Quantitative genotyping to estimate genetic contributions to pooled samples and genetic merit of the contributing entities

Abstract

Genotyping required to track family membership in aquaculture breeding programs is reduced dramatically by estimating the contributions of different families to pooled samples of tissue. This approach is relevant to widely differing scenarios involving animals, plants, and microbes. For the family membership scenario, SNP markers are genotyped for the contributing families' parents, and quantitatively genotyped to estimate allele frequencies within the mixed-family pooled tissue. Results are used to infer proportional contributions of the different families to the pool. Different computational strategies were tested for bias and sampling error. A correlation of 99% between estimated and true genetic contributions was achieved using 20 (50) randomly chosen SNPs at a standard error of allele frequency estimates of 0.01 (0.02). Optimal grouping of families and choice of markers further increases performance markedly. Trait means and distributions of families can be quite accurately estimated by tissue sampling across the range of trait values.     

PCR-RFLP molecular confirmation of color dilution alopecia in dogs in Brazil

Color dilution alopecia (CDA) is a dermatopathy observed exclusively in animals having a diluted coat color. In dogs, color dilution occurs as a result of a single-nucleotide variation (SNV) c.-22G > A in the melanophilin gene. We standardized a PCR–restriction-fragment length polymorphism (PCR-RFLP) technique to identify this mutation and determine its frequency in dogs in Brazil. The standardized PCR-RFLP technique could efficiently identify the SNV c.-22G > A in the melanophilin gene, with mutated allele frequencies of 0.1, 0.1, and 0.0875 in Dachshund, Miniature Pinscher, and Yorkshire Terrier breeds, respectively, with no statistical difference among the breeds (p = 0.252). The mutation was identified in 2 homozygous Dachshund dogs with alopecia, confirming the clinical characteristic of CDA. The standardization of a simpler and more accessible molecular technique for recognition of the SNV c.-22G > A in the melanophilin gene allows identification of heterozygous (phenotypically normal) dogs that can be excluded from reproduction, to avoid the birth of dogs with diluted coat color and consequently CDA.     

Genotyping‐by‐sequencing for construction of a new genetic linkage map and QTL analysis of growth‐related traits in Pacific bluefin tuna

Pacific bluefin tuna (Thunnus orientalis) has high market value, but its wild populations have decreased in recent years. The broodstock of Pacific bluefin tuna that were hatched artificially and reared under aquaculture conditions is beginning to be used for production. The creation of broodstock with commercially valuable traits, such as rapid growth, is therefore of great interest. Genetic linkage map‐based identification of markers associated with quantitative trait loci (QTLs) facilitates marker‐assisted selection (MAS) breeding and allows efficient genetic improvement of broodstock. Single nucleotide polymorphism (SNP)‐based genetic linkage map construction using the genotyping‐by‐sequencing method can expand the number of mapped markers and help identify growth‐related QTLs. In this study, we constructed sex‐specific maps for 24 linkage groups consisting of 677 SNP and 651 microsatellite markers. The total lengths of 93 progenies in the mapping population followed normal distribution, with an average length of 9.4 mm. We performed composite interval mapping in the mapping population. QTL analysis revealed one significant QTL in LG10 on the female linkage map. The genetic linkage map—the second such map generated for Pacific bluefin tuna—and the growth‐related QTLs detected in this study will be useful for tuna aquaculture MAS programs.     

应用荧光标记通用引物检测鲤鱼(Cyprinus Carpio)微卫星基因型

应用荧光标记通用引物检测微卫星是一种省成本、省时间、高效精确的基因型检测方法。本文介绍了该方法的基本原理和操作流程,并首次应用此方法检测鲤微卫星标记的基因型。结果显示,除位点HLJ179未检测到有效数据外,其它14个位点都采集到相应的基因型。该方法在鲤微卫星基因分型上的成功应用,为今后鲤大规模连锁分析提供了一种更经济有效的检测方法。     

禽霍乱巴氏杆菌的分离鉴定及基因分型

为确定疑似禽霍乱病例病原种类及其病原基因型,本研究采用细菌分离技术对病原菌进行实验室分离培养,应用传统方法和分子生物学方法对分离细菌进行鉴定,并应用PCR扩增和基因序列分析对分离细菌进行基因分型。结果显示,分离菌具有多杀性巴氏杆菌（Pasteurella multocida,Pm）典型培养特征,菌落形态和菌体染色特征、生理生化特性均与多杀性巴氏杆菌相符;PCR扩增到457 bp的基因片段。采用5对分型引物对分离菌进行基因分型显示,仅有A型引物扩增到大小1 050 bp的目的基因片段,序列分析也显示分离菌荚膜基因与A型多杀性巴氏杆菌参考菌株荚膜特异性基因同源性高达97.6%~100.0%,系统进化与A型多杀性巴氏杆菌处于同一进化分支。结果表明,疑似禽霍乱病例病原为A型多杀性巴氏杆菌,本研究结果将为禽霍乱的防控提供参考资料。     

我国新城疫分子流行病学研究进展

新城疫（Newcastle Disease,ND）是严重损害禽类健康的疾病之一，在世界范围内广泛流行，临床以高热、呼吸困难、下痢、神经紊乱、黏膜出血等症状为特征，严重危害禽类的生长繁殖及禽肉生产。新城疫由新城疫病毒（Newcastle Disease Virus,NDV）引起。NDV已有近100年的流行历史，能够感染鸡、鸭、鹅和鸽子等200多种禽类，其基因型众多，易变的基因型给新城疫防控带来巨大困难。鸟类迁徙在病毒跨境传播中起到重要作用，导致我国各地区新城疫疫情时有发生，给养禽业带来巨大的经济损失，严重制约了养禽业的健康发展。NDV分布范围广、宿主流动性强,是危害养禽业的重要病毒。为了解我国NDV的流行情况，通过对其分子流行病学及各基因型的时空分布进行分析，发现我国新城疫主要分布于广西、广东等华南地区，江苏、安徽等华东地区及陕西、甘肃等西北地区。这些地区分离出的高致病性Ⅱ类毒株包括多种基因型，其中基因Ⅱ型和基因Ⅶ型毒株为主要流行株。通过对NDV流行相关数据的整理与分析可为疫情防控和疫苗研究提供参考。