LDSO: a program to simulate pedigrees and molecular information under various evolutionary forces

Simulations are a major tool to evaluate new statistical methods and optimize experimental designs in the genomic era. However, this can only be achieved when the simulations are close enough to reality, as well as diverse enough to be realistic. For mapping studies, it is thus critical to re-create as much as possible the forces generating linkage (mutation, random drift, changes in population sizes, selection and pedigree structure) and the mechanisms producing trait genetic architecture (additivity, dominance, epistasis). We present here a computer program (ldso) simulating these phenomena. Optional outputs provide statistics on the linkage disequilibrium (LD) structure and the identity by descent between chromosomal segments, facilitating further data analyses. Furthermore, ldso enables the simulation of genomic data in known pedigrees, which sticks as precisely as possible to recent population history and structures of the long-range LD, allowing optimization of fine-mapping strategies.     

Identification of powdery mildew resistance loci in wheat by integrating genome-wide association study(GWAS) and linkage mapping

Wheat powdery mildew(Blumeria graminis f.sp.tritici, Bgt) is a disease of increasing importance globally due to the adoption of high yielding varieties and modern sustainable farming technologies.Growing resistant cultivars is a preferred approach to managing this disease, and novel powdery mildew resistance genes are urgently needed for new cultivar development.A genome-wide association study was performed on a panel of 1292 wheat landraces and historical cultivars using 5011 single nucleotide polymorphism(SNP)markers.The association panel was evaluated for reactions to three Bgt inoculants, OKS(14)-B-3-1, OKS(14)-C-2-1, and Bgt15.Linkage disequilibrum(LD) analysis indicated that genome-wide LD decayed to 0.1 at 23 Mb, and population structure analysis revealed seven subgroups in the panel.Association analysis using a mixed linear model(MLM) identified three loci for powdery mildew resistance on chromosome 2 B, designated QPm.stars-2BL1,QPm.stars-2BL2, and QPm.stars-2BL3.To evaluate the efficacy of GWAS in gene discovery,QPm.stars-2BL2 was validated using F2 and F2:3 populations derived from PI420646 × OK1059060-126135-3.Linkage analysis delimited the powdery mildew resistance gene in PI 420646 to an interval where QPm.stars-2BL2 was located, lending credence to the GWAS results.QPm.stars-2BL1 and QPm.stars-2BL3, which were associated with four SNPs located at 457.7–461.7 Mb and two SNPs located at 696.6–715.9 Mb in the Chinese Spring reference IWGSC RefSeq v1.0, respectively, are likely novel loci for powdery mildew resistance and can be used in wheat breeding to improve powdery mildew resistance.     

Linkage disequilibrium and effective population size in Gir cattle selected for yearling weight

Linkage disequilibrium (LD) plays an important role in genomic selection and mapping of quantitative trait loci (QTL). This study investigated the pattern of LD and effective population size (N_e) in Gir cattle selected for yearling weight. For this purpose, 173 animals with imputed genotypes (from 18 animals genotyped with the Illumina BovineHD BeadChip and 155 animals genotyped with the Bovine LDv4 panel) were analysed. The LD was evaluated at distances of 25–50 kb, 50–100 kb, 100–500 kb and 0.5–1 Mb. The N_e was estimated based on 5 past generations. The r² values (a measure of LD) were, respectively, .35, .29, .18 and .032 for the distances evaluated. The LD estimates decreased with increasing distance of SNP pairs and LD persisted up to a distance of 100 kb (r² = .29). The N_e was greater in generations 4 and 5 (24 and 30 animals, respectively) and declined drastically after the last generation (12 animals). The results showed high levels of LD and low N_e, which were probably due to the loss of genetic variability as a consequence of the structure of the Gir population studied.     

Phylogenetic analysis and genetic mapping of Chinese Hedychium using SRAP markers

In the present study, using the SRAP markers, we analyzed the interspecific phylogenetic relationship of 22 species of Chinese Hedychium to find out fine mapping population. Using the same technique, maps of two species selected by morphological characters were constructed. Phylogenetic analysis showed that 22 species were grouped into three clusters. The mapping parents selected were in one cluster, with a similarity coefficient of 0.31, which is lower than the mean value of 22 species. Two maps with medium-density were constructed. The maternal parent contained 139 loci and spanned 917.1 cM. These loci were distributed in 18 linkage groups. The paternal parent contained 203 loci and spanned 1386.8 cM, which spread over 23 linkage groups. Unfortunately, the number of loci with a segregation ratio of 3:1 was not sufficient for us to link two maps together. For parental selection, we suggested that the phylogenetic relationship as well as complements of characters should be considered. Moreover, our study showed that two species with similarity around or higher than the mean level tend to produce fine mapping population in Hedychium.     

The Estimation about a Type of Disequilibrium Model

A type of disequilibrium quantitative economic model i.e.,an orientation model,that sample may be distinguished is discussed.Also a method of estimation is obtained.And the estimate is unbiased.     

家畜基因组遗传多态标记—微卫星标记研究进展(下)

３微卫星标记的应用自微卫星被发现以来就受到了家畜遗传育种家们的高度重视,并且充分认识到了把它作为畜种的基因组变异研究所具有的巨大的潜在价值。现在它已被十分成功地作为富含信息、又容易获得的基因标记,广泛用于构建物种的遗传连锁图,基因鉴定（基因诊断）、物...     

Molecular genetic characterization of Central European soybean breeding germplasm

Soybean is the most important oilseed and protein crop worldwide, but in Europe, the acreage is comparably low. Thus, Europe strongly depends on imports of soy products and consequently recent efforts aim at expanding the acreage of soybean, particularly in Central Europe. The aim of this study was, therefore, to assist these breeding efforts by characterizing Central European soybean germplasm, employing a genotyping‐by‐sequencing approach yielding 7741 genomewide distributed markers. Our analysis on genetic diversity and population structure revealed that the Central European lines are most closely related to Swiss and Canadian lines and somewhat more distant from the investigated Chinese and US lines. In addition, we analysed patterns of allelic diversity and the extent of linkage disequilibrium. Collectively, our results can assist breeding of Central European soybean and suggest that further progress can be made by crosses among adapted material but a long‐term success also requires introgression of alleles from non‐European germplasm to further broaden the genetic diversity and incorporate novel traits.     

Fine mapping quantitative trait loci under selective phenotyping strategies based on linkage and linkage disequilibrium criteria

In fine mapping of a large‐scale experimental population where collection of phenotypes are very expensive, difficult to record or time‐demanding, selective phenotyping could be used to phenotype the most informative individuals. Linkage analyses based sampling criteria (LAC) and linkage disequilibrium‐based sampling criteria (LDC) for selecting individuals to phenotype are compared to random phenotyping in a quantitative trait loci (QTL) verification experiment using stochastic simulation. Several strategies based on LAC and LDC for selecting the most informative 30%, 40% or 50% of individuals for phenotyping to extract maximum power and precision in a QTL fine mapping experiment were developed and assessed. Linkage analyses for the mapping was performed for individuals sampled on LAC within families and combined linkage disequilibrium and linkage analyses was performed for individuals sampled across the whole population based on LDC. The results showed that selecting individuals with similar haplotypes to the paternal haplotypes (minimum recombination criterion) using LAC compared to random phenotyping gave at least the same power to detect a QTL but decreased the accuracy of the QTL position. However, in order to estimate unbiased QTL parameters based on LAC in a large half‐sib family, prior information on QTL position was required. The LDC improved the accuracy to estimate the QTL position but not significantly compared to random phenotyping with the same sample size. When applying LDC (all phenotyping levels), the estimated QTL effect were closer to the true value in comparison to LAC. The results showed that the LDC were better than the LAC to select individuals for phenotyping and contributed to detection of the QTL.     

构建多层次供求均衡的现代农村金融体系初探

为探讨现代农村金融运行机制,促进农村经济发展,对中国农村金融体系现状、金融供求矛盾和存在的主要问题进行了调研分析,认为中国农村金融表面上是供给量不足的问题,实际上是结构性失衡的问题.针对这些问题,提出了构建多层次供求均衡的现代农村金融体系的一种初步模式.