Replication and refinement of a quantitative trait locus influencing milk protein percentage on ovine chromosome 3

A previous genome scan that was conducted in Spanish Churra sheep identified a significant quantitative trait locus (QTL) for milk protein percentage (PP) on chromosome 3 (OAR3), between markers KD103 and OARVH34. The aim of this study was to replicate these results and to refine the mapped position of this QTL. To accomplish this goal, we analysed 14 new half‐sib families of Spanish Churra sheep including 1661 ewes from 29 different flocks. These animals were genotyped for 21 microsatellite markers mapping to OAR3. In addition to a classical linkage analysis (LA), a combined linkage disequilibrium and linkage analysis (LDLA) was performed with the aim of enhancing the resolution of the QTL mapping. The LA that was performed in this sheep population identified the presence of a highly significant QTL for PP near marker KD103 (P_c < 0.001; P_exp < 0.001). The phenotypic variance that was owing to the QTL was 2.74%. Two segregating families for the target QTL were identified in this population with QTL effect estimates of 0.47 and 0.95 SD. The LDLA identified the same QTL as the previous analyses with a high level of statistical significance (P = 9.184 E‐11) and narrowed the confidence interval (CI) to a 13 cM region. These results confirm the segregation of the previously identified OAR3 QTL that influences PP in Spanish Churra sheep. Future research will aim to increase the marker density across the refined CI and to analyse the corresponding candidate genes to identify the allelic variant or variants that underlie this genetic effect.     

两种常用数量性状连锁分析方法的原理和进展

在复杂性状疾病的家系连锁研究中,Haseman-Elston回归分析和方差组成模型是常用的两种数量性状连锁分析方法。前者主要针对同胞对的性状值差或和的平方进行回归分析;后者引用方差组成模型,将数量性状分解为遗传方差和环境方差,可估计二者对表型的影响。两种方法可应用于同胞对、核心家系或扩展家系,定位数量性状基因座。本文对这两种模型的原理、算法及其进展进行了综述,并给出了常用的统计软件包。Abstract：In this article, we discussed two model-free methods for detecting genetic linkage for quantitative traits, Haseman-Elston regression approach and variance components approach. The former is a regression approach for detecting linkage based on the squared difference or squared sums in quantitative trait values of sib-pairs and their estimated marker IBD scores. The latter can jointly model covariate effects along with variance components, including genetic component and non-genetic sources of variability. We have outlined the model assumption, the algorithm and the extensions for the both methods.     

关联分析及其在植物遗传学研究中的应用

植物的很多重要经济性状均属于复杂性状。基于连锁分析的QTL作图是研究复杂性状的有效手段, 但其尚存在一定的局限性。随着现代生物学的发展, 一种基于连锁不平衡的新剖分复杂性状方法--关联分析法, 开始应用于植物遗传学研究。与QTL作图法相比, 应用关联分析法具有不需要构建特殊的群体, 可同时对多个等位基因进行分析, 定位QTL精度可达到单基因水平等优势。该文介绍了关联分析方法学的基础和特性, 简述了其在植物遗传学研究中的进展情况, 并对其未来发展和在植物遗传学研究中的应用进行了展望。     

Distribution of clonal growth forms in wetlands

Clonal multiplication is a predominant type of reproduction in wetland species. However, both wetlands and plant organs of clonal growth are diverse, thus due to different stress factors operating in various wetlands preponderance of plants with specific clonal growth organs (CGOs) can be expected. To test this hypothesis the CGO spectra of wetland communities of the Netherlands were analysed, including a bog, a fen, heathland, a floodplain, river beds, fresh water pools, open salt water and a salt marsh. Moreover, it was evaluated whether different CGOs are characterised by different functional traits (shoot cyclicity, persistence of connections between ramets, number of offspring produced per year and lateral spread per year) in wetland species. Data on types of CGO, i.e., epigeogenous and hypogeogenous rhizomes, fragments and budding plants, stolons, tubers and bulbs, root-splitters, root-sprouters and special adaptations (turions) as well as their functional traits, were taken from the CLO-PLA 3 database. CGO spectra of wetland communities were analysed using two methods: comparison of observed vs. expected CGO spectra based on the presence/absence data and multivariate analysis (CCA) for inter-community differences considering species frequency. Moreover, relationships between CGOs and their functional traits were tested using multidimensional contingency tables. Apart from 26% of non-clonal species, the majority of wetland species was rhizomatous (51%). Other types of CGO were represented in less than 10% of species and root-derived CGOs were underrepresented (<2%) in comparison with terrestrial habitats. Among communities, fresh water pools and open salt water hosted higher proportion of species with fragments (∼10%) and turions (∼30%). Multivariate analysis divided wetland communities along the disturbance and hydric (water) gradients. Highly disturbed communities (salt marshes) were characterised by non-clonal species and species with root-derived CGOs. Aquatic communities (fresh water pools and open salt water) hosted species with the ability to spread by fragmentation and turions, contrary to permanently wet communities (bog and wet heathland) with the prevalence of species with epigeogenous rhizomes. It was also confirmed that the CGOs of wetland species differed in their traits. The most important functional trait characterising individual CGOs in the wetland flora was the degree of lateral spread (explained variability: 53%) followed by duration of persistence of connections between ramets (explained variability: 74%), which is in accordance with earlier distinguished strategies of clonal growth: integrator/splitter and spreading/non-spreading clones.     

关联分析及其在植物遗传学研究中的应用

植物的很多重要经济性状均属于复杂性状。基于连锁分析的QTL作图是研究复杂性状的有效手段,但其尚存在一定的局限性。随着现代生物学的发展,一种基于连锁不平衡的新剖分复杂性状方法——关联分析法,开始应用于植物遗传学研究。与QTL作图法相比,应用关联分析法具有不需要构建特殊的群体,可同时对多个等位基因进行分析,定位QTL精度可达到单基因水平等优势。该文介绍了关联分析方法学的基础和特性,简述了其在植物遗传学研究中的进展情况,并对其未来发展和在植物遗传学研究中的应用进行了展望。     

Genetic mapping of quantitative trait loci for resistance to Haemonchus contortus in sheep

This paper presents results from a mapping experiment to detect quantitative trait loci (QTL) for resistance to Haemonchus contortus infestation in merino sheep. The primary trait analysed was faecal worm egg count in response to artificial challenge at 6 months of age. In the first stage of the experiment, whole genome linkage analysis was used for broad-scale mapping. The animal resource used was a designed flock comprising 571 individuals from four half-sib families. The average marker spacing was about 20 cM. For the primary trait, 11 QTL (as chromosomal/family combinations) were significant at the 5% chromosome-wide level, with allelic substitution effects of between 0.19 and 0.38 phenotypic standard deviation units. In general, these QTL did not have a significant effect on faecal worm egg count recorded at 13 months of age. In the second stage of the experiment, three promising regions (located on chromosomes 1, 3 and 4) were fine-mapped. This involved typing more closely spaced markers on individuals from the designed flock as well as an additional 495 individuals selected from a related population with a deeper pedigree. Analysis was performed using a linkage disequilibrium–linkage approach, under additive, dominant and multiple QTL models. Of these, the multiple QTL model resulted in the most refined QTL positions, with resolutions of <10 cM achieved for two regions. Because of the moderate size of effect of the QTL, and the apparent age and/or immune status specificity of the QTL, it is suggested that a panel of QTL will be required for significant genetic gains to be achieved within industry via marker-assisted selection.     

Role of Genetic Factors in the Etiopathogenesis of Cerebrovascular Accidents: From an Animal Model to the Human Disease

1. The present work summarizes current knowledge on the genetic susceptibility to stroke, a complex cardiovascular phenotypic trait due to both gene/environment and gene/ gene interactions. 2. Evidence for the existence of genes directly contributing to stroke occurrence was first obtained in the animal model of the stroke-prone (sp) spontaneously hypertensive rat (SHR) through a linkage analysis approach in F2 segregating hybrid populations. In fact, several Quantitative Trait Loci (QTLs) were detected in different chromosomes of the rat. Candidate genes were identified (ANP, BNP, Adrenomedullin) and subsequently analyzed to obtain information on the fine disease mechanisms possibly dependent from specific sequence mutations. 3. The most important achievement was represented by the fact that the gene encoding ANP appeared to play a role in the disease of both rats and humans, thus providing a suggestive parallelism between the animal model and the human cerebrovascular disease. A more extensive analysis is required to identify the potential pathogenic role of genetic factors involved in human stroke.     

Changes in organ growth ofChenopodium rubrum due to suboptimal and multiple photoperiodic cycles with and without flowering effect

The growth changes of cotyledons, leaves, hypocotyls and roots due to photoperiodic induction in short day plantChenopodium rubrum were investigated in relation to flowering. Six-day old plants were induced by photoperiods with a different number of dark hours. We found that the degree of inhibition which occurred during induction in the growth of leaves, cotyledons and roots similarly as the stimulation of hypocotyl is proportional to the length of dark period. The photoperiods with 12, 16 and 20 dark hours bring about marked inhibition of growth and at the same time induce flowering in terminal and axillary meristems. The inhibitory effect of critical period for flowering,i.e. 8 dark hours, is not apparent in all criteria used and even the flower differentiation is retarded. The photoperiods of 4 and 6 dark hours did not affect growth and were ineffective in inducing flowering even if their number has been increased. The experiments with inductive photoperiod interrupted by light break have clearly shown that growth pattern characteristic for induced plants can be evoked in purely vegetative ones. Such statement did not exclude the possible importance of growth inhibition as a modifying factor of flower differentiation. We demonstrated that the early events of flower bud differentiation are accompanied by stimulation of leaf growth. The evaluation of growth and development of axillary buds at different nodes of insertion enabled us to quantify the photoperiodic effect and to detect the effects due to differences in dark period length not exceeding 2 hours.     

Plant growth analysis: towards a synthesis of the classical and the functional approach

A method of calculating relative growth rates (RGR) and net assimilation rates is presented. The method is based on the fitting of a polynomial through the relative growth rate values calculated by the 'classical' approach rather than through the In-transformed plant weights as in the 'functional' method. Additional ways of reducing the harvest-to-harvest variation characteristic of the classical approach are discussed. The main advantages of the present approach over the functional one are: (1) The degree of the polynomial can be increased (within certain limits) without inducing spurious fluctuations in RGR. Thus, quite complex trends in RGR can be described. (2) There is little interference between RGR values in different parts of the experiment. The main advantages over the classical approach are: (1) The erratic fluctuations in RGR are dampened. (2) As frequent small harvests are allowed, the workload at each harvest can be diminished and a more reliable impression of ontogenetic drift in RGR can be obtained. (3) RGR is described by a continuous function, thus facilitating further calculations and compilations.     

Constructing a new integrated genetic linkage map and mapping quantitative trait loci for vegetative mycelium growth rate in Lentinula edodes

The most saturated linkage map for Lentinula edodes to date was constructed based on a monokaryotic population of 146 single spore isolates (SSIs) using sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), insertion–deletion (InDel) markers, and the mating-type loci. Five hundred and twenty-four markers were located on 13 linkage groups (LGs). The map spanned a total length of 1006.1 cM, with an average marker spacing of 2.0 cM. Quantitative trait loci (QTLs) mapping was utilized to uncover the loci regulating and controlling the vegetative mycelium growth rate on various synthetic media, and complex medium for commercial cultivation of L. edodes. Two and 13 putative QTLs, identified respectively in the monokaryotic population and two testcross dikaryotic populations, were mapped on seven different LGs. Several vegetative mycelium growth rate-related QTLs uncovered here were clustered on LG4 (Qmgr1, Qdgr1, Qdgr2 and Qdgr9) and LG6 (Qdgr3, Qdgr4 and Qdgr5), implying the presence of main genomic areas responsible for growth rate regulation and control. The QTL hotspot region on LG4 was found to be in close proximity to the region containing the mating-type A (MAT-A) locus. Moreover, Qdgr2 on LG4 was detected on different media, contributing 8.07 %–23.71 % of the phenotypic variation. The present study provides essential information for QTL mapping and marker-assisted selection (MAS) in L. edodes.     

Evaluation of expected absolute error affecting the maximum specific growth rate for random relative error of cell concentration

Borzani's [(1994) World Journal of Microbiology and Biotechnology10, 475–476] idea of evaluation of absolute error affecting the 'maximum specific growth rate' (ESGR), calculated on the basis of the first and the last time points of the entire experimental time period, is generalized to the real-life situations where the relative errors of cell concentration cannot be assumed to be constant during the experiment. Visualizing the entire experimental time period as to comprise of several successive, mutually exclusive and exhaustive time intervals, we compute specific growth rates (SGRs) for each of these time intervals. Defining maximum of these SGR values as MSGR in contrast to Borzani's ESGR our aim is to study the effect of the expected absolute error on SGRs of different intervals. This will reveal the discrepancy between the true and observed MSGRs. Assuming the relative error distribution on (0,1) to be rectangular and symmetric truncated normal with mean at 0.5 and suitable variance, the expected values of the absolute errors are evaluated and numerically tabulated using the software packages MATHEMATICA and S-PLUS. Our results thus hold for situations involving varying relative errors where Borzani's results cannot be applied. A discussion with a concrete numerical example on the misidentification of the MSGR interval due to the effect of the random relative measuremental errors reveals to an experimental biologist that ignorance of this fact may lead to his/her entire experiment being futile.