Mapping of quantitative trait loci on porcine chromosome 4

A F₂ population derived from a cross between European Large White and Chinese Meishan pigs was established in order to study the genetic basis of breed differences for growth and fat traits. Chromosome 4 was chosen for initial study as previous work had revealed quantitative trait loci (QTLs) on this chromosome affected growth and fat traits in a Wild Boar × Large White cross. Individuals in the F₂ population were typed for nine markers spanning a region of approximately 124 c m . We found evidence for QTLs affecting growth between weaning and the end of test (additive effect: 43·4 g/day) and fat depth measured in the mid-back position (additive effect: 1·82 mm). There was no evidence of interactions between the QTLs and sex, grandparents or F₁ sires, suggesting that the detected QTLs were fixed for alternative alleles in the Meishan and Large White breeds. Comparison of locations suggests that these QTLs could be the same as those found in the Wild Boar × Large White cross.     

Mapping of QTL on chromosome X for fat deposition, muscling and growth traits in a wild boar x Meishan F2 family using a high-density gene map

Quantitative trait loci (QTL) for fat deposition, growth and muscling traits have been previously mapped on the basis of low-density linkage maps in a wild boar × Meishan F₂ family to the chromosome X region flanked by SW2456 and SW1943 . Improved QTL resolution was possible using data for F₂ animals with a marker density of 2.7 cM distance in the SW2456 to SW1943 region, including AR , SERPINA7 and ACSL4 as candidate genes. The resolution of the QTL scan was increased substantially, as evidenced by the higher F -ratio values for all QTL. Maxima of F -ratio values for fat deposition, muscling and growth traits were 28.6, 18.2 and 16.5 respectively, and those QTL positions accounted for 7.9%, 5.0% and 4.5% of the F₂ phenotypic variance (VF₂) respectively. QTL for fatness and growth and for most muscling traits mapped near ACSL4 , with the exception of the QTL for ham traits that mapped proximally, in the vicinity of AR . An analysis performed separately for F₂ male animals showed the predominant QTL affecting fat deposition traits (up to 13.6% VF₂) near AR and two QTL for muscling traits (up to 9.9% VF₂) mapped close to ACSL4 . In the F₂ female animals, QTL affecting muscling (up to 12.1% VF₂) mapped at ACSL4 and SW2456 , and QTL for fat deposition (10% VF₂) and growth (up to 10.5% VF₂) mapped at ACSL4 .     

Fertility of roach × bream hybrids, Rutilus rutilus (L.) ×Abramis brama (L.), and their identification

Adult roach, bream and their presumed F₁ hybrid from an Anglian Water reservoir were identified on the basis of morphological and meristic characteristics. The hybrid was clearly intermediate. Four hybrid breeding crosses were induced to spawn by hypophysis. A bream × roach cross (female named first) failed to produce fertile eggs, whereas F₁ hybrid × roach, roach × F₁ hybrid and F₁ hybrid × F₁ hybrid all produced fry. Fertility (defined as survival of eggs to hatching) was high for the F₁ hybrid × roach back-cross (56%) but low for the others (<2%), in comparison to the pure species controls (roach 69%, bream 76%). Progeny from these crosses were reared until anal fin rays could be counted. These counts indicated intermediacy between the parents and back-crossed individuals, and similarity between F₁ hybrids and their F₂ progeny.     

Genetic analysis of seed size, yield and days to flowering in a chickpea recombinant inbred line population derived from a Kabuli × Desi cross

Quantitative traits, seed size, yield and days to flowering were studied in a chickpea intraspecific recombinant inbred line (RIL) population (F_6:7) derived from a Kabuli × Desi cross. The population was evaluated in two locations over 2 years. Days to flowering was also evaluated in the greenhouse under short-day conditions. Seed size was the most heritable trait (0.90), followed by days to flowering (0.36) and yield (0.14). Negative and significant correlation was found between yield and seed size in the second year where environmental homogeneity was tested by analysing the controls included in each assay. During the first year, the environment was not considered homogeneous for yield in either location. Quantitative trait loci (QTLs) for the three characters were detected in linkage group (LG) 4. In relation to seed size, two QTLs were located in LG4 (QTL_SW1) and LG8 (QTL_SW2). QTL_SW1 accounted 20.3% of the total phenotypic variation and QTL_SW2 explained 10.1%. A QTL for yield (QTL_YD) was located in LG4 explaining around 13% of variation. QTL_YD might be pleiotropic with QTL_SW1. For days to flowering, a QTL (QTL_DF1) was located in LG4 for all environments analysed explaining around 20% of variation. QTL_DF1 was closely linked to QTL_SW1 and QTL_YD in LG4.     

Non-association between Rfp-Y major histocompatibility complex-like genes and susceptibility to Marek's disease virus-induced tumours in 63× 72 F2 intercross chickens

Marek's disease (MD) is a lymphoproliferative disease caused by a member of the herpesvirus family, and the best understood genetic resistance to MD involves the chicken major histocompatibility complex (MHC) B -complex. Preliminary observations have suggested that MHC-like Rfp-Y genes might also influence the incidence of MD. This study describes the differentiation and definition of unique Rfp-Y genes in inbred lines 6₃ and 7₂, lines that possess identical B -complex genes, but that are resistant or susceptible to MD, respectively. To assess if Rfp-Y genes affect susceptibility to MD, 265 6₃× 7₂ F₂ chickens were challenged with the JM strain of MD virus at 1 week of age and were evaluated for MD lesions at up to 10 weeks of age. Genotyping of the F₂ chickens for Rfp-Y haplotypes was performed by restriction fragment length polymorphism analysis of genomic DNA using Taq I and a B-FIV probe. Analysis of variance and interval mapping procedures were used to determine association between the Rfp-Y haplotypes and the phenotypic MD values of the F₂ chickens. The cosegregation analysis of 265 F₂ chickens indicated that there was no association between Rfp-Y haplotypes and MD susceptibility. Furthermore, the fact that the Rfp-Y haplotypes fit the 1:2:1 segregation ratio and the Rfp-Y allele frequencies did not differ significantly from 0·5 in the full population or in selected subpopulations (of either 40 MD-resistant or 39 MD-susceptible chickens) also indicated that Rfp-Y haplotypes do not significantly influence MD susceptibility. We conclude that Rfp-Y haplotypes do not play a major role in determining the genetic susceptibility to MD in 6₃× 7₂ F₂ White Leghorn chickens.     

Associations of GH gene variants with performance traits in F2 generations of European wild boar, Piétrain and Meishan pigs

The role of the porcine GH gene was investigated in 292 F₂ animals of mating Wild Boar × Piétrain and in 310 F₂ animals of mating Meishan × Piétrain. Forty-three traits of fattening, carcass composition, meat quality and stress resistance were recorded. For the analysis of associations between GH gene variants and quantitative traits, two restriction fragment length polymorphisms were examined. In the Meishan × Piétrain family eight traits related to fatness were significantly associated with GH genotypes, while in the Wild Boar × Piétrain family no significant associations were found. In the Meishan × Piétrain cross, the GH locus explained 11·7% to 17·7% of the total phenotypic variance in the F₂ population. The possibility of multiple alleles at the GH locus is discussed. Based on these results, we conclude that the GH locus should be further investigated in commercial breeds to determine its suitability for use in marker-assisted selection programmes.     

A comprehensive analysis of QTL for abdominal fat and breast muscle weights on chicken chromosome 5 using a multivariate approach

Quantitative trait loci (QTL) influencing the weight of abdominal fat (AF) and of breast muscle (BM) were detected on chicken chromosome 5 (GGA5) using two successive F₂ crosses between two divergently selected 'Fat' and 'Lean' INRA broiler lines. Based on these results, the aim of the present study was to identify the number, location and effects of these putative QTL by performing multitrait and multi-QTL analyses of the whole available data set. Data concerned 1186 F₂ offspring produced by 10 F₁ sires and 85 F₁ dams. AF and BM traits were measured on F₂ animals at slaughter, at 8 (first cross) or 9 (second cross) weeks of age. The F₀, F₁ and F₂ birds were genotyped for 11 microsatellite markers evenly spaced along GGA5. Before QTL detection, phenotypes were adjusted for the fixed effects of sex, F₂ design, hatching group within the design, and for body weight as a covariable. Univariate analyses confirmed the QTL segregation for AF and BM on GGA5 in male offspring, but not in female offspring. Analyses of male offspring data using multitrait and linked-QTL models led us to conclude the presence of two QTL on the distal part of GGA5, each controlling one trait. Linked QTL models were applied after correction of phenotypic values for the effects of these distal QTL. Several QTL for AF and BM were then discovered in the central region of GGA5, splitting one large QTL region for AF into several distinct QTL. Neither the 'Fat' nor the 'Lean' line appeared to be fixed for any QTL genotype. These results have important implications for prospective fine mapping studies and for the identification of underlying genes and causal mutations.     

Regional Distribution of Prostaglandins D2, E2, and F2α and Related Enzymes in Postmortem Human Brain

Abstract: The presence of prostaglandins D₂, E₂, and F_2α was demonstrated and their contents measured in various regions of postmortem human brain, pineal body, and pituitary by using specific radioimmunoassays and gas chromatography-mass spectrometry. The three prostaglandins were widely distributed in similar concentrations ranging from several hundred pg/g wet weight to about 40 ng/g wet weight. Prostaglandins D₂ and E₂ showed consistent and similar regional distributions in all six brains tested; amounts were high in pineal body, pituitary, olfactory bulb, and hypothalamus. On the other hand, prostaglandin F_2α was distributed more evenly. Prosta- glandin D synthetase and prostaglandin E synthetase activities were found in cerebrum homogenate from a single subject and were recovered from the 100,000 × g supernatant. The presence of 1 m M glutathione, reduced form, markedly stimulated the activity of prostaglandin E synthetase, but did not affect prostaglandin D synthetase activity. Activity of 15-hydroxyprostaglandin dehydrogenase was found in the cerebrum homogenate and was partially purified. This enzyme required NADP as a cofactor and copurified with prostaglandin E 9-ketoreductase.     

Reproductive trait divergence and hybrid fertility patterns between chromosomal races of the house mouse in Tunisia: analysis of wild and laboratory-bred males and females

The divergence in reproductive features and hybrid fertility patterns between two chromosomal races (2 n  = 40, 40St, and 2 n  = 22, 22Rb) of the house mouse in Tunisia were re-assessed on a larger sample of wild and laboratory-bred individuals than studied hitherto. Results showed that litter sizes were significantly smaller in 40St than in 22Rb mice, contrary to previous analyses. This suggests that variation in litter size between the two chromosomal races is more likely related to selective and/or environmental factors acting locally than to interracial reproductive trait divergence. However, the significantly reduced litter size of F₁ hybrids compared with parental individuals was confirmed, and further highlighted a sex difference in hybrid infertility, as F₁ females produced fewer litters and of smaller size than males. Histological analyses of F₁ and backcrosses showed a breakdown of spermatogenesis in males and a significantly reduced primordial follicle pool in females. The degree of gametogenic dysfunction was not related to the level of chromosomal heterozygosity per se , but a significant effect of two Rb fusions on follicle number was observed in hybrid females. These results suggest that genetic incompatibilities contribute to primary gametogenic dysfunction in hybrids between the chromosomal races in Tunisia.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 84 , 407–416.     

Effects of 5-azacytidine on the development of parthenogenetic mouse embryos

This study describes the effects of 5-azacytidine (5-azaC) on the development of diploid parthenogenetic embryos (PE) of CBA, C57BL/6 and (CBA × C57BL/6)F₁ mice in vitro at the 1-cell or the blastocyst stage or in vivo after implantation. Our findings indicate that genomic imprinting is modulated by genetic background. Non-fertilized C57BL/6 eggs form diploid parthenogenetic blastocysts at a much higher frequency than CBA eggs. Eggs from F₁ hybrid females form parthenogenetic blastocysts at an approximately intermediate level between these inbred strains of mice. C57BL/6 PE do not develop to the somite stages. In contrast, CBA PE and F₁ PE develop to various somite stages. Following administration of 5–azaC at 1.0 μmol/L in vitro at the 1- -cell stage, the number of implantations of C57BL/6 PE transferred to pseudopregnant females increased. In contrast, the number of implantations and somite F₁ PE did not significantly change following exposure to 5–azaC. However, administration of 5-azaC at the 1-cell stage stimulates development of somite F₁ PE. Administration of 5-azaC at 0.2 and 1.0 μmol/L in vitro at the blastocyst stage did not change the number of implantations of C57BL/6 PE. However, the number of implantations and somite CBA PE decreased. After injection of 5azaC at 0.24mg/kg in vivo at day 8 of gestation, some F₁ PE developed to 26–35 somites compared with a maximum of 25 somites in controls. The different effects of 5-azaC on the development of PE depend upon the mouse strain used and the stage of development.     

Serum albumin polymorphism and its relationship to economic traits in crossbred cattle

The serum albumin genotypes of 65 Jersey × Hariana (F₁), 75 Holstein Friesian × Hariana (F₁) and 47 Brown Swiss × Hariana (F₁) crossbred cows were determined by starch gel electrophoresis. Two albumin alleles Alb^F and Alb^s , but only either as Alb^F homozygotes or Alb^Fs heterozygotes, were observed amongst these animals. There were no Alb^S homozygotes or other genotypes. Highly significant relationships between albumin genotypes and both birth weights and first-lactation milk yields of these cows were observed. The Alb^F allele was associated with increased milk yield and greater birth weights.     

Peroxidase and polyphenol oxidase activities in Cyperus esculentus leaves following glyphosate applications

Following a 2-week treatment with glyphosate [N-(phosphonomethyl)glycine] changes in peroxidase (EC 1.11.1.7) and polyphenol oxidase (PPO; EC 1.14.18.1) activities of yellow nutsedge ( Cyperus esculentus L.) plants, were determined. Glyphosate caused significant increases of both activities. Isoelectric focusing gave 3 species (F₁, F₂ and F₃) of peroxidase activity, at pl 3.8, 4.4 and 4.8, and 4 species (F_a, F_b, F_c and F_d) of PPO activity at pl 7.0, 7.5, 7.8 and 9.5. The activity of the 4 active forms of PPO increased with increasing glyphosate dose up to 10⁻² M . The effect of the herbicide on the 3 fractions with peroxidase activity was to change their relative activities. Highest F₁ activity was found in control plants whereas the F₂ fraction was the predominant form in the plants treated with glyphosate at 10⁻² M and the highest F₃ activity occurred in plants treated with 5 × 10⁻³ M glyphosate. The increased PPO activity could produce phytotoxic o -quinones, and variations in peroxidase isoenzymes activity could enhance isoperoxidases with lignin biosynthetic activity.     

Alcohol dehydrogenase isozymes in the mouse: Genetic regulation, allelic variation among inbred strains and sex differences of liver and kidney A2 isozyme activity

Genetic analysis of a proposed cis-acting temporal locus ( Adh-3t ), which regulates alcohol dehydrogenase C₂ (ADH-C₂) acitivity in mouse epididymis extracts, among F₁ (ddN × BALB/c) × ddN male backcross progeny provided evidence for genetic distinctness between the structural ( Adh-3 ) and temporal ( Adh-3t ) loci on chromosome 3. Genetic analysis also confirmed the close, linkage of Adh-1 (encoding liver and kidney ADH-A₂) and Adh-3 (encoding stomach ADH-C₂) to within 0.3 centimorgans on the mouse genome. Evidence is presented for a proposed closely linked cis-acting temporal locus (designated Adh-1t ) for the A₂ isozyme (encoded by Adh-1 ) controlling the activity of this enzyme in mouse kidney extracts, but having no apparent affect on liver and intestine ADH-A₂ activities. An extensive survey of the distribution of Adh-1, Adh-3 and Adh-3t alleles among 65 strains of mice is reported — with the exception of two Japanese strains (ddN and KF), linkage disequilibrium between Adh-3 and Adh-3t was observed. Sex differences in mouse liver and kidney ADH-A₂ activities were observed, with male/female ratios of approximately 0.6 and 3 respectively for these tissue extracts.     

Isolation and imprinting analysis of the porcine DLX5 gene and its association with carcass traits

Imprinted genes play important roles in mammalian growth and development. However, reports on imprinted genes are limited in livestock. In this study, the complete ORF containing 289 amino acids of the porcine DLX5 gene was obtained. A C-to-T SNP mutation in exon 1 of the DLX5 gene was used to detect imprinting status with an RT-PCR/RFLP test (using HhaI) in eight heterozygous pigs from a population of Large White × Meishan F₁ hybrids. Imprinting analysis showed that the porcine DLX5 gene was maternally expressed in skeletal muscle, fat, lung, spleen, stomach and small intestine, but not imprinted in heart, liver, kidney, uterus, ovary, testicle or pituitary. A PCR–RFLP test was also used to detect the polymorphism in 310 pigs of a Large White × Meishan F₂ resource population. The statistical results showed significant association ( P  < 0.01) of the genotypes and fat meat percentage, carcass length, bone percentage, 6–7 rib fat thickness, average backfat thickness, thorax-waist fat thickness and buttock fat thickness.     

Two consensus quantitative trait loci clusters controlling anthesis–silking interval, ear setting and grain yield might be related with drought tolerance in maize

Unravelling the molecular basis of drought tolerance will provide novel opportunities for improving crop yield under water-limited conditions. The present study was conducted to identify quantitative trait loci (QTLs) controlling anthesis–silking interval (ASI), ear setting percentage (ESP) and grain yield (GY). The mapping population included 234 F₂ plants derived from the cross X178 (drought tolerant) × B73 (drought susceptible). The corresponding F_2:3 progenies, along with their parents, were evaluated for the above-mentioned traits under both well-watered and water-stressed field conditions in three different trials carried out in central and southern China. Interval mapping and composite interval mapping identified 45 and 65 QTLs for the investigated traits, respectively. Two QTL clusters influencing ASI and ESP on chromosomes 1 (bin 1.03) and 9 (bins 9.03–9.05) were identified in more than two environments, showing sizeable additive effects and contribution to phenotypic variance; these two QTL clusters influenced GY only in one environment. No significant interaction was detected between the two genomic regions. A comparative analysis of these two QTL clusters with the QTLs controlling maize drought tolerance previously described in three mapping populations confirmed and extended their relevance for marker-assisted breeding to improve maize production under water-limited conditions.     

Molecular evidence for repeated hybridization events involved in the origin of the genus × Crepidiastrixeris (Asteraceae) using RAPDs and ITS data

We investigated the hybrid origin of × Crepidiastrixeris denticulato-platyphylla using RAPDs and ITS sequence data. The putative parents Paraixeris denticulata and Crepidiastrum platyphyllum represent separate species, irrespective of geographical origin. The occurrence of species specific RAPD markers from P. denticulata and C. platyphyllum in × C. denticulato-platyphylla established unambiguously a hybrid origin between the two taxa. This was in line with the occurrence of a combination of morphological characters such as plant habit and floret numbers. The parent taxa differed from each other by 7 nucleotide substitutions and 2 indel events in the ITS region. The hybrids showed sequence additivity and most likely represent F₁ plants, with the exception of two plants which were of possible F₂ origin, possessing either the ITS sequences of one parent only, or one predominant ITS type. The hybrids occurred in two out of three localities where the parents occurred sympatrically. This fact, together with the short life-span of the plants, suggests that × C. denticulato-platyphylla exists as a result of repeated, frequent hybridization between the parent species.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 333–343.     

Mitigation using a tandem construct containing a selectively unfit gene precludes establishment of Brassica napus transgenes in hybrids and backcrosses with weedy Brassica rapa

Transgenic oilseed rape ( Brassica napus ) plants can interbreed with nearby weedy Brassica rapa , potentially enhancing the weediness and/or invasiveness of subsequent hybrid offspring. We have previously demonstrated that transgenic mitigation effectively reduces the fitness of the transgenic dwarf and herbicide-resistant B. napus volunteers. We now report the efficacy of such a tandem construct, including a primary herbicide-resistant gene and a dwarfing mitigator gene, to preclude the risks of gene establishment in the related weed B. rapa and its backcross progeny. The transgenically mitigated and non-transgenic B. rapa  ×  B. napus interspecific hybrids and the backcrosses (BC₁) with B. rapa were grown alone and in competition with B. rapa weed. The reproductive fitness of hybrid offspring progressively decreased with increased B. rapa genes in the offspring, illustrating the efficacy of the concept. The fitness of F₂ interspecific non-transgenic hybrids was between 50% and 80% of the competing weedy B. rapa , whereas the fitness of the comparable T₂ interspecific transgenic hybrids was never more than 2%. The reproductive fitness of the transgenic T₂ BC₁ mixed with B. rapa was further severely suppressed to 0.9% of that of the competing weed due to dwarfism. Clearly, the mitigation technology works efficiently in a rapeseed crop–weed system under biocontainment-controlled environments, but field studies should further validate its utility for minimizing the risks of gene flow.     

Sex ratio bias in the F1 adult progeny of African rice gall midge, Orseolia oryzivora H. and G. (Dipt., Cecidomyiidae)

Abstract:  Against the background of conflicting reports of variable sex ratio distribution in different populations of the African rice gall midge (AfRGM), Orseolia oryzivora Harris and Gagne, the number and sex ratios of F₁ adult progeny produced per female from wild and screen house populations were investigated in the screen house at 27 ± 3°C, 60–70% relative humidity and 12 : 12 h (light : dark) photoperiod. Results indicated the occurrence of a single sex-biased ratio in all the F₁ adult progeny produced per female of this pest. Regardless of the source, whether from wild or screen house population, each mated female AfRGM produced a full complement of either sex only but never both. The difference between the number of eggs laid and F₁ adult progeny that emerged per female from wild and screen house populations was not significant (P > 0.05), indicating consistency in the occurrence of this phenomenon among AfRGM populations. The reason for this could not be ascertained in this study but AfRGM eggs must be fertilized for development and eclosion to occur. No F₂ adults emerged when a cohort of emergents from the same female were allowed to re-infest susceptible seedlings, indicating absence of parthenogenesis.     

Genome-wide association analysis reveals cryptic alleles as an important factor in heterosis for fatness in chicken F2 population

Genome-wide association studies have become possible in the chicken because of the recent availability of the complete genome sequence, a polymorphism map and high-density single nucleotide polymorphism (SNP) genotyping platforms. We used these tools to study the genetic basis of a very high level of heterosis that was previously observed for fatness in two F₂ populations established by crossing one outbred broiler (meat-type) sire with dams from two unrelated, highly inbred, light-bodied lines (Fayoumi and Leghorn). In each F₂ population, selective genotyping was carried out using phenotypically extreme males for abdominal fat percentage (AF) and about 3000 SNPs. Single-point association analysis of about 500 informative SNPs per cross showed significant association ( P  < 0.01) of 15 and 24 markers with AF in the Broiler × Fayoumi and Broiler × Leghorn crosses respectively. These SNPs were on 10 chromosomes (GGA1, 2, 3, 4, 7, 8, 10, 12, 15 and 27). Interestingly, of the 39 SNPs that were significantly associated with AF, there were about twice as many homozygous genotypes associated with higher AF that traced back to the inbred lines alleles, although the broiler line had on average higher AF. These SNPs are considered to be associated with QTL with cryptic alleles. This study reveals cryptic alleles as an important factor in heterosis for fatness observed in two chicken F₂ populations, and suggests epistasis as the common underlying mechanism for heterosis and cryptic allele expression. The results of this study also demonstrate the power of high marker-density SNP association studies in discovering QTL that were not detected by previous microsatellite-based genotyping studies.     

Electron transfer reactions for the reduction of NADP+ in Methanosphaera stadtmanae

Abstract Methanosphaera stadtmanae , a member of the Methanobacteriales reduces methanol, but not CO₂ with H₂ or 2-propanol to produce methane. In cell-free extracts of M. stadtmanae the activities of several enzymes involved in electron transfer were measured. The activities of an F₄₂₀-nonreactive hydrogenase, NADP⁺: F₄₂₀ oxidoreductase, NADP⁺-dependent 2-propanol dehydrogenase, and a methyl viologen dependent F₄₂₀ dehydrogenase were observed. Based on the presence of these particular enzyme activities, their cofactor requirements and the absence of F₄₂₀-dependent hydrogenase activity, a model of the electron transport pathway through the coenzyme F₄₂₀ to provide electrons for biosynthesis, was formulated.