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BMC Genetics

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https://www.readbyqxmd.com/read/28525989/determination-of-genetic-effects-of-atf3-and-cdkn1a-genes-on-milk-yield-and-compositions-in-chinese-holstein-population
#1
REVIEW
Bo Han, Weijun Liang, Lin Liu, Yanhua Li, Dongxiao Sun
BACKGROUND: Our previous RNA-sequencing study revealed that the ATF3 and CDKN1A genes were remarkably differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein and fat percentage so that both of them were considered as candidates for milk composition. Herein, we further verified whether these genes have genetic effects on milk production traits in a Chinese Holstein cow population. RESULTS: By re-sequencing the entire coding and regulatory regions, we identified four SNPs in 5'promoter region, two in exons, seven in 3' un-translated region (UTR), and six in 3'flanking region of ATF3 gene, and one SNP in exon 5, two in 3'UTR, and two in 3'flanking region of CDKN1A gene...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525987/genetic-correlation-of-the-plasma-lipidome-with-type-2-diabetes-prediabetes-and-insulin-resistance-in-mexican-american-families
#2
Hemant Kulkarni, Manju Mamtani, Gerard Wong, Jacquelyn M Weir, Christopher K Barlow, Thomas D Dyer, Laura Almasy, Michael C Mahaney, Anthony G Comuzzie, Ravindranath Duggirala, Peter J Meikle, John Blangero, Joanne E Curran
BACKGROUND: Differential plasma concentrations of circulating lipid species are associated with pathogenesis of type 2 diabetes (T2D). Whether the wide inter-individual variability in the plasma lipidome contributes to the genetic basis of T2D is unknown. Here, we investigated the potential overlap in the genetic basis of the plasma lipidome and T2D-related traits. RESULTS: We used plasma lipidomic data (1202 pedigreed individuals, 319 lipid species representing 23 lipid classes) from San Antonio Family Heart Study in Mexican Americans...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525980/the-distribution-of-mitochondrial-dna-haplogroup-h-in-southern-iberia-indicates-ancient-human-genetic-exchanges-along-the-western-edge-of-the-mediterranean
#3
Candela L Hernández, Jean M Dugoujon, Andrea Novelletto, Juan N Rodríguez, Pedro Cuesta, Rosario Calderón
BACKGROUND: The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525967/candidate-gene-based-association-mapping-in-fusarium-culmorum-for-field-quantitative-pathogenicity-and-mycotoxin-production-in-wheat
#4
Valheria Castiblanco, Jose J Marulanda, Tobias Würschum, Thomas Miedaner
BACKGROUND: Quantitative traits are common in nature, but quantitative pathogenicity has received only little attention in phytopathology. In this study, we used 100 Fusarium culmorum isolates collected from natural field environments to assess their variation for two quantitative traits, aggressiveness and deoxynivalenol (DON) production on wheat plants grown in four different field environments (location-year combinations). Seventeen Fusarium graminearum pathogenicity candidate genes were assessed for their effect on the aggressiveness and DON production of F...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28514941/effects-of-marker-density-and-population-structure-on-the-genomic-prediction-accuracy-for-growth-trait-in-pacific-white-shrimp-litopenaeus-vannamei
#5
Quanchao Wang, Yang Yu, Jianbo Yuan, Xiaojun Zhang, Hao Huang, Fuhua Li, Jianhai Xiang
BACKGROUND: Due to the great advantages in selection accuracy and efficiency, genomic selection (GS) has been widely studied in livestock, crop and aquatic animals. Our previous study based on one full-sib family of Litopenaeus vannamei (L. vannamei) showed that GS was feasible in penaeid shrimp. However, the applicability of GS might be influenced by many factors including heritability, marker density and population structure etc. Therefore it is necessary to evaluate the major factors affecting the prediction ability of GS in shrimp...
May 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28511641/network-based-regularization-for-high-dimensional-snp-data-in-the-case-control-study-of-type-2-diabetes
#6
Jie Ren, Tao He, Ye Li, Sai Liu, Yinhao Du, Yu Jiang, Cen Wu
BACKGROUND: Over the past decades, the prevalence of type 2 diabetes mellitus (T2D) has been steadily increasing around the world. Despite large efforts devoted to better understand the genetic basis of the disease, the identified susceptibility loci can only account for a small portion of the T2D heritability. Some of the existing approaches proposed for the high dimensional genetic data from the T2D case-control study are limited by analyzing a few number of SNPs at a time from a large pool of SNPs, by ignoring the correlations among SNPs and by adopting inefficient selection techniques...
May 16, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28506298/fecx-bar-a-novel-bmp15-mutation-responsible-for-prolificacy-and-female-sterility-in-tunisian-barbarine-sheep
#7
Narjess Lassoued, Zohra Benkhlil, Florent Woloszyn, Ahmed Rejeb, Mohamed Aouina, Mourad Rekik, Stephane Fabre, Sonia Bedhiaf-Romdhani
BACKGROUND: Naturally occurring mutations in growth and differentiation factor 9 (GDF9) or bone morphogenetic protein 15 (BMP15) genes are associated with increased ovulation rate (OR) and litter size (LS) but also sterility. Observing the Tunisian Barbarine ewes of the "W" flock selected for improved prolificacy, we found prolific and infertile ewes with streaky ovaries. Blood genomic DNA was extracted from a subset of low-ovulating, prolific and infertile ewes of the "W" flock, and the entire coding sequences of GDF9 and BMP15 were sequenced...
May 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28506210/sucrose-non-ferment-1-related-protein-kinase-2-snrk2-genes-could-mediate-the-stress-responses-in-potato-solanum-tuberosum-l
#8
Jiangping Bai, Juan Mao, Hongyu Yang, Awais Khan, Aqi Fan, Siyan Liu, Junlian Zhang, Di Wang, Huijuan Gao, Jinlin Zhang
BACKGROUND: The SnRKs (sucrose non-fermenting 1 related protein kinase) are a gene family coding for Ser/Thr protein kinases and play important roles in linking the tolerance and metabolic responses of plants to abiotic stresses. To date, no genome-wide characterization of the sucrose non-ferment 1 related protein kinase 2 (SnRK2) subfamily has been conducted in potato (Solanum tuberosum L.). RESULTS: In this study, eight StSnRK2 genes (StSnRK2.1- StSnRK2.8) were identified in the genome of the potato (Solanum tuberosum L...
May 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28506208/a-strategy-to-apply-quantitative-epistasis-analysis-on-developmental-traits
#9
Marta K Labocha, Wang Yuan, Boanerges Aleman-Meza, Weiwei Zhong
BACKGROUND: Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. METHODS: In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement...
May 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28499390/high-content-behavioral-profiling-reveals-neuronal-genetic-network-modulating-drosophila-larval-locomotor-program
#10
Boanerges Aleman-Meza, Mario Loeza-Cabrera, Omar Peña-Ramos, Michael Stern, Weiwei Zhong
BACKGROUND: Two key questions in understanding the genetic control of behaviors are: what genes are involved and how these genes interact. To answer these questions at a systems level, we conducted high-content profiling of Drosophila larval locomotor behaviors for over 100 genotypes. RESULTS: We studied 69 genes whose C. elegans orthologs were neuronal signalling genes with significant locomotor phenotypes, and conducted RNAi with ubiquitous, pan-neuronal, or motor-neuronal Gal4 drivers...
May 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28476152/a-novel-nonsense-mutation-in-the-tyrosinase-gene-is-related-to-the-albinism-in-a-capuchin-monkey-sapajus-apella
#11
Felipe Tadeu Galante Rocha de Vasconcelos, Einat Hauzman, Leonardo Dutra Henriques, Paulo Roney Kilpp Goulart, Olavo de Faria Galvão, Ronaldo Yuiti Sano, Givago da Silva Souza, Jessica Lynch Alfaro, Luis Carlos de Lima Silveira, Dora Fix Ventura, Daniela Maria Oliveira Bonci
BACKGROUND: Oculocutaneous Albinism (OCA) is an autosomal recessive inherited condition that affects the pigmentation of eyes, hair and skin. The OCA phenotype may be caused by mutations in the tyrosinase gene (TYR), which expresses the tyrosinase enzyme and has an important role in the synthesis of melanin pigment. The aim of this study was to identify the genetic mutation responsible for the albinism in a captive capuchin monkey, and to describe the TYR gene of normal phenotype individuals...
May 5, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28464792/detection-and-comparison-of-micrornas-in-the-caprine-mammary-gland-tissues-of-colostrum-and-common-milk-stages
#12
Jinxing Hou, Xiaopeng An, Yuxuan Song, Binyun Cao, Heping Yang, Zhou Zhang, Wenzheng Shen, Yunpu Li
BACKGROUND: MicroRNAs (miRNAs) have a great influence on various physiological functions. A lot of high-throughput sequencing (HTS) research on miRNAs has been executed in the caprine mammary gland at different lactation periods (common milk lactation and dry period), but little is known about differentially expressed miRNAs in the caprine mammary gland of colostrum and peak lactation periods. RESULT: This study identified 131 differentially expressed miRNAs (P < 0...
May 2, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28420332/genetic-diversity-of-elaeis-oleifera-hbk-cortes-populations-using-cross-species-ssrs-implication-s-for-germplasm-utilization-and-conservation
#13
Maizura Ithnin, Chee-Keng Teh, Wickneswari Ratnam
BACKGROUND: The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Information on the genetic diversity of these collections can help achieve efficient conservation via maintenance of core collection. For this purpose, we have applied fourteen unlinked microsatellite markers to evaluate 532 E...
April 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28415964/quantitative-trait-locus-analysis-of-heterosis-for-plant-height-and-ear-height-in-an-elite-maize-hybrid-zhengdan-958-by-design-iii
#14
Hongjian Li, Qingsong Yang, Nannan Fan, Ming Zhang, Huijie Zhai, Zhongfu Ni, Yirong Zhang
BACKGROUND: Plant height (PH) and ear height (EH) are two important agronomic traits in maize selection breeding. F1 hybrid exhibit significant heterosis for PH and EH as compared to their parental inbred lines. To understand the genetic basis of heterosis controlling PH and EH, we conducted quantitative trait locus (QTL) analysis using a recombinant inbreed line (RIL) based design III population derived from the elite maize hybrid Zhengdan 958 in five environments. RESULTS: A total of 14 environmentally stable QTLs were identified, and the number of QTLs for Z1 and Z2 populations was six and eight, respectively...
April 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28412934/karyotype-diversity-and-chromosomal-organization-of-repetitive-dna-in-tityus-obscurus-scorpiones-buthidae
#15
Bruno Rafael Ribeiro de Almeida, Susana Suely Rodrigues Milhomem-Paixão, Renata Coelho Rodrigues Noronha, Cleusa Yoshiko Nagamachi, Marlyson Jeremias Rodrigues da Costa, Pedro Pereira de Oliveira Pardal, Johne Souza Coelho, Julio Cesar Pieczarka
BACKGROUND: Holocentric chromosomes occur in approximately 750 species of eukaryotes. Among them, the genus Tityus (Scorpiones, Buthidae) has a labile karyotype that shows complex multivalent associations during male meiosis. Thus, taking advantage of the excellent model provided by the Buthidae scorpions, here we analyzed the chromosomal distribution of several repetitive DNA classes on the holocentric chromosomes of different populations of the species Tityus obscurus Gervais, 1843, highlighting their involvement in the karyotypic differences found among them...
April 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28399816/ploidy-elicits-a-whole-genome-dosage-effect-growth-of-triploid-atlantic-salmon-is-linked-to-the-genetic-origin-of-the-second-maternal-chromosome-set
#16
A C Harvey, P G Fjelldal, M F Solberg, T Hansen, K A Glover
BACKGROUND: The Atlantic salmon aquaculture industry is investigating the feasibility of using sterile triploids to mitigate genetic interactions with wild conspecifics, however, studies investigating diploid and triploid performance often show contrasting results. Studies have identified dosage and dosage-compensation effects for gene expression between triploid and diploid salmonids, but no study has investigated how ploidy and parent-origin effects interact on a polygenic trait in divergent lines of Atlantic salmon (i...
April 11, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28388893/genome-wide-identification-and-expression-analysis-of-cllax-clpin-and-clabcb-genes-families-in-citrullus-lanatus-under-various-abiotic-stresses-and-grafting
#17
Chenliang Yu, Wenqi Dong, Yihua Zhan, Zong-An Huang, Zhimiao Li, Il Seop Kim, Chenghao Zhang
BACKGROUND: Auxin plays an important role in regulating plant growth and development as well as in the response of plants to abiotic stresses. Auxin is transported by three kinds of major protein families, including the AUXIN RESISTANT 1/LIKE AUX1 (AUX⁄LAX) influx carriers, the PIN-FORMED (PIN) efflux carriers and the ATP binding cassette B/P-glycoprotein/Multidrug-resistance (ABCB/MDR/PGP) efflux/condition carriers. The biological function of several auxin transporter genes has been well characterized in Arabidopsis thaliana...
April 7, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28381212/low-depth-genotyping-by-sequencing-gbs-in-a-bovine-population-strategies-to-maximize-the-selection-of-high-quality-genotypes-and-the-accuracy-of-imputation
#18
Jean-Simon Brouard, Brian Boyle, Eveline M Ibeagha-Awemu, Nathalie Bissonnette
BACKGROUND: Genotyping-by-sequencing (GBS) has emerged as a powerful and cost-effective approach for discovering and genotyping single-nucleotide polymorphisms. The GBS technique was largely used in crop species where its low sequence coverage is not a drawback for calling genotypes because inbred lines are almost homozygous. In contrast, only a few studies used the GBS technique in animal populations (with sizeable heterozygosity rates) and many of those that have been published did not consider the quality of the genotypes produced by the bioinformatic pipelines...
April 5, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28381206/transcriptome-profiling-of-arabian-horse-blood-during-training-regimens
#19
Katarzyna Ropka-Molik, Monika Stefaniuk-Szmukier, Kacper Żukowski, Katarzyna Piórkowska, Artur Gurgul, Monika Bugno-Poniewierska
BACKGROUND: Arabian horses are believed to be one of the oldest and most influential horse breeds in the world. Blood is the main tissue involved in maintaining body homeostasis, and it is considered a marker of the processes taking place in the other tissues. Thus, the aim of our study was to identify the genetic basis of changes occurring in the blood of Arabian horses subjected to a training regimen and to compare the global gene expression profiles between different training periods (T1: after a slow canter phase that is considered a conditioning phase, T2: after an intense gallop phase, and T3: at the end of the racing season) and between trained and untrained horses (T0)...
April 5, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28356074/a-deletion-in-the-intergenic-region-upstream-of-ednrb-causes-head-spot-in-the-rat-strain-kfrs4-kyo
#20
Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto, Mikita Suyama
BACKGROUND: Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could be the gene responsible for this phenotype, no mutations have been identified in its coding region. RESULTS: To identify mutations causative of this phenotype in KFRS4/Kyo, we analyzed target capture sequencing data that we recently generated...
March 29, 2017: BMC Genetics
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