Rflps for Somatotropic Genes Identify Quantitative Trait Loci for Growth in Mice

Restriction fragment length polymorphisms for somatotropic genes were tested for associations with body weight and postweaning growth rate in mice. Polymorphisms for growth hormone (GH) and insulin-like growth factor 2 (IGF-2) genes were identified in stock population lines which had been subjected to long-term selection for high 42-day body weight (H lines) or randomly mated (FP and C lines). Two F2 populations of mice (5F2 and MF2) were generated from crosses between a single H line of mice and two unselected control lines and subsequently, two divergently weight selected sublines were generated from each F2 population. The GHh allele which had originally been fixed in three of four H lines and absent from all FP and C lines was found to have a significant (P less than 0.01) effect on 42-day weight and postweaning growth rate in the F2 populations. However, GHh was associated with lower 42-day weight in the F2 populations, suggesting that the positive association between GHh and weight in the stock population was unique to the high weight selected genetic background of those lines. In agreement with this, the frequency of GHh increased in sublines selected for high 42-day weight and decreased in sublines selected for low 42-day weight. The IGF-2H5 allele was associated with higher weights in a sex-dependent manner in 5F2. In the high selected subline derived from 5F2, a significant increase in the frequency of IGF-2H5 was observed. Therefore this allele, in contrast to GHh, appears to be a positive indicator of growth irrespective of genetic background.     

Investigation of Obesity Candidate Genes On Porcine Fat Deposition Quantitative Trait Loci Regions

Objectives: To investigate possible obesity candidate genes in regions of porcine quantitative trait loci (QTL) for fat deposition and obesity‐related phenotypes. Research Methods and Procedures: Chromosome mapping and QTL analyses of obesity candidate genes were performed using DNA panels from a reference pig family. Statistical association analyses of these genes were performed for fat deposition phenotypes in several other commercial pig populations. Results: Eight candidate genes were mapped to QTL regions of pig chromosomes in this study. These candidate genes also served as anchor loci to determine homologous human chromosomal locations of pig fat deposition QTL. Preliminary analyses of relationships among polymorphisms of individual candidate genes and a variety of phenotypic measurements in a large number of pigs were performed. On the basis of available data, gene‐gene interactions were also studied. Discussion: Comparative analysis of obesity‐related genes in the pig is not only important for development of marker‐assisted selection on growth and fat deposition traits in the pig but also provides for an understanding of their genetic roles in the development of human obesity.     

Mapping Quantitative Trait Loci for Grain Appearance Traits of Rice Using a Recombinant Inbred Line Population

A linkage map consisting of 221 markers was constructed based on a recombinant inbred line (RIL) population from the cross between Zhenshan 97 and Minghui 63. Quantitative trait loci (QTL) mapping was carried out for grain appearance traits such as grain length, grain width and grain shape in rice in 1998 and 1999. Based on interval mapping method at the threshold LOD≥2.4, six, two and two QTLs were detected for grain length, grain width and grain shape, respectively, in 1998; In 1999, three, two and two QTLs were identified for the three traits, respectively. Of them, seven QTLs were simultaneously identified in both of the years. The QTL with large effects located in the interval RG393-C1087 on chromosome 3 not only controlled the grain length, but also influenced the grain shape. It explained 57.5%, 61.4% and 26.7%, 29.9% of phenotypic variation of the grain length and the grain shape in two years, respectively. The QTL with large effects located in the interval RG360-C734B on chromosome 5 affected the grain width and the grain shape. It explained 44.2%, 53.2% and 32.1%, 36.0% of phenotypic variation of the grain width and the shape in two years, respectively. Eight, five and five QTLs were identified for the grain length, width and shape, respectively, based on mixed linear-model composite interval mapping method at P =0.005. Their general contributions were 58.81%, 44.75%, and 57.47%. One QTL for the grain length was found to be significant interaction with environment.     

利用水稻重组自交系群体定位谷粒外观性状的数量性状基因

用区间作图和混合线性模型的复合区间作图两种方法,对水稻（Oryza sativa L）珍汕97和明恢63组合的重组自交系群体的谷粒外观性状－粒长,粒宽和粒形进行了数量性状基因（QTL）定位,用区间作图法在LOD≥2．4水平上（近拟于a=0.005),1998年对粒长,粒宽和粒形分别检测到6,2放2个QTLs,1999年对以上3个性状分别检测到3,2和2个QTLs,其中7个QTLs在两年均检测到,位于第3染色体RG393－C1087区间的QTL效应大,同时影响粒长和粒形,两年贡献分别为57．5％,61．4％和26．7％,29．9％,位于第5染色体RG360－C734B区间的QTL效应大,同时影响粒宽和粒形,两年贡献率分别为44．2％,53．2％和32．1％和36．0％,用混合线性模型的复合区间作图法在P＝0．005水平上,对粒长,粒宽和粒形分别检测到8,5和5个QTLs,共解释各自性状变异的58．81％,44．75％和57．47％,只检测到1个QTL与环境之间存在的显互作。     

Mixed Effects Models for Quantitative Trait Loci Mapping With Inbred Strains

Fixed effects models have dominated the statistical analysis of genetic crosses between inbred strains. In spite of their popularity, the traditional models ignore polygenic background and must be tailored to each specific cross. We reexamine the role of random effect models in gene mapping with inbred strains. The biggest difficulty in implementing random effect models is the lack of a coherent way of calculating trait covariances between relatives. The standard model for outbred populations is based on premises of genetic equilibrium that simply do not apply to crosses between inbred strains since every animal in a strain is genetically identical and completely homozygous. We fill this theoretical gap by introducing novel combinatorial entities called strain coefficients. With an appropriate theory, it is possible to reformulate QTL mapping and QTL association analysis as an application of mixed models involving both fixed and random effects. After developing this theory, our first example compares the mixed effects model to a standard fixed effects model using simulated advanced intercross line (AIL) data. Our second example deals with hormone data. Here multivariate traits and parameter identifiability questions arise. Our final example involves random mating among eight strains and vividly demonstrates the versatility of our models.     

Detection of Quantitative Trait Loci for Yield and Drought Tolerance Traits in Soybean Using a Recombinant Inbred Line Population

To investigate the genetic basis of drought tolerance in soybean （Glycine max L. Merr.） a recombinant inbred population with 184 F2：7：11 lines developed from a cross between Kefengl （drought tolerant） and Nannong1138-2 （drought sensitive） were tested under water-stressed and well-watered conditions in field and greenhouse trials. Traits measured included leaf wilting coefficient, excised leaf water loss and relative water content as indicators of plant water status and seed yield. A total of 40 quantitative trait loci （QTLs） were identified： 17 for leaf water status traits under drought stress and 23 for seed yield under well-watered and drought-stressed conditions in both field and greenhouse trials. Two seed yield QTLs were detected under both well-watered and drought-stressed conditions in the field on molecular linkage group H and Dlb, while two seed yield QTLs on molecular linkage group C2 were found under greenhouse conditions. Several QTLs for traits associated with plant water status were identified in both field and greenhouse trials, including two leaf wilting coefficient QTLs on molecular linkage group A2 and one excised leaf water loss QTL on molecular linkage group H. Phenotypic correlations of traits suggested several QTLs had pleiotropic or location-linked associations. These results will help to elucidate the genetic basis of drought tolerance in soybean, and could be incorporated into a marker-assisted selection breeding program to develop high-yielding soybean cultivars with improved tolerance to drought stress.     

Detection of Quantitative Trait Loci for Yield and Drought Tolerance Traits in Soybean Using a Recombinant Inbred Line Population

To investigate the genetic basis of drought tolerance in soybean ( Glycine max L. Merr.) a recombinant inbred population with 184 F_2:7:11 lines developed from a cross between Kefeng1 (drought tolerant) and Nannong1138-2 (drought sensitive) were tested under water-stressed and well-watered conditions in field and greenhouse trials. Traits measured included leaf wilting coefficient, excised leaf water loss and relative water content as indicators of plant water status and seed yield. A total of 40 quantitative trait loci (QTLs) were identified: 17 for leaf water status traits under drought stress and 23 for seed yield under well-watered and drought-stressed conditions in both field and greenhouse trials. Two seed yield QTLs were detected under both well-watered and drought-stressed conditions in the field on molecular linkage group H and D1b, while two seed yield QTLs on molecular linkage group C2 were found under greenhouse conditions. Several QTLs for traits associated with plant water status were identified in both field and greenhouse trials, including two leaf wilting coefficient QTLs on molecular linkage group A2 and one excised leaf water loss QTL on molecular linkage group H. Phenotypic correlations of traits suggested several QTLs had pleiotropic or location-linked associations. These results will help to elucidate the genetic basis of drought tolerance in soybean, and could be incorporated into a marker-assisted selection breeding program to develop high-yielding soybean cultivars with improved tolerance to drought stress.     

Identification of Quantitative Trait Loci for Bacterial Blight Resistance Derived from Oryza meyeriana and Agronomic Traits in Recombinant Inbred Lines of Oryza sativa

Bacterial blight (BB) is one of the major diseases that affect rice productivity. In previous studies, BB resistance was transferred to cultivated rice Oryza sativa from wild rice Oryza meyeriana using asymmetric somatic hybridization. One of the resistant hybrid progenies (Y73) has also been shown to possess novel resistance gene(s) different from any of those previously associated with BB resistance. We have mapped quantitative trait loci (QTLs) for BB resistance in a recombinant inbred line (RIL) population derived from a cross between Y73 and a BB‐susceptible cv. IR24. Five QTLs were detected where Y73 alleles contributed to increased BB resistance. Three minor QTLs were identified on chromosomes 3, 10 and 11, and two major QTLs on chromosomes 1 and 5, respectively. QTL on chromosome 5, designated qBBR5, had the strongest effect on BB resistance, explaining approximately 37% of the phenotypic variance. Using the same RIL population, we also mapped QTLs for agronomic traits including plant height (PH), heading date (HD), plant yield (PYD) and PYD component traits. A total of 21 QTLs were identified, of which four were detected for PH, six for HD, three for panicle number per plant (PNPP), one for spikelets per panicle (SPP), six for 1000‐grain weight (TGW) and one for PYD. qPH1 (a QTL for PH) was found in the same interval as qBBR1 for BB resistance, and qHD11 for HD and qBBR11 for BB resistance also shared a similar interval. Additionally, BB resistance was significantly correlated with PH or HD in the RIL population. This suggests that the resistance genes may have pleiotropic effects on, or close linkage to, genes controlling PH or HD. These results will help deduce the resistance mechanisms of the novel resistance gene(s) and provide the basis for cloning them and using them in marker‐assisted breeding.     

玉米叶形相关性状的Meta-QTL及候选基因分析

叶长、叶宽、叶面积及叶夹角不仅影响玉米(Zea mays)光合效率, 也是株型的重要构成因素。通过对620个叶形QTL进行整合, 构建不同遗传背景下的叶形QTL整合图谱, 利用元分析发掘出22个叶长、22个叶宽、12个叶面积以及17个叶夹角mQTL; 进一步运用生物信息学手段, 确定44个与叶片发育密切相关的候选基因。分析发现, 仅有NAL7-like、YABBY6- like和GRF2等13个基因位于mQTL区间内, 而玉米中已克隆的KNOTTED1、AN3/GIF1、rgd1/lbl1、mwp1及SRL2-like、HYL1-like和CYCB2;4-like等水稻(Oryza sativa)和拟南芥(Arabidopsis thaliana)叶形同源基因位于未被整合的QTL内; 对44个候选基因在叶片长、宽、厚发育过程中基部-末端、中央-边缘、远轴-近轴的调控机理进行归纳分析, 发现玉米中仅有少数几个候选基因被报道, 揭示了叶形发育的部分分子机理。因此, 对玉米叶形相关mQTL/QTL及基因进行全面深入的分析, 不仅有助于增加对其遗传结构的了解, 发掘更多候选基因, 阐明叶形发育和形成的分子机制, 还可为耐密理想株型的分子标记辅助选择提供依据。     

The Nxsm Recombinant Inbred Strains of Mice: Genetic Profile for 58 Loci Including the Mtv Proviral Loci

We report the construction of 17 recombinant inbred (RI) strains of mice derived from the progenitor strains NZB/BINRe and SM/J and the typing of this RI strain set, designated NXSM, for 58 loci distributed on 16 autosomes and the X chromosome. Two backcrosses involving NZB/BINJ and SM/J were constructed to confirm chromosomal assignments and determine gene orders suggested from NXSM RI strain data. From these results we recommend that chromosomal assignments and gene orders suggested from analyses of RI strain sets be confirmed using data obtained by other means. We also typed NZB/BINJ and SM/J for mammary tumor proviral (Mtv) loci. Both strains share three previously described Mtv loci: Mtv-7, Mtv-14 and Mtv-17. In addition, NZB/BINJ contains the previously described Mtv-3 and Mtv-9 loci and two new Mtv proviral loci: Mtv-27 located on chromosome (Chr) 1 and Mtv-28 located on the X chromosome. SM/J contains the previously described loci Mtv-6 and Mtv-8. Four LTR, mink cell focus-forming murine leukemia viral loci were identified and mapped: Ltrm-1 on Chr 12, Ltrm-2 on Chr 16, Ltrm-3 on Chr 5, and Ltrm-4 on Chr 13. The Tgn locus was positioned proximal to the Ly-6 locus on Chr 15.     

水稻QTL定位研究进展

水稻的许多重要农艺性状均属于数量性状,研究水稻数量性状遗传对水稻育种具有十分重要的意义.近年来大量的研究揭示了水稻QTL的基本特征,剖析了重要农艺性状的遗传基础,给水稻遗传改良带来了新策略,不断深入的研究已经完成了水稻特定数量基因的精细定位和克隆,到目前为止已经有一万多个水稻QTL进行了定位,其中有19个进行了克隆,这对水稻育种具有十分重要的意义.本文主要综述了QTL定位的理论基础,水稻QTL定位的研究进展,并对水稻QTL研究的趋势进行了展望.     

作物数量性状基因研究进展

分子生物技术的发展对作物数量性状基因(QTL)研究提供了条件,不同的定位群体各有其特点,相继出现的QTL定位方法也逐步完善.大量的研究揭示了QTL的基本特征,剖析了重要农艺性状的遗传基础,给作物遗传改良带来了新的策略,不断深入的研究已经完成了特定QTL的精细定位和克隆.本文从QTL的定位群体,定位方法,研究现状,精细定位与克隆,以及QTL利用等方面对作物数量性状基因的研究进行了综述。 Abstract:With the rapid development of molecular biotechnology,QTL analyses were executed for a lot of important agronomic traits in many crops.Different experimental populations and mapping methods had their own advantages in QTL analysis.Amounts of studies paid attention to locate the QTLs for important traits,and others tried to disect the genetic bases using molecular markers.Near isogenic lines were the best populations for QTL fine mapping and positional cloning,A few studies had been reported their results on materials with improvement traits using marker-assisted selection.This paper summarizes the recent progress on QTL mapping populations and methods,the status of QTL locating,QTL fine mapping and positional cloning,and QTL.application in breeding.     

作物数量性状基因研究进展

分子生物技术的发展对作物数量性状基因（QTL）研究提供了条件,不同的定位群体各有其特点,相继出现的QTL定位也逐步完善。大量的研究揭示了QTL的基本特征,剖析了重要农艺4性状的遗传基础,给作物遗传改良带来了新的策略,不断深入的研究已经完成了特定的QTL的精细定位和克隆。本从QTL的定位群体,定位方法,研究现状,精细定位与克隆,以及QTL利用等方面对作物数量性状基因的研究进行了综述。     

构建数量性状基因图谱的几种统计方法

以线性数学模型为线索,概述了用于构建数量性状基因图谱的几种主要统计方法,包括方差分析法、标记回归法、区间作图法、复合区间作图法、Jansen的复合区间作图法、双侧标记回归法以及新近发展的多区间作图法和多亲本作图法等.讨论了各种方法的优缺点. Abstract:Statistical methods for mapping QTLs were summarized, including one marker analysis, arker regression analysis,interval mapping (IM),composite interval mapping (CIM),Jansen's composite interval mapping, flanking marker regression analysis,multiple interval mapping (MIM) and multiple families mapping.Their advantages and disadvantages were discussed.     

Multiple Trait Analysis of Genetic Mapping for Quantitative Trait Loci

We present in this paper models and statistical methods for performing multiple trait analysis on mapping quantitative trait loci (QTL) based on the composite interval mapping method. By taking into account the correlated structure of multiple traits, this joint analysis has several advantages, compared with separate analyses, for mapping QTL, including the expected improvement on the statistical power of the test for QTL and on the precision of parameter estimation. Also this joint analysis provides formal procedures to test a number of biologically interesting hypotheses concerning the nature of genetic correlations between different traits. Among the testing procedures considered are those for joint mapping, pleiotropy, QTL by environment interaction, and pleiotropy vs. close linkage. The test of pleiotropy (one pleiotropic QTL at a genome position) vs. close linkage (multiple nearby nonpleiotropic QTL) can have important implications for our understanding of the nature of genetic correlations between different traits in certain regions of a genome and also for practical applications in animal and plant breeding because one of the major goals in breeding is to break unfavorable linkage. Results of extensive simulation studies are presented to illustrate various properties of the analyses.     

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。     

Polygenic Mutation in Drosophila Melanogaster: Genetic Interactions between Selection Lines and Candidate Quantitative Trait Loci

We have investigated genetic interactions between spontaneous mutations affecting abdominal and sternopleural bristle number that have accumulated in 12 long-term selection lines derived from an inbred strain, and mutations at 14 candidate bristle number quantitative trait loci. The quantitative test for complementation was to cross the selection lines to an inbred wild-type strain (the control cross) and to a derivative of the control strain into which the mutant allele at the candidate locus to be tested was substituted (the tester strain). Genetic interactions between spontaneous mutations affecting bristle number and the candidate locus mutations were common, and in several cases the interaction effects were different in males and females. Analyses of variance of the (tester - control) differences among and within groups of replicate lines selected in the same direction for the same trait showed significant group effects for several candidate loci. Genetically, the interactions could be caused by allelism of, and/or epistasis between, spontaneous mutations in the selection lines and the candidate locus mutations. It is possible that much of the response to selection was from new mutations at candidate bristle number quantitative trait loci, and that for some of these loci, mutation rates were high.