An integrated genetic linkage map for eucalypts using RFLP,RAPD and isozyme markers

An integrated genetic linkage map for E. nitens was constructed in an outbred three-generation pedigree. Analysis of 210 RFLP, 125 RAPD and 4 isozyme loci resulted in 330 markers linked in 12 linkage groups covering 1462 cM (n=11 in eucalypts). The 12th linkage group is comprised of only 5 markers and will probably coalesce with another linkage group when further linked loci are located. Co-dominant RFLP loci segregating in both parents were used to integrate linkages identified in the male and female parents. Differences in recombination frequencies in the two parents were observed for a number of pairs of loci, and duplication of sequences was identified both within and between linkage groups. The markers were distributed randomly across the genome except for the RFLPs in linkage group 10 and for some loci showing segregation distortion, which were clustered into three regions of the map. The use of a large number of co-dominant RFLP loci in this map enables it to be used in other pedigrees of E. nitens and forms a basis for the detection and location of QTL in E. nitens and other eucalypt species.     

马哈利樱桃矮化砧的DNA甲基化水平及模式分析

该研究利用MSAP技术,对25株矮化马哈利樱桃和25株半矮化马哈利樱桃进行甲基化水平和模式分析,以探讨其矮化的表观性状与其基因组甲基化修饰的关系。结果表明:(1)从64对引物中筛选出15对引物,在半矮化组中共扩增4 577个条带,其中半甲基化336个,全甲基化1 274个;在矮化组中共扩增4 444个条带,其中半甲基化349个,全甲基化1 383个;t检验和方差分析表明,矮化组与半矮化组在总甲基化水平和全甲基化水平上差异极显著,在半甲基化水平上差异显著,矮化组甲基化水平高于半矮化组。(2)半矮化组单态性位点23个,多态性位点136个;矮化组单态性位点17个,多态性位点142个,表明矮化组多态性高于半矮化组。(3)多态性类型分析表明,矮化组出现A4类型的频率较半矮化组高,A2类型的频率较半矮化组低,即矮化组中发生超甲基化的位点多于半矮化组,且‘马哈利’基因组甲基化多态性位点主要发生在双链内侧甲基化位点以及超甲基化位点上。研究认为,马哈利樱桃矮化和半矮化的基因组甲基化水平及模式存在差异,马哈利砧木的矮化性状与其基因组甲基化修饰有关。     

Genetic Analysis of Bemisia (Hemiptera: Aleyrodidae) Populations by Isoelectric Focusing Electrophoresis

Twenty-one whitefly populations in the genus Bemisia were evaluated for genetic variation at 3 allozyme loci. Nine of the 22 populations that exhibited polymorphic loci were subjected to allozyme analysis using a minimum of 10 enzymes, representing 10 to 14 distinct loci. Among those nine variants examined, calculated genetic distances ranged between 0.03 and 0.52, with three main groups emerging from the analysis. One group comprised two closely related Western Hemisphere variants of B. tabaci: type A from California, United States and a geographically proximal population from Culiacan, Mexico. A second cluster contained five collections previously identified as B. tabaci type B and Bemisia argentifolii, while a third group contained a single population from Benin, Africa. The latter two groups were grouped separately from New World populations and are thought to have a recent origin in the Eastern Hemisphere.     

Allotetraploidy of Zoysia species with 2n=40 based on a RFLP genetic map

 A RFLP linkage map of Zoysia spp. (2n=40), a warm-season turfgrass, was constructed by using the self-pollinated progenies obtained from an interspecific hybrid. Out of 115 DNA clones tested, 100 (87.0%), including 55 genomic clones, 38 cDNA clones, and seven gene clones encoding photosynthetic enzymes showed allelic-RFLP banding patterns among the parental accessions. We found that 26 probes detected two or more loci segregating in the self-pollinated progenies independently. The RFLP linkage map of Zoysia spp. consists of 115 loci in 22 linkage groups ranging in size from 12.5 cM to 141.3 cM with a total map distance of 1506 cM. Six RFLP loci (5.4%) showed significant segregation distortion (P<0.01). Two loci out of six were mapped to linkage group II, and another two loci were mapped to group VII. In the RFLP linkage map of zoysiagrass, five pairs of linkage groups sharing a series of duplicated loci with approximately the same order were identified. Therefore, we conclude that Zoysia spp. with 2n=40 should be considered as allotetraploids, which might have evolved from progenitors with a basic chromosome number of ten (x=10). Received: 20 March 1998 / Accepted: 17 September 1998     

Genetic Mapping of Laminaria japonica and L. Iongissima Using Amplified Fragment Length Polymorphism Markers in a ＂Two-Way Pseudo- Testcross＂ Strategy

With a ＂two-way pseudo-testcross＂ mapping strategy, we applied the amplified fragment length polymorphism （AFLP） markers to construct two moderate density genetic linkage maps for Laminaria. The linkage maps were generated from the 60 progenies of the F1 cross family （Laminaria iongissima Aresch. × L. Japonica Miyabe） with twenty pairs of primer combinations. Of the 333 polymorphic loci scored in 60 progenies, 173 segregated in a 1：1 ratio, corresponding to DNA polymorphisms heterozygous in a single parent, and the other 58 loci existing in both parents followed a 3：1 Mendelian segregation ratio. Among the loci with 1：1 segregating ratios, 79 loci were ordered in 14 linkage groups （648.6 cM） of the paternal map, and 72 loci were ordered in 14 linkage groups （601.9 cM） of the maternal map. The average density of loci was approximately 1 per 8 cM. To Investigate the homologies between two parental maps, we used 58 loci segregated 3：1 for further analysis, and deduced one homologous linkage group. The linkage data developed in these maps will be useful for detecting loci-controlling commercially important traits for Laminaria.     

The genetics of position-effect variegation modifying loci in Drosophila melanogaster

Summary The dose dependent effects of position-effect variegation (PEV) modifying genes were studied in chromosome arms2L, 2R and3R. Four groups of PEV modifying genes can be distinguished: haplo-abnormal suppressor and enhancer loci with or without a triplo-effect. using duplications four triplo-abnormal suppressor and four triplo-abnormal enhancer functions were localized. In two cases we proved that these functions correspond to a converse haplo-abnormal one. Altogether 43 modifier loci were identified. Most of these loci proved not to display significant triplo-effects (35). The group of haplo-abnormal loci with a triplo-effect may represent genes which play an important role in heterochromatin packaging.     

Inheritance of microsatellite DNA in bisexual gynogenesis complex of Fangzheng silver crucian carp,Carassius auratus gibelio (Bloch)

Five gynogenetic progeny groups of silver crucian carp Carassius auratus gibelio were produced and sex ratios (males:total progeny) of each of the progeny groups were analysed. About 110 males and 366 females were genotyped at 15 microsatellite loci for comparison with their parents to (1) verify the gynogenesis status of Fangzheng C. auratus gibelio, (2) detect the incorporation of paternal genetic material into the offspring and (3) study the possible association of genetic exchange at microsatellite loci with the existence of sex. The sex ratios in progenies of five groups were highly variable, but all had significant female bias. The sex ratio ranged from 0 to 0·37. Significant differences in the sex ratio within and between groups were also found. Microsatellite genotyping at 15 loci showed that 100 and 97% of the progeny shared the same genotype with the mother in four groups and in one group, respectively, confirming that gynogenesis is the general mechanism of reproduction in C. auratus gibelio. However, 0·63% of all offspring did show incorporation of paternal genetic material. No single loci tested were associated with the occurrence of male progeny, indicating unknown genetic mechanisms for sex determination in C. auratus gibelio.     

Primers for 22 candidate genes for ecological adaptations in Brassicaceae

There is an increasing interest in direct screening of polymorphisms at candidate loci to associate them with adaptations in natural situations. We report primers that amplify regions at 22 putatively orthologous functional loci in the family Brassicaceae: Arabidopsis thaliana, its two wild outcrossing relatives, and Brassica oleracea. Four groups of genes were known to have specific functions in the model species A. thaliana in ecologically important traits: timing of reproduction; metabolism of secondary compounds; defence against pathogens or light perception. In addition, genes of a fifth group were selected with no consideration of their function, as reference loci.     

Isolation and mapping of resistance gene analogs from the Avena strigosa genome

Degenerate primers based on conserved regions of the nucleotide binding site (NBS) domain (encoded by the largest group of cloned plant disease resistance genes) were used to isolate a set of 15 resistance gene analogs (RGA) from the diploid species Avena strigosa Schreb. These were grouped into seven classes on the basis of 60% or greater nucleic acid sequence identity. Representative clones were used for genetic mapping in diploid and hexaploid oats. Two RGAs were mapped at two loci of the linkage group AswBF belonging to the A. strigosa × A. wiestii Steud map, and ten RGAs were mapped at 15 loci in eight linkage groups belonging to the A. byzantina C. Koch cv. Kanota × A. sativa L. cv. Ogle map. A similar approach was used for targeting genes encoding receptor-like kinases. Three different sequences were obtained and mapped to two linkage groups of the hexaploid oat map. Associations were explored between already known disease resistance loci mapped in different populations and the RGAs. Molecular markers previously linked to crown rust and barley yellow dwarf resistance genes or quantitative trait loci were found in the Kanota × Ogle map linked to RGAs at a distance ranging from 0 cM to 20 cM. Homoeologous RGAs were found to be linked to loci either conferring resistance to different isolates of the same pathogen or to different pathogens. This suggests that these RGAs identify genome regions containing resistance gene clusters.     

Analysis of Heterozygosity at the PI, TF, PGM1, ACP1, HP, GC, GLO1, C3, and ESDLoci in Pulmonary Tuberculosis Patients Differing in Response to Treatment

Heterozygosity at nine genetic loci (PI, TF, PGM1, ACP1, HP, GC, GLO1, C3, and ESD) was analyzed in pulmonary tuberculosis patients with good (group 1, N= 71) and poor (group 2, N= 35) response to treatment. The observed heterozygosities were compared with the expected values, which were calculated from allele frequencies in a control sample of healthy individuals (N= 328 with all but one locus and 78 with ESD) according to Hardy–Weinberg expectations. The analysis showed that the observed heterozygosities g _l of patients significantly differed from the expected values h _lin the case of four loci (GC, PI, C3, and ACP1). The observed heterozygosity was higher than expected in three cases (PI, C3, and ACP1) and lower then expected (GC) in one case. When data on each individual locus were compared using Fisher's exact test, both groups of patients proved to significantly differ (P _F< 0.05) from the control group in the same four loci. No difference in observed heterozygosity was detected between the two groups of patients. The mean expected heterozygosity was h¯= 0.386 ± 0.00674; the mean observed heterozygosity was g¯ = 0.415 ± 0.02 in group 1, g¯ = 0.402 ± 0.026 in group 2, and g¯ = 0.371 ± 0.00955 in the control group. The ttest did not reveal a significant difference between the mean values of expected observed heterozygosities. Heterozygosity at individual loci, rather than mean heterozygosity, was proposed as an integral nonspecific indicator of the genetic control of a disease, because the former directly implicates individual marker loci in the development of a disorder, whereas effects of individual loci may eliminate each other when mean heterozygosity is computed. Based on the results obtained, a genetic control was assumed for the development of the tuberculosis process in the lungs.     

GENETIC MAPPING OF THE LAMINARIA JAPONICA (LAMINARALES,PHAEOPHYTA) USING AMPLIFIED FRAGMENT LENGTH POLYMORPHISM MARKERS1

To establish a molecular‐marker‐assisted system of breeding and genetic study for Laminaria japonica Aresch., amplified fragment length polymorphism (AFLP) was used to construct a genetic linkage map of L. japonica featuring 230 progeny of F₂ cross population. Eighteen primer combinations produced 370 polymorphic loci and 215 polymorphic loci segregated in a 3:1 Mendelian segregation ratio (P ≤ 0.05). Of the 215 segregated loci, 142 were ordered into 27 linkage groups. The length of the linkage groups ranged from 6.7 to 90.3 centimorgans (cM) with an average length of 49.6 cM, and the total length was 1,085.8 cM, which covered 68.4% of the estimated 1,586.9 cM genome. The number of mapped markers on each linkage group ranged from 2 to 12, averaging 5.3 markers per group. The average density of the markers was 1 per 9.4 cM. Based on the marker density and the resolution of the map, the constructed linkage map can satisfy the need for quantitative trait locus (QTL) location and molecular‐marker‐assisted breeding for Laminaria.     

Mapping of Mhc class I and class II regions to different linkage groups in the zebrafish, Danio rerio

 The mammalian major histocompatibility complex (Mhc) consists of three closely linked regions, I, II, and III, occupying a single chromosomal segment. The class I loci in region I and the class II loci in region II are related in their structure, function, and evolution. Region III, which is intercalated between regions I and II, contains loci unrelated to the class I and II loci, and to one another. There are indications that a similar Mhc organization exists in birds and amphibians. Here, we demonstrate that in the zebrafish (Danio rerio), a representative of the teleost fishes, the class II loci are divided between two linkage groups which are distinct from the linkage group containing the class I loci. The β₂-microglobulin-encoding gene is loosely linked to one of the class II loci. The gene coding for complement factor B, which is one of the region III genes in mammals, is linked neither to the class I nor to the class II loci in the zebrafish. These results, combined with preliminary data suggesting that the class I and class II regions in another order of teleost fish are also in different linkage groups, indicate that close linkage of the two regions is not necessary either for regulation of expression or for co-evolution of the class I and class II loci. They also raise the question of whether linkage of the class I and class II loci in tetrapods is a primitive or derived character. Received: 16 December 1996 / Revised: 6 February 1997     

Blood protein variation in a population of ethiopian vervet monkeys (Cercopithecus aethiops aethiops)

Seven small groups of vervet monkeys (Cercopithecus aethiops aethiops), totaling 124 individuals, from Awash National Park, Ethiopia, were trapped and blood samples were obtained. Twenty-three loci were examined by starch gel electrophoresis and four loci, Tf, E, ADA, and PMG2 were found to be polymorphic. The average heterozygosity (H?) of the population was calculated to be 5.6%. No significant deviations from Hardy-Weinberg equilibrium proportions occurred and a chi-square test for group homogeneity was also not significant. Average F_ST for all polymorphic loci was calculated to be 0.062. This suggests that the entire group functions as a single Mendelian population.     

Variation of allele composition and protein locus expression in the course of genetic differentiation of taxa of different ranks in the mammals

The contributions of different groups of loci, namely those identical (i), similar (s), and different (d) with respect to allele composition and the loci expressed in only one of two compared objects (0), into the differentiation of marsupial and placental mammals have been evaluated. An increase in the proportions of d and 0 loci with increasing taxon rank has been demonstrated. At the intraspecific level, identical loci are prevailing, and d loci are rare; the latter are more common in subspecies. At the species level, the proportions of different (d) and similar (s) loci are increased, but the proportion of i loci is still the highest. Only at the genus level does the proportion of different loci reach 41–49%; 0 loci are found in marsupials and small placental mammals, and the number of s loci is decreased. In large placental mammals, this trend is disrupted at the subspecies level, where the contribution of s loci is drastically increased, while the proportion of identical ones (i) is decreased. Comparison with data on other groups of vertebrates shows that the ratios between these groups of loci reflect the specificity of differentiation processes at the intraspecific level and the levels of species and taxa of higher ranks in all classes of animal analyzed. However, the species differentiation in amphibians approximately corresponds to the genus level in mammals and the family level in birds.     

The effect of population structure on the relationship between heterosis and heterozygosity at marker loci

The relationship between heterozygosity at neutral marker loci and heterosis of F₁ hybrids is investigated using a theoretical model. Results emphasize that linkage disequilibrium between the markers and the loci implicated in heterosis [quantitative trait loci (QTLs) that exhibit dominance effects] is a necessary condition to finding a correlation ( _mh ) between heterozygosity at marker loci and the heterosis. The effect of population structure, in which the parental inbred lines of the hybrids belong to different heterotic groups, is considered. _mh is investigated for: (1) hybrids between lines that belong to the same heterotic group (within-group hybrids); (2) hybrids between lines that belong to different groups (between-group hybrids); and (3) all hybrids, both within and between-groups. Within a group, significant values of ( _mh ) may arise because of linkage disequilibrium generated by drift. At the between-group level, no correlation is expected since link-age disequilibrium should differ randomly from one group to the other, which is consistent with recent experimental results. Possible ways to achieve prediction of the heterosis in this situation are discussed. When all hybrids are considered simultaneously, divergence of allelic frequencies among groups for the markers and the QTLs produces a correlation between heterosis and heterozygosity at marker loci. This correlation increases with the number of markers that are considered.     

Blood group antigens and the population genetics of Macaca mulatta on Cayo Santiago. I. Genetic differentiation of social groups

The red blood cell phenotypes for eight polymorphic loci were determined for 293 free-ranging Macaca mulatta living on Cayo Santiago; this number represents the total population of the island, disposed in four social groups plus peripheral males. The rhesus population shows significant genetic heterogeneity over blood group systems (loci) and social groups. No particular genetic locus or social group is solely responsible for the genetic heterogeneity observed. The distributions of genotypes for two loci (G and H) do not deviate significantly from Hardy-Weinberg expectations within social groups or in the population as a whole. Correction of the equilibrium expectations for the effect of population subdivision yields no statistically significant results. Overall, the results suggest that the interaction of a variety of processes (random genetic drift, founder effect, migration and selection) may be responsible for the diversity observed. These data, combined with those from further studies, may allow an application of behavioral and genetic knowledge to the study of microevolutionary processes among nonhuman primates.     

Characteristics, linkage-map positions, and allelic differentiation of Sorghum bicolor (L.) Moench DNA simple-sequence repeats (SSRs)

Fifty one clones isolated from a size-fractionated genomic DNA library of Sorghum bicolor (L.) Moench, that had been probed with four radiolabeled di- and tri-nucleotide oligomers, were sequenced. Fifty of the clones contained one or more simple-sequence repeats (SSRs) [72% of which were (AG/TC) _n SSRs] and, following analysis of the clones, polymerase-chain-reaction primer sets that amplify 38 unique SSR loci were developed. Genotyping of the 38 loci in 18 sorghum accessions, including the parents of a recombinant inbred (RI) mapping population, revealed polymorphism at 36 of the loci among the 18 accessions and at 31 of the loci (not including null alleles at two loci) between the parents of the RI population. All of the latter 31 loci were mapped. The genotypes at 17-mapped SSR loci were assayed in 190 S. bicolor accessions in order to determine δ* _T , the estimated level of allelic differentiation (the estimated probability that two members of a population, chosen at random and without replacement, differ in allelic composition), at each of the loci. The mean δ* _T value determined for S. bicolor overall was 0.89, the range of mean δ* _T values for ten S. bicolor races was from 0.88 to 0.83, and the range of mean δ* _T values for ten working groups (= sub-races) of the race caudatum, with only two exceptions, was from 0.87 to 0.79. The lowest δ* _T values for six of the loci among the ten race-caudatum working groups ranged from 0.86 to 0.70; thus, the probability that different alleles will be present at one or more of these loci in two accessions chosen at random from a working group is > 0.996 when three of the loci are genotyped, and > 0.9999 when all six of the loci are genotyped. The results of this study confirm that most S. bicolor SSR loci are sufficiently polymorphic to be useful in marker- assisted selection programs and they indicate that the levels of polymorphism at some loci are high enough to allow the vast majority of S. bicolor accessions, even accessions within working groups, to be distinguished from one another by determining the genotypes at a small number, perhaps as few as a half-dozen, SSR loci. Received: 13 September 1999 / Accepted: 2 December 1999     

Genetic structure of Glycine canescens,a perennial relative of soybean

Summary Allozyme variation as detected by starch gel electrophoresis was used to assess the extent and spatial organization of genetic variation across the entire range of Glycine canescens sensu lato. Eleven enzyme systems were assayed in 116 accessions of this taxon and 102 alleles were detected at a total of 31 loci. Eighty-one percent of loci were polymorphic. Most of this variation occurred between and very little within accessions. Three major groupings were detected. These groupings (groups 1, 2, and 3) also differed with respect to mean seed size and their geographic distribution. A further ten accessions stood out from these distinct groups. These accessions were most closely related to group 3 but were variable among themselves. In general, they were collected from highly dissected terrain, often in the remote interior of the continent. A final group of 18 problematic accessions (group X), originally tentatively identified as G. canescens on morphological grounds, was shown to be isozymically distinct from this species and was reclassified as one form of the polytypic species G. clandestina.     

Hybrid zones between two genetically differentiated forms of the pond frog Rana lessonae in southern Italy

Two distinct population groups of the pond frog Rana lessonae were detected in peninsular Italy and Sicily by multilocus electrophoresis: one group inhabits the peninsula down to northern Calabria, the second occurs in southern Calabria and on Sicily. Fixed alternative alleles distinguish the two groups at 5 of the 25 loci examined; marked allele frequency differences were observed at two additional loci. On average, the two groups differ by a Nei's standard genetic distance of 0.4. A wide hybrid zone (about 120 km) occurs between the two groups, with high genotypic diversity and absence of pure parental genotypes in central Calabria. Patterns of allozyme variation suggest that at least two distinct contact and hybridization events occurred, one in the Catanzaro, the other in the Crati-Sibari plains, about 70 km to the north. Geological evidence indicates that these areas correspond to two main marine-flooded grabens that would have repeatedly interrupted or reduced genetic exchange during Plio-Pleistocene times. The finding of a fixed difference at the Mdhp-1 locus between Sicilian and Calabrian R. lessonae witnesses their continuing differentiation following their last separation by definitive opening of the Strait of Messina, about 50 000 years ago. The wide hybrid zone, the diversity of genotypes and the agreement with Hardy-Weinberg expectations suggest complete hybrid fertility. Different patterns of introgression were observed at the various loci. The pattern of allelic variation at loci in R. lessonae is paralleled by the pattern of variation in lessonae genomes of the sympatric hemiclonal hybrid Rana esculenta, into which lessonae genomes are introduced each generation as a result of hybridogenesis.     

A genetic linkage map for Eucalyptus globulus with candidate loci for wood,fibre, and floral traits

A genetic linkage map containing potential candidate loci for wood, fibre and floral traits has been constructed for Eucalyptus globulus (Labill.) based on the segregation of 249 codominant loci in an outbred F₁ population of 148 individuals. The map contains 204 RFLP loci, including 31 cambium-specific expressed sequence tags (ESTs) and 14 known function genes, and 40 microsatellite and five isozyme loci. Independent male and female maps were constructed, and the 98 loci (39%) that segregated in both parents were used to combine the parental maps into an integrated map. The 249 loci mapped to 11 major linkage groups (n=11 in eucalypts) and a 12th small linkage group containing three loci that segregated in the male parent only. Total map distance is 1375 cM with an average interval of 6 cM. Forty one of the mapped loci identify known proteins (five isozymes) or sequences with known function (14 genes and 22 ESTs). The mapped genes include enzymes involved in lignin and cell-wall polysaccharide biosynthesis, and floral-development genes. This map will be used to locate quantitative trait loci for wood, fibre, and other traits in Eucalyptus. Received: 30 August 2000 / Accepted: 23 March 2001