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Molecular Genetics and Genomics: MGG

Javed Y Fowdar, Rebecca Grealy, Yi Lu, Lyn R Griffiths
Despite the success of genome-wide association studies (GWAS) in detecting genetic loci involved in complex traits, few susceptibility genes have been detected for essential hypertension (EH). We aimed to use pooled DNA GWAS approach to identify and validate novel genomic loci underlying EH susceptibility in an Australian case-control population. Blood samples and questionnaires detailing medical history, blood pressure, and prescribed medications were collected for 409 hypertensives and 409 age-, sex- and ethnicity-matched normotensive controls...
November 19, 2016: Molecular Genetics and Genomics: MGG
Taylor Gonchoroski, Veridiana G Virginio, Claudia E Thompson, Jéssica A Paes, Cláudio X Machado, Henrique B Ferreira
The minimal genome of the mollicute Mycoplasma hyopneumoniae, the etiological agent of porcine enzootic pneumonia, encodes a limited repertoire of antioxidant enzymes that include a single and atypical peroxiredoxin (MhPrx), whose evolution and function were studied here. MhPrx has only one catalytic cysteine, in contrast with some of its possible ancestors (2-Cys peroxiredoxins), which have two. Although it is more similar to 2-Cys orthologs, MhPrx can still function with a single peroxidatic cysteine (CysP), using non-thiolic electron donors to reduce it...
November 17, 2016: Molecular Genetics and Genomics: MGG
Hua-Hao Zhang, Guo-Yin Li, Xiao-Min Xiong, Min-Jin Han, Fang-Yin Dai
Helentrons represent a novel subtype of Helitrons. However, the evolutionary history of Helentrons in organisms is not clearly understood. In this study, we performed structure and autonomous partner analyses, which revealed that bm_455, a TE obtained from the Bombyx mori TE database, BmTEdb, was a member of Helentrons but not a long-terminal repeat (LTR) retrotransposon. Further analyses showed that bm_455 was also present in a wide range of insects including lepidopterans, coleopterans and hymenopterans using a homology-based search strategy...
November 16, 2016: Molecular Genetics and Genomics: MGG
Sergio Sebastián Samoluk, Germán Robledo, David Bertioli, José Guillermo Seijo
Satellite DNA (satDNA) is a major component of the heterochromatic regions of eukaryote genomes and usually shows a high evolutionary dynamic, even among closely related species. Section Arachis (genus Arachis) is composed of species belonging to six different genomes (A, B, D, F, G and K). The most distinguishing features among these genomes are the amount and distribution of the heterochromatin in the karyotypes. With the objective of gaining insight into the sequence composition and evolutionary dynamics of the heterochromatin fraction in Arachis, we investigated here the sequence diversity, genomic abundance, and chromosomal distribution of a satDNA family (ATR-2) among seven diploid species of section Arachis...
November 12, 2016: Molecular Genetics and Genomics: MGG
Lihua Li, Taozhi Ye, Xiaoling Gao, Rongjun Chen, Jinghong Xu, Chen Xie, Jianqing Zhu, Xiaojian Deng, Pingrong Wang, Zhengjun Xu
Low temperature may exert a negative impact on agronomical productivity. PsbR was known as the 10 kDa Photosystem II polypeptide. Although plant PsbR is thought to play important roles in photosynthesis, little is known about the contribution of plant PsbR to abiotic stress resistance. The expression patterns of three OsPsbR gene family members, OsPsbR1, OsPsbR2, and OsPsbR3, were characterized in rice 'Nipponbare'. Under normal condition, OsPsbR1 and OsPsbR3 showed tissue-specific expression, while the expression of OsPsbR2 could not be detected in all tested tissues...
November 10, 2016: Molecular Genetics and Genomics: MGG
Tao Zhou, Shikai Liu, Xin Geng, Yulin Jin, Chen Jiang, Lisui Bao, Jun Yao, Yu Zhang, Jiaren Zhang, Luyang Sun, Xiaozhu Wang, Ning Li, Suxu Tan, Zhanjiang Liu
Disease problems cause major economic losses for the aquaculture industries. In catfish, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the leading disease problem, causing tens of millions of dollars of annual economic losses. In this study, we conducted a genome-wide association study to determine quantitative trait loci (QTL) for resistance against ESC using an interspecific hybrid system. Five hundred fish were used in the analysis and 192 phenotypic extremes were used for genotyping with the catfish 250K SNP arrays...
November 8, 2016: Molecular Genetics and Genomics: MGG
Yuyan Sun, Yang Qiu, Mengmeng Duan, Jinglei Wang, Xiaohui Zhang, Haiping Wang, Jiangping Song, Xixiang Li
Anthocyanins are widely distributed water-soluble phytochemical pigments belonging to the flavonoid group. To date, limited knowledge is available about the regulatory roles of miRNAs in anthocyanin biosynthesis in plants. To identify the miRNAs associated with anthocyanin biosynthesis in radish, five small RNA (sRNA) libraries constructed from 'Xinlimei' radish roots at 11, 21, 44, 56 and 73 days (d) were examined using high-throughput sequencing technology. A total of 102.02 million (M) clean reads were generated, from which 483 known and 1415 novel miRNAs were identified...
November 5, 2016: Molecular Genetics and Genomics: MGG
Farzeen Kader, Meenu Ghai
Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development...
November 4, 2016: Molecular Genetics and Genomics: MGG
Jing Wu, Fangyun Cheng, Changfu Cai, Yuan Zhong, Xiao Jie
Tree peony (Paeonia Sect. Moutan) is an economically important ornamental plant, but little is known about the genetic architecture of important ornamental traits. To effectively improve ornamental value, we require a better understanding of genetic architecture in the complex traits of the tree peony. Association mapping is a powerful tool for detection of variation associated with traits. Thus, we examined the genetic diversity and the population structure of 462 unrelated cultivated P. rockii individuals, then performed association mapping to identify simple sequence repeat (SSR) markers associated with 12 floral traits...
November 2, 2016: Molecular Genetics and Genomics: MGG
Endre Neparáczki, Zoltán Juhász, Horolma Pamjav, Tibor Fehér, Bernadett Csányi, Albert Zink, Frank Maixner, György Pálfi, Erika Molnár, Ildikó Pap, Ágnes Kustár, László Révész, István Raskó, Tibor Török
We applied ancient DNA methods to shed light on the origin of ancient Hungarians and their relation to modern populations. Hungarians moved into the Carpathian Basin from the Eurasian Pontic steppes in the year 895 AD as a confederation of seven tribes, but their further origin remains obscure. Here, we present 17 mtDNA haplotypes and four Y-chromosome haplogroups, which portray the genetic composition of an entire small cemetery of the first generation Hungarians. Using novel algorithms to compare these mitochondrial DNA haplogroups with other ancient and modern Eurasian data, we revealed that a significant portion of the Hungarians probably originated from a long ago consolidated gene pool in Central Asia-South Siberia, which still persists in modern Hungarians...
November 1, 2016: Molecular Genetics and Genomics: MGG
Xiaoguang Shang, Chaoze Cheng, Jian Ding, Wangzhen Guo
Cotton is an economically important crop grown for natural fiber and seed oil production. Cottonseed oil ranks third after soybean oil and colza oil in terms of edible oilseed tonnage worldwide. The fatty acid composition of cottonseed oil determines its industrial application and nutritional values. However, little progress has been made in understanding cottonseed oil biogenesis. Stearoyl-acyl carrier protein desaturase (SAD), the only known enzyme to convert saturated fatty acids into unsaturated fatty acids in plants, plays key roles in determining the fatty acid composition of cottonseed oil...
October 28, 2016: Molecular Genetics and Genomics: MGG
Shaohua Hu, Tao Jiang, Yajun Zhou, Desong Ming, Hongzhi Gao, Mingxi Wang
Myroides odoratimimus (M. odoratimimus) has been gradually implicated as an important nosocomial pathogen that poses a serious health threat to immunocompromised patients owing to its multi-drug resistance. However, the resistance mechanism is currently unclear. To clarify the antibiotic resistance and infectivity mechanisms of M. odoratimimus, whole genome sequencing was performed on the multi-drug-resistant M. odoratimimus strain PR63039. The genome sequence was completed with single molecule real-time (SMRT) technologies...
October 28, 2016: Molecular Genetics and Genomics: MGG
Priyanka Agarwal, Rahul Kumar, Amit Pareek, Arun K Sharma
Isolation and functional characterization of tissue- and stage-specific gene promoters is beneficial for genetic improvement of economically important crops. Here, we have characterized a putative promoter of a ripening-induced gene RIP1 (Ripening induced protein 1) in tomato. Quantification of the transcript level of RIP1 showed that its expression is fruit preferential, with maximum accumulation in red ripe fruits. To test the promoter activity, we made a reporter construct by cloning 1450 bp putative RIP1 promoter driving the GUS (ß-glucuronidase) gene expression and generated stable transgenic lines in tomato and Arabidopsis...
October 27, 2016: Molecular Genetics and Genomics: MGG
Aung Kyaw Lwin, Edoardo Bertolini, Mario Enrico Pè, Andrea Zuccolo
Transposable elements (TEs) are the most abundant genetic material for almost all eukaryotic genomes. Their effects on the host genomes range from an extensive size variation to the regulation of gene expression, altering gene function and creating new genes. Because of TEs pivotal contribute to the host genome structure and regulation, their identification and characterization provide a wealth of useful data for gaining an in-depth understanding of host genome functioning. The giant reed (Arundo donax) is a perennial rhizomatous C3 grass, octadecaploid, with an estimated nuclear genome size of 2744 Mbp...
October 24, 2016: Molecular Genetics and Genomics: MGG
Ines Teichert, Miriam Lutomski, Ramona Märker, Minou Nowrousian, Ulrich Kück
During the sexual life cycle of filamentous fungi, multicellular fruiting bodies are generated for the dispersal of spores. The filamentous ascomycete Sordaria macrospora has a long history as a model system for studying fruiting body formation, and two collections of sterile mutants have been generated. However, for most of these mutants, the underlying genetic defect remains unknown. Here, we investigated the mutant spadix (spd) that was generated by X-ray mutagenesis in the 1950s and terminates sexual development after the formation of pre-fruiting bodies (protoperithecia)...
October 21, 2016: Molecular Genetics and Genomics: MGG
Nicolás Federico Villamil Munévar, Luiz Gustavo de Almeida, Beny Spira
Phosphate homeostasis is tightly regulated in bacteria. Phosphate scarcity is overcome by inducing the expression of genes associated with the scavenging of phosphate and phosphate-containing molecules, while phosphate surplus is stored in the form of polyphosphate (polyP). Regulation of the genes involved in polyP metabolism was investigated. Knockout of the most distal gene of the pstSCAB-phoU operon that encodes a Pi-transport system results in large accumulation of polyphosphate (polyP). Here, we show that the phoU mutation differentially affects the transcription of ppk and ppx, that respectively, encode a polyP kinase and a polyP exopolyphosphatase, by increasing the former and reducing the latter, further contributing the accumulation of polyP...
October 15, 2016: Molecular Genetics and Genomics: MGG
Sonika Ahlawat, Sachinandan De, Priyanka Sharma, Rekha Sharma, Reena Arora, R S Kataria, T K Datta, R K Singh
Hybrid sterility or reproductive isolation in mammals has been attributed to allelic incompatibilities in a DNA-binding protein PRDM9. Not only is PRDM9 exceptional in being the only known 'speciation gene' in vertebrates, but it is also considered to be the fastest evolving gene in the genome. The terminal zinc finger (ZF) domain of PRDM9 specifies genome-wide meiotic recombination hotspot locations in mammals. Intriguingly, PRDM9 ZF domain is highly variable between as well as within species, possibly activating different recombination hotspots...
October 15, 2016: Molecular Genetics and Genomics: MGG
Xiaozhu Wang, Shikai Liu, Chen Jiang, Xin Geng, Tao Zhou, Ning Li, Lisui Bao, Yun Li, Jun Yao, Yujia Yang, Xiaoxiao Zhong, Yulin Jin, Rex Dunham, Zhanjiang Liu
The ability to survive hypoxic conditions is important for various organisms, especially for aquatic animals. Teleost fish, representing more than 50 % of vertebrate species, are extremely efficient in utilizing low levels of dissolved oxygen in water. However, huge variations exist among various taxa of fish in their ability to tolerate hypoxia. In aquaculture, hypoxia tolerance is among the most important traits because hypoxia can cause major economic losses. Genetic enhancement for hypoxia tolerance in catfish is of great interest, but little was done with analysis of the genetic architecture of hypoxia tolerance...
October 12, 2016: Molecular Genetics and Genomics: MGG
Uwe Hoßfeld, Hans-Jörg Jacobsen, Christoph Plass, Benedikt Brors, Wilfried Wackernagel
No abstract text is available yet for this article.
October 11, 2016: Molecular Genetics and Genomics: MGG
Longxin Wang, Bowen Wang, Qingzhang Du, Jinhui Chen, Jiaxing Tian, Xiaohui Yang, Deqiang Zhang
Photosynthesis is one of the most important reactions on earth. PsbW, a nuclear-encoded subunit of photosystem II (PSII), stabilizes PSII structure and plays an important role in photosynthesis. Here, we used candidate gene-based linkage disequilibrium (LD) mapping to detect significant associations between allelic variations of PtoPsbW and traits related to photosynthesis, growth, and wood properties in Populus tomentosa. PtoPsbW showed the highest expression in leaves and it increased during the development of these leaves, suggesting that PtoPsbW may play an important role in plant growth and development...
October 8, 2016: Molecular Genetics and Genomics: MGG
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