Positive Alleles Research Articles

Two Loci Exert Major Effects on Chlorogenic Acid Synthesis in Maize Silks

Chlorogenic acid (CGA) in maize (Zea mays L.) silks has been implicated in resistance to corn earworm (Helicoverpa zea Boddie) with a mechanism similar to the flavone, maysin. However, the genetic basis of CGA synthesis is poorly understood. Our goal was to identify candidate loci affecting the biosynthesis of CGA using quantitative trait locus (QTL) analyses on three F 2 populations: (A619 × Mp708)F 2 , (A619 × Mo6)F 2 , and (Mo6 x Mp708)F 2 . Chlorogenic acid and flavone contents in silks were measured, linkage maps generated, and significant loci identified with composite interval mapping (CIM) and ANOVA multiple-effects models for the three populations. Of the QTLs detected, two exerted major effects; one corresponding to the p1 locus, and the other a novel locus we named qtl2. The main effect of the functional allele at the p1 locus was to increase both CGA and flavones, while the positive allele at the qtl2 locus only increased CGA. An epistatic interaction between p1 and qtl2 alleles in the (A619 × Mo6)F 2 population caused an increase in CGA with a concomitant decrease in flavones. The rare ability of Mo6 and Mp708 to synthesize CGA in excess of flavones is primarily a result from the effects at the qtl2 locus.

Expression analysis of RNA14, a gene involved in mRNA 3' end maturation in yeast: characterization of the rna14-5 mutant strain.

In Saccharomyces cerevisiae, Rna14 protein is involved in both cleavage and polyadenylation of mRNA in the nucleus. Previous work has demonstrated that this protein is also localized in mitochondria. Moreover, all known rna14 mutants can be separated into two distinct classes: the poly(A)-negative class, which contains mutants that are deficient in mRNA 3'-end processing, and the poly(A)-positive class, which includes those mutants that are not impaired in any of the steps in mRNA metabolism investigated. This suggests that in addition to its involvement in mRNA polyadenylation, Rna14p could have a second function related to mitochondrial metabolism. Here we investigated the regulation of RNA14 by characterizing the rna14-5 mutant, which is the only poly(A)-positive allele that also overproduces the RNA14 mRNA. We showed that both deregulation of RNA14 transcription and modification of RNA14 mRNA stability contribute to the strong accumulation of the transcripts in this mutant. Surprisingly, the RNA14 promoter itself is not essential for this phenotype of the rna14-5 mutant. However, the 3' UTR of the mRNA is necessary for overproduction of the transcripts, although it is not sufficient to deregulate a reporter gene by itself. Site-directed mutagenesis experiments provided additional data suggesting that the rna14-5 mutation acts at the protein level rather than modifying the properties of the RNA14 transcripts themselves. A tentative model accounting for the data is discussed, in light of the proposed extranuclear function of the Rna14p and its mitochondrial localization.

Origin of cytoplasm substituted rice cultivars found in Japan.

Genetic variation of Japanese rice cultivars were examined. Five of 450 lowland cultivars and another five of 200 upland cultivars were determined as the indica type by using isozyme genotypes and the remainder were of the japonica type. The major characteristics of these indica cultivars, revealed a slender shape of grains, a short apiculus hair length, a positive allele for Ph reaction, and allele-3 for the Pgd1 locus. Three of these indica cultivars showed a non-deletion ORF100, which is essential to the japonica-type plastid. The plastid subtype identity (PS-ID) sequences of these plastids is 6C7A, which is also a japonica-specific repeat unit. Thus, these cultivars were concluded to be naturally generated cytoplasm substituted lines. These plastids were introduced into a indica genetic background from japonica cultivars grown elsewhere. The rest of the indica cultivars revealed a deletion-type ORF100 and plastid subtype 8C8A, both of which are indica-specific. These cultivars carried indica-type allelic constitutions for diagnostic isozyme loci. However, other characters were identical to the cytoplasm-substituted cultivars in Japan. In East and Southeast Asia, cultivars carrying a indica-type nuclear genotype with a japonica-type plastid are restricted to Aus cultivars in the Bengal region. Genetic and historical records suggest that Japanese indica cultivars and the Aus cultivars are closely related. The Aus cultivars acquire necessary genetic constitutions from both indica and japonica cultivars through naturally occurring out-crossing to adapt to a particular cultivation condition in the region. The wide adaptability enabled them to be introduced into a northern region like Japan.

Identification of QTLs for early blight ( Alternaria solani) resistance in tomato using backcross populations of a Lycopersicon esculentum x L. hirsutum cross.

Most commercial cultivars of tomato, Lycopersicon esculentum Mill., are susceptible to early blight (EB), a devastating fungal ( Alternaria solani Sorauer) disease of tomato in the northern and eastern parts of the U.S. and elsewhere in the world. The disease causes plant defoliation, which reduces yield and fruit quality, and contributes to significant crop loss. Sources of resistance have been identified within related wild species of tomato. The purpose of this study was to identify and validate quantitative trait loci (QTLs) for EB resistance in backcross populations of a cross between a susceptible tomato breeding line (NC84173; maternal and recurrent parent) and a resistant Lycopersicon hirsutum Humb. and Bonpl. accession (PI126445). Sixteen hundred BC(1) plants were grown to maturity in a field in 1998. Plants that were self-incompatible, indeterminant in growth habit, and/or extremely late in maturity, were discarded in order to eliminate confounding effects of these factors on disease evaluation, QTL mapping, and future breeding research. The remaining 145 plants (referred to as the BC(1) population) were genotyped for 141 restriction fragment length polymorphism (RFLP) markers and 23 resistance gene analogs (RGAs), and a genetic linkage map was constructed. BC(1) plants were evaluated for disease symptoms throughout the season, and the area under the disease progress curve (AUDPC) and the final percent defoliation (disease severity) were determined for each plant. BC(1) plants were self-pollinated and produced BC(1)S(1) seed. The BC(1)S(1) population, consisting of 145 BC(1)S(1) families, was grown and evaluated for disease symptoms in replicated field trials in two subsequent years (1999 and 2000) and AUDPC and/or final percent defoliation were determined for each family in each year. Two QTL mapping approaches, simple interval mapping (SIM) and composite interval mapping (CIM), were used to identify QTLs for EB resistance in the BC(1) and BC(1)S(1) populations. QTL results were highly consistent across generations, years and mapping approaches. Approximately ten significant QTLs (LOD >/= 2.4, P </= 0.001) were identified (and validated) for EB resistance, with individual effects ranging from 8.4% to 25.9% and with combined effects of >57% of the total phenotypic variation. All QTLs had the positive alleles from the disease-resistant parent. The good agreement between results of the BC(1) and 2 years of the BC(1)S(1) generations indicated the stability of the identified QTLs and their potential usefulness for improving tomato EB resistance using marker-assisted selection (MAS). Further inspections using SIM and CIM indicated that six of the ten QTLs had independent additive effects and together could account for up to 56.4% of the total phenotypic variation. These complementary QTLs, which were identified in two generations and 3 years, should be the most useful QTLs for MAS and improvement of tomato EB resistance using PI126445 as a gene resource. Furthermore, the chromosomal locations of 10 of the 23 RGAs coincided with the locations of three QTLs, suggesting possible involvement of these RGAs with EB resistance and a potential for identifying and cloning genes which confer EB resistance in tomato.

Genetic diversity in populations of the fungi Phaeomoniella chlamydospora and Phaeoacremonium aleophilum on grapevine in France

Isolates of Phaeomoniella chlamydospora (Phc) and Phaeoacremonium aleophilum (Pha), two haploid, deuteromycetous fungi, were obtained from vines showing symptoms of esca disease in different localities in two French regions, and within a single vineyard in one of these regions. The population genetic structure was determined in both fungi using random amplified polymorphic DNA (RAPD) analysis. Populations of Phc showed similar levels of diversity at local and regional levels. The most frequent Phc haplotypes were found in every population, and the frequencies of positive alleles of markers were similar across populations. The hypothesis that recombination had occurred was rejected for the full set of samples, but not for the samples reduced to haplotypes, indicating that Phc may be a recombining species. Different features were identified in Pha populations. First, the southern population of Pha appeared more diverse than the south‐western populations. Second, genetic differentiation was identified between Pha populations from southern and south‐western regions for several RAPDs. Finally, in the southern population of Pha no evidence for recombination was obtained, even by reducing the sample to haplotypes. Within the single vineyard surveyed, several haplotypes of both fungi were recovered and randomly distributed. Thus different infection events appeared to have occurred on a low spatial scale. Data from this study showed that haplotypes of both fungi were distributed over long distances geographically, and that most of the vineyards surveyed were infested by more than one haplotype of Phc and Pha.

Quantitative inheritance in sunflower (helianthus annuus l.)

This study was conducted in order to estimate the gene effects which determine the inheritance of certain characters and to search the genetic structure of each group in a 9 x 9 diallel cross group established by crossing inbred lines of sunflower. (1) Significant positive heterotic effects were observed for all the characters studied but for different number of crosses. According to the results obtained, two to three parents were observed to be good general combiners for seed yield and eight hybrids were promising crosses for seed yield and plant height. (2) Both additive and dominance genetic variances were significant for all characters. Also, the overall mean dominance effect of heterozygous loci, h2 was significant for all characters. It was found that positive and negative alleles at these loci were not in equal proportions in the parents (i.e., H1 > H2). The average degree of dominance showed overdominance for all char acters.

Genetic mapping of QTLs conditioning soybean sprout yield and quality

Soybean sprouts have been used as a food in the Orient since ancient times. In this study, 92 restriction fragment length polymorphism (RFLP) loci and two morphological markers (W1 and T) were used to identify quantitative trait loci (QTLs) associated with soybean sprout-related traits in 100 F2-derived lines from the cross of ’Pureunkong’×’Jinpumkong 2’. The genetic map consisted of 76 loci which covered about 756 cM and converged into 20 linkage groups. Eighteen markers remained unlinked. Phenotypic data were collected in 1996 and 1997 for hypocotyl length, percentage of abnormal seedlings, and sprout yield 6 days after germination at 20°C. Hypocotyl length was determined as the average length from the point of initiation of the first secondary root to the point of attachment of the cotyledons. The number of decayed seeds and seedlings, plus the number of stunted seedlings (less than 2-cm growth), was recorded a s abnormal seedlings. Seed weight was determined based on the 50-seed sample. Sprout yield was recorded as the total fresh weight of soybean sprouts produced from the 50-seed sample divided by the dry weight of the 50-seed sample. Four QTLs were associated with sprout yield in the combined analysis across 2 years. For the QTL linked to L154 on the Linkage Group (LG) G the positive allele was derived from Pureunkong (R 2 = 0.19), whereas at the other three QTLs (A089 on LG B1, A668n on LG K and B046 on LG L) the positive alleles were from Jinpumkong 2. QTLs conditioning seed weight were linked to markers A802n (LG B1), A069 (LG E), Cr321 (LG F) and A235 (LG G). At these four markers, the Jinpumkong allele increased seed weight. Markers K011n on LG B1, W1 on LG F and A757 on LG L were linked to QTLs conditioning hypocotyl length; and Bng119, K455n and K418n to QTLs conditioning the abnormal seedlings. The QTLs conditioning sprout yield were in the same genomic locations as the QTLs for seed weight identified in this population or from previously published research, indicating that QTLs for sprout yield are genetically linked to seed-weight QTLs or else that seed-weight QTLs pleiotropically condition sprout yield. These data demonstrate that effective marker-assisted selection may be feasible for enhancing sprout yield in a soybean. The transgressive segregation of sprout yield, as well as the existence of two QTLs conditioning greater than 10% of the phenotypic variation in sprout yields provides an opportunity to select for progeny lines with a greater sprout yield than currently preferred cultivars such as Pureunkong.

Identification and validation of QTLs for salt tolerance during vegetative growth in tomato by selective genotyping

The purpose of this study was to identify quantitative trait loci (QTLs) for salt tolerance (ST) during vegetative growth (VG) in tomato by distributional extreme analysis and compare them with the QTLs previously identified for this trait. A BC1 population (N = 792) of a cross between a moderately salt-sensitive Lycopersicon esculentum Mill. breeding line (NC84173, maternal and recurrent parent) and a salt-tolerant L. pimpinellifolium (Jusl.) Mill. accession (LA722) was evaluated for ST in solution cultures containing 700 mM NaCl + 70 mM CaCl2 (electrical conductivity, EC = 64 dS/m and phiw approximately -35.2 bars). Thirty-seven BC1 plants (4.7% of the total) that exhibited the highest ST were selected (referred to as the selected population), grown to maturity in greenhouse pots and self-pollinated to produce BC1S1 progeny seeds. The 37 selected BC1S1 progeny families were evaluated for ST and their average performance was compared with that of the parental BC1 population before selection. A realized heritability of 0.50 was obtained for ST in this population. The 37 selected BC1 plants were subjected to restriction fragment length polymorphism (RFLP) analysis using 115 markers, and marker allele frequencies were determined. Allele frequencies for the same markers were also determined in an unselected BC1 population (N = 119) of the same cross. A trait-based marker analysis (TBA), which measures differences in marker allele frequencies between selected and unselected populations, was used to identify marker-linked QTLs. Five genomic regions were detected on chromosomes 1, 3, 5, 6, and 11 bearing significant QTLs for ST. Except for the QTL on chromosome 3, all QTLs had positive alleles contributed from the salt tolerant parent LA722. Of the five QTLs, three (those on chromosomes 1, 3, and 5) were previously identified for this trait in another study, and thus were validated here. Only one of the major QTLs that was identified in our previous study was not detected here. This high level of conformity between the results of the two studies indicates the genuine nature of the identified QTLs and their potential usefulness for ST breeding using marker-assisted selection (MAS). A few BC1S1 families were identified with most or all of the QTLs and with a ST comparable to that of LA722. These families should be useful for the development of salt tolerant tomato lines via MAS.

A Standard of AmpliType PM Typing from Aged Evidentiary Samples

In analyzing aged samples by the AmpliType PM PCR amplification and Typing kit, it was occasionally observed that color developed typing strips had dark allele dots on PM loci but no visible S dot. Since the S dot acts as a minimum dot intensity control to determine positive alleles on the PM loci, it is necessary to apply another control system. To achieve positive PM typing from a degraded DNA sample that is inferred to be derived from a single donor, a standard has been adopted wherein loci from which sufficient PCR products are observed on agarose gel can be typed. The objective determination of sufficient PCR was done by comparison between band peak height of each locus generated from a sample and that of the corresponding locus generated from two nanograms (recommended minimum quantity as template DNA) of the control DNA provided in the kit.

Protection against severe disease is conferred by DERAA-bearing HLA-DRB1 alleles among HLA-DQ3 and HLA-DQ5 positive rheumatoid arthritis patients

Experimental studies in transgenic mice have suggested that HLA-DQ predisposes to rheumatoid arthritis (RA), but could also modulate disease severity by presenting peptides derived from self-DR molecules. In particular, a short amino acid sequence, 70DERAA 74, in the third hypervariable region of HLA-DRB1 confers protection for the disease, while particular HLA-DQ [DQB1∗0501/DQA1∗01 (DQ5) and DQB1∗03/DQA1∗03 (DQ3)] molecules predispose to the disease. We have therefore analyzed the allelic distribution of HLA-DRB1, DQA1, and DQB1 and the presence of rheumatoid factor and nodules among 199 German RA patients and 196 healthy controls. Our results show that HLA-DQB1∗03/DQA1∗03 (or DRB1∗04) predisposes to RA more than HLA-DQB1∗0501/DQA1∗01 ( i.e., DRB1∗01 and DRB1∗10). Homozygosity for DQ3 confers the strongest genetic risk for RA (OR = 19.79 compared to OR = 10.05 for two doses of shared epitope (SE) positive HLA-DRB1 alleles). Furthermore, patients carrying both predisposing DQ and 70DERAA 74-positive HLA-DRB1 alleles are more often rheumatoid factor (RF) negative than patients carrying predisposing DQ alleles alone. Only one out of 14 patients (7%) with a protective combination (DQ3/ 70DERAA 74 and DQ5/ 70DERAA 74) had rheumatoid nodules compared to 67 out of 144 patients (46.5%) with predisposing DQ alleles alone (OR = 0.12, 95% CI: 0.02–0.72, p = 0.004). These results demonstrate a protective role of 70DERAA 74-positive DRB1 alleles against disease severity among RA patients.

Single intragenic microsatellite preimplantation genetic diagnosis for cystic fibrosis provides positive allele identification of all CFTR genotypes for informative couples.

This study is part of a strategy aimed at using fluorescent polymerase chain reaction (PCR) on informative genetic microsatellite markers as a diagnostic tool in preimplantation genetic diagnosis (PGD) of severe monogenic disease. Two couples, both of whom had previously had children who were compound heterozygote for severe cystic fibrosis mutations, were offered PGD using fluorescent PCR of the highly polymorphic cystic fibrosis transmembrane conductance regulator (CFTR) intragenic microsatellite marker IVS17bTA. Cleavage-stage embryo biopsy followed by PCR resulted in transfer of one unaffected carrier embryo for each couple. This approach eliminates the need for single cell multiplex PCR strategies to detect CF compound heterozygotes. It also provides a control of chromosome 7 ploidy in the blastomeres and a selection against allele dropout by positive detection of each CFTR copy of all genotypes in preimplantation embryos from genetically informative families.

RHD positive haplotypes in D negative Europeans

BackgroundBlood group genotyping is increasingly utilized for prenatal diagnosis and after recent transfusions, but still lacks the specificity of serology. In whites, the presence of antigen D is predicted, if two or more properly selected RHD-specific polymorphism are detected. This prediction must fail, if an antigen D negative RHD positive allele is encountered. Excluding RHDψ and CdeS frequent only in individuals of African descent, most of these alleles are unknown and the population frequency of any such allele has not been determined.MethodsWe screened 8,442 antigen D negative blood donations by RHD PCR-SSP. RHD PCR positive samples were further characterized by RHD exon specific PCR-SSP or sequencing. The phenotype of the identified alleles was checked and their frequencies in Germans were determined.ResultsWe detected 50 RHD positive samples. Fifteen samples harbored one of three new Del alleles. Thirty samples were due to 14 different D negative alleles, only 5 of which were previously known. Nine of the 14 alleles may have been generated by gene conversion in cis, for which we proposed a mechanism triggered by hairpin formation of chromosomal DNA. The cumulative population frequency of the 14 D negative alleles was 1:1,500. Five samples represented a D+/- chimera, a weak D and three partial D, which had been missed by routine serology; two recipients transfused with blood of the D+/- chimera donor became anti-D immunized.ConclusionThe results of this study allowed to devise an improved RHD genotyping strategy, the false-positive rate of which was lower than 1:10,000. The number of characterized RHD positive antigen D negative and Del alleles was more than doubled and their population frequencies in Europe were defined.

Quantitative trait loci influencing β-glucan content in oat (Avena sativa, 2n=6x=42)

The β-glucan content of oat grain is of inter-est due to its positive human health role as a dietary component influencing serum cholesterol levels and its relation to the energy intake of livestock feed. Two recombinant inbred populations sharing a common parent (Kanota × Ogle and Kanota × Marion), and containing 137 individual lines each, were used to identify genomic regions that influence the β-glucan content in cultivated oat. Single-factor ANOVA, a backward elimination process, simple interval mapping (SIM) and simplified composite interval mapping (sCIM) were used to identify quantitative trait loci (QTLs). Regions on linkage groups 11 and 14 of the hexaploid oat RFLP map influenced β-glucan levels in both populations and over environments. Other genomic regions were identified whose effects varied depending on the genetic background, but were significant over measurements for a given population. Kanota and Ogle exhibit similar β-glucan levels and each parent contributed about the same number of positive β-glucan alleles in the Kanota × Ogle cross. Marion is higher in β-glucan content than Kanota and contributed all of the positive alleles in the Kanota × Marion cross. Three of the β-glucan QTL regions identified have been previously implicated as having a significant influence on the groat oil content in oat. These correlated QTL regions were either in coupling phase, with a region from one parent having the same effect on both traits, or were in repulsion phase. Identification of coupling- and repulsion-phase QTL regions for β-glucan and oil content facilitates the use of markers in manipulating these traits in oat breeding.

Replication of Linkage of Familial Combined Hyperlipidemia to Chromosome 1q With Additional Heterogeneous Effect of Apolipoprotein A-I/C-III/A-IV Locus

Familial combined hyperlipidemia (FCHL), the most common familial dyslipidemia, is implicated in up to 20% of cases of premature coronary heart disease. Although underlying mutations for FCHL have yet to be identified, several candidate genes/regions have been identified. A positive linkage to chromosome 1q markers has been reported, with the highest lod score of 5.93 occurring at a location between D1S104 and D1S1677. Using the same diagnostic criteria, the Family Heart Study (FHS) has defined 71 FCHL families, comprising 170 cases, for a total of 137 possible affected sibling pairs. The FCHL criteria require elevation in serum low density lipoprotein cholesterol and triglyceride levels within the family, with at least 2 affected first-degree relatives. Markers D1S104 and D1S1677 were typed, and significant allele sharing was found in FCHL sibships (multipoint lod score with use of the model from the Finnish study was 2.52, and multipoint nonparametric score was 2.48; P=0.007), replicating linkage in this chromosome 1 region. In addition, previously reported linkage of FCHL to apolipoprotein A-I/C-III/A-IV has been investigated in FHS families. FHS results revealed positive but nonsignificant allele sharing among FCHL sibships with apolipoprotein A-I/C-III/A-IV by use of marker D11S4127 (nonparametric linkage score 1.11, P=0.13). Two-locus analyses of D1S104 and D11S4127 suggested possible heterogeneity rather than epistasis, with a maximum 2-locus lod score of 3.05. A nonparametric 2-locus analysis revealed significant improvement in the 2-locus versus single-locus scores. Finally, no linkage was found with markers near the lipoprotein lipase gene region.

QTLs and epistasis for aluminum tolerance in rice (Oryza sativa L.) at different seedling stages

To investigate the genetic background for aluminum (Al) tolerance in rice, a recombinant inbred (RI) population, derived from a cross between an Al-sensitive lowland indica rice variety IR1552 and an Al-tolerant upland japonica rice variety Azucena, was used in culture solution. A molecular linkage map, together with 104 amplified fragment length polymorphism (AFLP) markers and 103 restriction fragment length polymorphism (RFLP) markers, was constructed to map quantitative trait loci (QTLs) and epistatic loci for Al tolerance based on the segregation for relative root length (RRL) in the population. RRL was measured after stress for 2 and 4 weeks at a concentration of 1mM of Al3+ and a control with a pH 4.0, respectively. Two QTLs were detected at both the 2nd and the 4th weeks on chromosomes 1 and 12 from unconditional mapping, while the QTL on chromosome 1 was only detected at the 2nd stress week from conditional mapping. The effect of the QTL on chromosome 12 was increased with an increase of the stress period from 2 to 4 weeks. The QTL on chromosome 1 was expressed only at the earlier stress, but its contribution to tolerance was prolonged during growth. At least one different QTL was detected at the different stress periods. Mean comparisons between marker genotypic classes indicated that the positive alleles at the QTLs were from the Al-tolerant upland rice Azucena. An important heterozygous non-allelic interaction on Al tolerance was found. The results indicated that tolerance in the younger seedlings was predominantly controlled by an additive effect, while an epistatic effect was more important to the tolerance in older seedlings; additionally the detected QTLs may be multiple allelic loci for Al tolerance and phosphorus-uptake efficiency, or for Al and Fe2+ tolerance.

Genetic Analysis of Pre-Harvest Sprouting Resistance in a Wheat × Spelt Cross

Breeding for pre-harvest sprouting (PHS) resistance in wheat (Triticum aestivum L.) and spelt (Triticum spelta L.) is difficult because PHS is quantitatively inherited and strongly affected by environmental factors. The aim of this study was to detect molecular markers linked to quantitative trait loci (QTL) involved in PHS resistance to improve the breeding process. We measured falling number (FN) and α-amylase activity (AA) of 226 F 5 recombinant inbred lines (RILs) originating from a cross between the Swiss wheat cultivar Forno and the Swiss spelt cultivar Oberkulmer in four environments. QTL analysis was performed with 204 RILs and based on a genetic map of 183 loci. Across environments, 12 and 13 QTL were detected for FN and AA, respectively. Altogether the QTL explained more than 75% of the phenotypic variance. The two traits were highly correlated (r = -0.91) and of the 13 QTL for AA, nine coincided with QTL for FN. Three of the six QTL with major effects (R 2 ≥ 15%) on PHS resistance coincided with QTL for ear length. The QTL with the strongest impact had the positive allele from Oberkulmer and was located on 5AL at the q locus, which is responsible for the typical ear morphology of spelt. The QTL on 6A (with the positive allele from Forno), 3B, and 7B (both with the positive allele from Oberkulmer) improve PHS resistance without changing the ear morphology. Thus, these QTL could be important for marker assisted selection for PHS resistance in both the wheat and the spelt germplasm.

Association of MHC and rheumatoid arthritis: Association of RA with HLA-DR4 - the role of repertoire selection

Most patients with rheumatoid arthritis (RA) express HLA-DR4, HLA-DR1 or HLA-DR10. These alleles share a common amino acid motif in their third hypervariable regions: the shared epitope. In normals and patients with RA, HLA-DR genes exert a major influence on the CD4 αβ T-cell repertoire, as shown by studies of AV and BV gene usage and by BV BJ gene usage by peripheral blood CD4 αβ T-cells. However, the rheumatoid T-cell repertoire is not entirely under HLA-DR influence, as demonstrated by discrepancies in VB JB gene usage between identical twins discordant for RA and by contraction of the CD4 αβ T-cell repertoire in RA patients. Shared epitope positive HLA-DR alleles may shape the T-cell repertoire by presenting self peptides to CD4 T cells in the thymus. Peptides processed from HLA-DR molecules and encompassing the shared epitope may also be presented by HLA-DQ and select CD4 αβ T cells in the thymus. Thus, shared epitope-positive alleles impose a frame on the T-cell repertoire. This predisposing frame is further modified (by unknown factors) to obtain the contracted rheumatoid repertoire.

A combined RFLP and AFLP linkage map of upland rice (Oryza sativa L.) used to identify QTLs for root-penetration ability

Acombined RFLP and AFLP linkage map of an F6 recombinant inbred population, which was derived from a previously mapped F2 of a cross between the two drought resistant upland rice varieties Bala and Azucena, is presented. The map contains 101 RFLP and 34 AFLP markers on 17 linkage groups covering 1680 cM. Also presented is the approximate mapping position of a further four RFLP and 75 AFLP markers, which either could not be given a unique place on the map or for which the available data is not sufficient to allow confident positioning, and the result of quantitative trait locus (QTL) mapping of traits related to root-penetration ability. Root penetration was assessed by counting the number of root axes that penetrated a 3 mm-thick layer consisting of 80% wax and 20% white soft paraffin. Good root penetration would be expected to increase drought resistance where soil strength is high. Single-marker analysis revealed seven QTLs for the number of roots which penetrate the wax layer. In identical locations were seven QTLs for the ratio of penetrated to the total number of roots. Transgressive inheritance of positive alleles from Bala explained four of these QTLs. Comparison of the QTLs identified here with previous reports of QTLs for root morphology suggest that alleles which improve root penetration ability may also either make the roots longer or thicker.

Genetic analysis of apomixis in Citrus and Poncirus by molecular markers

Propagation of citrus rootstocks depends upon the production of clonal plants from nucellar seedlings. This makes apomixis one of the host important traits in breeding programs for citrus rootstocks. The genetic control of apomixis was studied in a 50-tree progeny derived from the cross C. volkameriana×P. trifoliata using 69 molecular markers and bulked segregant analysis. The proportion of nucellar seedlings was estimated by isoenzymatic analysis of 25 seedlings per tree for 2 consecutive years. The type of embryony (polyembryonic versus monoembryonic seeds) was also determined for fruit-yielding trees. Separate genetic maps for each parental species were developed. The integration and comparison of these maps could be accomplished using common multiallelic segregant loci. Differences in gene synteny between the two species-specific genetic maps were shown. Important distortions in the segregation of markers at several genomic regions, some of them also involving differences in the C-methylation pattern, have been observed, especially for the pollen parent. Analysis of quantitative trait loci (QTLs) revealed the presence of six genomic positions (two in P. trifoliata and four in C. volkameriana) contributing individually up to 24% of the total variation for apomixis. Within the same species, QTLs with positive and negative allele effects were present, even in the same linkage group. One of the markers associated to apomixis (Apo2) is also associated to embryony type. Therefore, the genetic control of apomictic reproduction found in citrus (nucellar embryony) is quite complex compared to what has been reported for gametophytic apomixis. Molecular markers linked to QTLs governing apomixis will be useful to assist selection of future apomictic rootstocks for citrus varieties.

RFLP mapping of QTLs conferring salt tolerance during the vegetative stage in tomato

Quantitative trait loci (QTLs) contributing to salt tolerance during the vegetative stage in tomato were investigated using an interspecific backcross between a salt-sensitive Lycopersicon esculentum breeding line (NC84173, maternal and recurrent parent) and a salt-tolerant Lycopersicon pimpinellifolium accession (LA722). One hundred and nineteen BC1 individuals were genotyped for 151 RFLP markers and a linkage map was constructed. The parental lines and 119 BC1S1 families (self-pollinated progeny of the BC1 individuals) were evaluated for salt tolerance in aerated saline-solution cultures with the salt concentration gradually raised to 700 mM NaCl+70 mM CaCl2 (equivalent to an electrical conductivity of approximately 64 dS/m and a water potential of approximately −35.2 bars). The two parental lines were distinctly different in salt tolerance: 80% of the LA722 plants versus 25% of the NC84173 plants survived for at least 2 weeks after the final salt concentration was reached. The BC1S1 population exhibited a continuous variation, typical of quantitative traits, with the survival rate of the BC1S1 families ranging from 9% to 94% with a mean of 51%. Two QTL mapping techniques, interval mapping (using MAPMAKER/QTL) and single-marker analysis (using QGENE), were used to identify QTLs. The results of both methods were similar and five QTLs were identified on chromosomes 1 (two QTLs), 3, 5 and 9. Each QTL accounted for between 5.7% and 17.7%, with the combined effects (of all five QTLs) exceeding 46%, of the total phenotypic variation. All QTLs had the positive QTL alleles from the salt-tolerant parent. Across QTLs, the effects were mainly additive in nature. Digenic epistatic interactions were evident among several QTL-linked and QTL-unlinked markers. The overall results indicate that tomato salt tolerance during the vegetative stage could be improved by marker-assisted selection using interspecific variation.