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D S J Groenenberg, J Harl, E Duijm, E Gittenberger
BACKGROUND: With the increasing capacity of present-day next-generation sequencers the field of mitogenomics is rapidly changing. Enrichment of the mitochondrial fraction, is no longer necessary for obtaining mitogenomic data. Despite the benefits, shotgun sequencing approaches also have disadvantages. They do not guarantee obtaining the complete mitogenome, generally require larger amounts of input DNA and coverage is low compared to sequencing with enrichment strategies. If the mitogenome could be amplified in a single amplification, additional time and costs for sample preparation might outweigh these disadvantages...
2017: Hereditas
Jialing He, Yingjun Xie, Shu Kong, Wenjun Qiu, Xiaoman Wang, Ding Wang, Xiaofang Sun, Deming Sun
A 1q42 deletion is a rare structure variation that commonly harbours various deletion breakpoints along with diversified phenotypes. In our study, we found a de novo 1q42 deletion in a boy who did not have a cleft palate or a congenital diaphragmatic hernia but presented with psychomotor retardation. A 1.9 Mb deletion located within 1q42.11-q42.12 was validated at the molecular cytogenetic level. This is the first report of a 1q42.11-q42.12 deletion in a patient with onlypsychomotor retardation. The precise break points could facilitate the discovery of potential causative genes, such as LBR, EPHX1, etc...
2017: Hereditas
Bing Zeng, Haidong Yan, Xinchun Liu, Wenjing Zang, Ailing Zhang, Sifan Zhou, Linkai Huang, Jinping Liu
BACKGROUND: While orchardgrass (Dactylis glomerata L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; however, genetic mechanisms of rust resistance are not well understood in orchardgrass. RESULTS: In this study, a genome-wide association study (GWAS) was performed using specific-locus amplified fragment sequencing (SLAF-seq) technology in orchardgrass. A total of 2,334,889 SLAF tags were generated to produce 2,309,777 SNPs...
2017: Hereditas
Christina M Rochus, Anna M Johansson
BACKGROUND: Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep...
2017: Hereditas
Thu Giang Thi Bui, Nguyen Thi Lan Hoa, Jo-Yi Yen, Roland Schafleitner
BACKGROUND: Single nucleotide polymorphism (SNP) markers are the method of choice for genetic analyses including diversity and quantitative trait loci (QTL) studies. Marker validation is essential for QTL studies, but the cost and workload are considerable when large numbers of markers need to be verified. Marker systems with low development costs would be most suitable for this task. RESULTS: We have tested allele specific polymerase chain reaction (PCR), tetra markers and a genotyping tool based on the single strand specific nuclease CEL-I to verify randomly selected SNP markers identified previously either with a SNP array or by genotyping by sequencing in rice and mungbean, respectively...
2017: Hereditas
Jianmin Yuan, Jianlin Hu, Zhiqiang Li, Fuquan Zhang, Dexiang Zhou, Chunhui Jin
BACKGROUND: Schizophrenia (SCZ) is a common, complex and severe psychiatric disorder associated with many different genetic and environmental risk factors. Evidence from genetic studies has revealed the role of genome structural variations, specifically copy number variants (CNVs), in the etiology of SCZ. Nevertheless, the occurrence of CNVs and their relation to SCZ has remained relatively unstudied in the diverse Han Chinese population. RESULTS: We used a case/control paradigm, including 476 cases and 1023 controls...
2017: Hereditas
Ranjith Kumar Manoharan, Hee-Jeong Jung, Indeok Hwang, Namhee Jeong, Kang Hee Kho, Mi-Young Chung, Ill-Sup Nou
BACKGROUND: Tomatoes provide a significant dietary source of the carotenoids, lycopene and β-carotene. During ripening, carotenoid accumulation determines the fruit colors while chlorophyll degradation. These traits have been, and continue to be, a significant focus for plant breeding efforts. Previous work has found strong evidence for a relationship between CYC-B gene expression and the orange color of fleshy fruit. Other work has identified a point mutation in SGR that impedes chlorophyll degradation and causes brown flesh color to be retained in some tomato varieties...
2017: Hereditas
Lei Sun, Xiucai Fan, Ying Zhang, Jianfu Jiang, Haisheng Sun, Chonghuai Liu
BACKGROUND: The color of berry skin is an important economic trait for grape and is essentially determined by the components and content of anthocyanins. The fruit color of Chinese wild grapes is generally black, and the profile of anthocyanins in Chinese wild grapes is significantly different from that of Vitis vinifera. However, V. davidii is the only species that possesses white berry varieties among Chinese wild grape species. Thus, we performed a transcriptomic analysis to compare the difference of transcriptional level in black and white V...
2016: Hereditas
Sakshi Chaudhary, Bharat Kumar Mishra, Thiruvettai Vivek, Santoshkumar Magadum, Jeshima Khan Yasin
BACKGROUND: Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. RESULTS: A total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences)...
2016: Hereditas
Göran Arnqvist, Zorana Kurbalija Novičić, José A Castro, Ahmed Sayadi
BACKGROUND: Recent experimental evidence for selection on mitochondrial DNA (mtDNA) has prompted the question as to what processes act to maintain within-population variation in mtDNA. Balancing selection though negative frequency dependent selection (NFDS) among sympatric haplotypes is a possibility, but direct empirical evidence for this is very scarce. FINDINGS: We extend the previous findings of a multi-generation replicated cage experiment in Drosophila subobscura, where mtDNA polymorphism was maintained in a laboratory setting...
2016: Hereditas
Weizhen Jiang, Qingling Li, Xiaolu Chen, Yi Ren, Rong Chen, Hong Wu, Yuesheng Yang
BACKGROUND: Aneuploid ermpglasm is an important resource for genetic studies and identification of individual chromosomes in the cells of the aneuploid is an important step. The karyotype has already been established for purple coneflower (Echinacea purpurea L.), but due to the high similarity in the morphology of several pairs of chromosomes in this species, it cannot be used to identify individual chromosomes in its own complement. The objectives of this study are to develop and evaluate the Giemsa C-banding technique for the purpose of identifying the individual chromosomes in Echinacea purpurea...
2016: Hereditas
Alma Delia Genis-Mendoza, Carlos Alfonso Tovilla-Zárate, Lilia López-Narvaez, Patricia Mendoza-Lorenzo, Patricia Ostrosky-Wegman, Humberto Nicolini, Thelma Beatriz González-Castro, Yazmin Hernández-Diaz
BACKGROUND: Neonatal lesion in the ventral hippocampus (NLVH) is a validated animal model to study schizophrenia from a neurodevelopmental perspective. This animal model is also used to investigate how neonatal lesions may alter the genetic expression of dopaminergic receptors. The present study compares mRNA expression levels of dopamine receptors (drd2 and drd3) in lymphocytes and brain of NLVH animals at two different age stages: young and adult. METHODS: The NLVH procedure was performed on 20 male Wistar rats at postnatal days 5-7...
2016: Hereditas
Hiroyo Kagami, Kazunori Taguchi, Takumi Arakawa, Yosuke Kuroda, Hideto Tamagake, Tomohiko Kubo
BACKGROUND: Obtaining dedifferentiated cells (callus) that can regenerate into whole plants is not always feasible for many plant species. Sugar beet is known to be recalcitrant for dedifferentiation and plant regeneration. These difficulties were major obstacles for obtaining transgenic sugar beets through an Agrobacterium-mediated transformation procedure. The sugar beet line 'NK-219mm-O' is an exceptional line that forms callus efficiently and is easy to regenerate, but the inheritance of these characters was unknown...
2016: Hereditas
Chandler C Roe, Kimberly S Horn, Elizabeth M Driebe, Jolene Bowers, Joel A Terriquez, Paul Keim, David M Engelthaler
BACKGROUND: Prevention of nosocomial transmission of infections is a central responsibility in the healthcare environment, and accurate identification of transmission events presents the first challenge. Phylogenetic analysis based on whole genome sequencing provides a high-resolution approach for accurately relating isolates to one another, allowing precise identification or exclusion of transmission events and sources for nearly all cases. We sequenced 24 methicillin-resistant Staphylococcus aureus (MRSA) genomes to retrospectively investigate a suspected point source of three surgical site infections (SSIs) that occurred over a one-year period...
2016: Hereditas
Firuz Odilbekov, Eva Edin, Larisa Garkava-Gustavsson, Helena Persson Hovmalm, Erland Liljeroth
BACKGROUND: Early blight, caused by the fungus Alternaria solani, occurs on potato mainly in the south-eastern part of Sweden, but also in other parts of the country. The aim of this study was to investigate the genetic diversity of A. solani populations from different potato growing regions in south-eastern Sweden using AFLP marker analysis. In addition, the cultured isolates were examined for substitutions in the gene encoding cytochrome b, associated with loss of sensitivity against QoI fungicides...
2016: Hereditas
Kaixin Fu, Zhihui Guo, Xinquan Zhang, Yan Fan, Wendan Wu, Daxu Li, Yan Peng, Linkai Huang, Ming Sun, Shiqie Bai, Xiao Ma
BACKGROUND: Genetic diversity of 19 forage-type and 2 turf-type cultivars of tall fescue (Festuca arundinacea Schreb.) was revealed using SSR markers in an attempt to explore the genetic relationships among them, and examine potential use of SSR markers to identify cultivars by bulked samples. RESULTS: A total of 227 clear band was scored with 14 SSR primers and out of which 201 (88.6 %) were found polymorphic. The percentage of polymorphic bands (PPB) per primer pair varied from 62...
2016: Hereditas
Fang Liu, Tengfei Shi, Sisi Huang, Linsheng Yu, Shoudong Bi
BACKGROUND: The Mount Huang eastern honey bees (Apis cerana) are an endemic population, which is well adapted to the local agricultural and ecological environment. In this study, the genetic structure of seven eastern honey bees (A. cerana) populations from Mount Huang in China were analyzed by SSR (simple sequence repeat) markers. RESULTS: The results revealed that 16 pairs of primers used amplified a total of 143 alleles. The number of alleles per locus ranged from 6 to 13, with a mean value of 8...
2016: Hereditas
Marjan Ghasemkhani, Larisa Garkava-Gustavsson, Erland Liljeroth, Hilde Nybom
BACKGROUND: Neonectria ditissima is one of the most important fungal pathogens of apple trees, where it causes fruit tree canker. Information about the amount and partitioning of genetic variation of this fungus could be helpful for improving orchard management strategies and for breeding apple cultivars with high levels of genetically determined resistance. In this study single-spore Neonectria isolates originating from both the same and from different perithecia, apple cultivars and apple orchards in Sweden and Belgium, were evaluated for AFLP- and SSR-based genetic similarity and for mating system...
2016: Hereditas
Fang Huang, Jiawei Shen, Qingli Guo, Yongyong Shi
BACKGROUND: Enhancers are tissue specific distal regulation elements, playing vital roles in gene regulation and expression. The prediction and identification of enhancers are important but challenging issues for bioinformatics studies. Existing computational methods, mostly single classifiers, can only predict the transcriptional coactivator EP300 based enhancers and show low generalization performance. RESULTS: We built a hybrid classifier called eRFSVM in this study, using random forests as a base classifier, and support vector machines as a main classifier...
2016: Hereditas
Pirjo Tanhuanpää, Maria Erkkilä, Ruslan Kalendar, Alan Howard Schulman, Outi Manninen
BACKGROUND: Timothy (Phleum pratense L.), a cool-season hexaploid perennial, is the most important forage grass species in Nordic countries. Earlier analyses of genetic diversity in a collection of 96 genebank accessions of timothy with SSR markers demonstrated high levels of diversity but could not resolve population structure. Therefore, we examined a subset of 51 accessions with REMAP markers, which are based on retrotransposons, and compared the diversity results with those obtained with SSR markers...
2016: Hereditas
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