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Molecular Genetics and Genomics: MGG

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https://www.readbyqxmd.com/read/28032277/genomic-strategies-to-understand-causes-of-keratoconus
#1
REVIEW
Justyna A Karolak, Marzena Gajecka
Keratoconus (KTCN) is a degenerative disorder of the eye characterized by the conical shape and thinning of the cornea. The abnormal structure of KTCN-affected cornea results in loss of visual acuity. While many studies examine how environmental factors influence disease development, finding the genetic triggers has been a major emphasis of KTCN research. This paper focuses on genomic strategies that were implemented for finding candidate genes, including linkage and association studies, and presents different approaches of mutation screening...
December 28, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28028612/qtls-for-cell-wall-bound-phenolics-in-relation-to-the-photosynthetic-apparatus-activity-and-leaf-water-status-under-drought-stress-at-different-growth-stages-of-triticale
#2
Tomasz Hura, Mirosław Tyrka, Katarzyna Hura, Agnieszka Ostrowska, Kinga Dziurka
The present study aimed at identifying the regions of triticale genome responsible for cell wall saturation with phenolic compounds under drought stress during vegetative and generative growth. Moreover, the loci determining the activity of the photosynthetic apparatus, leaf water content (LWC) and osmotic potential (Ψ o) were identified, as leaf hydration and functioning of the photosynthetic apparatus under drought are associated with the content of cell wall-bound phenolics (CWPh). Compared with LWC and Ψ o, CWPh fluctuations were more strongly associated with changes in chlorophyll fluorescence...
December 27, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28028611/comparative-analysis-of-the-gut-microbiota-of-black-bears-in-china-using-high-throughput-sequencing
#3
Can Song, Bochu Wang, Jun Tan, Liancai Zhu, Deshuai Lou, Xiaoxi Cen
The Asiatic black bear (Ursus thibetanus) is a protected species from eastern Asia. In China, the Asiatic black bear occurs in 17 provinces from northeast to southwest regions. To date, information on microbial diversity in the gut of the Asiatic black bears from different populations remains limited. To determine the species composition and community structure of the gut microbiota in the Asiatic black bear, we characterized 36 fecal samples from Sichuan, Yunnan, and Heilongjiang provinces, China, by pyrosequencing the 16S V3-V4 hypervariable regions using the Illumina Miseq platform...
December 27, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28013378/the-tandem-repeated-organization-of-nb-lrr-genes-in-the-clubroot-resistant-crb-locus-in-brassica-rapa-l
#4
Katsunori Hatakeyama, Tomohisa Niwa, Takeyuki Kato, Takayoshi Ohara, Tomohiro Kakizaki, Satoru Matsumoto
To facilitate prevention of clubroot disease, a major threat to the successful cultivation of Chinese cabbage (Brassica rapa L.), we bred clubroot-resistant (CR) cultivars by introducing resistance genes from CR turnips via conventional breeding. Among 11 CR loci found in B. rapa, we identified CRb in Chinese cabbage cultivar 'CR Shinki' as a single dominant gene for resistance against Plasmodiophora brassicae pathotype group 3, against which the stacking of Crr1 and Crr2 loci was not effective. However, the precise location and pathotype specificity of CRb have been controversial, because CRa and Rcr1 also map near this locus...
December 24, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28012016/the-ferredoxin-dependent-glutamate-synthase-osfd-gogat-participates-in-leaf-senescence-and-the-nitrogen-remobilization-in-rice
#5
Dong-Dong Zeng, Ran Qin, Mei Li, Md Alamin, Xiao-Li Jin, Yu Liu, Chun-Hai Shi
Ferredoxin-dependent glutamate synthase (Fd-GOGAT, EC 1.4.7.1) plays major roles in photorespiration and primary nitrogen assimilation. However, due to no mutant or knockdown lines of OsFd-GOGAT have been reported in rice (Oryza sativa L.), the contribution of OsFd-GOGAT to rice foliar nitrogen metabolism remains little up-to-date. Here, we isolated a rice premature leaf senescence mutant named gogat1, which was reduced in 67% of the total GOGAT enzyme activity in leaves. The gogat1 mutant exhibited chlorosis under natural condition, while showed less extent premature leaf senescence under low light treatment...
December 23, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28004182/cdk5rap2-interaction-with-components-of-the-hippo-signaling-pathway-may-play-a-role-in-primary-microcephaly
#6
Salil K Sukumaran, Maria Stumpf, Sarah Salamon, Ilyas Ahmad, Kurchi Bhattacharya, Sarah Fischer, Rolf Müller, Janine Altmüller, Birgit Budde, Holger Thiele, Muhammad Tariq, Naveed Altaf Malik, Peter Nürnberg, Shahid Mahmood Baig, Muhammad Sajid Hussain, Angelika A Noegel
Autosomal recessive primary microcephaly (MCPH) is characterized by a substantial reduction in brain size but with normal architecture. It is often linked to mutations in genes coding for centrosomal proteins; however, their role in brain size regulation is not completely understood. By combining homozygosity mapping and whole-exome sequencing in an MCPH family from Pakistan, we identified a novel mutation (XM_011518861.1; c.4114C > T) in CDK5RAP2, the gene associated with primary microcephaly-3 (MCPH3), leading to a premature stop codon (p...
December 21, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/27988808/inheritance-and-quantitative-trail-loci-mapping-of-adventitious-root-numbers-in-cucumber-seedlings-under-waterlogging-conditions
#7
Xuewen Xu, Jing Ji, Qiang Xu, Xiaohua Qi, Xuehao Chen
The hypocotyl-derived adventitious root (AR) is an important morphological acclimation to waterlogging stress; however, its genetic basis has not been adequately understood. In the present study, a mixed major gene plus polygene inheritance model was used to analyze AR numbers (ARN) 7 days after waterlogging treatment in six generations (P1, P2, F1, B1, B2, and F2), using cucumber waterlogging tolerant line Zaoer-N and sensitive Pepino as parents. The results showed that the genetic model D-4, mixed one negative dominance major gene and additive-dominance polygenes, is the best-fitting genetic model for waterlogging-triggered ARN phenotype...
December 17, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/27987057/transcriptome-analysis-of-the-freshwater-pearl-mussel-cristaria-plicata-mantle-unravels-genes-involved-in-the-formation-of-shell-and-pearl
#8
Xuefeng Wang, Zhiming Liu, Wenjian Wu
Cristaria plicata, a bivalve widespread in Eastern Asia fresh water, is utilized as the freshwater pearl mussel in China. With a high economic value in pearl production, it is also an ideal object used for the studies on biomineralization in freshwater. In the research, we performed a large-scale sequencing of Cristaria plicata mantle transcriptome using Illumina HiSeq™ 2500, obtaining 98,501 unigenes with 67,817,724 bases. 22.28 and 16.64% of the unigenes were annotated in the NR and Swiss-Prot databases, respectively...
December 16, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/27933381/genome-wide-identification-and-functional-analysis-of-s-rnase-involved-in-the-self-incompatibility-of-citrus
#9
Mei Liang, Wei Yang, Shiying Su, Lili Fu, Hualin Yi, Chuanwu Chen, Xiuxin Deng, Lijun Chai
S-RNase-based self-incompatibility is found in Solanaceae, Rosaceae, and Scrophulariaceae, and is the most widespread mechanism that prevents self-fertilization in plants. Although 'Shatian' pummelo (Citrus grandis), a traditional cultivated variety, possesses the self-incompatible trait, the role of S-RNases in the self-incompatibility of 'Shatian' pummelo is poorly understood. To identify genes associated with self-incompatibility in citrus, we identified 16 genes encoding homologs of ribonucleases in the genomes of sweet orange (Citrus sinensis) and clementine mandarin (Citrus clementine)...
December 8, 2016: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/27866268/a-genome-wide-association-study-of-essential-hypertension-in-an-australian-population-using-a-dna-pooling-approach
#10
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
https://www.readbyqxmd.com/read/27858147/evolution-and-function-of-the-mycoplasma-hyopneumoniae-peroxiredoxin-a-2-cys-like-enzyme-with-a-single-cys-residue
#11
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
https://www.readbyqxmd.com/read/27853884/horizontal-transfer-of-a-novel-helentron-in-insects
#12
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
https://www.readbyqxmd.com/read/27838847/evolutionary-dynamics-of-an-at-rich-satellite-dna-and-its-contribution-to-karyotype-differentiation-in-wild-diploid-arachis-species
#13
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
https://www.readbyqxmd.com/read/27832344/molecular-characterization-and-functional-analysis-of-the-ospsbr-gene-family-in-rice
#14
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
https://www.readbyqxmd.com/read/27826737/gwas-analysis-of-qtl-for-enteric-septicemia-of-catfish-and-their-involved-genes-suggest-evolutionary-conservation-of-a-molecular-mechanism-of-disease-resistance
#15
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
https://www.readbyqxmd.com/read/27817120/identification-of-anthocyanin-biosynthesis-related-micrornas-in-a-distinctive-chinese-radish-raphanus-sativus-l-by-high-throughput-sequencing
#16
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
https://www.readbyqxmd.com/read/27815639/dna-methylation-based-variation-between-human-populations
#17
REVIEW
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
https://www.readbyqxmd.com/read/27807670/association-mapping-for-floral-traits-in-cultivated-paeonia-rockii-based-on-ssr-markers
#18
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
https://www.readbyqxmd.com/read/27803981/genetic-structure-of-the-early-hungarian-conquerors-inferred-from-mtdna-haplotypes-and-y-chromosome-haplogroups-in-a-small-cemetery
#19
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
https://www.readbyqxmd.com/read/27796643/identification-of-candidate-genes-from-the-sad-gene-family-in-cotton-for-determination-of-cottonseed-oil-composition
#20
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
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