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1.
Natalia Sevane Hubert Leveziel Geoffrey R Nute Carlos Sanudo Alessio Valentini John Williams Susana Dunner the GeMQual Consortium 《畜牧与生物技术杂志(英文版)》2014,(2):154-162
Background： Consuming moderate amounts of lean red meat as part of a balanced diet valuably contributes to intakes of essential nutrients, in this study, we merged phenotypic and genotypic information to characterize the variation in lipid profile and sensory parameters and to represent the diversity among 15 cattle populations. Correlations between fat content, organoleptic characteristics and lipid profiles were also investigated. Methods： A sample of 436 largely unrelated purebred bulls belonging to 15 breeds and reared under comparable management conditions was analyzed. Phenotypic data -including fatness score, fat percentage, individual fatty acids （FA） profiles and sensory panel tests- and genotypic information from 11 polymorphisms was used. Results： The correlation coefficients between muscle total lipid measurements and absolute vs. relative amounts of polyunsaturated FA （PUFA） were in opposite directions. Increasing carcass fat leads to an increasing amount of FAs in triglycerides, but at the same time the relative amount of PUFAs is decreasing, which is in concordance with the negative correlation obtained here between the percentage of PUFA and fat measurements, as well as the weaker correlation between total phospholipids and total lipid muscle content compared with neutral lipids. Concerning organoleptic characteristics, a negative correlation between fiavour scores and the percentage of total PUFA, particularly to n-6 fraction, was found. The correlation between juiciness and texture is higher than with flavour scores. The distribution of SNPs plotted by principal components analysis （PCA） mainly reflects their known trait associations, although influenced by their specific breed allele frequencies. Conclusions： The results presented here help to understand the phenotypic and genotypic background underlying variations in FA composition and sensory parameters between breeds. The wide range of traits and breeds studied, along with the genotypic information on polymorphisms previo 相似文献
2.
Nadeau JH Balling R Barsh G Beier D Brown SD Bucan M Camper S Carlson G Copeland N Eppig J Fletcher C Frankel WN Ganten D Goldowitz D Goodnow C Guenet JL Hicks G Hrabe de Angelis M Jackson I Jacob HJ Jenkins N Johnson D Justice M Kay S Kingsley D Lehrach H Magnuson T Meisler M Poustka A Rinchik EM Rossant J Russell LB Schimenti J Shiroishi T Skarnes WC Soriano P Stanford W Takahashi JS Wurst W Zimmer A;International Mouse Mutagenesis Consortium 《Science (New York, N.Y.)》2001,291(5507):1251-1255
3.
Rice Full-Length cDNA Consortium;National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team Kikuchi S Satoh K Nagata T Kawagashira N Doi K Kishimoto N Yazaki J Ishikawa M Yamada H Ooka H Hotta I Kojima K Namiki T Ohneda E Yahagi W Suzuki K Li CJ Ohtsuki K Shishiki T;Foundation of Advancement of International Science Genome Sequencing & Analysis Group Otomo Y Murakami K Iida Y Sugano S Fujimura T Suzuki Y Tsunoda Y Kurosaki T Kodama T Masuda H Kobayashi M Xie Q Lu M 《Science (New York, N.Y.)》2003,301(5631):376-379
4.
J.W. Kijas M. Serrano R. McCulloch Y. Li J. Salces Ortiz J.H. Calvo M.D. Pérez‐Guzmán The International Sheep Genomics Consortium 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2013,130(6):468-475
Most published genomewide association studies (GWAS) in sheep have investigated recessively inherited monogenic traits. The objective here was to assess the feasibility of performing GWAS for a dominant trait for which the genetic basis was already known. A total of 42 Manchega and Rasa Aragonesa sheep that segregate solid black or white coat pigmentation were genotyped using the SNP50 BeadChip. Previous analysis in Manchegas demonstrated a complete association between the pigmentation trait and alleles of the MC1R gene, setting an a priori expectation for GWAS. Multiple methods were used to identify and quantify the strength of population substructure between black and white animals, before allelic association testing was performed for 49 034 SNPs. Following correction for substructure, GWAS identified the most strongly associated SNP (s26449) was also the closest to the MC1R gene. The finding was strongly supported by the permutation tree‐based random forest (RF) analysis. Importantly, GWAS identified unlinked SNP with only slightly lower p‐values than for s26449. Random forest analysis indicated these were false positives, suggesting interpretation based on both approaches was beneficial. The results indicate that a combined analytical approach can be successful in studies where a modest number of animals are available and substantial population stratification exists. 相似文献
5.
Withen KB Brüniche-Olsen A Pedersen BV;European Cattle Genetic Diversity Consortium Gravlund P 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2011,128(2):141-152
A phenotypically interesting strain of cattle existed on the small island of Agersoe, on the west coast of Zealand, Denmark, in the beginning of the last decade. The cattle share a great resemblance to the extinct Danish breed, the Island cattle. The objective of this study was to genetically characterize the Agersoe cattle, using microsatellites, amplified fragment length polymorphism (AFLP) and mtDNA markers, and analyse the genetic variability within the breed and the genetic relationship to 14 European breeds with focus on the Red Danish and Jutland breed. The results show diversity in nuclear markers comparable to that of modern breeds and that the Agersoe cattle are separable from the two native breeds. The absence of inbreeding and the degree of genetic diversity are taken as a sign of recent admixture. The Agersoe cattle did not exhibit a consistent association with any of the European breeds. Several arguments based on this survey have been put forward in favour of characterizing the Agersoe cattle as being the last remnants of the Danish Island Cattle. 相似文献
6.
Rhesus Macaque Genome Sequencing Analysis Consortium Gibbs RA Rogers J Katze MG Bumgarner R Weinstock GM Mardis ER Remington KA Strausberg RL Venter JC Wilson RK Batzer MA Bustamante CD Eichler EE Hahn MW Hardison RC Makova KD Miller W Milosavljevic A Palermo RE Siepel A Sikela JM Attaway T Bell S Bernard KE Buhay CJ Chandrabose MN Dao M Davis C Delehaunty KD Ding Y Dinh HH Dugan-Rocha S Fulton LA Gabisi RA Garner TT Godfrey J Hawes AC Hernandez J Hines S Holder M Hume J Jhangiani SN 《Science (New York, N.Y.)》2007,316(5822):222-234
7.
Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China 总被引：1，自引：0，他引：1
Chinese SARS Molecular Epidemiology Consortium 《Science (New York, N.Y.)》2004,303(5664):1666-1669
Sixty-one SARS coronavirus genomic sequences derived from the early, middle, and late phases of the severe acute respiratory syndrome (SARS) epidemic were analyzed together with two viral sequences from palm civets. Genotypes characteristic of each phase were discovered, and the earliest genotypes were similar to the animal SARS-like coronaviruses. Major deletions were observed in the Orf8 region of the genome, both at the start and the end of the epidemic. The neutral mutation rate of the viral genome was constant but the amino acid substitution rate of the coding sequences slowed during the course of the epidemic. The spike protein showed the strongest initial responses to positive selection pressures, followed by subsequent purifying selection and eventual stabilization. 相似文献
8.
The genome of the sea urchin Strongylocentrotus purpuratus 总被引：2，自引：0，他引：2
Sea Urchin Genome Sequencing Consortium Sodergren E Weinstock GM Davidson EH Cameron RA Gibbs RA Angerer RC Angerer LM Arnone MI Burgess DR Burke RD Coffman JA Dean M Elphick MR Ettensohn CA Foltz KR Hamdoun A Hynes RO Klein WH Marzluff W McClay DR Morris RL Mushegian A Rast JP Smith LC Thorndyke MC Vacquier VD Wessel GM Wray G Zhang L Elsik CG Ermolaeva O Hlavina W Hofmann G Kitts P Landrum MJ Mackey AJ Maglott D Panopoulou G Poustka AJ Pruitt K Sapojnikov V Song X Souvorov A Solovyev V Wei Z 《Science (New York, N.Y.)》2006,314(5801):941-952
We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes. 相似文献
9.
Precision Medicine in Cats: Novel Niemann‐Pick Type C1 Diagnosed by Whole‐Genome Sequencing 
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下载免费PDF全文 D.A. Mauler B. Gandolfi C.R. Reinero D.P. O'Brien J.L. Spooner L.A. Lyons and Lives Consortium 《Journal of veterinary internal medicine / American College of Veterinary Internal Medicine》2017,31(2):539-544
State‐of‐the‐art health care includes genome sequencing of the patient to identify genetic variants that contribute to either the cause of their malady or variants that can be targeted to improve treatment. The goal was to introduce state‐of‐the‐art health care to cats using genomics and a precision medicine approach. To test the feasibility of a precision medicine approach in domestic cats, a single cat that presented to the University of Missouri, Veterinary Health Center with an undiagnosed neurologic disease was whole‐genome sequenced. The DNA variants from the cat were compared to the DNA variant database produced by the 99 Lives Cat Genome Sequencing Consortium. Approximately 25× genomic coverage was produced for the cat. A predicted p.H441P missense mutation was identified in NPC1, the gene causing Niemann‐Pick type C1 on cat chromosome D3.47456793 caused by an adenine‐to‐cytosine transversion, c.1322A>C. The cat was homozygous for the variant. The variant was not identified in any other 73 domestic and 9 wild felids in the sequence database or 190 additionally genotyped cats of various breeds. The successful effort suggested precision medicine is feasible for cats and other undiagnosed cats may benefit from a genomic analysis approach. The 99 Lives DNA variant database was sufficient but would benefit from additional cat sequences. Other cats with the mutation may be identified and could be introduced as a new biomedical model for NPC1. A genetic test could eliminate the disease variant from the population. 相似文献
10.
Therése Bengtsson The PPP Barley Consortium Outi Manninen Ahmed Jahoor Jihad Orabi 《Genetic Resources and Crop Evolution》2017,64(8):2021-2033
Genetic diversity, population structure and genome-wide linkage disequilibrium (LD) was estimated in Nordic spring barley (Hordeum vulgare L. subsp. vulgare) by genotyping 180 breeding lines with 48 SSR markers and 7842 high-confidence SNPs using the Illumina Infinium 9K assay. In total 6208 SNPs were polymorphic and selected for further statistical analysis. A Mantel test revealed a strong positive correlation with a Pearson’s correlation coefficient (r) of 0.86, between the estimates of genetic distances based on SSR and SNP data. Population structure analysis identified two groups with a clear ancestry and one group with an admixed ancestry. The groups were primarily separated based on row-type and geographical origin. Average LD for the whole population decayed below a critical level of r2 = 0.20 within a range of 0–4 cM. To avoid confounding effects of the strong population structure, LD decay for the different groups was analysed separately and ranged from 0 to 12 cM. A slower LD decay was found within the two-rowed lines compared to the six-rowed lines and the two-rowed lines originating from the northern part, which could be the result of strong selection for malting quality and yield in the southern part. No large difference in genetic diversity was observed between population sub-groups, but differences at certain chromosomal regions were evident. 相似文献