembled for the current study. Read More

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http://dx.doi.org/10.1186/s12863-020-0825-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7017545PMC
February 2020

Reliability of genomic evaluation for egg quality traits in layers.

BMC Genet 2020 02 11;21(1):17. Epub 2020 Feb 11.

PEGASE, INRAE, Agrocampus Ouest, 16 Le Clos, Saint-Gilles, 35590, France.

Background: Genomic evaluation, based on the use of thousands of genetic markers in addition to pedigree and phenotype information, has become the standard evaluation methodology in dairy cattle breeding programmes over the past several years. Despite the many differences between dairy cattle breeding and poultry breeding, genomic selection seems very promising for the avian sector, and studies are currently being conducted to optimize avian selection schemes. In this optimization perspective, one of the key parameters is to properly predict the accuracy of genomic evaluation in pure line layers. Read More

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http://dx.doi.org/10.1186/s12863-020-0820-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7014768PMC
February 2020

Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis.

BMC Genet 2020 02 10;21(1):16. Epub 2020 Feb 10.

AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia.

Background: 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 regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~ 65,000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (F), excess of homozygosity (F), correlation between uniting gametes (F), and diagonal elements of the genomic relationship matrix (F); 2) to identify frequently occurring ROH (i. Read More

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http://dx.doi.org/10.1186/s12863-020-0824-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7011551PMC
February 2020

Genotype-by-environment interaction in coast redwood outside natural distribution - search for environmental cues.

BMC Genet 2020 02 10;21(1):15. Epub 2020 Feb 10.

The New Zealand Redwood Company, P.O. Box 1343, Taupō, 3351, New Zealand.

Background: Effective matching of genotypes and environments is required for the species to reach optimal productivity and act effectively for carbon sequestration. A common garden experiment across five different environments was undertaken to assess genotype x environment interaction (GxE) of coast redwood in order to understand the performance of genotypes across environments.

Results: The quantitative genetic analysis discovered no GxE between investigated environments for diameter at breast height (DBH). Read More

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http://dx.doi.org/10.1186/s12863-020-0821-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7011450PMC
February 2020

A genome-wide scan study identifies a single nucleotide substitution in the tyrosinase gene associated with white coat colour in a red deer (Cervus elaphus) population.

BMC Genet 2020 02 10;21(1):14. Epub 2020 Feb 10.

Department for Veterinary Clinical Science, Justus-Liebig-University, Frankfurter Strasse 112, D-35392, Giessen, Germany.

Background: Red deer with very pale coat colour are observed sporadically. In the red deer (Cervus elaphus) population of Reinhardswald in Germany, about 5% of animals have a white coat colour that is not associated with albinism. In order to facilitate the conservation of the animals, it should be determined whether and to what extent brown animals carry the white gene. Read More

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http://dx.doi.org/10.1186/s12863-020-0814-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7011275PMC
February 2020

Epistatic regulation of growth in Atlantic salmon revealed: a QTL study performed on the domesticated-wild interface.

BMC Genet 2020 02 7;21(1):13. Epub 2020 Feb 7.

Population Genetics Research group, Institute of Marine Research, P.O. Box 1870, Nordnes, NO-5817, Bergen, Norway.

Background: Quantitative traits are typically considered to be under additive genetic control. Although there are indications that non-additive factors have the potential to contribute to trait variation, experimental demonstration remains scarce. Here, we investigated the genetic basis of growth in Atlantic salmon by exploiting the high level of genetic diversity and trait expression among domesticated, hybrid and wild populations. Read More

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http://dx.doi.org/10.1186/s12863-020-0816-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7006396PMC
February 2020

Parental warmth interacts with several genes to affect executive function components: a genome-wide environment interaction study.

BMC Genet 2020 02 4;21(1):11. Epub 2020 Feb 4.

Faculty of Education, Beijing Normal University, Beijing, China.

Background: Executive function (EF) is vital to human beings. It has been linked to many genes and family environmental factors in separate studies, but few studies have examined the potential interactions between gene(s) and environmental factor(s). The current study explored the whole genome to identify SNPs, genes, and pathways that interacted with parental warmth (PW) on EF. Read More

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http://dx.doi.org/10.1186/s12863-020-0819-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001336PMC
February 2020

Genotype frequency distributions of 28 SNP markers in two commercial lines and five Chinese native chicken populations.

BMC Genet 2020 02 4;21(1):12. Epub 2020 Feb 4.

Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.

Background: 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 of lowly selected Chinese native chicken populations, we selected 14 representative SNP markers strongly associated with growth traits or carcass traits and 14 SNP markers strongly associated with egg laying traits through previous reports. By using the MassArray technology, we detected the genotype frequency distributions of these 28 SNP markers in seven populations including four lowly selected as well as one moderately selected Sichuan native chicken populations, one commercial broiler line and one commercial layer line. Read More

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http://dx.doi.org/10.1186/s12863-020-0815-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001339PMC
February 2020

Identification of QTL TGW12 responsible for grain weight in rice based on recombinant inbred line population crossed by wild rice (Oryza minuta) introgression line K1561 and indica rice G1025.

BMC Genet 2020 02 3;21(1):10. Epub 2020 Feb 3.

Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Jingzhou, People's Republic of China.

Background: Limited genetic resource in the cultivated rice may hinder further yield improvement. Some valuable genes that contribute to rice yield may be lost or lacked in the cultivated rice. Identification of the quantitative trait locus (QTL) for yield-related traits such as thousand-grain weight (TGW) from wild rice speices is desired for rice yield improvement. Read More

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http://dx.doi.org/10.1186/s12863-020-0817-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6998338PMC
February 2020
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Genome-wide association study on Fourier transform infrared milk spectra for two Danish dairy cattle breeds.

BMC Genet 2020 01 31;21(1). Epub 2020 Jan 31.

Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, DK-8830, Tjele, Denmark.

Background: Infrared spectral analysis of milk is cheap, fast, and accurate. Infrared light interacts with chemical bonds present inside the milk, which means that Fourier transform infrared milk spectra are a reflection of the chemical composition of milk. Heritability of Fourier transform infrared milk spectra has been analysed previously. Read More

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http://dx.doi.org/10.1186/s12863-020-0810-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6993354PMC
January 2020

The primordial tRNA acceptor stem code from theoretical minimal RNA ring clusters.

BMC Genet 2020 01 23;21(1). Epub 2020 Jan 23.

Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical & Labcom CNRS/UGA/OrangeLabs Telecoms4Health, Université Grenoble Alpes, F-38700, La Tronche, France.

Background: Theoretical minimal RNA rings code by design over the shortest length once for each of the 20 amino acids, a start and a stop codon, and form stem-loop hairpins. This defines at most 25 RNA rings of 22 nucleotides. As a group, RNA rings mimick numerous prebiotic and early life biomolecular properties: tRNAs, deamination gradients and replication origins, emergence of codon preferences for the natural circular code, and contents of early protein coding genes. Read More

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http://dx.doi.org/10.1186/s12863-020-0812-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979358PMC
January 2020

Distribution of allele frequencies for genes associated with physical activity and/or physical capacity in a homogenous Norwegian cohort- a cross-sectional study.

BMC Genet 2020 01 23;21(1). Epub 2020 Jan 23.

Department of Natural Sciences and Environmental Health, University of South-Eastern Norway, Gullbringvegen 36, 3800, Bø i, Telemark, Norway.

Background: There are large individual differences in physical activity (PA) behavior as well as trainability of physical capacity. Heritability studies have shown that genes may have as much impact on exercise participation behavior as environmental factors. Genes that favor both trainability and participation may increase the levels of PA. Read More

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http://dx.doi.org/10.1186/s12863-020-0813-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979285PMC
January 2020

Trait-based mapping to identify the genetic factors underlying anaerobic germination of rice: Phenotyping, GXE, and QTL mapping.

BMC Genet 2020 01 17;21(1). Epub 2020 Jan 17.

International Rice Research Institute, Los Baños, Laguna, Philippines.

Background: Anaerobic germination is one of the most important traits for rice under direct-seeded conditions. The trait reduces risk of crop failure due to waterlogged conditions after seeding and allows water to be used as a means of weed control. The identification of QTLs and causal genes for anaerobic germination will facilitate breeding for improved direct-seeded rice varieties. Read More

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http://dx.doi.org/10.1186/s12863-020-0808-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6969419PMC
January 2020