Positive Alleles Research Articles

Recovery of Environmental Human DNA by Insects*,†

We tested the hypotheses that foraging insects can acquire human DNA from the environment and that insect-delivered human DNA is of sufficient quantity and quality to permit standard forensic analyses. Houseflies, German cockroaches, and camel crickets were exposed to dusty surfaces and then assayed for human mitochondrial and nuclear loci by conventional and qPCR, and multiplex STR amplification. Over two experiments, 100% of insect groups and 94% of dust controls tested positive for human DNA. Of 177 individuals, 33-67% tested positive and 13 yielded quantifiable human DNA (mean = 0.022 ± 0.006 ng; mean dust control = 2.448 ± 0.960 ng); four had at least one positive allele call for one or more locus; eight others showed multiple peaks at some loci. Results imply that application to routine forensic casework is limited given current detection methodology yet demonstrate the potential use of insects as environmental samplers for human DNA.

Correlation between polymorphisms in ADSL and GARS-AIRS-GART genes with inosine 5′-monophosphate (IMP) contents in Beijing-you chickens

1. The association of single nucleotide polymorphisms identified within the ADSL (adenylosuccinate lyase deficiency) gene and GARS-AIRS-GART (glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide transformylase) gene with the content of inosine 5′-monophosphate (IMP) was studied in a population of male Beijing-you (BJY) chickens slaughtered at 90 d of age. 2. A single nucleotide polymorphism in exon 2 of the ADSL gene had an effect on IMP content. Chickens inheriting the positive allele at ADSL, both homozygous and heterozygous genotypes, had a higher content of IMP in breast muscle than did individuals without it. 3. Similar results were obtained for the GARS-AIRS-GART gene. The marker at the 5′ untranslated region (UTR) of the GARS-AIRS-GART gene was also significant for the IMP value. Chickens inheriting the genotypes with the positive allele at this locus had a much higher content of IMP than did those homozygous for the unfavourable one. 4. Interactions between ADSL and GARS-AIRS-GART were detected for such traits as body weight and muscle yields in the tested population. The two loci acted in an additive fashion. Because IMP is one of the most important flavour components in meat, markers developed at these two genes, as well as the combination genotypes, could be used as potential molecular markers for improving chicken quality.

Quantitative Trait Loci Associated with Resistance to Rice Stripe Virus and Small Brown Planthopper Infestation in Rice

ABSTRACTRice stripe is a serious viral disease of japonica rice (Oryza sativa L.) cultivars in Asia. Resistance to this disease can be divided into that to rice stripe virus (RSV) and to the pest (small brown planthopper, SBPH). Here we have used a doubled‐haploid (DH) population bred from the cross Zhaiyeqing8 (ZYQ8) × Jingxi17 (JX17) and four separate inoculation methods to genetically dissect the rice stripe resistance present in ZYQ8. Two linked RSV resistance quantitative trait loci (QTLs) were located on chromosome 1, and one on chromosome 11, jointly explaining 30 to 44% of the trait variance. The main‐effect qSTV11 was mapped close to the established RSV resistance gene Stvb‐i For resistance to SBPH, three QTLs were located, mapping to chromosomes 1, 2, and 11, and jointly explaining 44 to 51% of the trait variance. The large‐effect qSBPH1 appears to be a novel QTL conferring a degree of tolerance and antibiosis against SBPH. The positive alleles at all six QTLs were present in ZYQ8. Analysis of a set of chromosome segment substitution lines (CSSLs) in which chromosomal segments of various indica varieties were present in a japonica background showed that rice stripe resistance genes/QTLs are common on the long arm of chromosome 1.

QTL Analysis of Anoxic Tolerance at Seedling Stage in Rice

Coleoptile lengths of 7-day-old seedlings under anoxic stress and normal conditions were investigated in two permanently segregated populations and their parents in rice ( Oryza sativa L.). Using anoxic response index, a ratio of coleoptile length under anoxic stress to coleoptile length under normal conditions, as an indicator of seedling anoxic tolerance (SAT), QTLs for SAT were detected. Two loci controlling SAT, designated as qSAT-2-R and qSAT-7-R, were detected in a recombinant inbred line (RIL) population (247 lines) derived from a cross between Xiushui 79 (japonica variety) and C Bao (japonica restorer line). qSAT-2-R, explaining 8.7% of the phenotype variation, was tightly linked with the SSR marker RM525. qSAT-7-R, explaining 9.8% of the phenotype variation, was tightly linked with the marker RM418. The positive alleles of the two loci came from C Bao. Six loci controlling SAT, designated as qSAT-2-B, qSAT-3-B, qSAT-5-B, qSAT-8-B, qSAT-9-B and qSAT-12-B, were detected in a backcross inbred line (BIL) population (98 lines) derived from a backcross of Nipponbare (japonica)/Kasalath (indica)//Nipponbare (japonica). The positive alleles of qSAT-2-B, qSAT-3-B and qSAT-9-B, which explained 16.2%, 11.4% and 9.5% of the phenotype variation, respectively, came from Nipponbare. Besides, the positive alleles of qSAT-5-B, qSAT-8-B and qSAT-12-B, which explained 7.3%, 5.8% and 14.0% of the phenotype variation, respectively, were from Kasalath.

Acquired Antibody Responses against Plasmodium vivax Infection Vary with Host Genotype for Duffy Antigen Receptor for Chemokines (DARC)

BackgroundPolymorphism of the Duffy Antigen Receptor for Chemokines (DARC) is associated with susceptibility to and the severity of Plasmodium vivax malaria in humans. P. vivax uses DARC to invade erythrocytes. Individuals lacking DARC are ‘resistant’ to P. vivax erythrocytic infection. However, susceptibility to P. vivax in DARC+ individuals is reported to vary between specific DARC genotypes. We hypothesized that the natural acquisition of antibodies to P. vivax blood stages may vary with the host genotype and the level of DARC expression. Furthermore, high parasitemia has been reported to effect the acquisition of immunity against pre-erythrocytic parasites. We investigated the correlation between host DARC genotypes and the frequency and magnitude of antibodies against P. vivax erythrocytic stage antigens.Methodology/FindingsWe assessed the frequencies and magnitudes of antibody responses against P. vivax and P. falciparum sporozoite and erythrocytic antigens in Colombian donors from malaria-endemic regions. The frequency and level of naturally-acquired antibodies against the P. vivax erythrocytic antigens merozoite surface protein 1 (PvMSP1) and Duffy binding protein (PvDBP) varied with the host DARC genotypes. Donors with one negative allele (FY*B/FY*Bnull and FY*A/FY*Bnull) were more likely to have anti-PvMSP1 and anti-PvDBP antibodies than those with two positive alleles (FY*B/FY*B and FY*A/FY*B). The lower IgG3 and IgG1 components of the total IgG response may account for the decreased responses to P. vivax erythrocytic antigens with FY*A/FY*B and FY*B/FY*B genotypes. No such association was detected with P. falciparum erythrocytic antigens, which does not use DARC for erythrocyte invasion.Conclusion/SignificanceIndividuals with higher DARC expression, which is associated with higher susceptibility to P. vivax infection, exhibited low frequencies and magnitudes of P. vivax blood-stage specific antibody responses. This may indicate that one of the primary mechanisms by which P. vivax evades host immunity is through DARC indirectly down-regulating humoral responses against erythrocytic invasion and development.

Healthy newly weaned pigs require more tryptophan to maximize feed intake if they are susceptible to Escherichia coli K88

After challenging piglets with enterotoxigenic Escherichia coli K88 (ETEC), l-tryptophan addition limits the decrease in feed intake and weight gain in ETEC-susceptible subjects. Here we verified whether the susceptibility to ETEC affects the requirement of tryptophan in piglets reared in optimal sanitary conditions and without E. coli K88 challenge. The MUC4 gene was used as a marker to verify the susceptibility, to grouping 36 pigs after weaning, into homozygote for the negative and positive alleles (2 −/− and 2 +/+ pigs per litter). For 21 days pigs were fed using two different diets within each genotype per litter, varied for Trp to Lys ratio (17% or 22%, standardized ileal digestible basis — SID), by a supplementation of 0.5 g/kg l-Trp. In the first week feed intake increased with Trp in MUC4 +/+ pigs (P < 0.05), but not in MUC4 −/−. Without Trp addition a trend of decreased feed intake was seen in MUC4 +/+ ( P = 0.094). On average, for the two genotypes, Trp addition increased feed intake in the first week ( P < 0.05). The higher Trp to Lys ratio increased average daily weight gain in the first week ( P < 0.01) and in the whole trial ( P < 0.05). Growth performance was not affected by the genotype for MUC4. The results were also validated by an in vitro test of adhesion of E. coli K88 to the intestinal villi: we confirmed that there is a strong correlation between MUC4 genotype and the phenotype for the presence of ETEC receptor on the intestinal villi. Data confirm that a Trp to Lys ratio of 22% is necessary to maintain the body weight gain in the three weeks post-weaning. In the first week post-weaning pigs of the genotype MUC4 +/+ require more Trp than the MUC4 −/− pigs to maximize feed intake, when they are free from diseases and are kept in optimal sanitary conditions.

Genetic analysis of leaffolder resistance in rice

A double haploid (DH) population, which consists of 120 lines derived from anther culture of a typical indica and japonica hybrid 'CJ06'/'TN1', was used to investigate the genetic basis for rice leaffolder resistance. Using a constructed molecular linkage map, five QTLs for rolled leaves were detected on chromosomes 1, 2, 3, 4, and 8. The positive alleles from CJ06 on chromosomes 3, 4, and 8 increased the resistance to rice leaffolder, and the alleles from TN1 on chromosomes 1 and 2 also enhanced resistance to leaffolder. The interactions between QTLs were identified and tested, and four conditional interactions were acquired for resistance to rice leaffolder. These loci were located on chromosomes 2, 9, 10, and 11, respectively. QTL pyramiding indicated that the positive alleles affect resistance to leaffolder. The prospective application of this data in rice breeding was also discussed.

Analysis of QTLs Associated with Photosynthesis Characteristics in Wheat Seedlings

For the purpose of detecting QTLs associated with photosynthetic related traits, a set of 168 doubled haploid (DH) lines derived from the cross between Huapei 3 and Yumai 57 was tested with 324 SSR markers covering the whole genome of wheat (Triticum aestivum L.). The net photosynthetic rate, gas changes, chlorophyll content, and chlorophyll fluorescence in leaves were investigated in both DH population and the parents at seedling stage. QTL analysis was carried out using QTLNetwork version 2.0 based on the mixed linear model. A total of 17 additive QTLs and 20 pairs of epistatic QTLs were detected for the photosynthetic related traits. All additive QTLs and 16 pairs of epistatic QTLs had interactions with environments. In agreement with the high correlations of phenotypes, several traits shared common QTL regions, and showed tight linkages of these QTLs or pleiotropisms. In the interval between Xwmc215 and Xgdw63 on chromosome 5D, three major additive QTLs for chlorophyll a, chlorophyll b, and carotinoid contents explained the phenotypic variations by 18.23%, 10.40%, and 27.25%, respectively, whose positive alleles were all originated from Huapei 3. These QTLs are favorable for marker-assisted selection. In addition, this region was near the QTLs for net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO2 concentration (Ci), and the ratio of Ci to gas conductance (Cr). The QTL for Ci on chromosome 5B was a minor locus but explained relatively great phenotypic variation in the interactions between QTLs and environments.

Allele Interaction – Single Locus Genetics Meets Regulatory Biology

BackgroundSince the dawn of genetics, additive and dominant gene action in diploids have been defined by comparison of heterozygote and homozygote phenotypes. However, these definitions provide little insight into the underlying intralocus allelic functional dependency and thus cannot serve directly as a mediator between genetics theory and regulatory biology, a link that is sorely needed.Methodology/Principal FindingsWe provide such a link by distinguishing between positive, negative and zero allele interaction at the genotype level. First, these distinctions disclose that a biallelic locus can display 18 qualitatively different allele interaction sign motifs (triplets of +, – and 0). Second, we show that for a single locus, Mendelian dominance is not related to heterozygote allele interaction alone, but is actually a function of the degrees of allele interaction in all the three genotypes. Third, we demonstrate how the allele interaction in each genotype is directly quantifiable in gene regulatory models, and that there is a unique, one-to-one correspondence between the sign of autoregulatory feedback loops and the sign of the allele interactions.Conclusion/SignificanceThe concept of allele interaction refines single locus genetics substantially, and it provides a direct link between classical models of gene action and gene regulatory biology. Together with available empirical data, our results indicate that allele interaction can be exploited experimentally to identify and explain intricate intra- and inter-locus feedback relationships in eukaryotes.

Confirmation and refinement of a QTL on BTA5 affecting milk production traits in the Fleckvieh dual purpose cattle breed

We analysed a QTL affecting milk yield (MY), milk protein yield (PY) and milk fat yield (FY) in the dual purpose cattle breed Fleckvieh on BTA5. Twenty-six microsatellite markers covering 135 cM were selected to analyse nine half-sib families containing 605 sons in a granddaughter design. We thereby assigned two new markers to the public linkage map using the CRI-MAP program. Phenotypic records were daughter yield deviations (DYD) originating from the routinely performed genetic evaluations of breeding animals. To determine the position of the QTL, three different approaches were applied: interval mapping (IM), linkage analysis by variance component analysis (LAVC), and combined linkage disequilibrium (LD) and linkage (LDL) analysis. All three methods mapped the QTL in the same marker interval (BM2830-ETH152) with the greatest test-statistic value at 118, 119.33 and 119.33 cM respectively. The positive QTL allele simultaneously increases DYD in the first lactation by 272 kg milk, 7.1 kg milk protein and 7.0 kg milk fat. Although the mapping accuracy and the significance of a QTL effect increased from IM over LAVC to LDL, the confidence interval was large (13, 20 and 24 cM for FY, MY and PY respectively) for the positional cloning of the causal gene. The estimated averages of pair wise marker LD with a distance <5 cM were low (0.107) and reflect the large effective population size of the Fleckvieh subpopulation analysed. This low level of LD suggests a need for increase in marker density in following fine mapping steps.

Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) S18Y polymorphism in Alzheimer's disease

Alzheimer's disease (AD) is characterized by protein aggregates, i.e. senile plaques and neurofibrillary tangles. The ubiquitin-proteasome system has been proposed a role in proteolytic removal of these protein aggregates. Ubiquitin carboxy-terminal hydrolase L1 (UCHL1) is a de-ubiquitinating enzyme with important functions in recycling of ubiquitin. The S18Y polymorphism of the UCHL1 gene confers protection against Parkinson's disease. In this study, the genotype and allele frequencies of the UCHL1 S18Y polymorphism were investigated in 452 AD patients and 234 control subjects, recruited from four memory clinics in Sweden. Using a binary logistic regression model including UCHL1 allele A and APOE ε4 allele positivity, age and sex as covariates with AD diagnosis as dependent variable, an adjusted OR of 0.82 ([95% CI 0.55-1.24], P = 0.35) was obtained for a positive UCHL1 allele A carrier status. The present study thus do not support a protective effect of the UCHL1 S18Y polymorphism against AD.

HindIII-based restriction fragment length polymorphism in hemophilic and nonhemophilic patients

Hemophilia A is most common recessively inherited bleeding disorder, which affect one in five thousand male births throughout the world. In most of the hemophilic A patients, no common mutation is easily identifiable. This limitation has been overcome by the use of polymorphic DNA marker, i.e., restriction fragment length polymorphism (RFLP). This marker of polymorphism could only be detected by amplifying the polymorphic region and digestion the polymerase chain reaction (PCR) product with the restriction enzyme (PCR−RFLP), i.e., HindIII. The polymorphic region of HindIII is 608 bp in length and after the restriction digestion, different sizes of fragments, i.e., 427 and 181 bp were, respectively, obtained. However, in homozygous (+/+) condition three bands of 427, 100, and 81 bp were obtained and in the other negative allelic homozygous condition (-/-) two bands of 427 and 181 bp were obtained. Similarly fragments of different sizes, i.e., 427, 181, 100, and 81 bp were obtained in heterozygous conditions. Therefore, in this study, we have analyzed the factor VIII gene in the 17 different families using restriction enzyme HindIII-based RFLP molecular marker technique. Out of these, the observed heterozygosity for HindIII was found 47.5%, whereas, for positive allele it was 26%, and for negative allele the frequency was 74%.

The effect of missing marker genotypes on the accuracy of gene-assisted breeding value estimation: a comparison of methods

In livestock populations, missing genotypes on a large proportion of the animals is a major problem when implementing gene-assisted breeding value estimation for genes with known effect. The objective of this study was to compare different methods to deal with missing genotypes on accuracy of gene-assisted breeding value estimation for identified bi-allelic genes using Monte Carlo simulation. A nested full-sib half-sib structure was simulated with a mixed inheritance model with one bi-allelic quantitative trait loci (QTL) and a polygenic effect due to infinite number of polygenes. The effect of the QTL was included in gene-assisted BLUP either by random regression on predicted gene content, i.e. the number of positive alleles, or including haplotype effects in the model with an inverse IBD matrix to account for identity-by-descent relationships between haplotypes using linkage analysis information (IBD–LA). The inverse IBD matrix was constructed using segregation indicator probabilities obtained from multiple marker iterative peeling. Gene contents for unknown genotypes were predicted using either multiple marker iterative peeling or mixed model methodology. For both methods, gene-assisted breeding value estimation increased accuracies of total estimated breeding value (EBV) with 0% to 22% for genotyped animals in comparison to conventional breeding value estimation. For animals that were not genotyped, the increase in accuracy was much lower (0% to 5%), but still substantial when the heritability was 0.1 and when the QTL explained at least 15% of the genetic variance. Regression on predicted gene content yielded higher accuracies than IBD–LA. Allele substitution effects were, however, overestimated, especially when only sires and males in the last generation were genotyped. For juveniles without phenotypic records and traits measured only on females, the superiority of regression on gene content over IBD–LA was larger than when all animals had phenotypes. Missing gene contents were predicted with higher accuracy using multiple-marker iterative peeling than with using mixed model methodology, but the difference in accuracy of total EBV was negligible and mixed model methodology was computationally much faster than multiple iterative peeling. For large livestock populations it can be concluded that gene-assisted breeding value estimation can be practically best performed by regression on gene contents, using mixed model methodology to predict missing marker genotypes, combining phenotypic information of genotyped and ungenotyped animals in one evaluation. This technique would be, in principle, also feasible for genomic selection. It is expected that genomic selection for ungenotyped animals using predicted single nucleotide polymorphism gene contents might be beneficial especially for low heritable traits.

Identification and mapping of the leaf stripe resistance gene Rdg1a in Hordeum spontaneum

Leaf stripe of barley, caused by Pyrenophora graminea, is an important seed-borne disease in organically grown as well as in conventionally grown Nordic and Mediterranean barley districts. Two barley segregating populations represented by 103 recombinant inbred lines (RILs) of the cross L94 (susceptible) x Vada (resistant) and 194 RILs of the cross Arta (susceptible) x Hordeum spontaneum 41-1 (resistant) were analysed with two highly virulent leaf stripe isolates, Dg2 and Dg5, to identify loci for P. graminea resistance. A major gene with its positive allele contributed by Vada and H. spontaneum 41-1 was detected in both populations and for both pathogen isolates on chromosome 2HL explaining 44.1 and 91.8% R (2), respectively for Dg2 and Dg5 in L94 x Vada and 97.8 and 96.1% R (2), respectively for Dg2 and Dg5 in Arta x H. spontaneum 41-1. Common markers in the gene region of the two populations enabled map comparison and highlighted an overlapping for the region of the resistance locus. Since the map position of the resistance locus identified in this report is the same as that for the leaf stripe resistance gene Rdg1a, mapped earlier in Alf and derived from the 'botanical' barley line H. laevigatum, we propose that leaf stripe resistance in Vada and H. spontaneum 41-1 is governed by the same gene, namely by Rdg1a, and that Rdg1a resistance could be traced back to H. spontaneum, the progenitor of cultivated barley. PCR-based molecular markers that can be used for marker-assisted selection (MAS) of Rdg1a were identified. An Rdg1a syntenic interval with the rice chromosome arm 4L was identified on the basis of rice orthologs of EST-based barley markers. Analysis of the rice genes annotated into the syntenic interval did not reveal sequences strictly belonging to the major class (nucleotide-binding site plus leucine-rich repeat) of the resistance genes. Nonetheless, four genes coding for domains that are present in the major disease-resistance genes, namely receptor-like protein kinase and ATP/GTP-binding proteins, were identified together with a homolog of the barley powdery mildew resistance gene mlo. Three (out of five) homologs of these genes were mapped in the Rdg1a region in barley and the mlo homolog map position was tightly associated with the LOD score peak in both populations.

In essential thrombocythemia, multiple JAK2-V617F clones are present in most mutant-positive patients: a new disease paradigm

In essential thrombocythemia (ET), the JAK2-V617F mutation is usually restricted to a subpopulation of neutrophils and platelets, and production of JAK2 wild-type (WT) platelets is not suppressed. Nonmutated precursor cells may, therefore, be susceptible to the acquisition of further JAK2 mutations. We used a common single nucleotide polymorphism (SNP) in the JAK2 coding sequence to genotype V617F alleles obtained either by allele-specific restriction enzyme digestion (RED) or by cloning. Both SNP alleles were detected in JAK2 mutant-positive alleles from neutrophils of 10 of 11 ET patients studied using RED compared with 0 of 5 with polycythemia vera. These results were confirmed in cloned products from 5 ET patients and indicate the occurrence of at least 2 separate JAK2 mutation events in the majority of ET patients investigated. In a further ET patient, JAK2 mutant-positive erythroid colonies with either X-allele inactivated were detected, demonstrating they could not have arisen from a common clonal precursor. These results indicate that at least 2 independent JAK2-V617F events occur commonly in ET patients, and they may arise on a polyclonal background. The presence of a JAK2 mutation in ET patients should not, therefore, be equated with a malignant disease.

Marker assisted backcross breeding to improve cooking quality traits in Myanmar rice cultivar Manawthukha

Several components contribute to rice grain quality, and among these, fragrance and taste qualities are the most important to consumers. Manawthukha, an elite non-fragrant cultivar with high amylose content (AC), intermediate gel consistency (GC) and gelatinisation temperature (GT), occupies the largest number of acres in Myanmar. To improve fragrance and intermediate AC in Manawthukha, Basmati370 was used as a donor parent to introgress the Basmati alleles of genes conferring fragrance and intermediate AC into Manawthukha by Marker Assisted Backcrossing (MAB). Four backcrosses and one selfing were conducted to transfer positive alleles of badh2 and Wx from Basmati into Manawthukha. Twelve BC 4F 2 selected lines that carried the homozygous Basmati alleles were planted in multi-location trials (four in Myanmar and one in Thailand) and examined for their agronomic performance and cooking quality. The seeds of the improved lines and their parents, harvested from Kamphaeng Saen, Kuaukse, Kyauktada and Latpatan, were investigated for fragrance and AC. All improved lines had fragrance and intermediate AC similar to the donor parent Basmati, whereas their agronomic performances were the same as the original Manawthukha. All improved lines had medium plant heights, high tiller numbers, dense panicles, non-lodging phenotypes and high yielding potentials. Simultaneous improvement of fragrance and intermediate AC indicated that badh2 and Wx genes had major effects on the fragrance and AC, respectively. We show here the success of improving fragrance and intermediate AC by MAB and the high efficiency of selection in early generations. In the present study, MAB accelerated the development of superior qualities in the genetic background of Manawthukha. The improved Manawthukha should be immediately useful for Myanmar farmers and will help farmers to increase their incomes.

Identification and validation of quantitative trait loci for grain protein concentration in adapted Canadian durum wheat populations

Grain protein concentration (GPC) is one of the most important factors influencing pasta-making quality. Durum wheat (Triticum turgidum L. var durum) cultivars with high GPC produce pasta with increased tolerance to overcooking and greater cooked firmness. However, the large environmental effect on expression of GPC and the negative correlation with grain yield have slowed genetic improvement of this important trait. Understanding the genetics and identification of molecular markers associated with high GPC would aid durum wheat breeders in trait selection at earlier generations. The objectives of this study were to identify and validate molecular markers associated with quantitative trait loci (QTL) for elevated GPC in durum wheat. A genetic map was constructed using SSR and DArT markers in an F(1)-derived doubled haploid (DH) population derived from the cross DT695 x Strongfield. The GPC data were collected from replicated trials grown in six Canadian environments from 2002 to 2005. QTL associated with variation for GPC were identified on the group 1, 2, and 7 chromosomes and on 5B and 6B, but only QGpc.usw-B3 on 2B and QGpc.usw-A3 on 7A were expressed consistently in four and six environments, respectively. Positive alleles for GPC at these loci were contributed by the high-GPC parent Strongfield. The QGpc.usw-A3 QTL was validated in a second DH population, and depending on environment, selection for the Strongfield allele at barc108 resulted in +0.4% to +1.0% increase in GPC, with little effect on yield in most environments. Given the consistent expression pattern in multiple populations and environments, barc108 could be useful for marker-assisted selection for high GPC.

Identification of Quantitative Trait Loci for Alkaline Tolerance at Early Seedling Stage of Japonica Rice Under Alkaline Stress

Using an F 2:3 population with 200 lines derived from a cross between the japonica rice ( Oryza sativa L.) varieties Gaochan 106 and Changbai 9, quantitative trait loci (QTLs) for root number, root length, seedling height, and their relative alkaline damage rates at early seedling stage were identified under 0.15% Na 2CO 3 alkaline stress. A total of 26 QTLs associated with these traits were detected on chromosomes 1, 5, 6, 7, 8, 9, and 11, consisting of 4 QTLs for root number, 5 QTLs for relative alkaline damage rate of root number, 6 QTLs for root length, 2 QTLs for relative alkaline damage rate of root length, 5 QTLs for seedling height, and 4 QTLs for relative alkaline damage rate of seedling height. QTLs qRN6-1, qRN11, qRRN11-2, qRRL11-2, qSH1, qSH11-2, qRSH5, and qRSH6-2 accounted for 29.91, 13.42, 23.86, 21.06, 15.81, 16.53, 29.89, and 34.63% of the phenotypic variations, respectively. These QTLs, except for qRN6-1 with the marker flanking distance of 19.0 cM, were located with relatively large marker flanking distances over 26.3 cM. The positive alleles at 13 loci originated from the tolerant parent Changbai 9, and the positive alleles at other loci were from the sensitive parent Gaochan 106. Partial dominance and over dominance were the main effects at these loci.

Estimation of genetic parameters and regression line analysis for yield and its components in maize

Eight inbred lines of maize were crossed in half- diallel in spring season of 2002 to produce twenty eight F1 crosses. The parents and crosses were grown in Fall season of 2002 and in Spring season of 2003 using RCBD with four replicates to determine the nature and magnitude of gene effects through components analysis and graphic analysis for 50% silking date, plant and ear height, ear length, number of rows/ear, number of grain/row, kernel weight and grain yield/plant. Both the additive and dominance genetic variances were found to be significant for all characters, except for grain yield/plant where the additive genetic variance was not significant in Fall season. The estimates of dominance genetic variance were more than the additive one for plant and ear height, number of grain/row, kernel weight and grain yield/plant, while, it was inverse that in other characters, and this reflected the reduction of the values of the narrow sense heritability, and increased of the values of the average degree of dominance one for the mentioned characters and it was less than one for other characters, which indicated that the studied characters were under partial and over dominance gene action. Also the results showed that positive and negative alleles were not distributed equally among the parents for all characters. Indicating that from the estimates of the ratio H2/4H1 were different from 0.25, and excess of dominant genes in the parents for all characters, indicating that from the estimates of the ratio KD/KR were more than one. The graphic analysis suggested the presence of over dominance and genetic variability among parents for most characters. It was concluded from the results of this study that some inbred lines could be used in a breeding program to develop elite hybrids of higher yield/plant and other related traits.

Genetic Modifiers of Homozygous Beta Zero Thalassemia.

Introduction: Extensive studies over the last 50 years have derived two major modifiers of the clinical expression of beta-thalassemia: innate ability to produce fetal hemoglobin (Hb F) and co-inheritance of alpha-thalassemia. Recently genetic variants at the BCL11A locus and HBS1L-MYB intergenic region, that can modulate Hb F levels have been identified ( Thein et al 2007, Menzel et al 2007). Moreover, BCL11A variant has been shown to moderate the phenotype of homozygous beta-thalassemia (Uda et al 2008). In this study we evaluated the contribution of these Hb F modulating genetic markers and of alpha-thalassemia in ameliorating the severity of homozygous beta-thalassemia.Methods: We studied 50 patients with the mild non-tranfusion dependent thalassemia intermedia phenotype and 75 with the severe tranfusion dependent thalassemia major. All patients were homozygotes for the beta 39 non-sense C → T mutation and were negative for the Xmn I -158 Gγ polymorphism. Alpha thalassemia was detected by GAP-PCR technique (deletion defects) and restriction enzyme digestion (nondeletion defects).Genotyping of HbF modulating genetic variants was performed using TaqMan® SNP genotyping assay (Applied Biosystems, Warrington, UK) according to the manufacturer's protocol. Evaluation of the association, OR calculation and test for interaction were performed fitting a logistic regression.Results: We found that the frequency of the BCL11A and HBS1L-MYB Hb F modulating markers and of co-inherited alpha- thalassemia is significantly increased (p= 2.05 x 10−5, p= 8.1 x 10−4, and p= 9.9 x 10−5 respectively) in the group of patients with thalassemia intermedia. Interestingly, the contribution of BCL 11A gene appears to be greater than HBS 1L-MYB locus ( OR= 5.15 and 4.61 respectively) and both are striking larger than the effect attributable to the co-inheritance of alpha-thalassemia (OR= 3.32). Furthermore, to visualize the combined effects of all loci, we considered a score variable defined as the number of positive alleles (i.e. those associated with the amelioration of the phenotype) carried from each patient. When considered all together the three loci explain 79% of the variation, evaluated as the correlation between fitted and observed values in the logistic regression. All three analyzed loci act in an additive fashion, where each copy of the minor allele contributes to the amelioration of the phenotype expression.Conclusions: Molecular genetic analysis and particularly genome-wide association scans are producing rapid advances in defining the genetic variants for complex diseases and quantitative traits. The information reported are relevant in understanding the correlation between genotype and phenotype in thalassemia syndromes.