烟草根黑腐病抗性位点RBRR1的InDel分子标记开发与分析

  背景和目的  RBRR1是通过远缘杂交与回交导入栽培烟草的一个单显性广谱型根黑腐病抗病位点,为了开发基于该位点的简单高效稳定且成本低的紧密连锁分子标记。  方法  在已有酶切扩增多态性序列（Cleaved amplified polymorphism sequences, CAPS）标记相关序列基础上,利用云晒1号基因组与抗、感根黑腐病材料重测序信息,基于其序列插入/缺失（Insertion/Deletion, InDel）多态性设计抗病相关分子标记,并开展遗传效应和遗传变异分析。  结果  筛选到4对具有良好多态性的引物,在目标单株的分子标记辅助选择中具备便捷、高效且呈共显性的特点。遗传效应分析表明,通过分子标记辅助选择导入RBRR1位点能够极显著提高栽培烟草根黑腐病抗性。遗传变异分析结果显示,在烟草核心种质资源中仅有白肋烟TN90和SoTa2携带有RBRR1抗病基因,并发现4对引物在普通烟草自然群体中呈现2种基因型。  结论  RBRR1抗病位点在我国尚未进行广泛利用,具有较高的利用价值;而开发的4个InDel标记可用于该抗性位点的分子标记辅助选择育种和后续抗病基因的精细定位与克隆。      

一个与烟草TMV抗性基因N紧密连锁的共显性SSR标记

烟草普通花叶病（Tobacco Mosaic Virus,TMV）是烟叶生产的主要病害,为建立烟草抗TMV分子标记辅助选择体系,本研究以高抗TMV烤烟品种Coker176和易感TMV烤烟品种Y3以及它们的BC1F1群体为试材,采用分离集团分组分析法（Bulked Segregation Analysis,BSA）和简单序列重复（Simple Sequence Repeat,SSR）标记技术,筛选与TMV抗性基因N紧密连锁的共显性SSR标记。通过对18764对SSR引物的分析表明,有396对SSR引物在两亲本间有多态,选出1对SSR引物TM508-007扩增出的标记与TMV抗性的N基因紧密连锁,遗传连锁距离为0.41 cM,证实获得的与TMV抗性基因N紧密连锁的共显性SSR标记稳定可靠,可用于烟草抗TMV分子标记辅助选择。      

烟草种质的SSR标记遗传多样性及青枯病抗性的关联分析

烟草青枯病是影响烟草产质量的主要病害之一,开发出与烟草青枯病抗病性密切相关的优异等位基因,可加速抗病品种的选育进程。据此,本研究选用94份烟草种质材料作为研究对象,运用236个SSR标记对这些材料进行基因分型和群体结构分析,开展基于连锁不平衡的关联分析探测与青枯病抗性相关的分子标记。结果表明,236个SSR标记在94份烟草种质中检测到904个等位变异位点,平均每个SSR标记为3.83个位点;这些SSR标记的多态性信息量（PIC）值在0.1361~0.8760之间,平均为0.5136。基于SSR基因分型数据,构建了126个标记单倍型;在此基础上进行群体结构分析,将94份种质划分为2个类群,表明本研究烟草种质的群体结构简单,有利于减少伪关联。二年田间抗病性数据与单倍型的关联分析发现7个单倍型与青枯病抗病性密切相关,其中有3个单倍型在二年的田间试验中均表现出与青枯病抗性密切相关,平均解释率超过10%。研究结果可为烟草青枯病抗病材料的分子标记辅助筛选提供参考。      

Application of genomics to grapevine improvement

Imagine a breeder browsing a grape chromosome nucleotide-by-nucleotide around a trait locus, scrolling down the list of catalogued genes along a genetic interval, resequencing for a few thousand dollars a potential parent or a selected breeding line. In the past couple of years, this vision has become a reality. The availability of the reference genome sequence has provided significant assistance in the saturation of loci with targeted genetic markers. Grape breeders are now offered unprecedented possibilities for selecting plants using deoxyribonucleic acid (DNA) sequences within or near the gene that controls a desirable trait rather than handling their phenotypes. Genomics-assisted selection offers unique advantages in the correct choice of elite genotypes, in order to improve traits for which limitations of phenotyping technologies or low hereditability adversely affect the efficiency of phenotypic selection. DNA technologies enable the application of marker-assisted selection to thousands of grape seedlings every year, which was previously feasible only for cereals and annuals, enhancing the possibilities of finding an ideal recombinant in populations bred from highly heterozygous parents. The expected outcome is a renewal of the varietal choices available to viticulturists, with novel genotypes that meet the demand for disease-free vines and flavourful grapes. The depth of exploration and characterisation of the existing germplasm is crucial for translating natural diversity into new varieties that could perform beyond the fence of the experimental vineyards and gain substantial market share. We review here how current achievements in genomics and genome sequencing are expected to increase the efficiency of grapevine breeding programs.     

SSR和ISSR标记技术应用进展

介绍了SSR和ISSR标记的原理和特点,综述了这两种技术在种质遗传多样性、基因定位及分子标记辅助育种、遗传图构建及种子纯度和真伪鉴定等研究中的应用进展,并提出了在烟草遗传育种中应用的建议。     

花生SSR分子标记的开发与利用

主要介绍了基因组SSR、EST—SSR分子标记的开发及其在花生遗传图谱的构建、花生性状及相关基因的定位、遗传多样性研究及种质资源的鉴定等方面的应用,同时对SSR标记在花生中的应用前景进行了展望,以期为花生分子育种提供参考。     

SSR标记在甘蔗遗传育种中的应用

SSR(Simple sequence repeat)标记是建立在PCR基础上的一种新型DNA分子标记.SSR数量丰富,信息含量高,呈共显性遗传,易于分析,所以它是进行甘蔗遗传研究的理想工具.本文就SSR标记在甘蔗遗传多样性分析、遗传连锁图谱构建、鉴定品种和分子标记辅助育种等方面的应用进行了综述.     

231份烤烟种质资源SSR标记遗传多样性及其与农艺性状和化学成分的关联分析

本文旨在分析烤烟种质资源遗传多样性,通过关联分析寻找与烤烟农艺性状和化学成分相关联的分子标记,为分子标记辅助选择育种和提高烤烟育种效率奠定基础。利用均匀分布于烟草24个连锁群上的120个SSR标记分析了231份烤烟种质资源的遗传多样性及群体遗传结构,在此基础上采用TASSEL 5.0 GLM（general linear model）和MLM （mixed linear model）方法进行标记与表型性状变异（8个农艺性状和5个化学成分）的关联分析。通过遗传多样性分析,共检测出403个等位变异,变异范围2-21个,平均每个标记3.36个;引物的多态性信息含量（PIC）为0.036~0.785,平均值为0.408;供试材料间遗传距离为0.003~0.371,平均值为0.148。通过非加权组平均法（UPGMA）进行聚类分析,在遗传距离（GD）值为0.153水平上可将231份烤烟材料聚为4大类。通过群体遗传结构分析将供试材料划分成3个亚群,且每个亚群分别包含117、38和76份烤烟材料。通过GLM_Q和MLM_Q+K两种关联分析模型,分别检测出17个和9个与13个表型性状显著相关,其中9个标记在两个年份和两种模型中均被检测到与同一性状在P < 0.001水平上极显著相关,且MLM_Q+K未能检测到新的关联标记;3个株高相关标记（TM10481、PT54964和TM20580）、2个叶数相关标记（TM10846和PT60728）、1个茎围相关标记（TM25276）和1个叶长相关标记（TM11215）与已报道的QTL定位结果一致,可应用于烤烟分子标记辅助选择育种。      

一个与净叶黄抗赤星病基因紧密连锁的SSR标记

为了在分子水平上弄清烟草赤星病抗性的遗传规律,并进行遗传定位,以抗赤星病品种净叶黄和感赤星病品种NC82为亲本,构建了F₁、F₂、BC₁ 代群体。通过对该群体进行赤星病接种鉴定和抗性遗传分析,发现净叶黄对赤星病的抗性由显性多基因控制。通过分子标记群体扩增,在第M号连锁群上,筛选到一个与净叶黄的赤星病抗性基因紧密连锁的SSR标记,它与抗性基因间的遗传距离为4 cM。该标记可用于抗赤星病育种的辅助选择。     

Strategies for estimating genetic parameters in marker-assisted best linear unbiased predictor models in dairy cattle

An appropriate strategy to estimate variance components and breeding values in genetic models with quantitative trait loci (QTL) was developed for a dairy cattle breeding scheme by utilizing simulated data. Reliable estimates for variance components in QTL models are a prerequisite in fine-mapping experiments and for marker-assisted genetic evaluations. In cattle populations, only a small fraction of the population is genotyped at genetic markers, and only these animals are included in marker-assisted genetic evaluation models. Phenotypic information in these models are precorrected phenotypes [daughter yield deviations (DYD) for bulls, yield deviations (YD) for cows] estimated by standard animal models from the entire population. Because DYD and YD may represent different amounts of information, the problem of weighting these 2 types of information appropriately arises. To detect the best combination of phenotypes and weighting factors, a stochastic simulation for a trait representing milk yield was used. The results show that DYD models are generally optimal for estimating QTL variance components, but properties of estimates depend strongly on weighting factors. An example for the benefit in selection of using YD is shown for the selection among paternal half-sibs inheriting alternative QTL alleles. Even if QTL effects are small, marker-assisted best unbiased linear prediction can improve the selection among half-sibs, because the Mendelian sampling variance within family can be exploited, especially in DYD-YD models. Marker-assisted genetic evaluation models should also include YD for cows to ensure that marker-assisted selection improves selection even for moderate QTL effects (≥10%). A useful strategy for practical implementation is to estimate variance components in DYD models and breeding values in DYD-YD models.     

烟草糖酯SSR分子标记筛选及辅助育种应用

为明确与糖酯紧密连锁的SSR分子标记在烟草实际育种工作中的可用性,加快烤烟糖酯遗传改良进程,本研究利用聚丙烯酰胺凝胶电泳技术和GC-MS检测技术,以不同遗传背景的5个烟草种质以及192份重组自交系遗传群体为试验材料,对5个SSR分子标记开展了筛选和验证研究。结果表明,5个分子标记中,PT20315、PT30354两个分子标记在不同遗传背景中多态性稳定,并且其多态性条带与糖酯表型差异的对应性较好;在重组自交系群体中,两个分子标记鉴定的基因型与糖酯表型的一致率分别为93.75%和90.58%,可用于高糖酯烟草分子辅助育种中。目前,利用两个分子标记辅助选择,已经定向改良获得高糖酯K326等新品系材料。     

向日葵体细胞胚的QTL分析及标记辅助选择

为了定位向日葵体细胞胚基因和筛选相关标记用于辅助育种,以31个重组自交系为材料,利用下胚轴表皮细胞诱导体细胞胚,获得了与体细胞胚发生率相关的,位于第5、10、13连锁群上的3个QTL位点,可分别解释表型变异的14.61％、10.04％和14.07％.同时,获得了与每块胚数相关的9个QTL位点,分别位于第2、8、10、11、12和19连锁群上,可解释表型变异的6.64％～16.96％,其中4个QTL位点位于第10连锁群上且位置相邻（在34.57 ～ 47.1OcM之间）,可解释表型变异的40.39％.为了验证所获结果,在31个重组自交系中,筛选出2个体细胞胚发生率高的株系和1个低的株系杂交,构建了2个F2分离群体.利用AFLP和SSR标记对F2群体进行扫描,在与体细胞胚发生率相关的第5、10、13条连锁群上分别增加了24、6和18个新标记,标间距从6.80 ～11.40cM缩短到5.10～5.60cM.通过对F2群体与亲本基因型进行QTL区域的对比分析,预选出7个体细胞胚发生率高和7个低的株系,利用F3家系诱导体细胞胚进行验证.结果表明,预选结果与实际获得的结果完全一致,控制向日葵每块胚数的基因主要位于第10连锁群上,控制体细胞胚发生率的基因主要位于第5、13连锁群上;4个AFLP标记（e32m50-1、e38 m49-2、e40m49-1、e32m62-10）是最靠近控制体细胞胚发生基因的标记,可以作为该性状的辅助选择标记.     

谷子分子标记研究与应用

谷子是我国传统粮食作物,具有抗旱、耐瘠薄、营养价值高等优点,谷子的种质资源分析及育种研究非常重要,随着分子生物学的发展,分子标记技术的出现为谷子的遗传研究及育种开辟了新的思路和手段。分子标记包括DNA分子标记和蛋白质分子标记,其中DNA分子标记常被用于构建遗传连锁图谱、基因定位及QTL分析、遗传多样性研究、系谱分析与品种鉴定和比较基因组研究等,本文分别介绍了谷子常用的DNA分子标记和蛋白质分子标记及其特点,并综述了其在谷子上的研究应用情况,简要分析和展望了分子标记在谷子上的未来发展。     

Application of genomic technologies to the improvement of meat quality of farm animals

Meat quality is of economic importance in farm animals. It is controlled by multigenes and the environment. During the past few decades, advances in molecular genetics have led to the identification of genes, or markers associated with genes, that affect meat quality. Work on sequencing farm animal genomes will help us to understand how genes function in various organisms and might be applied in the field to study the molecular control of meat quality. Candidate gene and genome scans are two main strategies to identify loci associated with the trait of meat quality. Several genes that influence meat quality have already been, or are close to being, identified. Some of them have been applied to the breeding of farm animals by marker-assisted selection. This will accelerate cumulative and permanent genetic improvement of herds.     

Characterization and authenticity of virgin olive oil (<Emphasis Type="Italic">Olea europaea</Emphasis> L.) cultivars by microsatellite markers

Traceability and authenticity of olive oils have become a major instrument to guarantee the consumer’s protection. Recently, determination of adulteration of olive oils is based on the analysis of simple sequence repeats. In this study, we evaluate the feasibility of identifying above cultivars and the derived oils by the analysis of SSR markers. To this purpose, 22 virgin olive oils were prepared in the laboratory and DNA was extracted using a commercial kit, and 8 SSR markers were analyzed. The obtained results indicated that the comparison of the genetic profile of DNA extracted from oil and leaves of the cultivars studied concluded different genetic profiles in some cultivars when studied for their genome as well as for their oils. These additional alleles in oil’s profile appear as minor peaks can be originating from the pollinators and which are present in the genome of the seed embryo. Hierarchical classification of varieties based on similarity measures and clustering was globally inconsistent with the grouping of varieties by end use and the geographical origin. Finally, we set up a categorization means to discriminate all the types of oil among them with the minimum of markers (three markers).     

分子标记技术及其在植物育种中的应用

概述各种常用分子标记技术RFLP，RAPD，AFLP，SSR，ISSR，SCAR，STS，CAPs的原理，并从种质资源的鉴别、基因定位、基因累加、异源目的基因的筛选、遗传图谱的构建等方面综述了分子标记技术在植物育种中的应用。     

Potential improvements in rate of genetic gain from marker-assisted selection in dairy cattle breeding schemes.

The value of marker-assisted selection in dairy cattle breeding schemes is predicted by a deterministic model. In these schemes, associations between markers and milk production were assessed from production records of daughters of a grandsire by a multiple regression model with random marker effects. By tracing markers from the grandsire to grandoffspring, deviations of grandoffspring from their full-sib family mean were predicted. Predictions of the within-family variance of the grandoffspring accounted for by markers amounted to up to 13.3%. This figure decreased when the number of daughters of the grandsire analyzed decreased and, less markedly, when the distance between flanking markers increased. Prediction of within-family deviations hardly improved rates of genetic gain in conventional progeny testing schemes; equal numbers of young bulls were born annually. Genetic gain and improvement of genetic gain because of prediction of within-family deviations were much higher in nucleus schemes. In these shemes, with short optimized generation intervals, conventional selection was mainly for pedigree information and did not use the within-family variance. Analysis of highly polymorphic markers in daughters of both grandsires accounted for 4.1 to 13.3% of the within-family variance, which increased rates of gain by 9.5 to 25.8% and 7.7 to 22.4% in open and closed nucleus schemes, respectively. Risk of breeding schemes, measured by the variance of the selection response, was not increased by the use of markers.     

分子标记技术及其在植物育种中的应用

概述各种常用分子标记技术RFLP,RAPD,AFLP,SSR,ISSR,SCAR,STS,CAPs的原理,并从种质资源的鉴别、基因定位、基因累加、异源目的基因的筛选、遗传图谱的构建等方面综述了分子标记技术在植物育种中的应用。     

Major advances in genetic evaluation techniques

The past quarter-century in genetic evaluation of dairy cattle has been marked by evolution in methodology and computer capacity, expansion in the array of evaluated traits, and globalization. Animal models replaced sire and sire-maternal grandsire models and, more recently, application of Bayesian theory has become standard. Individual test-day observations have been used more effectively in estimation of lactation yield or directly as input to evaluation models. Computer speed and storage are less limiting in choosing procedures. The increased capabilities have supported evaluation of additional traits that affect the net profitability of dairy cows. The importance of traits other than yield has increased, in a few cases due to an antagonistic relationship with yield. National evaluations combined internationally provide evaluations for bulls from all participating countries on each of the national scales, facilitating choices from among many more bulls. Selection within countries has increased inbreeding and the use of similar genetics across countries reduces the previously available outcross population. Concern about inbreeding has prompted changes in evaluation methodology and mating practices, and has promoted interest in crossbreeding. In just the past decade, distribution of genetic evaluations has gone from mailed paper or computer tapes for a limited audience to publicly accessible, request-driven distribution via the Internet. Among the distributed information is a choice of economic indices that combine an increasing array of traits into numbers reflecting breeding goals under different milk-pricing conditions. Considerable progress in genomics and the mapping of the bovine genome have identified markers for some deleterious recessive genes, but broader benefits of marker-assisted selection are still in the future. A possible exception is the proprietary use of DNA testing by semen producers to select among potential progeny test bulls. The collection and analysis of industry-wide data to evaluate genetic merit will continue to be the most important tool for genetic progress into the foreseeable future.     

Beinhart1000-1抗赤星病基因的QTL定位

为了研究赤星病抗性的遗传规律,筛选与抗性基因紧密连锁的SSR标记,并将抗性基因进行QTL定位,用抗赤星病品种Beinhart1000-1作母本,感病品种G140作父本,构建了F1及F2代群体,并对其进行了抗性鉴定和遗传分析。结果表明,Beinhart1000-1的赤星病抗病性是由显性多基因控制的。利用混合群体分组分析法,从2653对SSR引物中,得到83对在抗感池间表现多态且扩增条带稳定清晰的SSR标记。以F2代群体115个单株为作图群体,将该83对引物进行扩增,并用WinQTLCart2.5分析数据。这83个标记分别连锁到18个连锁群上,同时定位到两个抗赤星病的QTL位点,分别位于7号和15号连锁群上。