Transferability of sequence tagged microsatellite site (STMS) primers across four major pulses

The transferability of genome-specific sequence tagged microsatellite site (STMS) primers from field pea (P. sativum) and chickpea (C. arietinum) to other major pulses was examined. Overall, field pea STMS primers amplified products in most of the accessions in comparison to that of the chickpea STMS primers, which amplified products in relatively few accessions. The highest level of successful amplifications with a single primer was 89% for field pea and 33% for chickpea primers respectively. The potential transferability of the STMS primers among species, expressed as the total mean percentage of positive amplifications, was 53% for the field pea STMS primers and 9% for the chickpea STMS primers. The individual mean percentage of successful transferability of field pea STMS primers across lentil, vetch and chickpea/Cicer sp. accessions was 60%, 39% and 62%, respectively. Whereas, for the chickpea STMS primers successful transferability was 5%, 3% and 18% for lentil, vetch and field pea, respectively. The trnasferability of these STMS primers indicates a high level of sequence conservation in these regions across species. Together with their locus-specificity, co-dominant nature and potential to amplify multiple alleles, their transferability makes STMS markers a powerful tool for genetic mapping, diversity analysis and genotyping.     

Inheritance and linkage relationships of isozyme and morphological loci in cucumber (Cucumis sativus L.)

Twenty-one polymorphic and 17 monomorphic cucumber (Cucumis sativus L.) isozyme loci were identified in 15 enzyme systems. Seven of the polymorphic loci (Ak-2, Ak-3, Fdp-1, Fdp-2, Mpi-1, Pep-gl, and Skdh) had not been described previously. Segregation in F₂ and BC families for isozyme and morphological loci demonstrated agreement with the expected 121 and 11 segregation ratio (P<0.01). Nine morphological markers were found to be linked to isozyme loci and were integrated to form a map containing four linkage groups spanning 584 cM with a mean linkage distance of approximately 19 cM. Linkage groups (A to D) contain the following loci in genetic order: A psl, Pep-la, B, Per, dm, Pgm, Mpi-1, Idh, Ar, Fdp-1, Ak-2, Pgd-1, Mpi-2 and gl; B lh, Mdh-2, Pep-gl, Pgd-2, Fdp-2, Ccu, Mdh-3, Ak-3, ll, de, F and Mdh-1, and Gr; C cor, Gpi, and Skdh; D Tu and ss. This study detected four new linkages between morphological markers (dm-psl, de-ll, ll-F, and de-F) and confirmed previously reported linkages, dm-Ar and Tu-ss. The isozyme/morphological map constructed in this study led to a more comprehensive understanding of the genetic relationships between several economically important traits.Mention of a trade name, proprietary product, or specific equipment does not constitute a guarantee or warranty by the USDA and does not imply its approval to the exclusion of other products that may be suitable.     

Linkages between restriction fragment length,isozyme, and morphological markers in lentil

Summary A genetic linkage map of lentil comprising 333 centimorgans (cM) was constructed from 20 restriction fragment length, 8 isozyme, and 6 morphological markers segregating in a single interspecific cross (Lens culinaris × L. orientalis). Because the genotypes at marker loci were determined for about 66 F₂ plants, linkages are only reported for estimates of recombination less than 30 cM. Probes for identification of restriction fragment length polymorphisms (RFLPs) were isolated from a cDNA and EcoRI and PstI partial genomic libraries of lentil. The cDNA library gave the highest frequency of relatively low-copy-number probes. The cDNAs were about twice as efficient, relative to random genomic fragments, in RFLP detection per probe. Nine markers showed significant deviations from the expected F₂ ratios and tended to show a predominance of alleles from the cultigen. Assuming a genome size of 10 Morgans, 50% of the lentil genome could be linked within 10 cM of the 34 markers and the map is of sufficient size to attempt mapping of quantitative trait loci.     

Inheritance and linkage relationships of ten isozyme genes in hazelnut

Summary The inheritance of 6-phosphogluconate dehydrogenase (6PGD), malate dehydrogenase (MHD), aconitase (ACO), phosphoglucomutase (PGM), phosphoglucoisomerase (PGI), and glutamate-oxalacetate transaminase (GOT) polymorphic isozymes was studied in leaf extracts of nine hazelnut progenies using horizontal starch gel electrophoresis. Evidence of Mendelian inheritance was obtained for ten loci: 6-Pgd-2, Mdh-1, Aco-1, Aco-2, Pgm-1, Pgm-2, Pgm-3, Pgi-2, Pgi-3, and Got-2, which permitted the analysis of 28 alleles (2.8 per locus). The presence of null alleles was detected in Pgm-1 and Pgm-3. Joint segregation analysis of pairs of isozymes revealed four linkages: Mdh-1-Pgi-2, Aco-2-Pgm-2, Pgm-1-Pgm-3, and 6Pdg-2-Pgm-2.     

Genetic control and linkage relations of additional isozyme markers in chick-pea

Summary Allozyme polymorphisms of nine enzymes — aspartate aminotransferase (AAT), diaphorase (DIA), esterase (EST), formate dehydrogenase (FDH), -galactosidase (GAL), -glucosidase (GLU), malate dehydrogenase (MDH), malic enzyme (ME), and peroxidase (PRX) — were described in chick-pea (Cicer L.). Thirteen isozyme loci, Aat-c, Dia-4, Est-2, Est-4, Est-10, Fdh, Gal-2, Gal-3, Gal-4, Glu-3, Mdh-2, Me-2, and Prx-2, were genetically defined. Alleles of each of these isozyme loci expressed codominantly in heterozygotes and exhibited a codominant, single-locus segregation ratio in F₂. The loci Est-2, Mdh-2, and Me-1 were expressed only in flower. Linkage relations were determined for these 13 and several previously defined isozyme loci. The following new genetic linkages were identified: Pgm-p (locus for plastid phosphoglucomutase) — Est-10; Ald-p1 (one of the duplicate loci for plastid aldolase) — Glu-3 — Gal-2 — Est-2,3; Gal-3 — Aco-m (locus for mitochondrial aconitase) — Prx-2,3; Gpi-c (locus for cytosolic glucosephosphate isomerase) — Fdh; and Est-4 — Me-1. This study provides further confirmation on the existence of several conserved linkage groups among Cicer, Pisum, and Lens.     

Genetics and mapping of new isozyme loci in Vicia faba L using trisomics

Polymorphism in ten enzyme systems (ACO, ACP, AAT, EST, FK, ME, NAG, PRX, 6PGD, and SOD) in Vicia faba L. was analyzed, revealing 13 loci, six of which have not been reported before. Inheritance, genetics, possible location, and linkage analysis were studied in 13 different F² populations trisomic for four of the six chromosomes (nos. 3, 4, 5, and 6) of the species. Each of these loci exhibited typical Mendelian inheritance except for those involved in the trisomic chromosome. Five loci have been assigned to a specific chromosome: Est-2 to chromosome 3, Fk-2 to chromosome 4, Prx-1 to chromosome 5, and Sod-1 and Pgd-p to chromosome 6. Nag-1 and Pgd-c displayed a linkage of 22.8 cM indicating a clear homology with chromosome 5 of garden pea on which both markers are syntenic.     

Isozyme gene markers in the dioecious species Asparagus officinalis L.

Summary Extracts from phylloclads of Asparagus officinails were electrophoretically analyzed for isozyme polymorphism. Fourteen enzyme systems were examined using four buffer systems: seven enzymes (acid phosphatase, catalase, glutamate-oxaloacetate transaminase, isocitrate dehydrogenase, malate dehydrogenase, peroxidase, and 6-phosphogluconate dehydrogenase) exhibited clear and consistent banding patterns. Isozyme polymorphism was studied in seven pairs of male and female doubled haploids and in their male F₁s. Segregation of polymorphic loci was examined in the backcross progenies and was found to be consistent with a simple Mendelian inheritance in all cases, except for three anodical peroxidases, where two factors have been hypothesized. No linkage could be found between isozyme markers that were segregating in the same cross, but association was demonstrated between one malate dehydrogenase locus and the sex determining genes. The availability of isozyme markers may be useful in breeding and, in particular, the localization of one malate dehydrogenase locus on the sex chromosomes may be helpful in mapping the sex genes.     

Linkage and cytogenetic maps of genes controlling endosperm storage proteins and isozymes in rye (Secale cereale L.)

Summary An F₁ plant fromSecale cereale ssp.ancestrale xtelocentric substitution lines3R of the cultivated rye Petkus spring was used as female in a cross with the inbred line Riodeva (I28), which has the standard chromosome arrangement. Single plants from this backcross progeny were analyzed for chromosome constitution, storage protein, and isozymic patterns. The seed protein loci were identified asSec-1a andSec-1b loci controlling 40-K-secalins and-secalins, respectively. These loci are located on the short arm of chromosome1R. TheSec-3 locus controlling high-molecular-weight secalins is located on the long arm of chromosome1R. A further seed protein locus,Pr-3 (55-K protein), was located on the short arm of chromosome1R. A linkage was found between the6Pgd-2 isozyme locus controlling 6-phosphogluconate dehydrogenase isozymes located on the long arm of chromosome1R and the four seed protein loci. The results favor the gene order:6Pgd-2 ...Sec-3 ... [centromere] ...Pr-3 ...Sec-1b ...Sec-1a. Other linkages detected werePer-3a andPer-3b (0.33±0.33 cM),Est-8 andEst-12 (0.33±0.33 cM), andGot-3 and centromere (20.57±2.42 cM). The proxidase (Per), glutamate oxaloacetate transaminase (Got), and esterase (Est) loci were located on chromosome arms2RS,3RL, and6RL, respectively. The distances and the maps obtained are compared with data available in the literature.     

Linkage among isozyme,RFLP and RAPD markers in Vicia faba

Summary Segregating allozyme and DNA polymorphisms were used to construct a preliminary linkage map for faba bean. Two F₂ populations were analyzed, the most informative of which was segregating for 66 markers. Eleven independently assorting linkage groups were identified in this population. One of the groups contained the 45s ribosomal array and could be assigned to the large metacentric chromosome I on which the nucleolar organizer region is located. This linkage group also contained two isozyme loci, Est and Tpi-p, suggesting that it may share some homology with chromosome 4 of garden pea on which three similar markers are syntenic. Additional aspects of the map and the extent of coverage of the total nuclear genome are discussed.     

Allozyme and morphological variability,outcrossing rate and core collection formation in lentil germplasm

Summary A survey of qualitative genetic variation at 3 morphological trait loci, 17 isozyme loci and a putative isozyme locus (amylase) was made for 105 lentil (Lens culinaris Medikus) germplasm accessions from Chile, Greece and Turkey. New alleles were found for Lap-1, Me-2, Pgm-c, Pgm-p and 6-Pgd-c. The average proportion of polymorphic loci per population was 0.19, with a range of 0 to 0.42 over populations. Germplasm from Chile was equally variable to that from Greece and Turkey on the basis of individual loci and in a multilocus sense, despite its post-Columbus introduction to the New World. Evidence was found from associations between allelic states at different loci of a complex multilocus structure of lentil populations. A single multilocus genotype represented 10.2% of all plants sampled. The rate of outcrossing varied from 2.2% and 2.9% in Turkish and Greek landraces to 6.6% among Chilean populations. Using the survey data, a random sampling strategy for core collection formation was compared with two stratified sampling methods. The advantage of stratified sampling over random sampling was only significant at P=0.28.     

Natural occurrence of Bacillus thuringiensis in leguminous phylloplanes in the New Delhi region of India

Bacillus thuringiensis (Bt) isolates were present on the phylloplanes of chickpea (Cicer arietinum), pigeon pea (Cajanus cajan), pea (Pisum sativum) and mung bean (Vigna radiata). Bt index (ratio of the number of Bt colonies to the total number of spore-forming colonies per g of leaves) differed significantly among these plants, with the highest (0.20) in the chickpea phylloplane, followed by pigeon pea (0.17). Bt population of the chickpea phylloplane varied with plant age, being maximal in 45-day-old plants. Diversity was observed among Bt isolates for growth (up to 10-fold difference), antibiotic resistance, PCR product profile and toxicity to Helicoverpa armigera. Two isolates with high activity towards H. armigera were found. This revised version was published online in July 2006 with corrections to the Cover Date.     

An RFLP linkage map for loblolly pine based on a three-generation outbred pedigree

A genetic linkage map for loblolly pine (Pinus taeda L.) was constructed using segregation data from a three-generation outbred pedigree consisting of four grandparents, two parents, and 95 F₂ progeny. The map was based predominantly on restriction fragment length polymorphism (RFLP) loci detected by cDNA probes. Sixty-five cDNA and three genomic DNA probes revealed 90 RFLP loci. Six polymorphic isozyme loci were also scored. One-fourth (24%) of the cDNA probes detected more than 1 segregating locus, an indication that multigene families are common in pines. As many as six alleles were observed at a single segregating locus among grandparents and it was not unusual for the progeny to segregate for three or four alleles per locus. Multipoint linkage analysis placed 73 RFLP and 2 isozyme loci into 20 linkage groups; the remaining 17 RFLP and 4 isozyme loci were unlinked. The mapped RFLP probes provide a new set of codominant markers for genetic analyses in loblolly pine.     

Distribution,inheritance and linkage relationships of ribosomal DNA spacer length variants in pea

Summary DNA restriction endonuclease fragment analysis is used to examine the genetic organization, inheritance and linkage associations of the ribosomal DNA in pea. The substantial variation observed in the length of the intergenic spacer region is shown to segregate in Mendelian fashion involving two independent genetic loci, designated Rrn1 and Rrn2. Linkage between Rrn1 and two marker loci on chromosome 4 establishes the approximate location of this tandem array. Rrn2 shows linkage with a set of isozyme loci which assort independently of other markers on all seven chromosomes. Combining these observations with previous cytological data, we suggest that Rrn2 and the isozyme loci linked to it constitute a new linkage group on chromosome 7. The general absence of spacer length classes common to both rRNA loci in any of the lines we examined indicates that little or no genetic exchange occurs between the nonhomologous nucleolar organizer regions.     

New isozyme systems for maize (Zea mays L.): Aconitate hydratase,adenylate kinase,NADH dehydrogenase,and shikimate dehydrogenase

Electrophoretic variation and inheritance of four novel enzyme systems were studied in maize (Zea mays L.). A minimum of 10 genetic loci collectively encodes isozymes of aconitate hydratase (ACO; EC 4.2.1.3.), adenylate kinase (ADK; EC 2.7.4.3), NADH dehydrogenase (DIA; EC 1.6.99.—), and shikimate dehydrogenase (SAD; EC 1.1.1.25). At least four loci are responsible for the genetic control of ACO. Genetic data for two of the encoding loci,Aco1 andAco4, demonstrated that at least two maize ACOs are active as monomers. Analysis of organellar preparations suggests that ACO1 and ACO4 are localized in the cytosolic and mitochondrial subcellular fractions, respectively. Maize ADK is encoded by a single nuclear locus,Adk1, governing monomeric enzymes that are located in the chloroplasts. Two cytosolic and two mitochondrial forms of DIA were electrophoretically resolved. Segregation analyses demonstrated that the two cytosolic isozymes are controlled by separate loci,Dia1 andDia2, coding for products that are functional as monomers (DIA1) and dimers (DIA2). The major isozyme of SAD is apparently cytosolic, although an additional faintly staining plastid form may be present. Alleles atSad1 are each associated with two bands that cosegregate in controlled crosses. Linkage analyses and crosses with B-A translocation stocks were effective in determining the map locations of six loci, including the previously described but unmapped locusAcp4. Several of these loci were localized to sparsely mapped regions of the genome.Dia2 andAcp4 were placed on the distal portion of the long arm of chromosome 1, 12.6 map units apart.Dia1 was localized to chromosome 2, 22.2 centimorgans (cM) fromB1. Aco1 was mapped to chromosome 4, 6.2 cM fromsu1. Adk1 was placed on the poorly marked short arm of chromosome 6, 8.1 map units fromrgd1. Less than 1% recombination was observed betweenGlu1 (on chromosome 10) andSad1. In contrast to many other maize isozyme systems, there was little evidence of gene duplication or of parallel linkage relationships for these allozyme loci. This work was supported by grants from Pioneer Hi-Bred International, Inc., of Johnston, Iowa, the National Institute of Health (Research Grant GM11546), and the United States Department of Agriculture (Competitive Research Grant 83-CRCR-1-1273). This is Paper No. 11372 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh.     

Isozyme gene markers in Vicia faba L.

Summary This study was conducted to assess the genetic basis of the variability observed for the glutamate oxaloacetate transaminase (GOT), Superoxide dismutase (SOD), esterase (EST), and malate dehydrogenase (MDH) isozyme systems in different open-pollinated Vicia faba varieties. Individual plants showing contrasting zymogram patterns were simultaneously selfed and cross-combined. Crossing was unsuccessful in producing progeny, and only selfed progenies were suitable for genetical analysis of isozyme variability. Three zones of GOT activity were made visible. The isozyme of GOT-2 and GOT-3 zones were dimeric and under the control of three alleles at the Got-2 locus and two alleles at the Got-3 locus, respectively. The isozymes of the GOT-1 zone did not show any variability. Three zones of SOD isozyme activity were made visible. The isozymes occurring in the SOD-1 (chloroplastic isozyme form) and SOD-2 (cytosol isozyme form) zones were dimeric and under the control of two alleles at the Sod-1 and Sod-2 loci. The isozyme visualized in the SOD-3 zone (mitochondrial isozyme form) were tetrameric and under the control of two alleles at the Sod-3 locus. Apparently the isozymes made visible in the most anodal esterase zones EST-1, EST-2, and EST-3 were monomeric, and the occurrence of two alleles at each of two different loci explained the variability observed in the EST-2 and EST-3 zones. For MDH, only two five-banded zymogram pattern types were found, and every selfed progeny showed only one of the two zymogram type, indicating that each individual possessed fixed alleles at the loci controlling MDH isozyme. Got-2, Got-3, Sod-1, Sod-2, and Sod-3 appear to be five new isozyme gene markers that can be useful in Vicia faba breeding for linkage study, varietal fingerprinting, outcrossing rate estimate, and indirect selection for quantitative characters.     

Analysis of glucose phosphate isomerase in near-isogenic lines,and cultivars of rice (Oryza sativa L.)

Using the near-isogenic lines, the possible location of glucose phosphate isomeras-2 (phosphoglucose isomerase-2) locus (Pgi-2) in relation to photoperiod sensitivity locus (Se-1) and blast resistance locus (Pi-z) was investigated. The recombination frequency data indicate thatPgi-2 locus locates betweenSe-1 andPi-z loci. Furthermore, 15 Indica cultivars possessed two types of glucose phosphate isomerase-2 (GPI-2) isozyme, whereas only one type of GPI-2 isozyme was found in 30 Japonica cultivars.     

The dynamics of interlocus associations in the three-locus hitchhiking model

The hitchhiking effects of a selected locus upon the dynamics of the pairwise association,D _nn between two neutral loci is examined analytically for the special case where at least one of the neutral loci is in linkage equilibrium with the selected locus. The results apply approximately whenever the product of the pairwise associations between the selected locus and each neutral locus is negligible with respect to the three-way linkage disequilibrium. It is shown that precisely four broad classes of trajectories are possible, whether the selected locus is between (nsn) or to one side (snn) of the neutral loci, and whatever the mode of selection operating.D _nn may: (1) decay rapidly to zero, at a rate faster in each generation than that expected for two isolated neutral loci; (2) monotonically decay to zero at a rate which is slower in every generation than under the usual neutral regime; (3) increase initially and/or in intermediate periods before eventually slowly decaying to zero; or (4) exhibit type 1 behavior in the first segment of the trajectory and either type 2 or 3 behavior in the subsequent generations, with the transition marked by a change in sign. The nature of a given trajectory is largely determined by the direction of gene frequency change at the selected locus, and the initial signs of bothD _nn and the three-way linkage disequilibrium.The single most important consequence of these results is that there is no simple relation between the amount of pairwise association between two neutral markers and the recombination fraction between them. Several factors influencing the magnitude of the hitchhiking effect are also examined. It is shown that, all else being equal, the greater the three-way linkage disequilibrium, the greater the departure ofD _nn from the expected neutral dynamic. Increased recombination among the loci reduces the hitchhiking effect onD _nn . The dependence of the behavior upon the exact position of the selected locus is also determined both within and betweennsn andsnn chromosomal systems. An interesting discovery is that given equivalentnsn andsnn systems, with each having the same recombination between their two neutral loci,D _nn will deviate more from the standard neutral dynamic in thesnn system if its selected locus is sufficiently tightly linked to the neutral loci.     

A genetic map of citrus based on the segregation of isozymes and RFLPs in an intergeneric cross

Summary Isozymes and restriction fragment length polymorphisms were used as markers in the construction of a genetic map of the citrus nuclear genome. The map was based on the segregation of 8 isozyme, 1 protein, and 37 RFLP loci in 60 progeny of a cross of two intergeneric hybrids, Sacaton citrumelo (Citrus paradisi Macf. x Poncirus trifoliata (L.) Raf.) and Troyer citrange (C. sinensis (L.) Osbeck x P. trifoliata), often used as rootstocks. The map contains 38 of 46 studied loci distributed on ten linkage groups. A genome size of 1,700 cM was estimated from partial linkage data. Approximately 35% of the genome should be within 10 cM and 58% within 20 cM of the mapped markers. Eight loci in three linkage groups and 1 unlinked locus deviated significantly from Mendelian segregation.     

Effect of Seed Treatment with Rhizobium leguminosarum on Pythium Damping-off, Seedling Height, Root Nodulation, Root Biomass, Shoot Biomass, and Seed Yield of Pea and Lentil

Field experiments were conducted in 2004 and 2005 to determine the effects of seed treatment with Rhizobium leguminosarum bv. viceae on damping‐off, seedling height, root nodule mass, root biomass, shoot biomass and seed yield of pea and lentil in a field naturally infested with Pythium spp. Compared with the untreated controls, treatment of pea seeds with R. leguminosarum bv. viceae strains R12, R20 or R21 significantly (P < 0.05) reduced incidence of damping‐off, promoted seedling growth and increased root nodule mass, root biomass and shoot biomass. Seed treatments with R12 or R21 also resulted in a significant (P < 0.05) increase in seed yield of pea. The strain R21 was most effective among the four strains of R. leguminosarum bv. viceae tested in peas. Although, the level of disease control by strain R21 was similar to seed treatment with the fungicide Thiram^TM, R21 was more effective in enhancing root nodule production and promoting plant growth. For lentil, treatment of seeds with R. leguminosarum bv. viceae strains R12 or R21 significantly (P < 0.05) reduced incidence of damping‐off compared with the untreated control. All of the four strains of R. leguminosarum bv. viceae tested increased lentil seedling height, root nodule mass and shoot biomass, and all except R20 increased root biomass. Seed yield was higher for the treatments of R12 and R21. The strain R12 was most effective among the four strains of R. leguminosarum bv. viceae tested in lentil. Although, strain R12 was as effective as Thiram^TM for control of damping‐off of lentil, it was more effective than Thiram^TM for the production of root nodules and promotion of plant growth. The study concludes that seed treatment with R. leguminosarum bv. viceae is effective in control of Pythium damping‐off of pea and lentil and that the efficacy of control is strain specific, strain R21 for control of the disease on pea and strain R12 for control of the disease on lentil.     

Utility of RAPD markers in identifying genetic linkages to genes of economic interest in peach

The identification of molecular markers linked to economically important traits for use in crop improvement is very important in long-lived perennial species. Three-hundred-and-sixty RAPD primers were used with bulked segregant analysis to identify markers linked to loci of specific interest in peach [(Prunus persica) L. Batch] and peach x almond [(Prunus dulcis) Batch] crosses. The traits analyzed included flesh color, adhesion, and texture; pollen fertility; plant stature; and three isozyme loci. The Mendelian behavior of the RAPD loci was established, and RAPD markers were mapped relative to the loci controlling flesh color, adhesion, and texture, and the isozyme loci Mdh-1, 6Pgd-2 and Aat-1, as well as the existing RFLP genetic linkage map constructed previously using a peach x almond F₂ population. This technique has facilitated rapid identification of RAPD and RFLP markers that are linked to the traits under study. Loci controlling these traits mapped predominantly to linkage groups 2 and 3 of the peach genetic linkage map. Linkages to genes with both dominant and co-dominant alleles were identified, but linkages to dominant genes were more difficult to find. In several crosses, RAPD marker bands proved to be allelic. One co-dominant RAPD formed a heteroduplex band in heterozygous individuals and in mixtures of alternate homozygotes. The Mendelian behavior of the RAPD loci studied was established and the results suggest that RAPD markers will be useful for plant improvement in peach.