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1. A nonsense mutation in the COL7A1 gene causes epidermolysis bullosa in Vorderwald cattle

Author:
Pausch, Hubert; Ammermüller, Simon; Wurmser, Christine; Hamann, Henning; Tetens, Jens; Drögemüller, Cord; Fries, Ruedi
Source:
BMC genetics 2016 v.17 no.1 pp. 149
ISSN:
1471-2156
Subject:
alleles; artificial insemination; calves; consultants; epidermolysis bullosa; farmers; genotyping; haplotypes; homozygosity; inheritance (genetics); loci; nonsense mutation; pedigree; phenotype; progeny; single nucleotide polymorphism; sires
Abstract:
... BACKGROUND: 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 manifestation of fatal phenotypes in their progeny. Breeding consultants and farmers reported on Vorderwald calves with a congenital skin disease. The clinical findings in affected ca ...
DOI:
10.1186/s12863-016-0458-2
PubMed:
27905875
PubMed Central:
PMC5131490

2. Characterization of novel SSR markers in diverse sainfoin (Onobrychis viciifolia) germplasm

Author:
Kempf, Katharina; Mora-Ortiz, Marina; Smith, Lydia M. J.; Kölliker, Roland; Skøt, Leif
Source:
BMC genetics 2016 v.17 no.1 pp. 124
ISSN:
1471-2156
Subject:
germplasm; microsatellite repeats; alleles; animal husbandry; landraces; loci; Onobrychis viciifolia; tetraploidy; forage legumes; agronomic traits; breeding programs; environmental factors; secondary metabolites; genetic markers
Abstract:
... BACKGROUND: Sainfoin is a perennial forage legume with beneficial properties for animal husbandry due to the presence of secondary metabolites. However, worldwide cultivation of sainfoin is marginal due to the lack of varieties with good agronomic performance, adapted to a broad range of environmental conditions. Little is known about the genetics of sainfoin and only few genetic markers are avail ...
DOI:
10.1186/s12863-016-0431-0
PubMed:
27576309
PubMed Central:
PMC5006395

3. Evaluation of forensic DNA mixture evidence: protocol for evaluation, interpretation, and statistical calculations using the combined probability of inclusion

Author:
Bieber, Frederick R.; Buckleton, John S.; Budowle, Bruce; Butler, John M.; Coble, Michael D.
Source:
BMC genetics 2016 v.17 no.1 pp. 125
ISSN:
1471-2156
Subject:
DNA; alleles; forensic sciences; loci; polymerase chain reaction; probability; statistical analysis; United States
Abstract:
... BACKGROUND: The evaluation and interpretation of forensic DNA mixture evidence faces greater interpretational challenges due to increasingly complex mixture evidence. Such challenges include: casework involving low quantity or degraded evidence leading to allele and locus dropout; allele sharing of contributors leading to allele stacking; and differentiation of PCR stutter artifacts from true alle ...
DOI:
10.1186/s12863-016-0429-7
PubMed:
27580588
PubMed Central:
PMC5007818

4. Flowering time adaption in Swedish landrace pea (Pisum sativum L.)

Author:
Vanhala, Tytti; Normann, Kjersti R.; Lundström, Maria; Weller, James L.; Leino, Matti W.; Hagenblad, Jenny
Source:
BMC genetics 2016 v.17 no.1 pp. 117
ISSN:
1471-2156
Subject:
Pisum sativum; Swedish Landrace; alleles; clearcutting; climatic factors; correlation; crops; cultivars; flowering date; genetic background; genetic variation; growing season; haplotypes; landraces; loci; models; peas; photoperiod; Sweden
Abstract:
... BACKGROUND: Cultivated crops have repeatedly faced new climatic conditions while spreading from their site of origin. In Sweden, at the northernmost fringe of Europe, extreme conditions with temperature-limited growth seasons and long days require specific adaptation. Pea (Pisum sativum L.) has been cultivated in Sweden for millennia, allowing for adaptation to the local environmental conditions t ...
DOI:
10.1186/s12863-016-0424-z
PubMed:
27521156
PubMed Central:
PMC4983087

5. Genetic diversity trend in Indian rice varieties: an analysis using SSR markers

Author:
Singh, Nivedita; Choudhury, Debjani Roy; Tiwari, Gunjan; Singh, Amit Kumar; Kumar, Sundeep; Srinivasan, Kalyani; Tyagi, R. K.; Sharma, A. D.; Singh, N. K.; Singh, Rakesh
Source:
BMC genetics 2016 v.17 no.1 pp. 127
ISSN:
1471-2156
Subject:
alleles; breeding; breeding programs; cluster analysis; crops; genetic background; genetic variation; genotyping; loci; microsatellite repeats; models; parents; population structure; rice; India
Abstract:
... BACKGROUND: The knowledge of the extent and pattern of diversity in the crop species is a prerequisite for any crop improvement as it helps breeders in deciding suitable breeding strategies for their future improvement. Rice is the main staple crop in India with the large number of varieties released every year. Studies based on the small set of rice genotypes have reported a loss in genetic diver ...
DOI:
10.1186/s12863-016-0437-7
PubMed:
27597653
PubMed Central:
PMC5011800

6. Genome-wide association mapping revealed a diverse genetic basis of seed dormancy across subpopulations in rice (Oryza sativa L.)

Author:
Magwa, Risper Auma; Zhao, Hu; Xing, Yongzhong
Source:
BMC genetics 2016 v.17 no.1 pp. 28
ISSN:
1471-2156
Subject:
Oryza sativa; abscisic acid; alleles; chromosome mapping; environmental factors; genome-wide association study; grain crops; grain yield; haplotypes; indole acetic acid; loci; population structure; quantitative trait loci; rice; seed dormancy; seed germination; seeds; vivipary (plants)
Abstract:
... BACKGROUND: Seed dormancy is an adaptive trait employed by flowering plants to avoid harsh environmental conditions for the continuity of their next generations. In cereal crops, moderate seed dormancy could help prevent pre-harvest sprouting and improve grain yield and quality. We performed a genome wide association study (GWAS) for dormancy, based on seed germination percentage (GP) in freshly h ...
DOI:
10.1186/s12863-016-0340-2
PubMed:
26810156
PubMed Central:
PMC4727300

7. Genome-wide imputation study identifies novel HLA locus for pulmonary fibrosis and potential role for auto-immunity in fibrotic idiopathic interstitial pneumonia

Author:
Fingerlin, Tasha E.; Zhang, Weiming; Yang, Ivana V.; Ainsworth, Hannah C.; Russell, Pamela H.; Blumhagen, Rachel Z.; Schwarz, Marvin I.; Brown, Kevin K.; Steele, Mark P.; Loyd, James E.; Cosgrove, Gregory P.; Lynch, David A.; Groshong, Steve; Collard, Harold R.; Wolters, Paul J.; Bradford, Williamson Z.; Kossen, Karl; Seiwert, Scott D.; du Bois, Roland M.; Garcia, Christine Kim; Devine, Megan S.; Gudmundsson, Gunnar; Isaksson, Helgi J.; Kaminski, Naftali; Zhang, Yingze; Gibson, Kevin F.; Lancaster, Lisa H.; Maher, Toby M.; Molyneaux, Philip L.; Wells, Athol U.; Moffatt, Miriam F.; Selman, Moises; Pardo, Annie; Kim, Dong Soon; Crapo, James D.; Make, Barry J.; Regan, Elizabeth A.; Walek, Dinesha S.; Daniel, Jerry J.; Kamatani, Yoichiro; Zelenika, Diana; Murphy, Elissa; Smith, Keith; McKean, David; Pedersen, Brent S.; Talbert, Janet; Powers, Julia; Markin, Cheryl R.; Beckman, Kenneth B.; Lathrop, Mark; Freed, Brian; Langefeld, Carl D.; Schwartz, David A.
Source:
BMC genetics 2016 v.17 no.1 pp. 74
ISSN:
1471-2156
Subject:
alleles; etiology; fibrosis; gene expression; gene expression regulation; genotype; genotyping; inflammation; linkage disequilibrium; loci; lungs; meta-analysis; pneumonia; protein structure; risk; sequence analysis; single nucleotide polymorphism
Abstract:
... BACKGROUND: Fibrotic idiopathic interstitial pneumonias (fIIP) are a group of fatal lung diseases with largely unknown etiology and without definitive treatment other than lung transplant to prolong life. There is strong evidence for the importance of both rare and common genetic risk alleles in familial and sporadic disease. We have previously used genome-wide single nucleotide polymorphism data ...
DOI:
10.1186/s12863-016-0377-2
PubMed:
27266705
PubMed Central:
PMC4895966

8. Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle

Author:
Biegelmeyer, Patrícia; Gulias-Gomes, Claudia C.; Caetano, Alexandre R.; Steibel, Juan P.; Cardoso, Fernando F.
Source:
BMC genetics 2016 v.17 no.1 pp. 32
ISSN:
1471-2156
Subject:
Hereford; alleles; cattle; effective population size; genetic markers; genetic variation; linkage disequilibrium; loci; marker-assisted selection; quantitative trait loci; single nucleotide polymorphism; Brazil
Abstract:
... BACKGROUND: The existence of moderate to high levels of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) affecting traits of interest is fundamental for the success of genome-wide association (GWAS) and genomic selection (GS) studies. Knowledge about the extent and the pattern of LD in livestock populations is essential to determine the density of single nucleo ...
DOI:
10.1186/s12863-016-0339-8
PubMed:
26832943
PubMed Central:
PMC4736111

9. Microsatellite markers from tea green leafhopper Empoasca (Matsumurasca) onukii: a powerful tool for studying genetic structure in tea plantations

Author:
Zhang, Li; Dietrich, Christopher H.; Qin, Daozheng
Source:
BMC genetics 2016 v.17 no.1 pp. 112
ISSN:
1471-2156
Subject:
Empoasca vitis; alleles; amplified fragment length polymorphism; genetic markers; genetic variation; heterozygosity; loci; male genitalia; pests; plantations; tea; variance; China; Japan
Abstract:
... BACKGROUND: Tea green leafhopper is one of the most dominant pests in Chinese tea plantations. Recent evidence, including morphological and molecular data, revealed that tea green leafhopper in China is the same species as in Japan, Empoasca (Matsumurasca) onukii Matsuda. Previous morphological study that revealed variation in the structure of the male genitalia within and among populations of thi ...
DOI:
10.1186/s12863-016-0420-3
PubMed:
27473717
PubMed Central:
PMC4966850

10. Multiple regulatory variants located in cell type-specific enhancers within the PKP2 locus form major risk and protective haplotypes for canine atopic dermatitis in German shepherd dogs

Author:
Tengvall, Katarina; Kozyrev, Sergey; Kierczak, Marcin; Bergvall, Kerstin; Farias, Fabiana H. G.; Ardesjö-Lundgren, Brita; Olsson, Mia; Murén, Eva; Hagman, Ragnvi; Leeb, Tosso; Pielberg, Gerli; Hedhammar, Åke; Andersson, Göran; Lindblad-Toh, Kerstin
Source:
BMC genetics 2016 v.17 no.1 pp. 97
ISSN:
1471-2156
Subject:
DNA fragmentation; German Shepherd; alleles; allergens; antibodies; atopic dermatitis; dogs; epithelial cells; epithelium; genetic variation; genotyping; haplotypes; immunoglobulin E; keratinocytes; loci; protective effect; risk; single nucleotide polymorphism; transcription (genetics)
Abstract:
... BACKGROUND: Canine atopic dermatitis (CAD) is a chronic inflammatory skin disease triggered by allergic reactions involving IgE antibodies directed towards environmental allergens. We previously identified a ~1.5 Mb locus on canine chromosome 27 associated with CAD in German shepherd dogs (GSDs). Fine-mapping indicated association closest to the PKP2 gene encoding plakophilin 2. RESULTS: Additiona ...
DOI:
10.1186/s12863-016-0404-3
PubMed:
27357287
PubMed Central:
PMC4928279

11. Polymorphisms of two loci at the oxytocin receptor gene in populations of Africa, Asia and South Europe

Author:
Butovskaya, Polina R.; Lazebny, Oleg E.; Sukhodolskaya, Evgeniya M.; Vasiliev, Vasily A.; Dronova, Daria A.; Fedenok, Juliya N.; Rosa, Aracelli; Peletskaya, Elena N.; Ryskov, Alexey P.; Butovskaya, Marina L.
Source:
BMC genetics 2016 v.17 no.1 pp. 17
ISSN:
1471-2156
Subject:
alleles; databases; gender; heterozygosity; humans; loci; oxytocin; oxytocin receptors; parenting; people; single nucleotide polymorphism; social behavior; variance; Africa; Asia; Europe
Abstract:
... BACKGROUND: The oxytocin (OT) system is known to be implicated in the regulation of complex social behavior, particularly empathy and parenting. The goal of this study was to estimate the gender and population differences in polymorphisms of two oxytocin receptor gene SNPs, rs53576 and rs2254298, in four populations. RESULTS: These data were compared with each other and with 14 samples from the co ...
DOI:
10.1186/s12863-015-0323-8
PubMed:
26738630
PubMed Central:
PMC4704389

12. The high frequency of GJB2 gene mutation c.313_326del14 suggests its possible origin in ancestors of Lithuanian population

Author:
Mikstiene, Violeta; Jakaitiene, Audrone; Byckova, Jekaterina; Gradauskiene, Egle; Preiksaitiene, Egle; Burnyte, Birute; Tumiene, Birute; Matuleviciene, Ausra; Ambrozaityte, Laima; Uktveryte, Ingrida; Domarkiene, Ingrida; Rancelis, Tautvydas; Cimbalistiene, Loreta; Lesinskas, Eugenijus; Kucinskas, Vaidutis; Utkus, Algirdas
Source:
BMC genetics 2016 v.17 no.1 pp. 45
ISSN:
1471-2156
Subject:
Whites; alleles; ancestry; cross-sectional studies; disease severity; gene deletion; gene frequency; genetic factors; genotype-phenotype correlation; hearing disorders; industrialization; loci; neonates; pathogenesis; patients; probability; regression analysis; Lithuania
Abstract:
... BACKGROUND: Congenital hearing loss (CHL) is diagnosed in 1 – 2 newborns in 1000, genetic factors contribute to two thirds of CHL cases in industrialised countries. Mutations of the GJB2 gene located in the DFNB1 locus (13q11-12) are a major cause of CHL worldwide. The aim of this cross-sectional study was to assess the contribution of the DFNB1 locus containing the GJB2 and GJB6 genes in the deve ...
DOI:
10.1186/s12863-016-0354-9
PubMed:
26896187
PubMed Central:
PMC4761217

13. Efficient disruption and replacement of an effector gene in the oomycete Phytophthora sojae using CRISPR/Cas9

Author:
Fang, Yufeng; Tyler, Brett M.
Source:
Molecular plant pathology 2016 v.17 no.1 pp. 127-139
ISSN:
1464-6722
Subject:
DNA; DNA damage; Phytophthora sojae; alleles; gene conversion; genomics; homozygosity; loci; models; mutants; pathogens; physiology; site-directed mutagenesis; soybeans; virulence
Abstract:
... Phytophthora sojae is an oomycete pathogen of soybean. As a result of its economic importance, P. sojae has become a model for the study of oomycete genetics, physiology and pathology. The lack of efficient techniques for targeted mutagenesis and gene replacement have long hampered genetic studies of pathogenicity in Phytophthora species. Here, we describe a CRISPR/Cas9 system enabling rapid and e ...
DOI:
10.1111/mpp.12318
Chorus Open Access:
10.1111/mpp.12318