标记辅助选择改良数量性状的研究进展

本文系统地介绍了近年来有关标记辅助选择改良数量性状的研究进展,主要包括标记辅助回交、指数选择与最佳线性无偏预测的理论和应用研究概况.理论与计算机模拟表明标记辅助选择比常规表型选择更有效,但在实际育种中并不理想.同时本文还就当前标记辅助选择存在的问题和前景进行了讨论。 Abstract:Recent advances on marker-assisted selection (MAS) in the improvement of quantitative traits are reviewed.These include theoretical researches and applications of marker-assisted backcrossing,index selection,and best linear unbiased prediction (BLUP) in animal and plant breeding.Theoretical and simulation studies show that marker-assisted selection can substantially increase the efficiency of selection in comparison to phenotypic selection,but is not yet a proven technology.Problems and prospects in MAS are also discussed.     

水稻回交世代中两个抗纹枯病主效数量基因的鉴定与标记辅助选择

对水稻品种特青与Lemont杂交组合的F2 单株无性系群体,进行 2年有重复的抗水稻纹枯病QTLs定位,在特青的第 9号染色体和Lemont的第 11号染色体上分别定位到了 1个主效抗纹枯病QTL,各自命名为qSB 9和qSB 11。从该F2 定位群体中,根据位点双侧标记带型,选取 2个位点均为感病等位基因纯合的 2个单株作为双感亲本,均为抗病等位基因纯合的 1个单株作为双抗亲本,分别与轮回亲本特青和Lemont进行回交。标记辅助选择始于BC2F1 及以后的各回交世代,并于BC2F1 和BC4F1 世代进行了病原菌人工接种鉴定。鉴定结果表明,qSB 9和qSB 11确实存在于原定位区间,各等位基因也在回交过程中被成功选择。BC3F2 采用秧田期大群体标记检测,从中选取符合要求的单株,分别混合得到特青背景下的双感纯合系, Lemont背景下的双感、双抗纯合系,将这些纯合系连同轮回亲本同时种植于扬州大学农学院试验田和江苏里下河农科所试验田, 2次重复,随机区组设计,进行接种实验。结果表明: 1 )相同背景下的不同纯合系间在发病程度上存在极显著的差异,不同纯合系的病情严重程度依次为:Lemont双感系>特青双感系>Lemont>特青 >Lemont双抗系; 2 )2个位点上的抗性等位基因qSB 9和qSB 11单独存在时,分别可减轻病级 1 2级左右,同时存在时可减轻病级 2级左右;     

作物数量性状(QTL)基因研究进展

从作物数量性状基因座QTL(quantitative trait locus)作图群体类型及特点,QTL定位的原理和方法,作物QTL研究现状,以及QTL精细定位、克隆、利用等方面进行了综述。对作物QTL分子标记辅助选择育种进行了探讨,并对目前QTL定位中存在的问题和今后QTL的研究方向提出了一些思考。     

作物分子标记辅助选择的研究进展、影响因素及其发展策略

随着分子标记技术及其检测手段的发展,开发和应用成本的降低,分子标记辅助选择(MAS)在作物育种上的应用优势日益明显。本文综述了近年来MAS在基因聚合、基因转移和数量性状改良上的研究进展。总结了MAS的影响因素,包括标记与基因间的距离、目标性状的遗传率、群体大小、所用分子标记的数目、类型和相位等。并提出育种和定位同步进行、选择合适分子标记类型和数量、简化DNA提取方法、背景选择的逐步选择法、确定合适选择方案等MAS发展策略。     

小麦数量性状分子标记的研究进展

小麦的许多重要经济性状是受多基因控制的数量性状。综述了近年来小麦QTL的研究进展,包括QTL定位原理、研究涉及的性状、QTL分布情况、贡献率、数据统计分析使用的方法和应用软件等,列举了小麦重要农艺性状QTL在育种中的应用实例,分析了小麦QTL分子标记的发展和应用前景。     

性状遗传力与QTL方差对标记辅助选择效果的影响

在采用动物模型标记辅助最佳线性无偏预测方法对个体育种值进行估计的基础上,模拟了在一个闭锁群体内连续对单个性状选择10个世代的情形,并系统地比较了性状遗传力和QTL方差对标记辅助选择所获得的遗传进展、QTL增效基因频率和群体近交系数变化的影响。结果表明：在对高遗传力和QTL方差较小的性状实施标记辅助选择时,可望获得更大的遗传进展;遗传力越高,QTL方差越大,则QTL增效基因频率的上升速度越快;遗传力较高时,群体近交系数上升的速度较为缓慢,而QTL方差对群体近交系数上升速度的影响则不甚明显。结合前人关于标记辅助选择相对效率的研究结果,可以认为：当选择性状的遗传力和QTL方差为中等水平时,标记辅助选择可望获得理想的效果。     

泡桐无性系数量性状的遗传分析和指数选择研究

以１０年的泡桐无性系为材料,对包括材积、胸径、树高以内的８个主要数量性状进行了遗传参数分析,并在相关分析的基础上通过指数选择法,分别对材积、胸径、树高进行了选择指数研究。结果表明：材积的遗传变异系数较大,胸径、叶基宽中等,树高、叶干重等最小。遗传力以材积、胸径、叶柄长最高,叶干重、叶面积、叶基凹入、叶基宽中等,树高最低。多性状选择指数优于单一性状。根据材积、胸径、树高的选择指数,选出了２个材积,胸     

标记辅助回交育种中所需最小样本容量的近似估计

回交育种是把有利基因从供体亲本向受体亲本转移的一种有效方法,标记辅助选择可加速其进程。为了制定合理的标记辅助选择计划,育种家必须知道所需的后代群体大小。该文提出了一种估算在标记辅助回交育种中同时进行前景选择和背景选择所需群体大小的方法。在假定所需转移的目标基因座与遗传背景之间为相互独立的简化假设下,可以通过将解析方法（针对前景选择）与基于回交亲本图示基因型的模拟方法（针对背景选择）相结合,近似地估计出在每一世代中选到所需基因型的概率,进而估算出在一定概率水平下至少获得一个符合要求的个体所需的最小样本容量,用假想的例子演示了该方法的使用情况。该方法可以很方便地应用于实际的回交育种。     

多个连锁数量性状位点的多性状最优化选择

一种扩展的方法能够在多个世代对具有多个数量性状位点的多性状选择进行最优化。这种方法的基础是在目标雨数中用综合遗传值替代单个性状遗传值,并在整个规划期内最大化所有世代选择反应的加权和。利用多阶段系统优化控制理论,整个最优化问题通过一个向前和向后的迭代循环解决。用一个实际育种猪群的育种参数来评价该方法的选择效果,并和标准QTL选择和常规BLUP选择进行比较。结果表明,优化选择要优于标准QTL选择和常规BLUP选择。经济权重对优化选择的影响较明显,随着达100kg日龄赋予的经济权重的增加,优化选择的优势越明显。优化选择通过两种方式增加总选择反应：1）选择早期减少一部分QTL选择反应;2）对达100kgH龄给予更大的权重。选择后期优化累积贴现选择比优化终端选择给予达100kgH龄更大的权重。     

作物数量性状研究进展

作物主要农艺性状和经济性状大多属于数量性状。传统数量遗传学采用数理统计方法,把控制数量性状的多基因系统作为一个整体进行研究。DNA分子标记技术的出现和发展,为数量性状研究提供了重要工具。自20世纪80年代以来,QTL定位的统计分析方法发展很快,先后提出单标记分析法、区间作图法及复合区间作图法等。目前,作物QTL研究取得了重要进展,一些重要作物、重要农艺性状的主效QTL基因已被相继克隆成功,作物数量性状的研究已经成为一个具有勃勃生机的热门领域。     

A rapid method for computing the inverse of the gametic covariance matrix between relatives for a marked Quantitative Trait Locus

The inverse of the gametic covariance matrix between relatives, G^-1, for a marked quantitative trait locus (QTL) is required in best linear unbiased prediction (BLUP) of breeding values if marker data are available on a QTL. A rapid method for computing the inverse of a gametic relationship matrix for a marked QTL without building G itself is presented. The algorithm is particularly useful due to the approach taken in computing inbreeding coefficients by having to compute only few elements of G. Numerical techniques for determining, storing, and computing the required elements of G and the nonzero elements of the inverse are discussed. We show that the subset of G required for computing the inbreeding coefficients and hence the inverse is a tiny proportion of the whole matrix and can be easily stored in computer memory using sparse matrix storage techniques. We also introduce an algorithm to determine the maximum set of nonzero elements that can be found in G^-1 and a strategy to efficiently store and access them. Finally, we demonstrate that the inverse can be efficiently built using the present techniques for very large and inbred populations.     

植物抗病育种中的标记辅助选择与甘蔗

抗病基因的分子标记具有稳定、准确、高效的特点,通过对基因型而不是表型的直接选择,抗病基因分子标记应用于辅助选择可大大加快常规育种进程,提高育种效率。本文评述了植物抗病育种中标记辅助选择的发展概况,介绍了各种DNA分子标记技术及植物抗病基因连锁标记的筛选方法,重点介绍了甘蔗抗病基因分子标记研究的现状,展望了分子标记辅助选择在甘蔗抗病育种中的前景。     

Impacts of QTL × Environment Interactions on Genetic Response to Marker-Assisted Selection

Genotype × environment (GE) interaction is a common characteristic for quantitative traits, and has been a subject of great concern for breeding programs. Simulation studies were conducted to investigate the effects of GE interaction on genetic response to marker-assisted selection (MAS). In our study we demonstrated that MAS is generally more efficient than phenotypic selection in the presence of GE interaction, and this trend is more pronounced for developing broadly adaptable varieties. The utilization of different QTL information dramatically influences MAS efficiency. When MAS is based on QTLs evaluated in a single environment, the causal QTL × environment (QE) interactions usually reduce general response across environments, and the reduction in the cumulative general response is a function of the proportion of QE interactions for the trait studied. However, MAS using QTL information evaluated in multiple environments not only yields higher general response, but the general response obtained is also reasonably robust to QE interactions. The total response achieved by MAS in a specific environment depends largely on the total heritability of traits and is slightly subject to relative changes between general heritability and GE interaction heritability. Two breeding strategies, breeding experiments conducted in one environment throughout and in two environments alternately, were also examined for the implementation of marker-based selection. It was thus concluded that plant breeders should be cautious to utilize QTL information from only one environment and execute breeding studies in another.     

Partition of the genetic trend to validate multiple selection decisions

In this note, a procedure to partition the genetic trend of a selected population is presented. Each part of the genetic gain accounts for the Mendelian sampling terms of different groups of animals, which can be sometimes assigned to different selection policies. The method is based on a simple transformation of the predicted breeding values. The procedure was illustrated with two simulated examples. In the first example, the genetic trend is partitioned into two pieces, one coming from the selection on sires and the other coming from the selection on dams. The second example shows how the impact of an artificial insemination center in the genetic gain of the whole population can be evaluated.     

Efficiency of genomic prediction for boar taint reduction in Danish Landrace pigs

Genetic selection against boar taint, which is caused by high skatole and androstenone concentrations in fat, is a more acceptable alternative than is the current practice of castration. Genomic predictors offer an opportunity to overcome the limitations of such selection caused by the phenotype being expressed only in males at slaughter, and this study evaluated different approaches to obtain such predictors. Samples from 1000 pigs were included in a design which was dominated by 421 sib pairs, each pair having one animal with high and one with low skatole concentration (≥0.3 μg/g). All samples were measured for both skatole and androstenone and genotyped using the Illumina SNP60 porcine BeadChip for 62 153 single nucleotide polymorphisms. The accuracy of predicting phenotypes was assessed by cross‐validation using six different genomic evaluation methods: genomic best linear unbiased prediction (GBLUP) and five Bayesian regression methods. In addition, this was compared to the accuracy of predictions using only QTL that showed genome‐wide significance. The range of accuracies obtained by different prediction methods was narrow for androstenone, between 0.29 (Bayes Lasso) and 0.31 (Bayes B), and wider for skatole, between 0.21 (GBLUP) and 0.26 (Bayes SSVS). Relative accuracies, corrected for h², were 0.54–0.56 and 0.75–0.94 for androstenone and skatole respectively. The whole‐genome evaluation methods gave greater accuracy than using only the QTL detected in the data. The results demonstrate that GBLUP for androstenone is the simplest genomic technology to implement and was also close to the most accurate method. More specialised models may be preferable for skatole.     

Identification of gametes and treatment of linear dependencies in the gametic QTL-relationship matrix and its inverse

The estimation of gametic effects via marker-assisted BLUP requires the inverse of the conditional gametic relationship matrix G. Both gametes of each animal can either be identified (distinguished) by markers or by parental origin. By example, it was shown that the conditional gametic relationship matrix is not unique but depends on the mode of gamete identification. The sum of both gametic effects of each animal – and therefore its estimated breeding value – remains however unaffected. A previously known algorithm for setting up the inverse of G was generalized in order to eliminate the dependencies between columns and rows of G. In the presence of dependencies the rank of G also depends on the mode of gamete identification. A unique transformation of estimates of QTL genotypic effects into QTL gametic effects was proven to be impossible. The properties of both modes of gamete identification in the fields of application are discussed.     

Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

DNA markers have enormous potential to improve the efficiency and precision of conventional plant breeding via marker-assisted selection (MAS). The large number of quantitative trait loci (QTLs) mapping studies for diverse crops species have provided an abundance of DNA marker-trait associations. In this review, we present an overview of the advantages of MAS and its most widely used applications in plant breeding, providing examples from cereal crops. We also consider reasons why MAS has had only a small impact on plant breeding so far and suggest ways in which the potential of MAS can be realized. Finally, we discuss reasons why the greater adoption of MAS in the future is inevitable, although the extent of its use will depend on available resources, especially for orphan crops, and may be delayed in less-developed countries. Achieving a substantial impact on crop improvement by MAS represents the great challenge for agricultural scientists in the next few decades.     

Restricted best linear unbiased prediction and a selection model

Summary An equivalence between restricted best linear unbiased prediction (and thus restricted selection index) and a particular example of a selection model is presented. Specifically, the equivalence is between restricted selection and a model of selection on the residuals of the general mixed linear model. This result illustrates that restricted selection acts by nonrandomly sampling those genes that act pleiotropically in multiple trait genetic models. An expression for a mixed linear model which includes restrictions is also presented.     

Priors in Whole-Genome Regression: The Bayesian Alphabet Returns

Whole-genome enabled prediction of complex traits has received enormous attention in animal and plant breeding and is making inroads into human and even Drosophila genetics. The term “Bayesian alphabet” denotes a growing number of letters of the alphabet used to denote various Bayesian linear regressions that differ in the priors adopted, while sharing the same sampling model. We explore the role of the prior distribution in whole-genome regression models for dissecting complex traits in what is now a standard situation with genomic data where the number of unknown parameters (p) typically exceeds sample size (n). Members of the alphabet aim to confront this overparameterization in various manners, but it is shown here that the prior is always influential, unless n ≫ p. This happens because parameters are not likelihood identified, so Bayesian learning is imperfect. Since inferences are not devoid of the influence of the prior, claims about genetic architecture from these methods should be taken with caution. However, all such procedures may deliver reasonable predictions of complex traits, provided that some parameters (“tuning knobs”) are assessed via a properly conducted cross-validation. It is concluded that members of the alphabet have a room in whole-genome prediction of phenotypes, but have somewhat doubtful inferential value, at least when sample size is such that n ≪ p.     

5种红树林植物叶片SPAD值比较

以5种红树林植物为研究材料,分析测试其叶片相对叶绿素含量(SPAD值),并比较红树林树种、样区对其叶片SPAD值的影响。结果表明,各样区、各树种以及单株之间SPAD值均存差异,对不同样区进行多重比较,可将其分为7类,5个红树林树种在叶绿素含量上差异较明显。各树种中以秋茄Kandelia obvolata最大(70.4),其次是红海榄Rhizophora stylosa (65.9)和木榄Bruguiera gymnorrhiza (62.9),白骨壤Avicennia marina为51.9,最小为桐花树Aegiceras corniculatum(48.6),树种平均为60.5。试验分析表明,树种因子效应极显著(P<0.01),强于样区因子效应,说明红树林树种是影响其叶片SPAD值的重要因子,同时也表明不同的立地环境条件对叶绿素含量存在影响。5种红树林植物叶片SPAD值均与其树高、基径生长性状存在显著正相关。