Method for mapping a partial lethal-factor locus on a molecular-marker linkage map of a backcross and doubled-haploid population

 Distorted segregation has been repeatedly observed in various plant species in molecular-marker linkage mapping where distant crosses were made. It may be caused by a partial lethal-factor acting in the filial generations. A method is presented for estimating the recombination values between a partial lethal-factor locus and a linked molecular marker and the relative viability or fertilization ability of zygotes or gametes, respectively affected by the partial lethal factor in backcross (BC) and doubled-haploid (DH) populations using the maximum-likelihood method associated with the expectation maximization (EM) algorithm. The method was applied to segregation data of molecular markers for a population of 150 DH lines developed from the ‘Steptoe’בMorex’ cross in barley. The presence of a partial lethal-factor locus, located on chromosome 4, causing partial selection was suggested. This locus was tightly linked to the ABG500B marker, and the chance of fertilization of female gametes possessing the partial lethal factor was, on average, 59.8% that of a normal one. Two additional partial lethal factors were found on chromosome 5. Received: 3 December 1997 / Accepted: 25 February 1998     

A genetic linkage map for tef [Eragrostis tef (Zucc.) Trotter]

Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4x = 40) and a genome size of 730 Mbp. Ninety-four F₉ recombinant inbred lines (RIL) derived from the interspecific cross, Eragrostis tef cv. Kaye Murri × Eragrostis pilosa (accession 30-5), were mapped using restriction fragment length polymorphisms (RFLP), simple sequence repeats derived from expressed sequence tags (EST–SSR), single nucleotide polymorphism/insertion and deletion (SNP/INDEL), intron fragment length polymorphism (IFLP) and inter-simple sequence repeat amplification (ISSR). A total of 156 loci from 121 markers was grouped into 21 linkage groups at LOD 4, and the map covered 2,081.5 cM with a mean density of 12.3 cM per locus. Three putative homoeologous groups were identified based on multi-locus markers. Sixteen percent of the loci deviated from normal segregation with a predominance of E. tef alleles, and a majority of the distorted loci were clustered on three linkage groups. This map will be useful for further genetic studies in tef including mapping of loci controlling quantitative traits (QTL), and comparative analysis with other cereal crops.Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

遗传群体偏分离研究进展

偏分离是指观察到的基因型比例偏离预期的孟德尔分离频率方式,无法用传统的遗传理论和方法加以分析。偏分离被认为是一种重要的进化动力,并对遗传连锁图谱的构建造成影响。本文针对偏分离的现象、偏分离的影响因素和形成原因,以及对QTL定位的影响等方面进行综合分析,系统阐述了植物分离群体偏分离的研究进展,为后续研究提供有益的参考。     

遗传群体偏分离研究进展

偏分离是指观察到的基因型比例偏离预期的孟德尔分离频率方式,无法用传统的遗传理论和方法加以分析。偏分离被认为是一种重要的进化动力,并对遗传连锁图谱的构建造成影响。本文针对偏分离的现象、偏分离的影响因素和形成原因,以及对QTL定位的影响等方面进行综合分析,系统阐述了植物分离群体偏分离的研究进展,为后续研究提供有益的参考。     

远缘杂交中不育基因的位置和效应的最大似然估计

提出了一种统计方法,利用标记位点的异常分离,来估计远缘杂交中不育基因位点的位置和效应,在回交群体中,用最大似然法对不育基因与标记位点之间的生组值和配子存活率进行估计。将表现连续分布的育性指标转化为百连续变异的遗传标记的分离,可以避免对育性直接观测所带来的重组值估计结果的不稳定,还可以同时估计雌雄配子的存活率。     

Method for the mapping of a female partial-sterile locus on a molecular marker linkage map

The female gametophyte is an absolutely essential structure for angiosperm reproduction, and female sterility has been reported in a number of crops. In this paper, a maximum-likelihood method is presented for estimating the position and effect of a female partial-sterile locus in a backcross population using the observed data of dominant or codominant markers. The ML solutions are obtained via Bailey’s method. The process for the estimating of the recombination fractions and the viabilities of female gametes are described, and the variances of the estimates of the parameters are also presented. Application of the method is demonstrated using a set of simulated data. This method circumvents the problems of the traditional mapping methods for female sterile genes which were based on data from seed set or embryo-sac morphology and anatomy.     

Segregation,linkage, and diversity of allozymes in knobcone pine

Summary Female gametophytes of knobcone pine were used to study genetic variation at 58 loci in 26 enzyme systems. Mendelian segregation and linkage were tested at 21 loci. Got1, Pgi2, Mnr3, Adh2, and Lap2 were linearly arrayed in a single linkage group. Est and Acp3, and Flest and Lap1, formed two independent linkage groups. Although Mendelian segregation was the rule, several cases of segregation distortion were observed. Pooled over trees, Lap1 and Aap1 showed significant distortion. Of 11 cases of distortion observed for individual trees, 10 showed an excess of common alleles. Pooled over both loci and trees, giving a total sample of 17,183 gametes, the common alleles were significantly overrepresented by 1.1%, and heterogeneity was highly significant. Our results, and others in the literature, suggest that segregation distortion may affect the genetic structure of conifer populations.     

Estimation of unbiased recombination values in the presence of misclassification of a trait using RFLP maps

The effect of misclassification of phenotypes of a trait on the estimation of recombination value was investigated. The effect was larger for closer linkage. If a locus is dominant and linked with the misclassfied trait locus in the repulsion phase, then the effect on the recombination value between the two loci is largest. A method for estimating the unbiased recombination value and the misclassification rate using maximum likelihood associated with an EM algorithm is also presented. This method was applied to a numerical example from rice genome data. It was concluded that the present method combined with the metric multi-dimensional scaling method is useful for the detection of misclassified markers and for the estimation of unbiased recombination values.     

A linkage map based on information from four F2 populations of maize (Zea mays L.)

Summary Recently, maize (Zea mays L.) genetic maps based primarily upon segregating restriction fragment length polymorphisms (RFLPs) have been developed by several research groups. Some of the reported maps were based upon data from a single segregating population, whereas others were based upon information from several segregating populations. Potential problems with pooling information from several segregating populations have not been reported. These include the fact that few genetic markers are polymorphic in all populations, estimates of linkage may differ among populations, and population sizes may differ. We utilize the log-likelihood statistic to genetically map partially overlapping sets of informative genetic markers, to test homogeneity of recombination among populations, and to present a composite RFLP linkage map based upon data pooled from four F₂ populations.     

A molecular marker-based linkage map of diploid bananas (Musa acuminata)

A partial molecular linkage map of the Musa acuminata diploid genome is presented. This map is based on 58 RFLP, four isozyme and 28 RAPD markers segregating in an F₂ population of 92 individuals. A total of 90 loci was detected, 77 of which were placed on 15 linkage groups while 13 segregated independently. Segregation distortions were shown by 36% of all loci, mostly favoring the male parent. Chromosome structural rearrangements were believed to be one of the main causes of these distortions. The use of genetic linkage data to further the genetic and evolutionary knowledge of the genus Musa, as well as to help improve the design of breeding strategies, is discussed.     

Selective genotyping for determination of linkage between a marker locus and a quantitative trait locus

Summary Selective genotyping is the term used when the determination of linkage between marker loci and quantitative trait loci (QTL) affecting some particular trait is carried out by genotyping only individuals from the high and low phenotypic tails of the entire sample population. Selective genotyping can markedly decrease the number of individuals genotyped for a given power at the expense of an increase in the number of individuals phenotyped. The optimum proportion of individuals genotyped from the point of view of minimizing costs for a given experimental power depends strongly on the cost of completely genotyping an individual for all of the markers included in the experiment (including the costs of obtaining a DNA sample) relative to the cost of rearing and trait evaluation of an individual. However, in single trait studies, it will almost never be useful to genotype more than the upper and lower 25% of a population. It is shown that the observed difference in quantitative trait values associated with alternative marker genotypes in the selected population can be much greater than the actual gene effect at the quantitative trait locus when the entire population is considered. An expression and a figure is provided for converting observed differences under selective genotyping to actual gene effects.     

Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers

Sweetpotato genomic research is minimal compared to most other major crops despite its worldwide importance as a food crop. The development of a genetic linkage map in sweetpotato will provide valuable information about the genomic organization of this important species that can be used by breeders to accelerate the introgression of desired traits into breeding lines. We developed a mapping population consisting of 240 individuals of a cross between ‘Tanzania’, a cream-fleshed African landrace, and ‘Beauregard’, an orange-fleshed US sweetpotato cultivar. The genetic linkage map of this population was constructed using Amplified Fragment Length Polymorphism (AFLP) markers. A total of 1944 (‘Tanzania’) and 1751 (‘Beauregard’) AFLP markers, of which 1511 and 1303 were single-dose markers respectively, were scored. Framework maps consisting of 86 and 90 linkage groups for ‘Tanzania’ and ‘Beauregard’ respectively, were developed using a combination of JoinMap 3.0 and MAPMAKER/EXP 3.0. A total of 947 single-dose markers were placed in the final framework linkage map for ‘Tanzania’. The linkage map size was estimated as 5792 cM, with an average distance between markers of 4.5 cM. A total of 726 single-dose markers were placed in the final framework map for ‘Beauregard’. The linkage map length was estimated as 5276 cM, with an average distance between markers of 4.8 cM. Duplex and triple-dose markers were used to identify the corresponding homologous groups in the maps. Our research supports the hypothesis that sweetpotato is an autopolyploid. Distorted segregation in some markers of different dosages in this study suggests that some preferential pairing occurs in sweetpotato. However, strict allopolyploid inheritance in sweetpotato can be ruled out due to the observed segregation ratios of the markers, and the proportion of simplex to multiple-dose markers. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. This paper is a portion of a dissertation submitted by Jim C. Cervantes-Flores.     

Property and efficiency of the maximum likelihood method for molecular phylogeny

Summary The maximum likelihood (ML) method for constructing phylogenetic trees (both rooted and unrooted trees) from DNA sequence data was studied. Although there is some theoretical problem in the comparison of ML values conditional for each topology, it is possible to make a heuristic argument to justify the method. Based on this argument, a new algorithm for estimating the ML tree is presented. It is shown that under the assumption of a constant rate of evolution, the ML method and UPGMA always give the same rooted tree for the case of three operational taxonomic units (OTUs). This also seems to hold approximately for the case with four OTUs. When we consider unrooted trees with the assumption of a varying rate of nucleotide substitution, the efficiency of the ML method in obtaining the correct tree is similar to those of the maximum parsimony method and distance methods. The ML method was applied to Brown et al.'s data, and the tree topology obtained was the same as that found by the maximum parsimony method, but it was different from those obtained by distance methods.     

On the maximum likelihood method for estimating molecular trees: Uniqueness of the likelihood point

Summary Studies are carried out on the uniqueness of the stationary point on the likelihood function for estimating molecular phylogenetic trees, yielding proof that there exists at most one stationary point, i.e., the maximum point, in the parameter range for the one parameter model of nucleotide substitution. The proof is simple yet applicable to any type of tree topology with an arbitrary number of operational taxonomic units (OTUs). The proof ensures that any valid approximation algorithm be able to reach the unique maximum point under the conditions mentioned above. An algorithm developed incorporating Newton's approximation method is then compared with the conventional one by means of computers simulation. The results show that the newly developed algorithm always requires less CPU time than the conventional one, whereas both algorithms lead to identical molecular phylogenetic trees in accordance with the proof. Contribution No. 1780 from the National Institute of Genetics, Mishima 411, Japan     

A high-resolution linkage map of the lethal spotting locus: a mouse model for Hirschsprung disease

Mice homozygous for the lethal spotting (ls) mutation exhibit aganglionic megacolon and a white spotted coat owing to a lack of neural crest-derived enteric ganglia and melanocytes. The ls mutation disrupts the migration, differentiation, or survival of these neural crest lineages during mammalian development. A human congenital disorder, Hirschsprung disease (HSCR), is also characterized by aganglionic megacolon of the distal bowel and can be accompanied by hypopigmentation of the skin. HSCR has been attrrbuted to multiple loci acting independently or in combination. The ls mouse serves as one animal model for HSCR, and the ls gene may represent one of the loci responsible for some cases of HSCR in humans. This study uses 753 N₂ progeny from a combination of three intersubspecific backcrosses to define the molecular genetic linkage map of the ls region and to provide resources necessary for positional cloning. Similar to some cases of HSCR, the ls mutation acts semidominantly, its phenotypic effects dependent upon the presence of modifier genes segregating in the crosses. We have now localized the ls mutation to a 0.8-cM region between the D2Mit113 and D2Mit73/D2Mit174 loci. Three genes, endothelin-3 (Edn3), guanine nucleotide-binding protein -stimulating polypeptide 1 (Gnas), and phosphoenolpyruvate carboxykinase (Pck1) were assessed as candidates for the ls mutation. Only Edn3 and Gnas did not recombine with the ls mutation. Mutational analysis of the Edn3 and Gnas genes will determine whether either gene is responsible for the neural crest deficiencies observed in ls/ls mice.Both authors contributed equally to this research.     

基于EM算法的遗传重组率估计方法

EM算法是在不完全信息资料下实现参数极大似然估计的一种通用方法．本文导出了双位点不同标记类型,包括共显性-共显性,共显性-显性和显性-显性3种模式下,估计遗传重组率的EM算法,以及获得重组率抽样方差的Bootstrap方法;并将之推广到部分个体缺失标记基因型(未检测到电泳谱带)下的重组率估计．通过大量Monte Carlo模拟研究发现: (1)连锁紧密时,样本容量对重组率的估计影响不大;连锁松散时,需要较大样本容量才可检测到连锁以及实现重组率的较精确估计．(2)用包含缺失标记的所有个体估计重组率比仅用其中的非缺失标记个体估计更准确,且可显著提高连锁检测的统计功效．     

Detection of segregation distortions in an indica-japonica rice cross using a high-resolution molecular map

We have constructed a high-resolution rice genetic map containing 1383 DNA markers covering 1575 cM on the 12 linkage groups of rice using 186 F₂ progeny from a cross between a japonica variety, Nipponbare, and an indica variety, Kasalath. Using this high-resolution molecular linkage map, we detected segregation distortion in a single wide cross of rice. The frequencies of genotypes for 1181 markers with more than 176 genotype data were plotted along this map to detect segregation distortion. Several types of distorted segregation were observed on 6 of the chromosomes. We could detect 11 major segregation distortions at ten positions on chromosomes 1, 3, 6, 8, 9, and 10. The strongest segregation distortion was at 107.2 cM on chromosome 3 and may be the gametophyte gene 2 (ga-2). The Kasalath genotype at this position was transmitted to the progeny with about a 95% probability through the pollen gamete. At least 8 out of the 11 segregation distortions detected here are new. The use of the high-resolution molecular linkage map for improving our understanding of the genetic nature and cause of these segregation distortions is discussed.     

Introgression and DNA marker analysis of Lycopersicon peruvianum, a wild relative of the cultivated tomato, into Lycopersicon esculentum, followed through three successive backcross generations

 Segregation of the Lycopersicon peruvianum genome was followed through three generations of backcrossing to the cultivated tomato L. esculentum cv ‘E6203’ using molecular markers. Thirteen BC₁ plants were genotyped with 113 markers, 67 BC₂ plants with 84 markers, and finally 241 BC₃ plants were genotyped with 177 markers covering the entire genome and a BC₃ map constructed. Several segments of the genome, including parts of chromosomes 3, 4, 6, and 10, quickly became fixed for esculentum alleles, possibly due to sterility problems encountered in the BC₁. Observed overall heterozygosity and chromosome segment lengths at each generation were very near the expected theoretical values. Markers located near the top telomeric region of chromosome 9 showed segregation highly skewed towards the wild allele through all generations, suggesting the presence of a gamete promoter gene. One markers, TG9, mapped to a new position on chromosome 9, implying an intrachromosomal translocation event. Despite the great genetic distance between the two parents, overall recombination was only 25% less than that observed in a previous tomato cross, indicating that L. peruvianum genes may be more readily introgressed into cultivated germplasm than originally believed. Received: 9 April 1997 / Accepted : 20 May 1997     

A genetic linkage map of five marker loci in and around the Duchenne muscular dystrophy locus

Linkage analysis of five marker loci in and around the Duchenne muscular dystrophy (DMD) locus, DXS84, DXS206, DXS164, DXS270, and DXS28, was conducted with 499 families. Overall, the best multipoint distances were found to be DXS84-3.7 +/- 0.6 cM-DXS206-1.0 +/- 0.4 cM-DXS164-1.9 +/- 0.6 cM-DXS270-12.0 +/- 1.1 cM-DXS28. A comparison of this linkage map with the established physical map suggests the presence of hot spots for recombination in the DMD locus.     

Development of simple sequence repeat DNA markers and their integration into a barley linkage map

Simple sequence repeats (SSRs), or microsatellites, are a new class of PCR-based DNA markers for genetic mapping. The objectives of the present study were to develop SSR markers for barley and to integrate them into an existing barley linkage map. DNA sequences containing SSRs were isolated from a barley genomic library and from public databases. It is estimated that the barley genome contains one (GA)_n repeat every 330 kb and one (CA)_n repeat every 620 kb. A total of 45 SSRs were identified and mapped to seven barley chromosomes using doubled-haploid lines and/or wheat-barley addition-line assays. Segregation analysis for 39 of these SSRs identified 40 loci. These 40 markers were placed on a barley linkage map with respect to 160 restriction fragment length polymorphism (RFLP) and other markers. The results of this study demonstrate the value of SSRs as markers in genetic studies and breeding research in barley.