Inheritance of nuclear DNA content in leaf epidermal cells of Zea mays L.

 The nuclear DNA content (ploidy level) of maize leaf-epidermal cells was investigated by Feulgen cytophotometry in two lines, Illinois High Protein (IHP) and Illinois Low Protein (ILP), their reciprocal hybrids, and their F₂s. Epidermal cells have a 2C, 4C or 8C nuclear DNA content. The mean DNA content per nucleus in IHP was significantly higher than in ILP; the mean DNA content per nucleus in hybrids was intermediate between the parental lines, and the same DNA content was measured in reciprocal crosses. In F₂s the same mean DNA content as in F₁s was observed but with larger variability than in the F₁, possibly indicating genetic segregation. It is inferred that the ploidy level in the leaf epidermis is inherited, and incomplete dominance occurs in hybrids. The same behaviour in the different genotypes was observed for epidermal cell-surface area, except that an increase of mean surface area occurred in the F₁, probably due to heterotic effects. The difference in the accumulation of 4C and 8C nuclei in leaf epidermis parallels that reported between two genotypes for the endosperm tissue: to the greater chromosome endoreduplication found in the endosperm there were correspondingly higher frequencies of 4C and 8C nuclei in the leaf epidermis, indicating a higher general tendency to chromosome endoreduplication in IHP than in ILP. It is suggested that the accumulation of 4C nuclei (G₂-block) in the leaf epidermis may be regarded as the initial step of chromosome endoreduplication, the two phenomena being related to the control of the sequence DNA synthesis-mitosis, possibly involving the same genes in both endosperm and leaf. However, the inheritance of DNA content per nucleus in epidermal tissue seems to be different from that observed in endosperm tissue of the same genotypes, suggesting that differences may occur in the regulation of the activity of these genes. Received: 19 November 1996 / Accepted: 29 November 1996     

Chromosome endoreduplication in endosperm cells of two maize genotypes and their progenies

Summary Chromosome endoreduplication is a very common process in higher plants but its function and genetic control are still to be clarified. In our experiments we analyzed, by Feulgen cytophotometry, chromosome endoreduplication in endosperm cells of two maize genotypes, IHP and ILP, having high and low protein content in their seed, respectively. Chromosome endoreduplication occurs in both lines within 24 days after pollination, attaining a maximum ploidy level of 384C (7 DNA replication rounds) in IHP and of 192C (6 replication rounds) in ILP. In the mature seed, endosperms of the two lines show different mean ploidy level. In reciprocal crosses between IHP and ILP the f₁ endosperms have mean ploidy levels analogous to that of the maternal parent, showing that the difference in ploidy level between the two genotypes is maintained. After selfing of the f₁ plants, the difference in ploidy level between the two F₂ populations is reduced. In F₂ the mean ploidy level is as variable as in f₁, indicating the absence of genetic segregation. From our data, it is apparent that both the genetic constitution (cytoplasmic and nuclear) of the maternal parent and the genotype of the individual endosperms influence the ploidy level. An analysis of the protein content in endosperms carried out on the same seed sample as analyzed cytophotometrically showed that the protein content increases, during seed development, parallel to chromosome endoreduplication and varies, in the two lines, in reciprocal crosses and their progeny, according to the same trend as mean ploidy level, suggesting a correlation between the two parameters.     

Quantitative trait loci influencing protein and starch concentration in the Illinois Long Term Selection maize strains

A study was initiated to determine the number, chromosomal location, and magnitude of effect of QTL (quantitative trait loci or locus depending on context) controlling protein and starch concentration in the maize (Zea mays L.) kernel. Restriction fragment length polymorphism (RFLP) analysis was performed on 100 F₃ families derived from a cross of two strains, Illinois High Protein (IHP), X Illinois Low Protein (ILP), which had been divergently selected for protein concentration for 76 generations as part of the Illinois Long Term Selection Experiment. These families were analyzed for kernel protein and starch in replicated field trials during 1990 and 1991. A series of 90 genomic and cDNA clones distributed throughout the maize genome were chosen for their ability to detect RFLP between IHP and ILP. These clones were hybridized with DNA extracted from the 100 F₃ families, revealing 100 polymorphic loci. Single factor analysis of variance revealed significant QTL associations of many loci with both protein and starch concentration (P < 0.05 level). Twenty-two loci distributed on 10 chromosome arms were significantly associated with protein concentration, 19 loci on 9 chromosome arms were significantly associated with starch concentration. Sixteen of these loci were significant for both protein and starch concentration. Clusters of 3 or more significant loci were detected on chromosome arms 3L, 5S, and 7L for protein concentration, suggesting the presence of QTL with large effects at these locations. A QTL with large additive effects on protein and starch concentration was detected on chromosome arm 3L. RFLP alleles at this QTL were found to be linked with RFLP alleles at the Shrunken-2 (Sh2) locus, a structural gene encoding the major subunit of the starch synthetic enzyme ADP-glucose pyrophosphorylase. A multiple linear regression model consisting of 6 significant RFLP loci on different chromosomes explained over 64 % of the total variation for kernel protein concentration. Similar results were detected for starch concentration. Thus, several chromosomal regions with large effects may be responsible for a significant portion of the changes in kernel protein and starch concentration in the Illinois Long Term Selection Experiment.     

Development of RAPD and SCAR markers linked to the Russian wheat aphid resistance gene Dn2 in wheat

 RAPD (random amplified polymorphic DNA) analysis was used to identify molecular markers linked to the Dn2 gene conferring resistance to the Russian wheat aphid (Diuraphis noxia Mordvilko). A set of near-isogenic lines (NILs) was screened with 300 RAPD primers for polymorphisms linked to the Dn2 gene. A total of 2700 RAPD loci were screened for linkage to the resistance locus. Four polymorphic RAPD fragments, two in coupling phase and two in repulsion phase, were identified as putative RAPD markers for the Dn2 gene. Segregation analysis of these markers in an F₂ population segregating for the resistance gene revealed that all four markers were closely linked to the Dn2 locus. Linkage distances ranged from 3.3 cM to 4.4 cM. Southern analysis of the RAPD products using the cloned RAPD markers as probes confirmed the homology of the RAPD amplification products. The coupling-phase marker OPB10_880c and the repulsion-phase marker OPN1_400r were converted to sequence characterized amplified region (SCAR) markers. SCAR analysis of the F₂ population and other resistant and susceptible South African wheat cultivars corroborated the observed linkage of the RAPD markers to the Dn2 resistance locus. These markers will be useful for marker-assisted selection of the Dn2 gene for resistance breeding and gene pyramiding. Received: 1 July 1997 / Accepted: 20 October 1997     

Detecting and mapping repulsion-phase linkage in polyploids with polysomic inheritance

It has been suggested that ratios of coupling- to repulsion-phase linked markers can be used to distinguish between allopolyploids and autopolyploids, because repulsion-phase linkages are much more difficult to detect in autopolyploids with polysomic inheritance than allopolyploids with disomic inheritance. In this report, we analyze the segregation pattern of repulsion-phase linked markers in polyploids without complete preferential pairing. The observed repulsion-phase recombination fraction (R) in such polyploids is composed of a fraction due to crossing-over (R_c) and another fraction due to independent assortment (R_i). R_i is the minimum distance that can be detected between repulsion-phase linked markers. Because R_i is high in autopolyploids (0.3373, 0.4000, 0.4286 and 0.4444) for autopolyploids of 2n=4x, 6x, 8x and 10x), large population sizes are required to reliably detect repulsion linkages. In addition, the default linkage used in mapping-programs must be greater than the corresponding R_i to determine whether a polyploid is a true autopolyploid. Unfortunately, much lower default linkages than the R_is have been used in recent polyploid studies to determine polyploid type, and markers have been incorporated into polyploid maps based on the R values. Herein, we describe how mapping repulsion linkages can result in spurious results, and present methods to accurately detect the degree of preferential pairing in polyploids using repulsion linkage analysis. Received: 29 February 2000 / Accepted: 17 July 2000     

Coupling- and repulsion-phase RAPDs for marker-assisted selection of PI 181996 rust resistance in common bean

The Guatemalan black bean (Phaseolus vulgaris L.) plant introduction (PI) 181996 is resistant to all known US races of the bean rust fungus Uromyces appendiculatus (Pers. ex Pers.) Unger var. appendiculatus [syn. U. phaseoli (Reben) Wint.]. We report on two random amplified polymorphic DNA (RAPD) markers OAC20₄₉₀ tightly linked (no recombinants) in coupling phase and OAE19₈₉₀ linked in repulsion phase (at 6.2±2.8 cM) to PI 181996 rust resistance. These RAPDs, generated by single decamer primers in the polymerase chain reaction, were identified in near-isogenic bulks of non-segregating resistant and susceptible BC₄F₂ (NX-040*4/PI 181996) lines. Linkage of the RAPD markers was confirmed by screening 19 BC₄F₂ and 57 BC₄F₃ individuals segregating for PI 181996 resistance. Utility of the RAPDs OAC20₄₉₀ and OAE19₈₉₀ was investigated in a diverse group of common bean cultivars and lines. All cultivars into which the PI 181996 resistance was introgressed had the RAPD OAC20₄₉₀. A RAPD similar in size to OAC20₄₉₀, observed in some susceptible common bean lines, was confirmed by Southern blotting to be homologous to the RAPD OAC20₄₉₀. Use of the RAPDs OAC20₄₉₀ and OAE19₈₉₀ in marker-assisted selection (MAS) is proposed. The coupling-phase RAPD is most useful for MAS of resistant BC_nF₁individuals during traditional backcross breeding. The repulsion-phase RAPD has greatest utility in MAS of homozygous-resistant individuals in F₂ or later-segregating generations.Mention of a trademark or a proprietary product does not constitute a guarantee or warranty of the product by the USDA and does not imply its approval to the exclusion of other products that may also be suitable.     

Effect of Mating Structure on Variation in Linkage Disequilibrium

Measurement of linkage disequilibrium involves two sampling processes. First, there is the sampling of gametes in the population to form successive generations, and this generates disequilibrium dependent on the effective population size (N_e) and the mating structure. Second, there is sampling of a finite number (n) of individuals to estimate the population disequilibrium.——Two-locus descent measures are used to describe the mating system and are transformed to disequilibrium moments at the final sampling. Approximate eigenvectors for the transition matrix of descent measures are used to obtain formulae for the variance of the observed disequilibria as a function of N_e, mating structure, n, and linkage or recombination parameter.——The variance of disequilibrium is the same for monoecious populations with or without random selfing and for dioecious populations with random pairing for each progeny. With monogamy, the variance is slightly higher, the proportional difference being greater for unlinked loci.     

Multigenerational outbreeding effects in Chinook salmon (Oncorhynchus tshawytscha)

Outbreeding, mating between genetically divergent individuals, may result in negative fitness consequences for offspring via outbreeding depression. Outbreeding effects are of notable concern in salmonid research as outbreeding can have major implications for salmon aquaculture and conservation management. We therefore quantified outbreeding effects in two generations (F₁ hybrids and F₂ backcrossed hybrids) of Chinook salmon (Oncorhynchus tshawytscha) derived from captively-reared purebred lines that had been selectively bred for differential performance based on disease resistance and growth rate. Parental lines were crossed in 2009 to create purebred and reciprocal hybrid crosses (n = 53 families), and in 2010 parental and hybrid crosses were crossed to create purebred and backcrossed hybrid crosses (n = 66 families). Although we found significant genetic divergence between the parental lines (F_ST = 0.130), reciprocal F₁ hybrids showed no evidence of outbreeding depression (hybrid breakdown) or favorable heterosis for weight, length, condition or survival. The F₂ backcrossed hybrids showed no outbreeding depression for a suite of fitness related traits measured from egg to sexually mature adult life stages. Our study contributes to the current knowledge of outbreeding effects in salmonids and supports the need for more research to better comprehend the mechanisms driving outbreeding depression.     

A comparison of inbred lines derived by doubled haploidy and single seed descent in spring barley (Hordeum vulgare)

Samples of F_x inbred lines, derived by doubled haploidy (DH) and single seed descent (SSD) from five spring barley crosses were compared for agronomic characters. It was shown that, over this range of diverse crosses, inbreds derived by either technique could surpass the better parent or even the heterotic F₁. The means of the DH and SSD were, however, different for a number of characters, as well as differing from the mid-parent value. It was concluded that these differences stemmed from the presence of interacting genes showing linkage disequilibrium, although there was no unambiguous test to distinguish this from differential survival during the production of inbreds. This view was further supported by the finding that the DH sample, which tends to preserve existing linkages, produced a higher proportion of lines exceeding the better scoring parent when compared with the SSD population.     

Occurrence of genetic tumours in Triticum interspecies hybrids

Summary F₁ interspecific hybrids involving nine tetraploid Triticum species were studied. Some developed leaf tumours at the seedling stage. Tumorous hybrids were restricted to crosses involving either T. timopheevi or T. araraticum as one parent. The hybrids from the rest of the crosses, including those of T. timopheevi × T. araraticum, were non-tumorous. Genetically divergent and non-integrated parental species appeared to be inducing spontaneous tumour formation in their hybrids.     

Biochemical polymorphism in the rat,Rattus norvegicus: Genetic study of four markers

The linkage of the hemoglobin (Hbb) and albino (c) loci has been determined from backcross progeny of the mating (WAG/Orl × Long Evans/Orl)F ₁ × WAG/Orl. The data give 9.1 ± 1.8% recombination. The backcross (August/Orl × WAG/Orl)F ₁ × August/Orl segregating for Hbb and pink-eyed yellow (p) shows 21.5±4.2% recombination. The proposed gene order on linkage group I is p-c-Hbb. Linkage of the seminal vesicle protein (Svp-1) and the nonagouti (a) loci has been determined from backcross progeny of the mating (August/Orl × Long Evans/Orl)F ₁ × Long Evans/Orl. The data show 7.1±3.4% recombination. Svp-1 thus represents an additional marker in linkage group V. Two new autosomal variants have been reported: The locus which controls a plasma protein's polymorphism has been designated Gl-1 with two codominant alleles Gl-1a and Gl-1b. The other locus, controlling a testis esterases polymorphism, has been assigned the symbol Es-3 and has two codominant alleles Es-3a and Es-3b. The absence of linkage of Gl-1 and Es-3 to each other and to five different loci has also been reported. Rat and mouse analogy with respect to these markers and established linkages is discussed.     

Two-trait selection response with marker-based assortative mating

 Marker-based assortative mating (MAM) – the mating of individuals that have similar genotypes at random marker loci – can increase selection response for a single trait by 3–8% over random mating (RM). Genetic gain is usually desired for multiple traits rather than for a single trait. My objectives in this study were to (1) compare MAM, phenotypic assortative mating (PAM), and RM of selected individuals for improving two traits and (2) determine when MAM will be most useful for improving two traits. I simulated 20 generations of selecting 32 out of 200 individuals in an F₂ population. The individuals were selected based on an index (SI) of two traits and were intermated by MAM, PAM, or RM. I studied eight genetic models that differed in three contrasts: (1) weight, number of quantitative trait loci (QTL), and heritability (h ²) for each trait; (2) linkage of QTL for each trait; and (3) trait means of the inbred parents of the F₂. For SI and the two component traits, MAM increased short-term selection response by 5–8% in six out of the eight genetic models. The MAM procedure was least effective in two genetic models, wherein the QTL for one trait were unlinked to the QTL for the other trait and the parents of the F₂ had divergent means for each trait. The loss of QTL heterozygosity was much greater with MAM than with PAM or RM. Consequently, the advantage of MAM over RM dissipated after 5–7 generations. Differences were small between selection responses with PAM and RM. The MAM procedure can enhance short-term selection response for two traits when selection is not stringent, h ² is low, and the means of the parents of the F₂ are equal for each trait. Received: 10 June 1998 / Accepted: 5 August 1998     

Prediction of testcross means and variances among F3 progenies of F1 crosses from testcross means and genetic distances of their parents in maize

 Prediction of the means and genetic variances in segregating generations could help to assess the breeding potential of base populations. In this study, we investigated whether the testcross (TC) means and variances of F₃ progenies from F₁ crosses in European maize can be predicted from the TC means of their parents and F₁ crosses and four measures of parental genetic divergence: genetic distance (GD) determined by 194 RFLP or 691 AFLP^{TM 1} markers, mid-parent heterosis (MPH), and absolute difference between the TC means of parents (∣P₁−P₂∣). The experimental materials comprised six sets of crosses; each set consisted of four elite inbreds from the flint or dent germplasm and the six possible F₁ crosses between them, which were evaluated for mid-parent heterosis. Testcross progenies of these materials and 20 random F₃ plants per F₁ cross were produced with a single-cross tester from the opposite heterotic group and evaluated in two environments. The characters studied were plant height, dry matter content and grain yield. The genetic distance between parent lines ranged between 0.17 and 0.70 for RFLPs and between 0.14 and 0.57 for AFLPs in the six sets. Testcross-means of parents, F₁ crosses, and F₃ populations averaged across the six crosses in a particular set generally agreed well for all three traits. Bartlett’s test revealed heterogeneous TC variances among the six crosses in all sets for plant height, in four sets for grain yield and in five sets for dry matter content. Correlations among the TC means of the parents, F₁ crosses, and F₃ populations were highly significant and positive for all traits. Estimates of the TC variance among F₃ progenies for the 36 crosses showed only low correlations with the four measures of parental genetic divergence for all traits. The results demonstrated that for our material, the TC means of the parents or the parental F₁ cross can be used as predictors for the TC means of F₃ populations. However, the prediction of the TC variance remains an unsolved problem. Received: 4 August 1997 / Accepted: 17 November 1997     

High-resolution genetic mapping of the pepper (Capsicum annuum L.) resistance loci Me3 and Me4 conferring heat-stable resistance to root-knot nematodes (Meloidogyne spp.)

The PM687 line of Capsicum annuum L. has a single dominant gene, Me ₃ , that confers heat-stable resistance to root-knot nematodes (RKN). Me ₃ was mapped using doubled-haploid (DH) lines and F₂ progeny from a cross between the susceptible cultivar ’Yolo Wonder’ (’YW’) and the highly resistant line ’PM687’. Bulked-segregant analysis with DNA pools, from susceptible or resistant DH lines, was performed to identify RAPD and AFLP markers linked to Me ₃ . There was no polymorphism between bulks of ten DH lines using over 800 RADP primers (4,000 amplified fragments analysed). Using 512 AFLP primers (74,000 amplified fragments analysed), and bulked DNA templates from 20 resistant and 20 susceptible plants, we identified eight repulsion-phase and four coupling-phase markers linked to Me _3. Analysed in 103 DH progeny, they defined a 56.1-cM interval containing the target gene. The nearest were located 0.5, 1.0, 1.5 and 3.0 centimorgans (cM) on both sides of the gene. Analysis of the F₂ progeny (162 plants) with the nearest coupling-phase marker confirmed its close position. Another resistance gene to RKN, present in ’PM687’ (Me ₄ ), was shown to be linked to Me ₃ , 10 cM from it. In order to localize Me ₃ and Me ₄ on our reference intraspecific pepper linkage map, two AFLP markers were mapped. The Me ₃ nearest marker was 10.1cM from a RAPD marker named Q04_0.3 and 2.7cM from a RFLP marker named CT135. We investigated map-position orthologies between Me ₃ and two other nematode resistance genes, the tomato Mi-3 and the potato Gpa ₂ genes, which mapped in the telomeric region of the short arm of the tomato and potato chromosome 12 (or XII for potato). Received: 23 March 2000 / Accepted: 2 January 2001     

Linkage analysis of quantitative trait loci in multiple line crosses

Simple line crosses, for example, backcross and F₂, are commonly used in mapping quantitative trait loci (QTL). However, these simple crosses are rarely used alone in commercial plant breeding; rather, crosses involving multiple inbred lines or several simple crosses but connected by shared inbred lines may be common in plant breeding. Mapping QTL using crosses of multiple lines is more relevant to plant breeding. Unfortunately, current statistical methods and computer programs of QTL mapping are all designed for simple line crosses or multiple line crosses but under a regular mating system. It is not straightforward to extend the existing methods to handle multiple line crosses under irregular and complicated mating designs. The major hurdle comes from irregular inbreeding, multiple generations, and multiple alleles. In this study, we develop a Bayesian method implemented via the Markov chain Monte Carlo (MCMC) algorithm for mapping QTL using complicated multiple line crosses. With the MCMC algorithm, we are able to draw a complete path of the gene flow from founder alleles to their descendents via a recursive process. This has greatly simplified the problem caused by irregular mating and inbreeding in the mapping population. Adopting the reversible jump MCMC algorithm, we are able to simultaneously search for multiple QTL along the genome. We can even infer the posterior distribution of the number of QTL, one of the most important parameters in QTL study. Application of the new MCMC based QTL mapping procedure is demonstrated using two different mating designs. Design I involves two inbred lines and their derived F₁, F₂, and BC populations. Design II is a half-diallel cross involving three inbred lines. The two designs appear different, but can be handled with the same robust computer program.     

Evidence of Different Ploidy Eggs Produced by Diploid F2 Hybrids of Carassius auratus (♀) × Cyprinus carpio (♂)

Based on the presence of three types of eggs with different diameters 0.13, 0.17 and 0.2 cm, we made two crosses: F₂ (♀) × diploid red crucian carp (♂), and F₂ (♀) × F₁₀ tetraploid (♂). The ploidy levels of the progeny of the two crosses were examined by chromosome counting and DNA content measurement by flow cytometer. In the offspring of the former cross, tetraploids, trip-loids, and diploid were obtained. In the progeny of the latter cross, tetraploids and triploids were observed. The production of the different ploidy level fish in the progeny of the two crosses provided a further evidence that F₂ might generate triploid, diploid and haploid eggs. The presence of the male tetraploid found in F₂ (♀) × diploid red crucian carp (♂) suggested that the genotype of XXXY probably existed in the tetraploid progeny. The gonadal structures of the tetraploids and triploids indicated that both female and male tetraploids were fertile and the triploids were sterile. We concluded that the formations of different ploidy level eggs from F₂ were contributed by endoreduplication and fusion of germ cells.     

Verifying an F1 screen for identification and quantification of rare Bacillus thuringiensis resistance alleles in field populations of the sugarcane borer,Diatraea saccharalis

Using an F₁ screen, 352 feral individuals of the sugarcane borer, Diatraea saccharalis (F.) (Lepidoptera: Crambidae), were examined for the presence of Bacillus thuringiensis (Bt)‐resistance alleles. These insects represented four geographical populations collected in central and northeastern Louisiana, USA, and one field population from the Gulf Coast area of Texas, USA, during 2006. The F₁ screen used various crosses between field‐collected insects and a laboratory strain of Cry1Ab‐resistant D. saccharalis, including both reciprocal crosses and group mating. F₁ neonates of the crosses were screened for Bt resistance on Bt maize leaf tissue. One field‐collected individual of D. saccharalis was shown to have a Bt‐resistance allele. Based on Bayesian analysis procedures, the Bt‐resistance allele frequency in the five populations of D. saccharalis was 0.0028 with a 95% confidence interval of 0.0003–0.0079. The successful identification of a resistance allele in a field collection of insects suggests that the F₁ screening technique could be an effective tool for detecting and monitoring rare Bt‐resistance alleles in field populations of D. saccharalis.     

Genetic aspects of wheat gliadin proteins

Inheritance of gliadin components unique to three different varieties of common wheat (Triticum aestivum L.) was studied in F₁ and F₂ seeds of intervarietal crosses using protein patterns obtained by polyacrylamide gel electrophoresis in aluminum lactate buffer (pH 3.2). The patterns of F₁ seeds of the crosses Cheyenne × Justin and INIA 66R × Justin evidenced all the bands present in the patterns of the parents; band intensities reflected gene dosage levels dependent on whether the contributing parent was maternal or paternal in accordance with the triploid nature of endosperm tissue. Most of the gliadin components examined segregated in accordance with control by a single dominant gene, but in two instances single bands in the one-dimensional electrophoretic patterns segregated in the F₂ as expected if controlled by two genes. A method of two-dimensional electrophoresis was developed that resolved these apparently single bands into two components each, which could segregate independently. Linkage analysis provided evidence of codominant alleles and closely linked genes coding for gliadin protein components in both coupling and repulsion situations. The gliadin protein components seem to be coded for by clusters of genes located on chromosomes of homoeologous groups 1 and 6 in hexaploid wheats.Reference to a company or product name does not imply approval by the U.S. Department of Agriculture to the exclusion of others which may also be suitable.     

Inheritance of grain proteins in wheat

Summary Diallel crosses between five divergent vulgare wheat cultivars were made in order to evaluate the mode of inheritance and combining ability of grain proteins. Significant differences in grain protein content were found between cultivars and their hybrids. It was established that the inheritance of seed protein in the F₁ generation included both additive and non-additive gene action.