Positive Alleles Research Articles

1031-LBP: Evaluation of uracil dna glycosylase (UDG) with the LinkSeq™ real-time pcr hla typing method

Aim Post-PCR amplification products can pose a problem in clinical laboratories. Great care is needed to ensure post and pre-PCR areas minimize the risk of unwanted amplicons affecting results. Linkage Biosciences designed the LinkS e ¯ q™ real-time PCR HLA test to include deoxyuridine triphosphate (dUTP) rather than the standard deoxythmidine triphosphate (dTTP) in the PCR reaction as a preventive measure so that Uracil DNA Glycosylase enzyme (UDG) can be used as an optional additive to eliminate unwanted uracil-containing amplicons during PCR set-up. The aim of this study was to evaluate the effectiveness of adding UDG to the LinkS e ¯ q™ test in a laboratory setting with False Positive and False Negative issues. Methods To validate the usefulness of UDG reagent (provided by Linkage Biosciences) we selected 10 clinical DNA samples that contained aberrant primer dimer peaks which may have contributed to False Positive and False Negative allele amplification. All samples were typed with the standard LinkS e ¯ q™ protocol and with the UDG protocol. The 2 real-time kits that were used were the LinkS e ¯ q™ 384 well tray, Cat #1575 and the 192 well tray, Cat#1554 with SYBR Green dye for melting curve analysis. All samples were amplified using the Roche LightCycler® 480. Results All 10 samples showed improved results in the reduction of False Positives and removal of dimeric peaks using the UDG reagent. The data shows a total reduction of 93.6% of the False Positives, 66.6% reduction in False Negatives, and 86.7% reduction of software forced calls. The samples demonstrated concordance with PCR-SSP (Invitrogen), or UNET reported results. Conclusions In summary, the LinkS e ¯ q™ real-time PCR assay is a fast and reliable HLA typing method. The UDG reagent works well when necessary to remove suspect peaks which may interfere with SureTyper Software data analysis.

ACTN3 genotype predicts metabolic, anthropometric and cardiovascular phenotypes in a young, healthy population (711.8)

Exercise‐related polymorphisms have played an important role in shaping human evolution. One such polymorphism, ACTN3 R577X, is overrepresented in endurance athletes and centenarians suggesting an association with favorable metabolic health. As such, we examined the influence of ACTN3 genotype on health‐related phenotypes in young subjects (age 18‐35) from the Assessing Inherent Markers for Metabolic syndrome in the Young (AIMMY) study (n=188). Cardiovascular, anthropometric, metabolic and body composition characteristics were assessed. ACTN3 genotype was associated with BMI in a sex specific manner, with null (XX) females having higher scores, while male positive (RR/RX) allele carriers had greater scores compared to XX males (p<0.05). Similarly, body fat percentage and waist circumference measurements were higher in females of the XX genotype compared to RR/RX allele carriers (p<0.05). In males, body circumferences and waist:hip ratio were higher in RR/RX allele carriers compared to XX individuals. Interestingly, Male RR/RX allele carriers had higher blood glucose and diastolic blood pressure than XX males. It was also found that female RR/RX carriers had higher VO2 peak scores than XX females (p<0.05). Metabolic and cardiovascular associations with ACTN3 genotype may offer novel insight into predicted athletic performance and disease risk.

Identification and fine mapping of quantitative trait loci for seed vigor in germination and seedling establishment in rice

Seed vigor is an index of seed quality that is used to describe the rapid and uniform germination and the establishment of strong seedlings in any environmental conditions. Strong seed vigor in low-temperature germination conditions is particularly important in direct-sowing rice production systems. However, seed vigor has not been selected as an important breeding trait in traditional breeding programs due to its quantitative inherence. In this study, we identified and mapped eight quantitative trait loci (QTLs) for seed vigor by using a recombinant inbred population from a cross between rice (Oryza sativa L. ssp. indica) cultivars ZS97 and MH63. Conditional QTL analysis identified qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-11 influenced seedling establishment and that qSV-5a, qSV-5c, and qSV-8 influenced only germination. Of these, qSV-1, qSV-5b, qSV-6a, qSV-6b, and qSV-8 were low-temperature-specific QTLs. Two major-effective QTLs, qSV-1, and qSV-5c were narrowed down to 1.13-Mbp and 400-kbp genomic regions, respectively. The results provide tightly linked DNA markers for the marker-assistant pyramiding of multiple positive alleles for increased seed vigor in both normal and low-temperature germination environments.

Streptococcal infection as possible trigger for dense deposit disease (C3 glomerulopathy)

Dense deposit disease (DDD, formerly known as membranoproliferative glomerulonephritis (MPGN) type II) is a subtype of C3 glomerulopathy (C3G). Electron-dense deposits in the glomerular basement membrane characterize this glomerulonephritis. DDD typically presents with a nephritic syndrome that progresses to end-stage renal failure in 50 % of patients despite treatment. The pathogenic basis of DDD is uncontrolled activation of the alternative complement cascade although the potential triggering events that precipitate the development of complement dysregulation are typically unknown. There are isolated reports of an apparent association between streptococcal infection and DDD, as well as with MPGN types I and III. However, this association has not been deemed compelling, perhaps because so few cases have been reported or because of a current lack of evidence for a plausible hypothesis to connect a streptococcal infection with subsequent disease. In this report, we describe two patients with DDD who definitely had an antecedent streptococcal infection with the phenotype of acute post-streptococcal glomerulonephritis and whose initial kidney biopsy findings on light microscopy were indistinguishable from acute post-streptococcal glomerulonephritis. These patients had additional points of interest: recurrence of gross hematuria with recurrent streptococcal infections, slowly progressive course, persistently low serum C3 concentration, positive C3 nephritic factor, and positive risk alleles in the complement factor H (CFH) gene. We suggest that streptococcal infection may trigger DDD in individuals genetically predisposed by virtue of a disorder in complement regulation.

RNA-Seq analysis of two elite lines ofWithania somniferato evaluate potential of heterosis

Metabolite targeted breeding is one of the prime need in Ashwagandha (Withania somnifera) to meet its fast growing demand at domestic and international level owing to its vast spectral pharmaceutical potential. Till date only scanty breeding efforts exists majority being introductions or selections from the wilds/landraces through which active bio constituent increase is limited. Hybridization based heterotic positive QTL alleles can be introgressed in a fine quality good agronomic genetic base using marker assisted selection. Investigations under this study generated a large resource of Withania specific genomic microsatellite markers and SNP through RNA seq. Using an RNA-seq approach, the expression of 101245 unigenes were quantified in parents. The expression levels of 30% of transcripts differed between parents, a majority of which had more than 1.5 fold-changes. RNA seq will help to decipher the Withanolide biosynthesis pathway and SNP responsible for functional polymorphism in pathway genes and hence predicting the potential of heterosis.

Identification of putative quantitative trait loci associated with a flavonoid related to resistance to cabbage seedpod weevil (Ceutorhynchus obstrictus) in canola derived from an intergeneric cross, Sinapis alba × Brassica napus.

Kaempferol 3- O -sinapoyl-sophoroside 7- O -glucoside was putatively identified as the major component of a characteristic HPLC peak previously correlated with the reduction of cabbage seedpod weevil larval infestation in a novel canola genotype. The cabbage seedpod weevil (Ceutorhynchus obstrictus [Marsham]) (CSPW) is a serious pest of brassicaceous oilseed crops such as canola in both Europe and more recently in North America. At present, the only control strategy against CSPW is the application of insecticides. As an alternative more environmentally-friendly control strategy, we developed novel canola germplasm resistant to weevil attack through introgression of Sinapis alba DNA into Brassica napus by making the wide cross followed by embryo rescue and backcrossing to the B. napus parent. We have previously characterized resistant canola lines by metabolic profiling and were able to correlate reduction of larval infestation to the presence of a characteristic HPLC peak. In this study, we have putatively identified the major component in the peak using mass spectrometry as kaempferol 3-O-sinapoyl-sophoroside 7-O-glucoside (KSSG). We have also identified quantitative trait loci (QTL) associated with this HPLC peak in a mapping population consisting of more than 200 individual doubled haploid (DH) lines derived from a cross between CSW428 (the resistant parent) and SC030686 (the susceptible parent). This QTL accounted for approximately 9.5% of the phenotypic variation in KSSG content. The observation that only one QTL was identified as surpassing the LOD threshold of 3.0 suggests that both parents may possess the positive alleles for other QTL that have not been detected in our study. This finding also indicates a complex regulatory mechanism for KSSG levels and provides an appropriate explanation for the large transgressive segregation observed in the DH lines of the QTL mapping population.

Engraftment Of Human Polycythemia Vera CD34+ Cells In hSIRPα-Transgenic-Human-TPO-Expressing RAG2-/-, IL2Rγ-/- Immunodeficient Mice

IntroductionXenotransplantation of human hematopoietic malignancies into immunodeficient mice represents the most appropriate in vivo model system for human malignant hematopoiesis. While a diversity of immunodeficient mouse strains on the NOD/SCID and RAG2-/-/IL2Rγ-/--BALB/C background are described for the most aggressive human malignancies like acute leukemias, xenotransplantation models of less aggressive human hematologic disorders like myeloproliferative neoplasms and myelodysplastic syndromes show only limited engraftment levels. We recently developed next generation mouse strains expressing human cytokines and key factors of xenogeneic cell acceptance (e.g. hSIRPα to inactivate mouse macrophage activation by human cells) and hypothesized that these would represent suitable models for the assessment of human less aggressive hematologic disorders in vivo by providing an optimized “humanized” microenvironment. MethodsPeripheral blood (PB) and bone marrow (BM) samples of polycythemia vera (PV) patients were collected after informed consent at the Division of Hematology, Zurich University Hospital. Human CD34+ cells were isolated by density gradient centrifugation followed by immunomagnetical selection using anti-CD34 coupled beads. Purity of magnetical selection process was confirmed by FACS analysis. Newborn (24h-48h old) hSIRPα-tg-hTPO-knockin mice on the RAG2-/-/IL2Rγ-/--BALB/C background received sublethal irradiation (split dose of 2x1.5 Gy) and were transplanted intra-hepatically 24 hours later. Transplanted cell dose was dependent on availability of CD34+ stem and progenitor cells isolated from one phlebotomy sample (∼400ml of PB) of the respective patient. Mice were bled 4 weeks after transplantation and chimerism in peripheral blood was analyzed by flow cytometry using a panel of antigens (mCD45.2, hCD45, hCD33, hCD34, hCD3, hCD19). Mice showing positive chimerism in PB (i.e.>0.1% hCD45+ of total MNCs) at week 4 were sacrificed between week 8-16 and engraftment in BM, spleen and PB was analyzed by flow cytometry. To verify engraftment of human malignant hematopoiesis we quantified allele-burden of JAK2V617F point mutation in mouse BM using allele specific (AS)-PCR for the pathognomonic point mutation of the JAK2 gene. ResultsBy transplantation of 4-10x105 CD34+ cells into newborn hSIRPα-tg-hTPO-RAG2-/-/IL2Rγ-/- mice we could detect engraftment of hCD45+ cells in PB at week 4 (median 0.68%, range 0.12-23.8%). At week 8, BM engraftment of hCD45+ cells ranged 0.88-54.1% (median 4.43%) with a high proportion of human myeloid cells detected by hCD45/hCD33 co-staining (median 3.07 %, range 0.6-17.6% of total MNCs). We could detect engraftment until week 16, the latest timepoint assessed. Since all transplanted PV patient samples were positive for the common point mutation JAK2V617F, AS-PCR was used to quantify human malignant hematopoiesis. In tested BM samples of engrafted mice we found JAK2V617F positive alleles with a frequency of 2-12% (median 8%). To further assess the clonal composition of the engrafted population we established single cell sorting of primary and engrafted human PV-CD34+ cells in a 96 well format followed by liquid culture expansion and AS-PCR. In pilot studies we could show the clonal composition of a BM engrafted CD34+ population that split into 80% JAK2 WT expressing, 10% JAK2V617F heterozygous and 10 % JAK2V617F homozygous clones. We are currently extending these findings by side by side comparison of the clonal composition of primary vs. xenografted human PV-CD34+ cells of the same patient to test for the influence of a xenogeneic humanized microenvironment on maintenance of malignant cells in vivo. ConclusionsBy using hSIRPα-tg-hTPO-RAG2-/-/IL2Rγ-/- mice we could show engraftment of PV-CD34+ cells that extends previous reported engraftment levels in other model organisms. To our knowledge this is the first study assessing the clonal composition of human PV engrafted cells in the xenogeneic environment aiming at identifying components that are critical for the maintenance of human malignant hematopoiesis in vivo. This model will thus be a useful tool to test targeted therapies in vivo. Disclosures:No relevant conflicts of interest to declare.

QTL Scanning for Rice Yield Using a Whole Genome SNP Array

High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line (RIL) population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length of 1.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.

Application of a posteriori granddaughter and modified granddaughter designs to determine Holstein haplotype effects

A posteriori and modified granddaughter designs were applied to determine haplotype effects for Holstein bulls and cows with BovineSNP50 [~50,000 single nucleotide polymorphisms (SNP); Illumina Inc., San Diego, CA] genotypes. The a posteriori granddaughter design was applied to 52 sire families, each with ≥100 genotyped sons with genetic evaluations based on progeny tests. For 33 traits (milk, fat, and protein yields; fat and protein percentages; somatic cell score; productive life; daughter pregnancy rate; heifer and cow conception rates; service-sire and daughter calving ease; service-sire and daughter stillbirth; 18 conformation traits; and net merit), the analysis was applied to the autosomal segment with the SNP with the greatest effect in the genomic evaluation of each trait. All traits except 2 had a within-family haplotype effect. The same design was applied with the genetic evaluations of sons corrected for SNP effects associated with chromosomes besides the one under analysis. The number of within-family contrasts was 166 without adjustment and 211 with adjustment. Of the 52 bulls analyzed, 36 had BovineHD (high density; Illumina Inc.) genotypes that were used to test for concordance between sire quantitative trait loci and SNP genotypes; complete concordance was not obtained for any effects. Of the 31 traits with effects from the a posteriori granddaughter design, 21 were analyzed with the modified granddaughter design. Only sires with a contrast for the a posteriori granddaughter design and ≥200 granddaughters with a record usable for genetic evaluation were included. Calving traits could not be analyzed because individual cow evaluations were not computed. Eight traits had within-family haplotype effects. With respect to milk and fat yields and fat percentage, the results on Bos taurus autosome (BTA) 14 corresponded to the hypothesis that a missense mutation in the diacylglycerol O-acyltransferase 1 (DGAT1) gene is the main causative mutation, although other polymorphisms in that gene also modify fat yield and percentage. The positive allele for protein concentration was less frequent, which indicated that selection on that locus could be effective. Although the results can be used to determine causative polymorphisms for most of the analyzed traits, complete DNA sequencing of most of the analyzed sires probably will be required.

FRI0022 Relationships between radiographic damage, shared epitope alleles and circulating cytokines in dmard-naïve early ra patients

BackgroundAlthough therapeutic targeting of humoral and cellular inflammatory biomarkers has improved outcomes in subsets of patients with severe RA, the identification of novel targets based on insights into disease immunopathogenesis...

HLA-DRB1 Genotypes and the Risk of Developing Anti Citrullinated Protein Antibody (ACPA) Positive Rheumatoid Arthritis

ObjectiveTo provide a table indicating the risk for developing anti citrullinated protein antibody (ACPA) positive rheumatoid arthritis (RA) according to one’s HLA-DRB1 genotype.MethodsWe HLA-DRB1 genotyped 857 patients with ACPA positive RA and 2178 controls from South Eastern and Eastern France and calculated Odds Ratios (OR) for developing RA for 106 of 132 possible genotypes accounting for 97% of subjects.ResultsHLA-DRB1 genotypic ORs for developing ACPA positive RA range from 28 to 0.19. HLA-DRB1 genotypes with HLA-DRB1*04SE (HLA-DRB1*0404, HLA-DRB1*0405, HLA-DRB1*0408), HLA-DRB1*04∶01, HLA-DRB1*01 are usually associated with high risk for developing RA. The second HLA-DRB1 allele in genotype somewhat modulates shared epitope associated risk. We did not identify any absolutely protective allele. Neither the Reviron, nor the du Montcel models accurately explains our data which are compatible with the shared epitope hypothesis and suggest a dosage effect among shared epitope positive HLA-DRB1 alleles, double dose genotypes carrying higher ORs than single dose genotypes.ConclusionHLA-DRB1 genotypic risk for developing ACPA positive RA is influenced by both HLA-DRB1 alleles in genotype. We provide an HLA-DRB1 genotypic risk table for ACPA positive RA.

The Use of Combining Ability Analysis to Identify Elite Parents for Artemisia annua F1 Hybrid Production

Artemisia annua is an important medicinal crop used for the production of the anti-malarial compound artemisinin. In order to assist in the production of affordable high quality artemisinin we have carried out an A. annua breeding programme aimed at improving artemisinin concentration and biomass. Here we report on a combining ability analysis of a diallel cross to identify robust parental lines for hybrid breeding. The parental lines were selected based on a range of phenotypic traits to encourage heterosis. The general combining ability (GCA) values for the diallel parental lines correlated to the positive alleles of quantitative trait loci (QTL) in the same parents indicating the presence of beneficial alleles that contribute to parental performance. Hybrids generated from crossing specific parental lines with good GCA were identified as having an increase in both artemisinin concentration and biomass when grown either in glasshouse or experimental field trials and compared to controls. This study demonstrates that combining ability as determined by a diallel cross can be used to identify elite parents for the production of improved A. annua hybrids. Furthermore, the selection of material for breeding using this approach was found to be consistent with our QTL-based molecular breeding approach.

QDTY12.1: a locus with a consistent effect on grain yield under drought in rice

BackgroundSelection for grain yield under drought is an efficient criterion for improving the drought tolerance of rice. Recently, some drought-tolerant rice varieties have been developed using this selection criterion and successfully released for cultivation in drought-prone target environments. The process can be made more efficient and rapid through marker-assisted breeding, a well-known fast-track approach in crop improvement. QTLs have been identified for grain yield under drought with large effects against drought-susceptible varieties. Most of the identified QTLs show large QTL × environment or QTL × genetic background interactions. The development of mapping populations in the background of popular high-yielding varieties, screening across environments, including the target environments, and the identification of QTLs with a consistent effect across environments can be a suitable alternative marker-assisted breeding strategy. An IR74371-46-1-1 × Sabitri backcross inbred line population was screened for reproductive-stage drought stress at the International Rice Research Institute, Philippines, and Regional Agricultural Research Station, Nepalgunj, Nepal, in the dry and wet seasons of 2011, respectively. A bulk segregant analysis approach was used to identify markers associated with high grain yield under drought.ResultsA QTL, qDTY12.1, significantly associated with grain yield under reproductive-stage drought stress was identified on chromosome 12 with a consistent effect in two environments: IRRI, Philippines, and RARS, Nepalgunj, Nepal. This QTL explained phenotypic variance of 23.8% and contributed an additive effect of 45.3% for grain yield under drought. The positive QTL allele for qDTY12.1 was contributed by tolerant parent IR74371-46-1-1.ConclusionsIn this study, qDTY12.1 showed a consistent effect across environments for high grain yield under lowland reproductive-stage drought stress in the background of popular high-yielding but drought-susceptible recipient variety Sabitri. qDTY12.1 was also reported previously [Crop Sci 47:507–516, 2007] to increase grain yield under upland reproductive-stage drought stress situations. qDTY12.1 is the only QTL reported so far in rice to have shown a large effect against multiple recipient genetic backgrounds as well as under highly diverse upland and lowland rice ecosystems. qDTY12.1 can be successfully introgressed to improve grain yield under drought of popular high-yielding but drought-susceptible lowland as well as upland adapted varieties following marker-assisted breeding.

Validation of candidate gene markers for marker-assisted selection of potato cultivars with improved tuber quality

Tuber yield, starch content, starch yield and chip color are complex traits that are important for industrial uses and food processing of potato. Chip color depends on the quantity of reducing sugars glucose and fructose in the tubers, which are generated by starch degradation. Reducing sugars accumulate when tubers are stored at low temperatures. Early and efficient selection of cultivars with superior yield, starch yield and chip color is hampered by the fact that reliable phenotypic selection requires multiple year and location trials. Application of DNA-based markers early in the breeding cycle, which are diagnostic for superior alleles of genes that control natural variation of tuber quality, will reduce the number of clones to be evaluated in field trials. Association mapping using genes functional in carbohydrate metabolism as markers has discovered alleles of invertases and starch phosphorylases that are associated with tuber quality traits. Here, we report on new DNA variants at loci encoding ADP-glucose pyrophosphorylase and the invertase Pain-1, which are associated with positive or negative effect with chip color, tuber starch content and starch yield. Marker-assisted selection (MAS) and marker validation were performed in tetraploid breeding populations, using various combinations of 11 allele-specific markers associated with tuber quality traits. To facilitate MAS, user-friendly PCR assays were developed for specific candidate gene alleles. In a multi-parental population of advanced breeding clones, genotypes were selected for having different combinations of five positive and the corresponding negative marker alleles. Genotypes combining five positive marker alleles performed on average better than genotypes with four negative alleles and one positive allele. When tested individually, seven of eight markers showed an effect on at least one quality trait. The direction of effect was as expected. Combinations of two to three marker alleles were identified that significantly improved average chip quality after cold storage and tuber starch content. In F1 progeny of a single-cross combination, MAS with six markers did not give the expected result. Reasons and implications for MAS in potato are discussed.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-012-2035-z) contains supplementary material, which is available to authorized users.

Resistance QTL Mapping Analysis for Storage Pest Sitophilus zeamais in Wheat

Quantitative trait loci(QTLs) associated with Sitophilus zeamais resistance were identified using a population(127 re-combined inbred lines) from wheat cross Chuannong 16×Chuanmai 42.In a stimulated storage environment,adult,larva,and egg of S.zeamais were artificially fed with wheat seeds harvested in 2008 and 2009,respectively.Five QTLs located on chromosomes 3B,2D,3D,and 4B were detected with phenotypic contributions of 10.2%,8.5%,8.3%,8.5%,and 11.3%,respectively.The QTLs lo-cated between Xbarc6 and Xgwm112 on chromosome 3D were identified in seeds from both growing years,which explained 8.3-8.5% of the phenotypic variance.The positive allele on this locus was from parent Chuannong 16.

Molecular mapping of quantitative trait loci for grain chalkiness in rice (Oryza sativaL.)

Chalkiness of rice grain is an important but undesirable quality component, which has a profound influence on milling, cooking and eating qualities. Therefore, it is one of the key factors which determine the market value of rice grains. In this study, QTL mapping to determine the genomic regions governing percent grain with white core (PGWC) and chalkiness score (CS) was conducted using a population of 310 RILs, generated from the cross Pusa 1266/Jaya. Both the parents were extremely contrasting with Pusa 1266 with fully chalky and Jaya with translucent grains. RILs were evaluated at IARI, New Delhi during Kharif 2008 and 2009 and at RBGRC, Aduthurai during Rabi 2009–10. Several QTL signals could be detected by single marker analysis. Among them, two QTLs, one each for PGWC and CS, were prominently detected by composite interval mapping between a marker interval RM 6273-RM204 on the short arm of chromosome 6.The QTL for PGWC, qPGWC6 was consistently detected during all the three seasons, explaining a phenotypic variation of 17.75%, 18.79% and 12.20% respectively. Similarly, the QTL for CS, qCS6 was also consistent across three seasons, accounting for a phenotypic variation of 24.3%, 24.75% and 24.03% respectively. Co-localization of both these QTLs may be representing a single genomic region, strongly implying the presence of Wxb locus in contributing to grain chalkiness of Pusa1266. The positive allele for the reduced grain chalkiness was contributed by Jaya. These results will be useful in fine mapping and validation of the identified QTLs.

Improving yield and quality traits of durum wheat by introgressing chromosome segments from hexaploid wheat

Durum wheat (Triticum turgidum durum; 2n = 4x = 28; genome AABB) has long been an important food resource for human diets. The projected increase of the world's population to 9.1 billion by 2050 has highlighted the importance and urgency for improving the yield and quality performance of durum wheat. A backcrossed population, which was derived from the durum wheat variety 'Bellaroi' (recurrent parent) and the hexaploid genotype 'CSCR6' (donor parent), was used to investigate the feasibility of improving yield- and quality-related traits of durum wheat by introgressing chromosome fragments from hexaploid wheat. The population means for grain protein content, gluten content, spike length, and spikelet number were improved compared with those of the recurrent parent 'Bellaroi'. A small proportion of the backcross population lines showed significant improvements in spike length and spikelet number compared with the recurrent parent 'Bellaroi'. Some loci with significant effects for plant height, spike length, spikelet number, and thousand-grain weight were identified. Several of these loci affected more than one trait. These results showed that the introgression of chromosome fragments from 'CSCR6' into the durum genetic background could be an effective method for improving yield and quality traits of durum wheat. In addition, the loci showing significant effects on desired traits in this study could be fine mapped using an F2 population obtained by backcrossing the lines that carry the positive allele(s) with the recurrent parent.

Genetic Analysis of Carotenoids Content in Red Pepper (Capsicum annuum L.) Fruit using Complete Diallel Cross

Regarding carotenoids content, the genetic basis, heritability and combining ability in six red pepper inbred lines were investigated using full diallel crosses. Both additive and non-additive gene actions govern inheritance of carotenoids content. The mean square of array through variance and covariance analysis (Wr-Vr) was insignificant, which suggest that inbred lines involved in diallel cross may have no epistatic effects. The Vr/Wr graph revealed the influence of partial dominant gene action towards low carotenoids content and the absence of non-allelic interaction. The H2 component was smaller than the H1 and the [H2/4H1] component was 0.187 less than 0.25, indicating unequal proportion of positive and negative alleles in the parents. The estimates of broad and narrow sense heritability for carotenoids content were 0.956 and 0.832, respectively. The variance of general combining ability (GCA) was relatively higher than that of specific combining ability (SCA), which implied that the additive gene effects were predominant as compared to both dominant and epistatic effects for the accumulation of carotenoids in this genetic population. The values of GCA of ``62024L1`` and ``62067L2`` were higher than those of the other parents. These 2 inbred lines, therefore, can be considered as useful breeding materials to enhance fruit carotenoids content in other red pepper varieties.

Molecular Breeding to Improve Salt Tolerance of Rice (Oryza sativa L.) in the Red River Delta of Vietnam

Rice is a stable food in Vietnam and plays a key role in the economy of the country. However, the production and the cultivating areas are adversely affected from the threats of devastation caused by the rise of sea level. Using marker-assisted backcrossing (MABC) to develop a new salt tolerance rice cultivar is one of the feasible methods to cope with these devastating changes. To improve rice salt tolerance in BT7 cultivar, FL478 was used as a donor parent to introgress the Saltol QTL conferring salt tolerance into BT7. Three backcrosses were conducted and successfully transferred positive alleles of Saltol from FL478 into BT7. The plants numbers IL-30 and IL-32 in BC3F1 population expected recurrent genome recovery of up to 99.2% and 100%, respectively. These selected lines that carried the Saltol alleles were screened in field for their agronomic traits. All improved lines had Saltol allele similar to the donor parent FL478, whereas their agronomic performances were the same as the original BT7. We show here the success of improving rice salt tolerance by MABC and the high efficiency of selection in early generations. In the present study, MABC has accelerated the development of superior qualities in the genetic background of BT7.

Genetic Analysis and QTL Mapping of Large Flag Leaf Angle Trait in Japonica Rice

Genetic segregation analysis for flag leaf angle was conducted using six generations of P1, P2, F1, B1, B2 and F2 derived from a cross of 863B (a maintainer line of japonica rice) and A7444 (a germplasm with large flag leaf angle). Genotypes and phenotypes of flag leaf angle were investigated in 863B (P1), A7444 (P2) and 141 plants in BC1F1 (863B/A7444//863B) population. An SSR genetic linkage map was constructed and QTLs for flag leaf angle were detected. The genetic map containing 79 information loci was constructed, which covers a total distance of 441.6 cM, averaging 5.6 cM between two neighboring loci. Results showed that the trait was controlled by two major genes plus polygene and the major genes were more important. Fifteen markers showed highly significant correlations with flag leaf angle based on single marker regression analysis. Two QTLs (qFLA2 and qFLA8) for flag leaf angle were detected by both composite interval method in software WinQTLCart 2.5 and composite interval method based on mixed linear model in QTL Network 2.0. The qFLA2 explained 10.50% and 13.28% of phenotypic variation, respectively, and was located at the interval of RM300 and RM145 on the short arm of chromosome 2. The qFLA8 explained 9.59% and 7.64% of phenotypic variation, respectively, and was located at the interval flanking RM6215 and RM8265 on the long arm of chromosome 8. The positive alleles at the two QTLs were both contributed from A7444.