Methylation potential associated with diet,genotype, protein,and metabolite levels in the Delta Obesity Vitamin Study

Micronutrient research typically focuses on analyzing the effects of single or a few nutrients on health by analyzing a limited number of biomarkers. The observational study described here analyzed micronutrients, plasma proteins, dietary intakes, and genotype using a systems approach. Participants attended a community-based summer day program for 6–14 year old in 2 years. Genetic makeup, blood metabolite and protein levels, and dietary differences were measured in each individual. Twenty-four-hour dietary intakes, eight micronutrients (vitamins A, D, E, thiamin, folic acid, riboflavin, pyridoxal, and pyridoxine) and 3 one-carbon metabolites [homocysteine (Hcy), S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH)], and 1,129 plasma proteins were analyzed as a function of diet at metabolite level, plasma protein level, age, and sex. Cluster analysis identified two groups differing in SAM/SAH and differing in dietary intake patterns indicating that SAM/SAH was a potential marker of nutritional status. The approach used to analyze genetic association with the SAM/SAH metabolites is called middle-out: SNPs in 275 genes involved in the one-carbon pathway (folate, pyridoxal/pyridoxine, thiamin) or were correlated with SAM/SAH (vitamin A, E, Hcy) were analyzed instead of the entire 1M SNP data set. This procedure identified 46 SNPs in 25 genes associated with SAM/SAH demonstrating a genetic contribution to the methylation potential. Individual plasma metabolites correlated with 99 plasma proteins. Fourteen proteins correlated with body mass index, 49 with group age, and 30 with sex. The analytical strategy described here identified subgroups for targeted nutritional interventions.

Electronic supplementary material

The online version of this article (doi:10.1007/s12263-014-0403-9) contains supplementary material, which is available to authorized users.     

Genetic drift on networks: ploidy and the time to fixation

Genetic drift in finite populations ultimately leads to the loss of genetic variation. This paper examines the rate of neutral gene loss for a range of population structures defined by a graph. We show that, where individuals reside at fixed points on an undirected graph with equal degree nodes, the mean time to loss differs from the panmictic value by a positive additive term that depends on the number of individuals (not genes) in the population. The effect of these spatial structures is to slow the time to fixation by an amount that depends on the way individuals are distributed, rather than changing the apparent number of genes available to be sampled. This relationship breaks down, however, for a broad class of spatial structures such as random, small-world and scale-free networks. For the latter structures there is a counter-intuitive acceleration of fixation proportional to the level of ploidy.     

Genetic associations and serum paraoxonase levels with atherosclerosis in western Iranian patients

Molecular Biology Reports - The oxidative modification of low-density lipoprotein (LDL) in the arterial wall plays a pivotal role in the initiation and progression of atherosclerosis which is a...     

Genetic variation in immune parameters and associations to survival in Atlantic salmon

Lysozyme activity, haemolytic activity, total level of IgM, and levels of antibodies against A-layer from Aeromonas salmonicida and O-antigen from Vibrio salmonicida , respectively, were determined in 77 full-sib groups of Atlantic salmon in order to evaluate their possible use as immune parameters for indirect selection to improve disease resistance. Fish from parallel full-sib groups had previously been challenged with Aeromonas salmonicida (causing furunculosis), Renibacterium salmoninarum (causing bacterial kidney disease, BKD) and Vibrio salmonicida (causing cold-water vibriosis). Heritabilities were estimated for each of the immune parameters and correlations between the least square means of the full-sib groups for the different immune parameters and survival rates in the parallel full-sib groups were determined. A significant genetic variation in lysozyme activity was found, as well as an apparent genetic association between low lysozyme activity and high survival rates. Low heritabilities and low univariate correlations with survival in the full-sib groups were estimated for all of the other immune parameters. An analysis of the multivariate associations between the full-sib mean values of the complete set of immune parameters, and survival rates in the parallel full-sib groups in each of the challenge tests, revealed that, at low levels of lysozyme activity and with low antibody titres against V. salmonicida O-antigen, increased IgM levels seemed to increase survival from furunculosis.     

Multiple QTLs influencing triglyceride and HDL and total cholesterol levels identified in families with atherogenic dyslipidemia

We conducted a genome-wide scan using variance components linkage analysis to localize quantitative-trait loci (QTLs) influencing triglyceride (TG), high density lipoprotein-cholesterol (HDL-C), low density lipoprotein-cholesterol, and total cholesterol (TC) levels in 3,071 subjects from 459 families with atherogenic dyslipidemia. The most significant evidence for linkage to TG levels was found in a subset of Turkish families at 11q22 [logarithm of the odds ratio (LOD)=3.34] and at 17q12 (LOD=3.44). We performed sequential oligogenic linkage analysis to examine whether multiple QTLs jointly influence TG levels in the Turkish families. These analyses revealed loci at 20q13 that showed strong epistatic effects with 11q22 (conditional LOD=3.15) and at 7q36 that showed strong epistatic effects with 17q12 (conditional LOD=3.21). We also found linkage on the 8p21 region for TG in the entire group of families (LOD=3.08). For HDL-C levels, evidence of linkage was identified on chromosome 15 in the Turkish families (LOD=3.05) and on chromosome 5 in the entire group of families (LOD=2.83). Linkage to QTLs for TC was found at 8p23 in the entire group of families (LOD=4.05) and at 5q13 in a subset of Turkish and Mediterranean families (LOD=3.72). These QTLs provide important clues for the further investigation of genes responsible for these complex lipid phenotypes. These data also indicate that a large proportion of the variance of TG levels in the Turkish population is explained by the interaction of multiple genetic loci.     

Genetic structure,allozyme-habitat associations and reproductive fitness in Gypsophila fastigiata (Caryophyllaceae)

Relationships between allozyme differentiation, habitat variation and individual reproductive success were examined in local populations of a perennial herb, Gypsophila fastigiata, on the Baltic island of Öland (Sweden). Relatively little (c. 2%) of the total allozyme diversity in this largely outcrossing species is explained by differentiation between sites tens of kilometres apart. The low level of geographic differentiation suggests that gene flow between sites is, or has recently been, extensive. Yet the component of allozyme diversity due to differentiation between plots (only tens of meters apart) within sites is 3 times larger than the between-site component of diversity. Allozyme variation, especially at the Pgi-2 locus, is significantly associated with habitat variation within sites. Different allele x habitat combinations for the Pgi-2 locus are associated with differences in individual reproductive fitness. Differential selection in different local habitats may thus contribute to the fine-scale structuring of genetic diversity within sites.     

Genetic diversity and environmental associations of wild wheat,Triticum dicoccoides,in Israel

Summary Allozyme variation in the tetraploid wild progenitor of wheat, Triticum dicoccoides, was studied for the proteins encoded by about 50 gene loci in 457 individuals representing 12 populations from Israel. Six spikelet morphological traits were measured in the same populations. The results indicate that: (a) 16 loci (= 32%) were monomorphic in all 12 populations, 15 loci (= 30%) were locally polymorphic, and 19 loci (= 38%) were regionally polymorphic. All polymorphic loci (but one) displayed high levels of polymorphism ( 10%). In Israel, the proportion of polymorphic loci per population, P, in wild wheat averaged 0.25 (range, 0.16–0.38), and the genetic diversity index, H_e averaged 0.07, (range, 0.03 – 0.12). (b) Altogether there were 110 alleles at the 50 putative loci tested (c) Genetic differentiation of populations included regional and local patterns: (i) The coefficients of genetic distance between populations were high (mean D = 0.10 range, 0.02 – 0.25), and indicated sharp genetic differentiation over short distances, (ii) Common ( 10%) but sporadic and localized alleles were frequent (76%), and (iii) Rare alleles were few (only 5 alleles). (d) The patterns of allozyme and spikelet variation in the wild gene pool were significantly correlated with, and partly predictable by, water factors, including those of precipitation, evaporation, and relative humidity as well as of soil type, (e) All six spikelet characters showed statistically significant variation among localities and (f) Allozymic variation was correlated with spikelet variation.These results suggest in T. dicoccoides: (i) the operation of natural selection in population genetic structure, (ii) local adaptive genetic differentiation caused by diversifying selection through climate and soil, and (iii) the guidelines for sampling these resources for use in wheat breeding programs.     

Genetic loci for blood lipid levels identified by linkage and association analyses in Caribbean Hispanics

To identify genetic loci influencing blood lipid levels in Caribbean Hispanics, we first conducted a genome-wide linkage scan in 1,211 subjects from 100 Dominican families on five lipid quantitative traits: total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), high density lipoprotein cholesterol (HDL-C), triglycerides (TG), and LDL-C/HDL-C ratio. We then investigated the association between blood lipid levels and 21,361 single nucleotide polymorphisms (SNP) under the 1-logarithm of odds (LOD) unit down regions of linkage peaks in an independent community-based subcohort (N = 814, 42% Dominican) from the Northern Manhattan Study (NOMAS). We found significant linkage evidence for LDL-C/HDL-C on 7p12 (multipoint LOD = 3.91) and for TC on 16q23 (LOD = 3.35). In addition, we identified suggestive linkage evidence of LOD > 2.0 on 15q23 for TG, 16q23 for LDL-C, 19q12 for TC and LDL-C, and 20p12 for LDL-C. In the association analysis of the linkage peaks, we found that seven SNPs near FLJ45974 were associated with LDL-C/HDL-C with a nominal P < 3.5 × 10(-5), in addition to associations (P < 0.0001) for other lipid traits with SNPs in or near CDH13, SUMF2, TLE3, FAH, ARNT2, TSHZ3, ZNF343, RPL7AL2, and TMC3. Further studies are warranted to perform in-depth investigations of functional genetic variants in these regions.     

Ecogeographical distribution and differential adaptedness of multilocus allelic associations in Spanish Avena sativa L.

We determined the nine-locus isozyme genotype of 267 landrace accessions of Avena sativa from 31 provinces of Spain. Our results establish that level of genetic variability is usually high both within and among accessions of this heavily self-fertilizing hexaploid grass and that multilocus genetic structure differs in various ecogeographical regions of Spain. We concluded that selection favoring different multilocus genotypes in different environments was the main integrating force that shaped the internal genetic structure of local populations as well as the overall adaptive landscape of A. sativa in Spain. Implications in genetic resource conservation and utilization are discussed.     

Genetic diversity in Australian wheat varieties and breeding material based on RFLP data

 Restriction fragment length polymorphisms (RFLPs) have been used to characterise the genetic diversity of wheat (Triticum aestivum) germplasm. One hundred and twenty-four accessions comprising all major Australian wheat varieties and lines important for breeding purposes were assayed for RFLPs with clones of known genetic location and selected to give uniform genome coverage. The objectives of this study were to determine RFLP-based genetic similarity between accessions and to derive associations between agronomically significant traits and RFLP phenotypes. Ninety-eight probes screened against genomic DNA digested with five restriction endonucleases detected a total of 1968 polymorphic fragments. Genetic similarity (GS) calculated from the RFLP data ranged from 0.004 to 0.409 between accessions, with a mean of 0.18. Cluster analysis based on GS estimates produced four groupings that were generally consistent with available pedigree information. Comparisons of the RFLP phenotypes of accessions containing disease resistance genes present on introgressed alien segments enabled the identification of specific alleles characteristic of these regions. Associations were derived for a range of stem-rust, leaf-rust and yellow-rust resistance genes. These results suggest that RFLP analysis can be used for the characterisation and grouping of elite breeding material of wheat and RFLP profiling can identify chromosome segments associated with agronomic traits. Received: 10 March 1997 / Accepted: 28 July 1997     

Systems Biology in Aging: Linking the Old and the Young

Aging can be defined as a process of progressive decline in the physiological capacity of an organism, manifested by accumulated alteration and destabilization at the whole system level. Systems biology approaches offer a promising new perspective to examine the old problem of aging. We begin this review by introducing the concepts of systems biology, and then illustrate the application of systems biology approaches to aging research, from gene expression profiling to network analysis. We then introduce the network that can be constructed using known lifespan and aging regulators, and conclude with a look forward to the future of systems biology in aging research. In summary, systems biology is not only a young field that may help us understand aging at a higher level, but also an important platform that can link different levels of knowledge on aging, moving us closer to a more comprehensive control of systematic decline during aging.     

分蘖型谷子资源的表型和遗传多样性分析

本研究选用了来自国外及国内的68份分蘖型谷子进行了表型及遗传多样性分析。表型分析表明,质量性状以绿鞘、白谷黄米、圆锥穗、松散穗码居多,数量性状变异系数除出谷率较小外,其他性状表现了丰富的遗传变异,来自山西的小软谷单株穗重、单株穗粒重、千粒重均为最高,而来自黑龙江的大青谷单株穗粒重、出谷率、千粒重均为最低。遗传多样性分析结果表明,77对引物共检测出202个等位位点,每对引物可检测到1~6个位点不等,平均为2.62个;77对引物多态性信息含量(PIC)在0.0283~0.6974之间,平均多态性信息量(PIC)为0.4169,68份材料间的遗传相似系数变化范围为0.59~0.96,平均值为0.68。利用软件NTSYSpc 2.10的UPGMA聚类方法对68份谷子分蘖材料进行了聚类,这些材料被划分为4个类群,即Ⅰ、Ⅱ、Ⅲ和Ⅳ。Ⅰ类群主要来自西北地区谷子分蘖种质,Ⅱ类群主要来自国外谷子分蘖种质,Ⅲ类群包括华北、华东和东北的谷子分蘖种质,Ⅳ类群仅包括一个种质。结合表型鉴定出10份优势谷子分蘖种质。这些结果揭示68份谷子分蘖种质遗传多样性较好,研究结果为挖掘谷子分蘖优良基因及谷子分蘖育种提供理论依据。     

Genetic diversity and multilocus associations in Cunninghamia lanceolata (Lamb.) Hook from The People's Republic of China

Open-pollinated seeds were assayed for allozyme polymorphisms at 24 loci to assess genetic diversity and multilocous associations in 16 populations of Cunninghamia lanceolata (Lamb.) Hook in the People's Republic of China. On average, the percentage of polymorphic loci was 88.0, the number of alleles per locus was 3.0, and the expected heterozygosity was 0.394. The distribution of genetic diversity was not correlated with the geographic and climatic variables of the populations. However, allele frequencies correlated linearly with the mean annual temperature of the populations at Mdh-1, Mdh-2, Mnr-2, Pgi-1, and Skdh-1 and with the altitude of the populations at Aph-4 and 6Pg-2. Of the total gene diversity 6% was attributed to among-population differentiation; 94% resided within populations. Two-locus gametic disequilibria were found in 15 of the 16 populations, and higher-order gametic disquilibria were significant in most populations. The gametic disequilibria did not correlate with geographic and climatic variables. The results suggest that population subdivision, founder effect, occurrence across diverse environments, a mating system dominated by inbreeding, and historical events from 2000 years of cultivation are contributing factors in the generation and maintenance of the multilocus genetic structure in this conifer.     

花生表型及SSR遗传多样性的研究

对山西省农业科学院经济作物研究所保存的75份花生材料(包括28个已审定的花生品种和47个地方品种)进行了包括株型、茸毛的有无、叶色、粒形、叶形、生长习性、开花习性、粒大小、粒色等表型性状的Shannon-Weaver遗传多样性指数(简称SWI)和Simpson遗传多样性指数(简称SI)分析。结果表明:参试的75份花生品种遗传多样性指数分别为SWI=0.924,SI=0.500,其中以开花习性最低(SWI=0.139,SI=0.014),而Shannon-Weaver指数以粒色最高为1.841,Simpson指数为0.712。利用48对SSR引物对这些材料进行了遗传多样性分析,结果如下:(1)在48对花生的SSR引物中,有35对(占所用引物总数的72.9%)具有多态性,共检测到215条多态性条带,平均每对引物可扩增6条多态性带。(2)根据SSR扩增结果对75份材料的聚类分析结果表明,这些材料的相似系数(GS)为0.25～0.85,平均GS值为0.55。28个审定品种的相似系数为0.39～0.85,平均为0.60。     

Donor Perspectives on Issues Associated with Donation of Genetic Samples and Information: An Australian Viewpoint

This paper provides a legal overview of key issues associated with donation of genetic samples and information from a donor perspective. In particular, it addresses the property status of samples as well as issues in respect of consent, privacy, commercialisation and benefit sharing. The paper highlights the need for appropriate protection and safeguards for individuals, but also, importantly, for understanding what donors actually think and want in terms of genetic research and the use of their samples and information. The paper seeks to emphasise the importance of transparency and accountability in the conduct of research in order to maximise donor participation and confidence and public trust in general.

水稻籽粒矿质元素含量遗传及主要农艺性状相关性分析

通过了解水稻子粒钙、镁、铜、铁、锌和硒等矿质元素含量,以绿旱1号作为父本与102S、KD36S、7HS012及7HS013不育系为母本进行配组,对父本与杂交后代主要农艺及经济性状、水稻子粒中的矿质元素含量进行了遗传分析,并对各杂交后代的主要农艺性状和子粒中矿质元素含量以及各矿质元素含量间进行了相关性分析.结果表明,杂交后代农艺及经济性状多数表现出超高亲分离现象,且LK3的农艺及经济性状均表现为最好.水稻子粒矿质元素含量与部分农艺和经济性状存在明显的正相关或负相关关系,且K、Mg、Zn、Se等元素含量与水稻产量密切相关.水稻子粒中矿质元素含量大小依次为P＞K ＞Mg ＞S＞ Ca＞ Mn ＞Fe ＞Zn ＞Cu ＞Se,4个杂交后代的K元素含量表现出超高亲分离现象,LK2、LK3和LK4的Fe元素含量也表现出超高亲分离现象.水稻子粒大量与微量元素之间相关性最高,微量元素之间相关性次之,大量元素之间相关性最小,以7HS012不育系为母本得到的杂交后代农艺性状表现较好,矿质元素含量最高,7HS013次之,其他不育系表现一般.本研究为选育出耐旱及营养价值高的水稻新品种母本的选择提供了理论依据.     

北方冬麦区小麦抗旱种质资源遗传多样性分析

遗传多样性分析对于作物资源评价和利用具有重要的意义。本研究以我国北方冬麦区136份小麦抗旱种质资源为材料,分析10个农艺性状及其耐旱指数的相关性,以及抗旱种质的遗传多样性。结果表明:在雨养和灌溉条件下,穗叶距的变异系数最高,分别为42.1%和37.2%,单穗总小穗数的变异系数最低,为6.4%和5.7%;不同水分条件下,植株稳产性主要受单株穗数、有效小穗数及穗下节长的影响;性状耐旱指数的多样性指数在1.95到2.07之间变化,平均值为2.02;根据性状耐旱指数将供试材料分为7个类群,其中第I、第III类群材料表现为对水分条件不敏感,而第II类群材料更适于在干旱条件下种植。材料之间的抗旱性差异可以作为抗旱育种中亲本选配的依据。     

云南甘蔗细茎野生种82-114测交后代主要性状遗传分析

利用云南甘蔗细茎野生种82-114(简称:云割82-114)为父本,与甘蔗栽培原种、生产品种和含野生血缘F1等3类亲本进行测交.对后代锤度、茎径、株高、有效茎、蔗产量等5个主要数量性状进行方差、遗传力和配合力分析,结果表明:①组合后代锤度、茎径、株高、有效茎4个性状差异极显著;②组合后代锤度、茎径、株高、有效茎的遗传力表现较突出,均超89.0%;③3类组合中,栽培原种×云割82.114后代有效茎配合力表现明显的正效应,生产品种×云割82-114后代锤度、茎径、株高、蔗产量配合力有比较明显的正效应,舍野生血缘F1×云割82-114后代锤度、茎径、株高、有效茎、蔗产量等5个指标的配合力效应取向不明显.     

Genetic variation in constitutive and inducible pyrrolizidine alkaloid levels inCynoglossum officinale L.

The constitutive pyrrolizidine alkaloid (PA) concentration of both shoots and roots differed significantly between 17 selfed families. The broad-sense heritability accounted for 33–43% of the variation in PA levels. Families also differed significantly in the amount and the direction of PA induction in both shoots and roots, 24 h after punching 15 holes in the leaves. We found a significantly negative relationship between the changes in PA content of the shoots and changes in PA content of the roots. The total PA content of the plants did not increase. We thus concluded that changes in PA distribution over the plant resulted from transport of PAs within the plant. The direction of transport differed between families: some transported PAs to the shoots, others to the roots. This makes it questionable whether PAs act as damage-induced defences. The effect of damage on the PA concentration is far less than the differences found between families in the constitutive PA concentration. This again strongly suggests that damage-induced defences inCynoglossum officinale do not play an important role. We argue that the general lack of attention that is given to genotype in induction experiments, has led to false conclusions.