Single gene inheritance of occurrence of head spots in mice

Results from earlier selection studies indicated that while the size of head spots in mice descended from the Goodale head-spot strain was a quantitative, polygenic trait, head-spot occurrence was probably a qualitative trait inherited by one or two genes. The present study was undertaken to examine this possibility by crossing a head-spot stock with three inbred strains and with two noninbred stocks carrying mutant genes. Observed segregation ratios in the F2 and backcross generations of these crosses were compared to results expected under various models of qualitative inheritance. Evidence of linkage between known loci and a putative head-spot gene also was sought. Results indicated that head spotting was inherited primarily by the action of a recessive autosomal gene, head spot (hs). The action of this gene was subject to modification, in some crosses, by other genes or by environmental factors. Attempts to demonstrate linkage between the head spots and known single-locus traits were unsuccessful.     

Parentage testing and linkage analysis in the horse using a set of highly polymorphic microsatellites

Ten (TG)_n positive clones, isolated from an equine genomic library and sequenced, contained 12–19 uninterrupted TG repeats. Primers for polymerase chain reaction (PCR) were synthesized and nine of these (TG)_n loci (HTG7-15) were successfully amplified and utilized in this study together with five previously reported equine microsatellite loci (HTG2-6). The PCR products were analysed by polyacrylamide gel electrophoresis followed by automated laser fluorescence detection or autoradiography. All microsatellites showed polymorphism and stable Mendelian inheritance. Differences in microsatellite variability between horse breeds were detected. A linkage analysis comprising HTG2-15, one coat colour gene and 16 genetic blood markers enabled addition of HTG2 to linkage group U2 and a new linkage group (U6) was established comprising the loci HTG7 and HTG12. Close linkage was excluded within a set of eight microsatellites. The estimated probability of exclusion in four breeds for a parentage test based on these eight loci varied between 0.96 and 0.99.     

Genetic analysis of floral anthocyanin pigmentation traits in Asiatic hybrid lily using molecular linkage maps

To understand the genetic background of two floral anthocyanin pigmentation traits, anthocyanin pigmentation in the flower tepals and spot formation, in the Asiatic hybrid lily (2n = 24), segregation of the two traits among 96 F₁ plants derived from a cross between commercial cultivars 'Montreux' and 'Connecticut King' were investigated. 'Montreux' has anthocyanin pigmentation in the tepals with many spots, and 'Connecticut King' has flowers with carotenoid pigmentation without spots. The F₁ plants with or without anthocyanin pigment in the tepals segregated with a 1:1 segregation ratio, indicating that a single gene controls anthocyanin pigmentation in the tepals. The number of spots per square centimeter of all tepals showed continuous distribution in the F₁ plants. To map the loci for the two anthocyanin pigmentation traits, molecular linkage maps in the Asiatic hybrid lily were constructed using a double pseudo-testcross strategy, with the same F₁ plants used for phenotypic evaluation, and 212 PCR-based DNA markers. The trait for anthocyanin pigmentation in tepals was used as a trait marker. The map of 'Montreux' comprised 95 markers in 26 linkage groups, and the map of 'Connecticut King' used 119 markers in 24 linkage groups. The total map lengths were 867.5 and 1,114.8 cM, respectively. The trait locus for anthocyanin pigmentation in the tepals was between markers ASR35-180 and P506-40 in linkage group 1 of the 'Montreux' map with a map distance of 1.2 cM and 2.6 cM, respectively. A single-point analysis of quantitative trait loci (QTLs) for tepal spot number identified two putative QTLs in linkage groups 1 and 19 of the 'Connecticut King' map. One putative QTL in linkage group 19 explained 64% of the total phenotypic variation. Because both putative QTLs were mapped on the linkage map of 'Connecticut King' that has no spots, dominant alleles of them might suppress spot formation.     

常染色体显性遗传小眼球病与12个微卫星多态标志的初步连锁分析

本文报道了一个常染色体显性遗传小眼球的大家系,初步排除了此家系致病基因在目前已知位点(CHX10、MITF、RX、MCOP、NNO1、NNO2)的可能,并探讨了与11号染色体上的微卫星DNA标志的连锁关系。采用聚合酶链(PCR)扩增微卫星DNA片段,扩增产物进行聚丙烯酰胺凝胶电泳,用银染显示结果;用MLINK连锁分析软件计算LOD值。结果显示,本家系小眼球致病基因与6个已知位点及11号染色体上的微卫星DNA标志之间不存在连锁,提示此家系的致病位点目前尚未被定位。     

马尾松GOT、LDH和MDH同工酶的遗传方式和连锁关系

本文采用聚丙烯酰胺凝胶电泳研究了马尾松三种同工酶的遗传方式和连锁关系。结果表明,GOT、LDH和MDH三种同工酶的遗传表达稳定,分别受4个、2个和4个位点控制。只有一对位点(MDH-3和MDH-4)间存在着紧密的连锁关系。     

常染色体显性遗传小眼球病与12个微卫星多态标志的初步连锁分析

本文报道了一个常染色体显性遗传小眼球的大家系,初步排除了此家系致病基因在目前已知位点(CHXl0、MITF、RX、MCOP、NN01、NN02)的可能,并探讨了与11号染色体上的微卫星DNA标志的连锁关系。采用聚合酶链(PCR)扩增微卫星DNA片段,扩增产物进行聚丙烯酰胺凝胶电泳,用银染显示结果;用MLINK连锁分析软件计算LOD值。结果显示,本家系小眼球致病基因与6个已知位点及ll号染色体上的微卫星DNA标志之间不存在连锁,提示此家系的致病位点目前尚未被定位。     

Mapping of the hooded,Gc protein,and albumin gene loci in linkage group VI of the laboratory rat

Crosses to determine the position of the three gene loci, h, Gc, and Alb, in the sixth linkage group of the rat used three strains, the TM strain, the ACI-alb analbuminemic congenic strain, and the abh-alb tester strain established by crossing the abh coat color tester strain and analbuminemic rats. Their genotypes were [C/C, h/h, GcB/GcB, Alb/Alb], [C/C, hi/hi, GcA/GcA, alb/alb] and [C/C, h/h, GcA/GcA, alb/alb], respectively. Determination of genotypes was performed by coat color and polyacrylamide gel electrophoresis (PAGE of serum protein for the Gc and albumin genes. The positions of the three gene loci in the VI linkage group were calculated from the recombination values from the phenotypes of progenies. According to this data, the three gene loci were in h-Gc-Alb tandem and the distances were 15.5 +/- 1.0% in h-Gc, 15.8 +/- 1.0% in h-Alb, and 0.32 +/- 0.16% in Gc-Alb. These data confirmed the relationship among the Gc, Alb, and Afp genes in the rat as well as in humans.     

A microsatellite-based genetic linkage map for channel catfish, Ictalurus punctatus

Microsatellite loci were identified in channel catfish gene sequences or random clones from a small insert genomic DNA library. Outbred populations of channel catfish contained an average of eight alleles per locus and an average heterozygosity of 0.70. A genetic linkage map of the channel catfish genome (N = 29) was constructed from two reference families. A total of 293 microsatellite loci were polymorphic in one or both families, with an average of 171 informative meioses per locus. Nineteen type I loci, 243 type II loci, and one EST were placed in 32 multipoint linkage groups covering 1958 cM. Nine more type II loci were contained in three two-point linkage groups covering 24.5 cM. Twenty-two type II loci remained unlinked. Multipoint linkage groups ranged in size from 11.9 to 110.5 cM with an average intermarker distance of 8.7 cM. Seven microsatellite loci were closely linked with the sex-determining locus. The microsatellite loci and genetic linkage map will increase the efficiency of selective breeding programs for channel catfish.     

Genetic control of PI and GC variants in the American Mink

Genetic polymorphism of the serum α-protease inhibitor (PI) and group-specific component (GC) in minks was revealed using one-dimensional polyacrylamide gel electrophoresis and immunoblotting. Two codominant alleles were identified at each of the two loci. The data ruled out the possibility of any linkage between the PI, GC and the coat colour gene Crystal ( Cr ).     

Development and characterization of microsatellite markers for the endangered Chinese yew Taxus chinensis var. mairei (Taxaceae)

We isolated and characterized 11 microsatellite loci for the Chinese yew, Taxus chinensis var. mairei, an endangered tree species in China, by constructing a (CA)(12)-enriched library. The number of alleles per locus ranged from 5 to 10. The observed heterozygosities ranged from 0.2500 to 0.8333 and the expected heterozygosities ranged from 0.5196 to 0.8680. No significant linkage disequilibrium was detected at these loci. However, four loci significantly deviated from Hardy-Weinberg equilibrium. The null alleles were found to be present at locus Tach9 and locus Tach11 by the Micro-checker test (P < 0.001). These polymorphic loci could be employed in research of gene flow and spatial genetic patterns of T. chinensis var. mairei.     

Two-Dimensional DNA Typing of Human Pedigrees: Spot Pattern Characterization and Segregation

By two-dimensional (2-D) genome typing, i.e., electrophoretic separation of restriction enzyme-digested genomic DNA on the basis of both size and sequence in denaturing gradient gels followed by hybridization analysis, several hundred alleles (spots) can be analyzed in parallel, using a micro- or minisatellite core probe. We studied the segregation of 213 and 214 spots detected by microsatellite core probe (CAC)_nand mini- satellite core probe 33.6, respectively, in two three-generation human pedigrees. Reproducibility of the spot patterns was such that particular spot variants could be scored in both pedigrees. Between 73 and 74% of the spots scored were variant and were transmitted in a Mendelian manner. Very little cosegregation among the 2-D spots themselves was observed, suggesting a random distribution over the genome. Several pairs of spots that appeared to contain both alleles from single loci were identified. The few spots detected by both probes (overlapping spots) showed different segregation patterns, indicating that each probe detects independent sets of genetically informative loci. These results provide a firm basis for using 2-D DNA typing to identify disease loci and for constructing a 2-D spot genetic linkage map of the human genome.     

Nonuniform linkage disequilibrium within a 1,500-kb region of the human immunoglobulin heavy-chain complex.

We have characterized 10 VH polymorphic loci of the VH2, VH3, VH4, and VH5 families. Eight of 10 VH polymorphisms were found to be insertion/deletion polymorphisms, probably the result of nonhomologous recombination over the course of evolution of the current human VH repertoire. The 10 VH polymorphic loci were analyzed in 10 three-generation and 10 two-generation Canadian caucasoid families. Linkage disequilibrium (allelic association) was measured between pairs of VH polymorphic loci, and 12 significant associations were found. The degree of linkage disequilibrium measured between IGH polymorphic loci was then compared with the physical distance separating the loci. The physical distance between IGH polymorphic loci does not entirely determine the degree of linkage disequilibrium between polymorphic loci. Two regions, one in the VH region (between VH3f-2 and VH5-2 and one in the CH region (between C delta and C gamma 3), were found to have linkage disequilibrium values approximately 1/3,000 of that observed in other portions of the IGH region. The previous identification of recombinants in the C delta-to C gamma 3 region indicates that these areas of low linkage disequilibrium are consistent with the presence of recombination hot spots. The observed high amount of recombination in the subtelomeric portion of chromosome 14 therefore appears to be the result of specific hot spots for recombination, rather than a general increase in recombination in this region.     

Gene Flow and Selection in a Two-Locus System

A model of gene flow and selection in two linked loci is analyzed. The problems considered are the effects of linkage on the clines in frequencies at the two loci and the role of gene flow in producing linkage disequilibrium between the loci. Also, the possible significance of linkage as a mechanism for permitting a population of "track" spatial changes in the environment is considered. The results are that when the recombination fraction between the loci is of the same order of magnitude as the selection coefficients or smaller, then linkage is important in determining the gene frequencies and a substantial amount of linkage disequilibrium is present in the cline. Depending on the spatial pattern of selection on the two loci, linkage can either decrease or increase a population's response to local selection.     

The concordance of gene trees and species trees at two linked loci

The gene genealogies of two linked loci in three species are analyzed using a series of Markov chain models. We calculate the probability that the gene tree of one locus is concordant with the species tree, given that the gene tree of the other locus is concordant. We define a threshold value of the recombination rate, r*, to be the rate for which the difference between the conditional probability of concordance and its asymptotic value is reduced to 5% of the initial difference. We find that, although r* depends in a complicated way on the times of speciation and effective population sizes, it is always relatively small, <10/N4, where N4 is the effective size of the species represented by the internal branch of the species tree. Consequently, the concordance of gene trees of neutral loci with the species tree is expected to be on roughly the same length scale on the chromosome as the extent of significant linkage disequilibrium within species unless the effective size of contemporary populations is very different from the effective sizes of their ancestral populations. Both balancing selection and selective sweeps can result in much longer genomic regions having concordant gene trees.     

Mendelian inheritance, linkage and genotypic disequilibrium in microsatellite loci isolated from Hymenaea courbaril (Leguminosae)

The Neotropical tree Hymenaea courbaril, locally known as Jatobá, is a valuable source of lumber and also produces comestible and medicinal fruit. We characterized Mendelian inheritance, linkage and genotypic disequilibrium at nine microsatellite loci isolated from H. courbaril, in order to determine if they would provide accurate estimates of population genetic parameters of this important Amazon species. The study was made on 250 open-pollinated offspring originated from 14 seed trees. Only one of nine loci presented significant deviation from the expected Mendelian segregation (1:1). Genotypic disequilibrium between pairwise loci was investigated based on samples from 55 adult and 56 juvenile trees. No genetic linkage between any paired loci was observed. After Bonferroni's corrections for multiple tests, we found no evidence of genotypic disequilibrium between pairs of loci. We conclude that this set of loci can be used for genetic diversity/ structure, mating system, gene flow, and parentage analyses in H. courbaril populations.     

Genetics of three esterase loci in Anopheles stephensi liston

A survey of laboratory strains of Anopheles stephensi for nonspecific esterases by polyacrylamide gel electrophoresis revealed 10 zones of esterase activity. In 3 of the 10 zones, three electromorphs were observed. Genetic analysis revealed that these three zones are controlled by three loci, viz., Est-3, Est-4, and Est-5, and that the electromorphs are codominant alleles at each locus. The three esterase loci were found linked to each other and to an autosomal marker colorless-eye. The esterase loci have tentatively been placed in linkage group II. The probable gene sequence on chromosome 2 is either c-Est-3-Est-4-Est-5 or c-Est-4-Est-3-Est-5.     

巴西橡胶树SSR遗传图谱的构建

以热研88-13×IAN873的94个F1群体为试材, 利用简单序列重复(Simple sequence repeat, SSR)标记, 采用FsLinkageMAP 1.0软件, 构建了巴西橡胶树热研88-13×IAN873的遗传连锁图谱。从441对SSR引物中筛选出160对具有多态信息的引物, 在分离群体中共检测到206个多态性位点, 176个位点用于遗传图谱的构建; χ²检验结果显示, 有147个位点符合1:1分离比例, 有12个符合1:2:1分离比例, 有17个符合1:1:1:1的分离比例, 共有13个偏分离位点, 偏分离率低(7.38%); 91个SSR位点被分为18个连锁群, 覆盖橡胶树基因组1 937.06 cM, 每个连锁群包含2～16个位点, 标记间的平均距离为21.29 cM。     

Identification of the stem rust resistance gene Pg9 and its association with crown rust resistance and endosperm proteins in 'Dumont' oat.

The Canadian oat cultivar 'Dumont' is known to have genes Pc38 and Pc39 for crown rust resistance and genes Pg2 and Pg13 for stem rust resistance. When crossed to a susceptible oat line OT328, 'Dumont' was shown to have an additional dominant gene for crown rust resistance, designated PcX. Tests of segregating progeny indicated that the stem rust resistance gene Pg9 is present and is tightly linked in coupling to PcX. The presence of Pg9 in 'Dumont' was confirmed in crosses involving the cultivar 'Ukraine', which has Pg9 and a crown rust resistance gene tightly linked to it. The association of rust resistance with endosperm proteins in 'Dumont' was investigated. The linkage of gene Pg13 with a 56.6-kDa polypeptide locus (map distance of 10.47 +/- 2.70 cM) was demonstrated using sodium dodecylsulfate - polyacrylamide gel electrophoresis (SDS-PAGE). A 27.9-kDa polypeptide was shown to be associated with the linked PcX/Pg9 loci by SDS-PAGE but appeared to be more reliably separated as an avenin band, designated B4, using acid-PAGE. Another avenin band, designated B2, also was shown to be associated with the PcX/Pg9 loci using acid-PAGE. The loci conditioning the B2 and B4 bands appeared to be tightly linked or allelic and are separated from the linked PcX/Pg9 loci by a map distance of 1.03 +/- 0.36 cM. The association of Pg13 with a 56.6-kDa polypeptide and the tight linkage between PcX/Pg9 and the B2 (in coupling) and B4 (in repulsion) avenin loci offer a useful tool to breeders to detect the presence of these genes in oat breeding.     

A linkage map for sugi (Cryptomeria japonica) based on RFLP,RAPD, and isozyme loci

A linkage map for sugi was constructed on the basis of restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), and isozyme loci using a three-generation pedigree prepared for genetic analysis of heartwood color. A total of 128 RFLP (123 cDNA and 5 genomic probes), 33 RAPD, 2 isozyme, and 1 morphological (dwarf) loci segregated in 73 progeny. Of the 164 segregating loci, 145 loci were distributed in 20 linkage groups. Of these loci, 91 with confirmed map positions were assigned to 13 linkage groups, covering a total of 887.3 cM. A clustering of markers with distorted segregation was observed in 6 linkage groups. In the four clusters, distortions with a reduction in the number of homozygotes from one parent only were found.Abbreviations MAS marker-assisted selection - PAGE polyacrylamide gel electrophoresis - QTL quantitative traits of loci - RAPD random amplified polymorphic DNA - RFLP restriction fragment length polymorphism This work was supported by a Grant-in-Aid from the Ministry of Agriculture, Forestry and Fisheries of Japan (Integrated Research Program for the Use of Biotechnological Procedures for Plant Breeding) and by a Grant-in-Aid from the Ministry of Education, Science and Culture of Japan (Cooperative Research, no. 04304017)     

Gene-based sequence diversity analysis of field pea (Pisum)

Sequence diversity of 39 dispersed gene loci was analyzed in 48 diverse individuals representative of the genus Pisum. The different genes show large variation in diversity parameters, suggesting widely differing levels of selection and a high overall diversity level for the species. The data set yields a genetic diversity tree whose deep branches, involving wild samples, are preserved in a tree derived from a polymorphic retrotransposon insertions in an identical sample set. Thus, gene regions and intergenic "junk DNA" share a consistent picture for the genomic diversity of Pisum, despite low linkage disequilibrium in wild and landrace germplasm, which might be expected to allow independent evolution of these very different DNA classes. Additional lines of evidence indicate that recombination has shuffled gene haplotypes efficiently within Pisum, despite its high level of inbreeding and widespread geographic distribution. Trees derived from individual gene loci show marked differences from each other, and genetic distance values between sample pairs show high standard deviations. Sequence mosaic analysis of aligned sequences identifies nine loci showing evidence for intragenic recombination. Lastly, phylogenetic network analysis confirms the non-treelike structure of Pisum diversity and indicates the major germplasm classes involved. Overall, these data emphasize the artificiality of simple tree structures for representing genomic sequence variation within Pisum and emphasize the need for fine structure haplotype analysis to accurately define the genetic structure of the species.