Statistical confidence in parentage analysis with incomplete sampling: how many loci and offspring are needed?

We have recently presented models to estimate parentage in breeding systems with multiple mating and incomplete sampling of the candidate parents. Here we provide formulas to calculate the statistical confidence and the optimal trade-off between the number of loci and offspring. These calculations allow an understanding of the statistical significance of the parentage estimates as well as the appropriate sampling regime required to obtain a desired level of confidence. We show that the trade-off generally depends on the parentage of the putative parents. When parentage is low, sampling effort should concentrate on increasing the number of loci. Otherwise, there are similar benefits from increasing the number of loci or offspring. We demonstrate these methods using genetic data from a nest of the bluegill sunfish (Lepomis macrochirus).     

A high-throughput system for genome-wide measurement of genetic recombination in Arabidopsis thaliana based on transgenic markers

A high-throughput system for the measurement of recombination frequencies in the genetic model plant, Arabidopsis thaliana, is described. It is based on 21 mono-transgenic isogenic lines harboring antibiotic resistance genes on all five chromosomes. Recombination between pairs of gene insertions in repulsion phase that confer resistance against kanamycin (kan) and hygromycin (hyg) is determined by a phenotypic assay of progeny (DART: Double Antibiotic Resistance Technique). DART allows testing for the influence of numerous environmental and genetic factors, including candidate genes, on recombination frequencies in specific genomic regions as well as the entire genome. Its usefulness is demonstrated by investigating the effects of UV treatment, different temperature and phosphorus supply regimes, and sex on recombination frequencies for all five chromosomes of A. thaliana. Electronic Publication     

Mapping quantitative trait loci associated with days to flowering and photoperiod sensitivity in rice (Oryza sativa L.)

This study was undertaken to identify putative quantitative trait loci (QTLs) associated with days to flowering (DTF) and photoperiod response in rice. A population of 143 recombinant inbred lines derived from a cross between CO39 and Moroberekan was grown under greenhouse conditions and exposed to two different photoperiod regimes. DTF of individual plants was evaluated under 10 h and 14 h day lengths, and loci associated with photoperiod sensitivity were identified based on the delay in flowering under the 14 h photoperiod (DTF at 14 h minus DTF at 10 h). An RFLP data set consisting of 127 markers provided the basis for the QTL analysis. Both single marker and interval analysis were used and interactions between putative QTLs were estimated based on two-way ANOVA. Out of 15 QTLs associated with DTF, only 4 were identified as influencing the response to photoperiod. Interactions between flowering QTLs indicated the complex nature of the control of flowering in rice. The effectiveness of using a single recombinant inbred population to study a variety of complex phenotypes is discussed in relation to practical plant breeding.     

QTLs for a component of partial resistance to cucumber mosaic virus in pepper: restriction of virus installation in host-cells

 Ninety four doubled-haploid (DH) lines obtained from the F₁ between Perennial, a cucumber mosaic virus (CMV)-partially resistant Capsicum annuum line, and Yolo Wonder, a CMV-susceptible C. annuum line, were analysed with 138 markers including mostly RFLPs and RAPDs. Clustering of RAPD markers was observed on five linkage groups of the intraspecific linkage map. These clusters could correspond to the centromeric regions of pepper chromosomes. The same progenies were evaluated for restriction of CMV installation in pepper cells in order to map quantitative trait loci (QTLs) controlling CMV resistance. This component of partial resistance to CMV was quantitatively assessed using a CMV strain that induced necrotic local lesions on the inoculated leaves. The number of local lesions gave an estimation of the density of the virus-infection sites. Genotypic variance among the DH lines was highly significant for the number of local lesions, and heritability was estimated to be 0.94. Using both analysis of variance and non-parametric tests, three genomic regions significantly affecting CMV resistance were detected on chromosomes Noir, Pourpre and linkage group 3, together explaining 57% of the phenotypic variation. A digenic epistasis between one locus that controlled significant trait variation and a second locus that by itself had no demonstrable effect on the trait was found to have an effect on CMV resistance. For each QTL, the allele from Perennial was associated with an increased resistance. Implications of QTL mapping in marker-based breeding for CMV resistance are discussed. Received: 16 September 1996     

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

The identification of individuals’ breed of origin has several practical applications in livestock and is useful in different biological contexts such as conservation genetics, breeding and authentication of animal products. In this paper, penalized multinomial regression was applied to identify the minimum number of single nucleotide polymorphisms (SNPs) from high-throughput genotyping data for individual assignment to dairy sheep breeds reared in Sicily. The combined use of penalized multinomial regression and stability selection reduced the number of SNPs required to 48. A final validation step on an independent population was carried out obtaining 100% correctly classified individuals. The results using independent analysis, such as admixture, F_st, principal component analysis and random forest, confirmed the ability of these methods in selecting distinctive markers. The identified SNPs may constitute a starting point for the development of a SNP based identification test as a tool for breed assignment and traceability of animal products.     

Expansion of GARP-Expressing CD4+CD25−FoxP3+ T Cells and SATB1 Association with Activation and Coagulation in Immune Compromised HIV-1-Infected Individuals in South Africa

Virologica Sinica - Although antiretroviral treatment lowers the burden of human immunodeficiency virus (HIV)-related disease, it does not always result in immunological recovery. This manifests as...     

Tumour shape-dependent microwave hyperthermia using a novel coaxial micro-cut slot antenna

Given that the effectiveness of interstitial hyperthermia for cancer treatment is related to the temperature achieved during the ablation process, there is a need for an accurate understanding of the required temperature distribution which is affected by the physical shape and form of tumours. Although a maximum peak temperature value and minimum backward heating are desired, the temperature distribution needs to be not only high but also uniformly extended over a section instead of at one peak point, especially when a roughly oval-shaped tumour is aligned with the antenna. In this case, achieving a high temperature peak destroys only the central cancerous cells after the first minutes of ablation, leaving the cells on the side alive. In this paper, a complex model was extended for the study of the heat distribution of an antenna over a porous liver composed of blood, cancerous cells, and normal tissue. Three different types of antenna were analysed: single-slot, double-slot, and dipole-tip. A novel structure made up of the single-slot antenna with a micron cut, named the micro-cut slot (MCS) antenna, was proposed and analysed. Thanks to the new structure, high uniform temperature distribution with minimum backward heating was achieved. The extended model equations, which encompass a coupled nonlinear set of transient Maxwell's electromagnetic equations, extended Darcy–Brinkman equation, and local thermal non-equilibrium equations for porous medium approximation, were solved numerically using the novel alternating direction implicit, finite–difference time–domain approach. The results showed that each type of antenna could be useful if chosen according to the shape of the tumour. In comparison with previously used antennas, the MCS antenna presented a good combination of the required goals of achieving uniform high temperature distribution and minimum backward heating.     

DNA marker analysis for pyramided of Fusarium head blight (FHB) resistance QTLs from different germplasm

A pyramided FHB resistance line of wheat (WSY) was previously developed from three FHB resistant cultivars (Sumai 3, Wangshuibai, and Nobeokabouzu) in the Jiangsu Academy of Agricultural Sciences, China. In the present study, we analyzed the genetic relationship between WSY and the three parental cultivars using DNA markers in order to clarify how many and which resistance genes had accumulated in WSY. We analyzed 282 DNA markers from the 21 wheat chromosomes. WSY was found to include different chromosome regions that harbored putative FHB QTLs of the three parental germplasm. Haplotypes of DNA markers on these QTL regions revealed that the 1BL, 2BL, 5AS, and 7AL QTL regions were from Sumai 3, the 2AS, 2DS, 3AS, and 6BS QTL regions were from Wangshuibai, and the 3BS QTL region was from Nobeokabouzu. This study showed that different resistance genes from the different resistant germplasm had indeed accumulated in WSY. WSY is a potential resistant resource for FHB resistance in wheat breeding programs.     

凉山半细毛羊1号染色体微卫星遗传连锁图谱的构建

实验选择绵羊1号条染色体上的9个微卫星标记,采用父系半同胞家系群体（共387个个体）构建凉山半细毛羊1号染色体遗传连锁图。建立的资源参考家系通过20个微卫星标记进行了系谱确证。试验结果表明,9个标记的等位基因数变化范围为5~15个,杂合度在0.202~0.831之间,平均杂合度为0.617,各标记的平均多态信息含量PIC=0.604。构建的凉山半细毛羊1号条染色体遗传连锁图总长度311.0 cM,与美国肉畜中心（USDA）和国际绵羊作图中心（IMF）构建的绵羊1号条染色遗传连锁图结果基本一致。可用于下一步的QTL定位研究。