Single-parent segregant pools for allocation of markers to a specified chromosomal region in outcrossing species

Bulked co-segregant analysis is a method of rapidly allocating unmapped genetic markers to a specific chromosomal region. Although originally developed for utilization in populations derived from crosses between fully inbred lines, it has been proposed that co-segregant pools could also serve the same purpose in outbreeding populations, if individuals from only a single large family are pooled. Large, fully mapped, single-sire backcross and half-sib families are presently available as part of the international chicken and bovine reference family panels respectively. In this study, power and tests of significance for single-parent co-segregant analysis are derived for full-sib, single-parent back-cross and single-parent half-sib families, as a function of proportion of recombination between index marker and linked marker, proportion of single-parent alleles among the mates, number of individuals in each segregant pool and technical error variance. Power was found to be greater than 0–80 for many reasonable parameter combinations. The method is illustrated using microsatellite markers and a large single-sire bovine family, part of the international bovine reference family panel.     

Logical Structures of Young Chimpanzees' Spontaneous Object Grouping

I investigated sensorimotor precursors of logicoarithmetic operations involved in spontaneous object grouping of five common chimpanzees aged 1 to 4 years. I considered three basic logical relations between objects or sets of objects: equivalence, order, and reversibility relations. Chimpanzees introduced equivalence and order relations within sets of objects as well as between sets. They showed a higher level of logical organization than monkeys do. Compared to human infants, chimpanzees manifested a specific difference and a specific delay. First, chimpanzees only partially mapped the logical properties of their action organization on sets of objects. For example, chimpanzees' simultaneous acts on two sets of objects, though increasing with age, almost never resulted in spatial correspondences between the sets. Secondly, they showed a specific delay in that they produced scarcely any form of reversibility.     

A repeated measures approach to pooled and calibrated biomarker data

Participant-level meta-analysis across multiple studies increases the sample size for pooled analyses, thereby improving precision in effect estimates and enabling subgroup analyses. For analyses involving biomarker measurements as an exposure of interest, investigators must first calibrate the data to address measurement variability arising from usage of different laboratories and/or assays. In practice, the calibration process involves reassaying a random subset of biospecimens from each study at a central laboratory and fitting models that relate the study-specific “local” and central laboratory measurements. Previous work in this area treats the calibration process from the perspective of measurement error techniques and imputes the estimated central laboratory value among individuals with only a local laboratory measurement. In this work, we propose a repeated measures method to calibrate biomarker measurements pooled from multiple studies with study-specific calibration subsets. We account for correlation between measurements made on the same person and between measurements made at the same laboratory. We demonstrate that the repeated measures approach provides valid inference, and compare it to existing calibration approaches grounded in measurement error techniques in an example describing the association between circulating vitamin D and stroke.     

A genome‐wide association study using selective DNA pooling identifies candidate markers for fertility in Holstein cattle

The decline in the reproductive efficiency of dairy cows, especially those with high producing potential, has become a challenging problem. In this study, a selective DNA pooling approach was applied to a cow population whose oocytes were fertilized and cultured to obtain phenotypic records of fertilization rate and blastocyst rate. Using a stringent 5% genome‐wide significance level, 22 and five single nucleotide polymorphisms (SNPs) were found to be associated with fertilization rate and blastocyst rate, respectively. SNPs that showed significant association in selective DNA pooling were further evaluated by individual genotyping. Interestingly, the majority of the SNP associations were confirmed by individual genotyping, testifying to the effectiveness of selective DNA pooling using a high‐density SNP genotyping array. This study is the first application of the selective DNA pooling approach using the BovineSNP50 array in cattle.     

福建漳州青花菜栽培钾肥施用技术优选

以青花菜品种‘炎秀’Brassica oleracea var．italica ‘yanxiu’为材料,通过设置钾肥横向与纵向施肥的田间试验,探讨青花菜最佳钾肥用量和最佳钾肥运筹。结果表明,在设定氮、磷肥施用量分别为30.0 kg/667.7 m2、10.0 kg/667.7 m2的条件下,钾肥不同施用量对青花菜的株高、苗期功能叶片数、植株扩展度及全株重（去根）、单球重均有一定的影响,当钾肥施用量为19.1 kg/667.7 m2时,其产量最高,为1763.5 kg/hm2;在同样氮、磷肥的背景条件下,钾肥施用量以15.0 kg/667.7 m2,按基肥/追肥不同比例进行施用,青花菜所表现的株高、苗期功能叶片数、植株扩展度及全株重、单球重等形态及产量指标均有所差异,当基肥∶追肥按0.2∶0.8进行施用时,该产量指标均明显高于其它配比的处理。     

石器研究中“操作链”的概念、内涵及应用

作为旧石器研究中十分重要的研究概念之一, 本文对"操作链"的发展史、理论内涵、实践方法等方面进行讨论, 认为"操作链"概念是一种动态的、综合的理论视角和研究体系, 强调了石器技术系统的两个行为过程(技术表现与思维运作)和一个互动关系(操作序列)。实践应用和术语对比, 为更好地运用"操作链"研究石器并复原史前技术体系提供了参考。文章还提出了"操作链"概念本身存在的问题, 希望能在今后的工作中得到完善。     

Isolation and characterization of microsatellite loci in the ant Myrmica scabrinodis

Five polymorphic microsatellite loci were developed for the ant Myrmica scabrinodis using a magnetic bead hybridization selection protocol. The number of alleles per locus varied between three and six. Cross‐species amplification of four of the loci yielded positive amplification products in four Myrmica species, suggesting their general suitability for microsatellite analysis within this taxonomic group.     

两种混合样品策略对揭示杜鹃花根部真菌多样性的影响

由于土壤微生物群落物种组成的高度空间异质性,混合样品(sample pooling)被广泛应用于微生物多样性与群落结构研究。在根部真菌的分子检测中,样品混合策略以及测序的克隆数或序列数均对揭示真菌群落结构的准确性有影响。【目的】为建立一套能快速准确地反映杜鹃花属植物根部真菌的物种组成与群落结构的分子检测技术平台,【方法】本研究采集锈红杜鹃和亮鳞杜鹃多份根系样品分别提取DNA,比较PCR扩增前和扩增后混合策略构建的克隆文库中真菌物种组成的差异。【结果】在2种宿主植物根系中,多份样品在PCR扩增后混合构建的克隆文库检测到的根部真菌物种丰富度、真菌群落的Shannon-Wiener多样性指数均高于扩增前混合的克隆文库。高频度的根部真菌在2种克隆文库中均检测到,但低频度的真菌物种组成在2种克隆文库中完全不同。更重要的是,当采用广泛应用的真菌通用引物ITS1f和ITS4扩增根部真菌ITS序列时,PCR扩增后混合的方法能有效地减轻杜鹃花属植物ITS序列被优先扩增的现象。真菌物种累积曲线显示,当测序的真菌ITS片段克隆数达到50个左右,即能较全面地反映2种杜鹃花根部真菌物种组成。【结论】独立扩增多份根系样品DNA,再将PCR产物混合构建克隆文库的方法能更全面地揭示杜鹃花属植物根部真菌物种丰富度与物种组成。     

Estimation of relative allele frequencies of single-nucleotide polymorphisms in different populations by microarray hybridization of pooled DNA

Single-nucleotide polymorphisms (SNPs) are considered useful polymorphic markers for genetic studies of polygenic traits. A new practical approach to high-throughput genotyping of SNPs in a large number of individuals is needed in association study and other studies on relationships between genes and diseases. We have developed an accurate and high-throughput method for determining the allele frequencies by pooling the DNA samples and applying a DNA microarray hybridization analysis. In this method, the combination of the microarray, DNA pooling, probe pair hybridization, and fluorescent ratio analysis solves the dual problems of parallel multiple sample analysis, and parallel multiplex SNP genotyping for association study. Multiple DNA samples are immobilized on a slide and a single hybridization is performed with a pool of allele-specific oligonucleotide probes. The results of this study show that hybridization of microarray from pooled DNA samples can accurately obtain estimates of absolute allele frequencies in a sample pool. This method can also be used to identify differences in allele frequencies in distinct populations. It is amenable to automation and is suitable for immediate utilization for high-throughput genotyping of SNP.