基于F3种子的胚乳性状QTL区间定位

文章提出了包括胚乳效应和母体效应的胚乳性状QTL定位的统计方法,该方法的实验设计是分子标记基因型信息来自F2母体植株和F3种子胚(或植株),胚乳性状表型值来自F3单粒种子胚乳,称之为两步等级设计。同时,用计算机全面模拟以验证该模型的可行性,模拟结果表明,只要群体足够大,该模型能较有效地进行胚乳性状QTL定位并精确地估计出胚乳QTL的各种遗传效应和母体效应。     

水稻亚种间杂交粒重及加工品质性状的遗传效应分析

用4个广亲和粳型品种和5个籼型品种为材料,按NCⅡ设计配制杂交组合,获得同一环境下的亲本及F_1植株上的籽粒群体(F_2),对其稻谷千粒重、糙米千粒重、出糙率、总精米率以及整精米率等粒重和加工品质性状进行测定,并按胚乳性状遗传模型和混合线性模型的分析方法对籼粳亚种间杂交稻粒重及加工品质性状的遗传效应进行了研究,结果表明:籼粳交籽粒的粒重及各加工品质性状同时受到胚乳直接基因效应、母体基因效应以及微弱的细胞质效应的影响,但其主要受制于母体加性效应,并且存在一定的胚乳杂种优势和母体杂种优势;不同亲本品种对于粒重及加工品质性状的遗传改良具有不同的作用.     

家畜抗性等级性状的QTL定位方法

在广义线性模型的框架内模拟研究了家畜抗性等级性状的QTL定位方法,QTL参数的估计采用最大似然方法,比较了阈模型方法与一般线性方法的QTL定位效率,并对影响等级性状QTL定位效率的主要因素（QTL效应、性状的遗传力）进行了模拟研究,实验设计为多个家系的女儿设计,资源群体大小为500头。研究结果表明：在QTL位置参数估计及检验功效方面,阈模型方法具有一定的优势,对抗性等级性状QTL定位的功效也高于线性方法。另外,性状遗传力和QTL效应的大小对QTL定位的准确度也有直接的影响,随着性状遗传力QTL效应的     

杂交一代作图群体大小对茶树QTL效应估计的影响

利用杂交一代(F_1)作图群体进行遗传定位是研究茶树数量性状的重要手段,然而F_1群体大小对定位有显著影响。本研究以327份龙井43×白毫早F_1群体及它们的春季发芽期、新梢颜色和叶形指数3个性状的田间观测数据为基础,采用随机抽样的方法生成60个不同大小的作图群体(n=50,100,150,200,250,300),并利用基于SSR分子标记的连锁图谱进行QTL定位分析,以探讨F_1群体大小对茶树QTL定位结果的影响。结果表明QTL效应估计受群体大小的影响显著;当群体达150份时可基本保证检出效应在10%以上的QTL,但并不能实现对QTL效应值的准确估计,且最高与最低估计值相差可达2. 83倍。因此在研究和育种工作中,建议在条件允许的情况下应尽量扩大作图群体,对于从较小F_1群体中得到的QTL效应值应谨慎对待。     

胚乳性状数量基因的定位方法

将三倍体胚乳性状的数量遗传模型和二倍体性状数量基因（QTL）图构建方法相结合,导出双侧标记基因型下有关胚乳性状QTL的遗传组成、平均数和遗传方差分量,据之提出以某一区间双侧标记基因型胚乳性状的平均值为依变数,以该区间内任一点假定存在的QTL的加性效应d、显性效应h1和／或h2的系数为自变数,进行有重复观察值的多元线性回归分析,根据多元线性回归的显著性测验该点是否存在QTL,并估计出QTL的遗传效应。给定区间内任一点,皆可以此进行分析,从而可在整条染色体上作图,并以之确定QTL的数目和最可能位置,同时,在检测某一区间时,利用多元线性回归方法将该区间外可能存在的QTL的干扰进行统计控制,以提高QTL检测的精度。此外,还讨论了如何将之推广应用于其他类型的DNA不对应资料以及具复杂遗传模型的胚乳性状资料。     

离散性状QTL区间定位的最大似然方法

采用最大似然区间定位法对阈模型与一般线性模型的QTL定位效率进行了比较,并对影响离散性状QTL检测效率的主要因素（QTL效应、性状的遗传力和表型发生率）进行了模拟研究,实验设计为多个家系的女儿设计．资源群体大小为500头。研究结果表明：在QTL参数估计及检验功效方面,阈模型方法具有较大的优势,对离散性状QTL定位的效率明显高于LM（Linear Model）方法,定位的准确性也较高。另外,性状遗传力、QTL效应的大小和性状表型发生率对QTL定位的准确度也有直接的影响,随着性状遗传力和表型发生率的提高,随着QTL效应的增大,QTL定位的效率也进一步提高。     

作物杂种后代基因型值和杂种优势的预测方法

本文提出了利用作物亲本和F_1预测杂种后代基因型值和杂种优势的统计分析方法.该方法运用加性-显性遗传模型,分析双列杂交试验资料,用MINQUE(1)法估算方差分量以及预测遗传效应值.由加性和显性效应预测值可进一步预测F_1,F_2,BC_1,BC_2,等不同世代的基因型值,在预测F_1群体平均优势和群体超亲优势的基础上,可以推导出其它各世代的杂种优势.提出了预测杂种后代保持超亲优势世代数的简单公式,根据杂交组合F_1群体平均优势和双亲相对遗传差异,便可预测该组合能在生产上直接利用的世代数.以棉花六个品种完全双列杂交试验资料为例,分析了各组合F_1和F_2的基因型值、超亲优势和保持5％超亲优势的世代数.     

玉米籽粒性状的遗传效应分析

采用二倍体胚和三倍体胚乳种子遗传模型及其分析方法,以5个玉米自交系及其配制的F1,F2,BC1,BC2世代为材料,研究5个玉米种子性状的胚直接效应、胚乳直接效应、母体效应和细胞质效应。分析结果表明,除粒宽外,各性状的遗传同时由细胞质效应和胚、胚乳、母体基因效应所控制,百粒重主要受胚乳和母体效应的影响,粒长的遗传以母体效应为主,粒宽和粒厚以胚乳效应为主。各部位籽粒百粒重的胚乳直接加性效应与母体加性效应的协方差达到显著或极显著水平,其余性状的胚、胚乳直接效应与母体效应间的协方差均不显著,通过母体植株的遗传表现可以对这些性状进行有效的选择。S22 是改良百粒重的优良亲本。 Abstract：The embryo,endosperm and cytoplasm effects of seven seed traits were studied by genetic model for diploid embryo and triploid endosperm plant seeds using five inbreds and their F1, F2, BC1 and BC2 generations. The estimates of genetic variance components indicated that the inheritance of all other kernel traits was controlled by the four effects except kernel width. The 100?kernel weight was mainly controlled by endosperm and maternal effects , and kernel length was controlled by the maternal effects,while endosperm conrrolled kernel width and kernel thickness. Except the significant or highly significant covariances between the endosperm direct additive and maternal additive effects for 100－kernel weight,all other traits between the embryo or endosperm direct effect and the maternal were not significant. So,maize inbreds could be developed by direct selection based on maternal plants for these traits. S22 was the best inbred of the improvement for kernel weight in this study.     

利用Bayesian-MCMC方法进行畜禽复杂离散性状QTL定位

复杂离散性状由于表型数据呈离散分布并且提供信息量过小, 因此很难用常规的统计方法对此类性状的QTL进行定位研究. Bayesian-MCMC方法是复杂离散性状QTL定位的重要手段, 该方法通过所有先验信息来推导QTL参数的后验分布并利用Markov Chain随机过程进行抽样的方法对目标参数进行统计推断. 利用Monte Carlo方法, 针对畜禽远交群体模拟产生多个全同胞家系的2级分类复杂离散性状, 然后基于IBD方差组分的随机模型的定位策略, 同时利用MCMC的3种不同抽样技术(Gibbs抽样、Metropolis抽样和Reversible Jump MCMC抽样)产生相应QTL参数的后验样本, 并进行了目标参数的Bayesian统计推断. 结果表明: Bayesian-MCMC方法能够对不同家系结构和QTL效应水平下复杂离散性状QTL进行有效检测; 当家系含量增加时, QTL定位的精确性和准确性提高, 并可适用于效应更小QTL的检测.     

籼稻糙米厚度的发育遗传研究

应用包括３套遗传体系基因效应的数量性状发育遗传模型,分析了１２个籼稻亲本在４个不同稻米发育时期的糙米厚性状。结果表明,三倍体胚乳、二倍体母体植株基因的加性和显性效应以及细胞质效应均可以明显影响各个稻米发育时期的糙米厚度,其中灌浆始期以二倍体母体植株效应为主,灌浆中后期以三倍体胚乳效应为主,成熟期则以细胞质效应为主。在４个不同发育时期中,控制糙米厚的基因加性效应和显性效应交替为主。胚乳显性方差和母体     

Experimental designs and statistical methods for mapping quantitative trait loci underlying triploid endosperm traits without maternal genetic variation

Many endosperm traits are related to grain quality in cereal crops. Endosperm traits are mainly controlled by the endosperm genome but may be affected by the maternal genome. Studies have shown that maternal genotypic variation could greatly influence the estimation of the direct effects of quantitative trait loci (QTLs) underlying endosperm traits. In this paper, we propose methods of interval mapping of endosperm QTLs using seeds of F2 or BC1 (an equal mixture of F1 x P1 and F1 x P2 with F1 as the female parent) derived from a cross between 2 pure lines (P1 x P2). The most significant advantage of our experimental designs is that the maternal effects do not contribute to the genetic variation of endosperm traits and therefore the direct effects of endosperm QTLs can be estimated without the influence of maternal effects. In addition, the experimental designs can greatly reduce environmental variation because a few F1 plants grown in a small block of field will produce sufficient F2 or BC1 seeds for endosperm QTL analysis. Simulation studies show that the methods can efficiently detect endosperm QTLs and unbiasedly estimate their positions and effects. The BC1 design is better than the F2 design.     

Statistical model for characterizing epistatic control of triploid endosperm triggered by maternal and offspring QTLs

To study the effects of maternal and endosperm quantitative trait locus (QTL) interaction on endosperm development, we derive a two-stage hierarchical statistical model within the maximum-likelihood context, implemented with an expectation-maximization algorithm. A model incorporating both maternal and offspring marker information can improve the accuracy and precision of genetic mapping. Extensive simulations under different sampling strategies, heritability levels and gene action modes were performed to investigate the statistical properties of the model. The QTL location and parameters are better estimated when two QTLs are located at different intervals than when they are located at the same interval. Also, the additive effect of the offspring QTLs is better estimated than the additive effect of the maternal QTLs. The implications of our model for agricultural and evolutionary genetic research are discussed.     

水稻丽粳2号近等基因系杂种后代耐冷性遗传研究

在昆明低温冷害条件下,以十和田×(十和田和丽粳2号BC4F5)配制的杂种BC5F1、BC5F2、BC5F3和BC5F4及亲本为材料,用主基因-多基因混合遗传模型对丽粳2号作耐冷基因供体培育出的近等基因系进行孕穗期耐冷性遗传研究。结果表明:(1)杂种BC5F2、BC5F3和BC5F4分离群体在同一世代每穗实粒数与总粒数、结实率呈极显著的正相关;(2)以结实率为耐冷性鉴定指标,近等基因系孕穗期耐冷性受2对主基因和多基因共同控制,其主效基因的遗传率为90.97%,微效基因遗传率为3.83%,主基因和微效基因都存在加性-显性-上位性效应。     

Statistical methods for dissecting triploid endosperm traits using molecular markers. An autogamous model

The endosperm, a result of double fertilization in flowering plants, is a triploid tissue whose genetic composition is more complex than diploid tissue. We present a new maximum-likelihood-based statistical method for mapping quantitative trait loci (QTL) underlying endosperm traits in an autogamous plant. Genetic mapping of quantitative endosperm traits is qualitatively different from traits for other plant organs because the endosperm displays complicated trisomic inheritance and represents a younger generation than its mother plant. Our endosperm mapping method is based on two different experimental designs: (1) a one-stage design in which marker information is derived from the maternal genome and (2) a two-stage hierarchical design in which marker information is derived from both the maternal and offspring genomes (embryos). Under the one-stage design, the position and additive effect of a putative QTL can be well estimated, but the estimates of the dominant and epistatic effects are upward biased and imprecise. The two-stage hierarchical design, which extracts more genetic information from the material, typically improves the accuracy and precision of the dominant and epistatic effects for an endosperm trait. We discuss the effects on the estimation of QTL parameters of different sampling strategies under the two-stage hierarchical design. Our method will be broadly useful in mapping endosperm traits for many agriculturally important crop plants and also make it possible to study the genetic significance of double fertilization in the evolution of higher plants.     

云南元江普通野生稻株高和抽穗期QTL定位研究

以云南元江普通野生稻为供体亲本,在特青的遗传背景下构建了一套BC3高代回交群体。利用117个SSR标记分析383个BC3F2株系的基因型,采用单标记分析法对控制元江普野株高和抽穗期的QTL进行分析。在北京和合肥两个地点试验结果表明,控制株高的QTL分布在第1染色体上,在RM104附近有一个QTL,与sd-1位置相当,其对表现型变异的贡献率在两个地点分别为27％和28％,其加性效应值分别为26．24cm和26．28cm,来自野生稻的等位基因显著提高回交群体的株高;在第1、3、7、8、11染色体共检测到6个控制抽穗期QTL,其中第8染色体RM25附近控制抽穗期的QTL在两个地点的贡献率分别为13％和15％,加性效应值为4．60d和3．65d,来自野生稻的等位基因使回交群体抽穗期延迟。     

Mixed linear model approach for mapping quantitative trait loci underlying crop seed traits

The crop seed is a complex organ that may be composed of the diploid embryo, the triploid endosperm and the diploid maternal tissues. According to the genetic features of seed characters, two genetic models for mapping quantitative trait loci (QTLs) of crop seed traits are proposed, with inclusion of maternal effects, embryo or endosperm effects of QTL, environmental effects and QTL-by-environment (QE) interactions. The mapping population can be generated either from double back-cross of immortalized F₂ (IF₂) to the two parents, from random-cross of IF₂ or from selfing of IF₂ population. Candidate marker intervals potentially harboring QTLs are first selected through one-dimensional scanning across the whole genome. The selected candidate marker intervals are then included in the model as cofactors to control background genetic effects on the putative QTL(s). Finally, a QTL full model is constructed and model selection is conducted to eliminate false positive QTLs. The genetic main effects of QTLs, QE interaction effects and the corresponding P-values are computed by Markov chain Monte Carlo algorithm for Gaussian mixed linear model via Gibbs sampling. Monte Carlo simulations were performed to investigate the reliability and efficiency of the proposed method. The simulation results showed that the proposed method had higher power to accurately detect simulated QTLs and properly estimated effect of these QTLs. To demonstrate the usefulness, the proposed method was used to identify the QTLs underlying fiber percentage in an upland cotton IF₂ population. A computer software, QTLNetwork-Seed, was developed for QTL analysis of seed traits.     

A statistical model for estimating maternal-zygotic interactions and parent-of-origin effects of QTLs for seed development

Proper development of a seed requires coordinated exchanges of signals among the three components that develop side by side in the seed. One of these is the maternal integument that encloses the other two zygotic components, i.e., the diploid embryo and its nurturing annex, the triploid endosperm. Although the formation of the embryo and endosperm contains the contributions of both maternal and paternal parents, maternally and paternally derived alleles may be expressed differently, leading to a so-called parent-of-origin or imprinting effect. Currently, the nature of how genes from the maternal and zygotic genomes interact to affect seed development remains largely unknown. Here, we present a novel statistical model for estimating the main and interaction effects of quantitative trait loci (QTLs) that are derived from different genomes and further testing the imprinting effects of these QTLs on seed development. The experimental design used is based on reciprocal backcrosses toward both parents, so that the inheritance of parent-specific alleles could be traced. The computing model and algorithm were implemented with the maximum likelihood approach. The new strategy presented was applied to study the mode of inheritance for QTLs that control endoreduplication traits in maize endosperm. Monte Carlo simulation studies were performed to investigate the statistical properties of the new model with the data simulated under different imprinting degrees. The false positive rate of imprinting QTL discovery by the model was examined by analyzing the simulated data that contain no imprinting QTL. The reciprocal design and a series of analytical and testing strategies proposed provide a standard procedure for genomic mapping of QTLs involved in the genetic control of complex seed development traits in flowering plants.     

The QTL analysis on maternal and endosperm genome and their environmental interactions for characters of cooking quality in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L<Emphasis Type="Italic">.</Emphasis>)

Investigations to identify quantitative trait loci (QTLs) governing cooking quality traits including amylose content, gel consistency and gelatinization temperature (expressed by the alkali spread value) were conducted using a set of 241 RIL populations derived from an elite hybrid cross of “Zhenshan 97” × “Minghui 63” and their reciprocal backcrosses BC₁F₁ and BC₂F₁ populations in two environments. QTLs and QTL × environment interactions were analyzed by using the genetic model with endosperm and maternal effects and environmental interaction effects on quantitative traits of seed in cereal crops. The results suggested that a total of seven QTLs were associated with cooking quality of rice, which were subsequently mapped to chromosomes 1, 4 and 6. Six of these QTLs were also found to have environmental interaction effects.