Positive Alleles Research Articles

Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits.

Green Revolution (GR) rice varieties are high yielding but typically drought sensitive. This is partly due to the tight linkage between the loci governing plant height and drought tolerance. This linkage is illustrated here through characterization of qDTY1.1, a QTL for grain yield under drought that co-segregates with the GR gene sd1 for semi-dwarf plant height. We report that the loss of the qDTY1.1 allele during the GR was due to its tight linkage in repulsion with the sd1 allele. Other drought-yield QTLs (qDTY) also showed tight linkage with traits rejected in GR varieties. Genetic diversity analysis for 11 different qDTY regions grouped GR varieties separately from traditional drought-tolerant varieties, and showed lower frequency of drought tolerance alleles. The increased understanding and breaking of the linkage between drought tolerance and undesirable traits has led to the development of high-yielding drought-tolerant dwarf lines with positive qDTY alleles and provides new hope for extending the benefits of the GR to drought-prone rice-growing regions.

CYP2D6 Genotype and Risk of Recurrence in Tamoxifen Treated Breast Cancer Patients

Despite consistent pharmacogenetic effects of CYP2D6 on tamoxifen exposure, there is considerable controversy regarding the validity of CYP2D6 as a predictor of tamoxifen outcome. Understanding the current state of evidence in this area and its limitations is important for the care of patients who require endocrine therapy for breast cancer. A total of 101 patients with breast cancer who received tamoxifen therapy for at least 3 years, were genotyped for common alleles of the CYP2D6 gene by nested-PCR and restriction fragment length polymorphism PCR. Patients were classified as extensive or poor metabolizers (PM) based on CYP2D6*4 alleles in 3 different groups according to the menopause, Her2-neu status, and stage 3. The mean age of the patients with the disease recurrence was 50.8±6.4 and in non recurrent patients was 48.2±6.8. In this study 63.3% (n=64) patients were extensive metabolizers and 36.6% (n=37) were poor metabolizers. Sixty four of the 101 patients (63.3%) were Her2-neu positive. For tamoxifen- treated patients, no statistically significant difference in rate of recurrence observed between CYP2D6 metabolic variants in stage 3 and post-menopausal patients. However, there was a significant association between CYP2D6 genotype and recurrence in tamoxifen-treated Her2-neu positive patients. Compared with other women with breast cancer, those with Her2-neu positive breast cancer and extensive metabolizer alleles had a decreased likelihood of recurrence. This study for the first time demonstrated significant effects of CYP2D6 extensive metabolizer alleles on risk of recurrence in Her2-neu positive breast cancer patients receiving adjuvant tamoxifen therapy. Therefore, CYP2D6 metabolism, as measured by genetic variation, can be a predictor of breast cancer outcome in Her2-neu positive women receiving tamoxifen.

Diverse regulatory factors associate with flowering time and yield responses in winter-type Brassica napus.

BackgroundFlowering time, plant height and seed yield are strongly influenced by climatic and day-length adaptation in crop plants. To investigate these traits under highly diverse field conditions in the important oilseed crop Brassica napus, we performed a genome-wide association study using data from diverse agroecological environments spanning three continents.MethodsA total of 158 European winter-type B.napus inbred lines were genotyped with 21,623 unique, single-locus single-nucleotide polymorphism (SNP) markers using the Brassica 60 K-SNP Illumina® Infinium consortium array. Phenotypic associations were calculated in the panel over the years 2010–2012 for flowering time, plant height and seed yield in 5 highly diverse locations in Germany, China and Chile, adding up to 11 diverse environments in total.ResultsWe identified 101 genome regions associating with the onset of flowering, 69 with plant height, 36 with seed yield and 68 cross-trait regions with potential adaptive value. Within these regions, B.napus orthologs for a number of candidate adaptation genes were detected, including central circadian clock components like CIRCADIAN CLOCK- ASSOCIATED 1 (Bna.CCA1) and the important flowering-time regulators FLOWERING LOCUS T (Bna.FT) and FRUITFUL (Bna.FUL).DiscussionGene ontology (GO) enrichment analysis of candidate regions suggested that selection of genes involved in post-transcriptional and epigenetic regulation of flowering time may play a potential role in adaptation of B. napus to highly divergent environments. The classical flowering time regulators Bna.FLC and Bna.CO were not found among the candidate regions, although both show functional variation. Allelic effects were additive for plant height and yield, but not for flowering time. The scarcity of positive minor alleles for yield in this breeding pool points to a lack of diversity for adaptation that could restrict yield gain in the face of environmental change.ConclusionsOur study provides a valuable framework to further improve the adaptability and yield stability of this recent allopolyploid crop under changing environments. The results suggest that flowering time regulation within an adapted B. napus breeding pool is driven by a high number of small modulating processes rather than major transcription factors like Bna.CO. In contrast, yield regulation appears highly parallel, therefore yield could be increased by pyramiding positively associated haplotypes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1950-1) contains supplementary material, which is available to authorized users.

Abstract 4925: Liquid biopsy using the ion AmpliSeq v2 cancer panel

Abstract Introduction: Plasma cell-free circulating tumor DNA (ctDNA) has the potential to serve as a noninvasive surrogate to determine tumor genotype and monitor treatment response. Here we report the analytical validation of the Ion AmpliSeq v2 Cancer Panel (ACP) in plasma ctDNA samples. Methods: Mutations were assessed using the ACP, designed to survey 2800 mutations in 50 cancer-related genes. TruQ reference standards were used to determine LOD. Healthy donor and cancer patient plasma samples were used for other studies. Eight libraries were barcoded and sequenced with PGM sequencing 200 kit v2 on a 318 v2 chip. The sequencing data were analyzed with a combination of Torrent Suite 3.4.2, VarScan, our proprietary analysis pipeline and IGV. The background noise level of hotspot nt positions was calculated from multiple runs of known wild type DNA. In order to increase the sensitivity of the assay to detect low-level mutation, a custom program was developed to detect variants clearly different from background noise (95% confidence) and not reported by the two variant callers. PCR methods were used for concordance testing. Results: The performance characteristics of the AmpliSeq v2 Cancer Panel were demonstrated in 1) Minimum DNA input and LOD: With 10 ng DNA input, 43/43 and 42/43 expected mutations were detected at 2.5% or 1%, respectively. With 1 ng DNA input, 42/43 and 40/43 expected mutations were detected at 2.5% and 1%, respectively. 2) Coverage: The mean library coverage for 40 plasma libraries was 2912x with only 5 non-critical regions below 250x coverage. 3) Baseline error rate: 95% of 2290 hot-spots for SBS showed <0.5% background error frequency assessed in 10 healthy control ctDNA samples. The mean background error frequency plus two folds of SD falls below 0.5% for 91% of SBS hot-spots. 4)Precision: All mutations expected for TruQ6 were detected in 4 independent runs at observed allele frequencies with 0.6% mean SD and 0.1% mean deviation from the true value. A 2% TP53 mutation R174W was reproducibly detected in a lung cancer plasma sample in 2 independent runs. 5) Concordance study: Consistent results were observed for 3 positive (Allele Freq 40%, 3% and 0.2%, respectively) and 3 negative melanoma plasma samples previously genotyped by AS-PCR for Braf V600E/K mutations. Additional cancer patient ctDNA samples are being assessed for concordance in the detection of other mutations. Conclusions: The ACP offers a useful tool for comprehensive somatic mutation profiling in ctDNA. The limit of detection is 1-2% mutation frequency for most mutations with slight variation across different nucleotide positions. The low concentration of ctDNA obtained from plasma samples can present a challenge. Less than 10 ng DNA input may result in allele drop out for low level mutations due to the inefficient amplification of multiplex PCR compared with PCR methods using a short length single amplicon. Higher DNA input to rescue allele drop-out is under evaluation. Citation Format: WeiHua Liu, Zhenyu Yan, Candice L. Horn, Fabio Nunes, Steven M. Bray, Philip J. Ebert, Peng Fang, Jennifer Biroschak, Cindy Spittle, Chad Galderisi, Jin Li. Liquid biopsy using the ion AmpliSeq v2 cancer panel. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4925. doi:10.1158/1538-7445.AM2015-4925

Gender differences in risk factors for transition from mild cognitive impairment to Alzheimer’s disease: A CREDOS study

BackgroundWomen are subject to a disproportionate burden from Alzheimer’s disease (AD) and sex differences exist in treatment response and prognosis of the disease. Yet gender-specific risk factors have not been widely studied. We aimed to investigate gender-specific risk factors for AD in subjects with mild cognitive impairment (MCI). MethodsParticipants (n=294) with MCI were recruited from a nationwide, prospective cohort study of dementia and were followed for a median (range) of 13.8 (6.0–36.0) months. Sex-stratified associations of progression to AD with baseline characteristics were explored. ResultsSeventy-four individuals (25.2%) developed incident dementia (67AD) during follow-up. Significant risk factors for probable AD differed by sex. In men, the significant risk factors were severe periventricular white matter hyperintensities, and poorer global cognitive function. In women, older age, clinically significant depressive symptoms at baseline, and positive APOE ε4 alleles were the significant risk factors. ConclusionsRisk factors for progression from MCI to probable AD differed in men and women. These results may translate to gender-specific preventative or therapeutic strategies for patients with MCI.

Impact of the D genome and quantitative trait loci on quantitative traits in a spring durum by spring bread wheat cross.

The impact of the D genome and QTL in the A and B genomes on agronomic performance of hexaploid wheat and tetraploid durum was determined using novel recombinant inbred line populations derived from interploid crosses. Genetic differences between common hexaploid (6X) bread wheat (Triticum aestivum, 2n = 6x = 42, genome, AABBDD) and tetraploid (4X) durum wheat (T. turgidum subsp. durum, 2n = 4x = 28, genome, AABB) may exist due to effects of the D genome and allelic differences at loci in the A and B genomes. Previous work allowed identification of a 6X by 4X cross combination that resulted in a large number of fertile recombinant progeny at both ploidy levels. In this study, interspecific recombinant inbred line populations at both 4X and 6X ploidy with 88 and 117 individuals, respectively, were developed from a cross between Choteau spring wheat (6X) and Mountrail durum wheat (4X). The presence of the D genome in the 6X population resulted in increased yield, tiller number, kernel weight, and kernel size, as well as a decrease in stem solidness, test weight and seed per spike. Similar results were found with a second RIL population containing 152 lines from 18 additional 6X by 4X crosses. Several QTL for agronomic and quality traits were identified in both the 4X and 6X populations. Although negatively impacted by the lack of the D genome, kernel weight in Mountrail (4X) was higher than Choteau (6X) due to positive alleles from Mountrail on chromosomes 3B and 7A. These and other favorable alleles may be useful for introgression between ploidy levels.

Single nucleotide polymorphism markers linked to QTL for wheat yield traits

Continuous improvement in grain yield is one of the major challenges for wheat (Triticum aestivum L.) breeding worldwide. This study characterized quantitative trait loci (QTL) underlying wheat grain yield and its components using a high-density genetic linkage map developed from a recombinant inbred line (RIL) population derived from ‘Ning7840’ × ‘Clark’. The map consisted of 594 single nucleotide polymorphism and 404 simple sequence repeat markers covering a genetic distance of 4225.7 cM. The RIL population was evaluated for grain yield (GY), spike number per m2 (SNPM), kernel number per spike (KNPS), and thousand-kernel weight (TKW) in three Oklahoma locations from 2001 to 2003. A total of 29 additive QTL (eight for GY, two for SNPM, five for KNPS, and 14 for TKW) were mapped on 13 chromosomes. Eight pairs of epistatic QTL were detected for different yield components: four for GY, two for KNPS, and two for TKW. Four additive QTL, including two for GY and two for KNPS, showed additive × environment interactions. QTL that were repeatable in multiple environments were identified for all traits except SNPM. Positive alleles were dispersed between the two parents for all traits, with ‘Clark’ contributing slightly more. Seven pleiotropic loci were co-localized for at least two traits. Interestingly, all co-localized loci overlapped for TKW, and four of them overlapped for GY. Thus, selecting QTL for TKW may simultaneously select for or against yield or other yield components in breeding.

Estimates of genetic parameters for grain yield, agro-morphological traits and quality attributes in bread wheat (Triticum aestivum)

A study for estimating genetic parameters was carried out by involving 10 parents and their 45 F1's planted in randomized block design (RBD) having three replications revealed significant variance for all the characters under study. The analysis of genetic components showed that significant additive and dominant components for all the traits. Positive and significant value of "F" for yield and quality components in F1 crosses indicated the preponderance of dominant and positive genes in the parents. The estimates of h2 were found highly significant for number of productive tillers/ plant, flag leaf area, spike length, spikelets/ spike, biological yield/ plant, grain yield/ plant, harvest index, ash content and gluten content, whereas, non-significant values were reported for rest of the traits. The value of (H2/4H1) for all the traits indicated the asymmetrical distribution of positive and negative alleles among the parents. The proportion of dominant and recessive genes indicated presence of dominant alleles in the parents for these traits. The ratio of h2/H21 generation revealed that more than one major gene group was responsible for controlling these traits. Estimates of SCA effects revealed that the best cross combinations namely; DBW 58/ HD 2687, DBW 58/ DBW 17, PBW 590/HD 2687, PBW 373/DBW 17, PBW 373/RAJ 3765, HD 2687/WH 711, MP 1236/PBW 373, MP 1236/HD 2687, MP 1236/PBW 590, PBW 550/HD 2687 and PBW 550/DBW 17 for respective yield components and quality traits may be exploited through heterosis breeding programme to improve these traits in wheat (Triticum aestivum L.). It may be concluded from the present investigation that these parental lines can be used as donors for improving both components in future by following bi-parental mating and diallel selective mating system could be the best breeding method in early segregating generations for improvement in these traits.

Marker-assisted breeding for transgressive seed protein content in soybean [Glycine max (L.) Merr

After two cycles of marker-assisted breeding on three loci, lines with transgressive segregation of 8.22-9.32 % protein content were developed based on four original soybean parents with 35.35-44.83 % protein content. Marker-assisted breeding has been an innovative approach in conventional breeding, which is to be further demonstrated, especially for quantitative traits. A study on continuous transgressive breeding for seed protein content (SPC) in soybean using marker-assisted procedures is reported here. The SPC of the recombinant inbred line (RIL) population XG varied in 38.04-47.54 % under five environments with P 1 of 35.35 %, P 2 of 44.34 % and total heritability of 89.11 %. A transgressive segregant XG30 with SPC 45.53 % was selected for further improvement. The linkage mapping of XG showed its genetic constitution composed of five additive QTL (32.16 % of phenotypic variation or PV) and two pairs of epistatic QTL (2.96 % PV) using 400 SSR markers with the remnant heritability 53.99 % attributed to the undetected collective of minor QTL. Another transgressive segregant WT133 with SPC 48.39 % was selected from the RIL population WT (44.83 % SPC for both parents). XG30 and WT133 were genotyped on the three major additive QTL (Prot-08-1, Prot-14-1 and Prot-19-2) as A 2 A 2 B 2 B 2 L 1 L 1 and A 1 A 1 B 1 B 1 L 2 L 2 , respectively. From WT133×XG30, surprising transgressive progenies were obtained, among which the recombinants with all three positive alleles A 2 _B 2 _L 2 _ performed the highest SPC, especially that of Prot-08-1. The five F 2-derived superior families showed their means higher than the high parent value in F 2:3 and F 2:4 and more transgressive effect in F 2:5:6, with the highest as high as 54.15 %, or 4.82 and 9.32 % more than WT133 and its original high parent, respectively. This study demonstrated the efficiency of marker-assisted procedure in breeding for transgressive segregation of quantitative trait.

New QTL alleles for quality-related traits in spring wheat revealed by RIL population derived from supernumerary × non-supernumerary spikelet genotypes.

A population developed from an exotic line with supernumerary spikelets was genetically dissected for eight quality traits, discovering new genes/alleles with potential use in wheat breeding programs. Identifying new QTLs and alleles in exotic germplasm is paramount for further improvement of quality traits in wheat. In the present study, an RIL population developed from a cross of an elite wheat line (WCB414) and an exotic genotype with supernumerary spikelets (SS) was used to identify QTLs and new alleles for eight quality traits. Composite interval mapping for 1,000 kernels weight (TKW), kernel volume weight (KVW), grain protein content (GPC), percent of flour extraction (FE) and four mixograph-related traits identified a total of 69 QTLs including 19 stable QTLs. These QTLs were located on 18 different chromosomes (except 4D, 5D, and 6D). Thirteen of these QTLs explained more than 15% of phenotypic variation (PV) and were considered as major QTLs. In this study, we identified 11 QTLs for TKW (R (2) = 7.2-17.1 %), 10 for KVW (R (2) = 6.7-22.5%), 11 for GPC (R (2) = 4.7-16.9%), 6 for FE (R (2) = 4.8-19%) and 31 for mixograph-related traits (R (2) = 3.2-41.2%). In this population, several previously identified QTLs for SS, nine spike-related and ten agronomic traits were co-located with the quality QTLs, suggesting pleiotropic effects or close linkage among loci. The traits GPC and mixogram-related traits were positively correlated with SS. Indeed, several loci for quality traits were co-located with QTL for SS. The exotic parent contributed positive alleles that increased PV of the traits at 56% of loci demonstrating the suitability of germplasm with SS to improve quality traits in wheat.

Multiplex genotyping of cytokine gene SNPs using fluorescence bead array.

Single nucleotide polymorphisms (SNPs) of genes that affect cytokine production and function are known to influence the susceptibility and progression of immune-related conditions such as infection, autoimmune diseases, transplantation, and cancer. We established a multiplex genotyping method to analyze the SNPs of cytokine genes by combining the multiplex PCR and bead array platform. Thirteen cytokine gene regions, including 20 SNPs, were amplified, and allele-specific primer extension was performed in a single tube. High-quality allele-specific primers were selected for signals greater than 1000 median fluorescence intensity (MFI) for positive alleles, and less than 500 MFI for negative alleles. To select and improve the extension primers, modifications for the reverse direction, length or refractory were performed. 24 primers in the forward or reverse direction step and 12 primers in length or refractory modifications were selected and showed high concordance with results by nucleotide sequencing. Among the 13 candidate cytokine genes, the SNPs of 12 cytokine genes, including IL-1α, IL-1R, IL-1RA, IL-1β, IL-2, IL-4, IL-4Rα, IL-6, IL-10, IL-12, TGF-β1, and TNF-α, were successfully defined with the selected allele-specific primers in healthy Korean subjects. Our genotyping system provides a fast and accurate detection for SNPs of multiple cytokine genes to investigate their association with immune-related diseases and transplantation outcomes.

Mapping quantitative trait loci determining seed longevity in tobacco (Nicotiana tabacum L.)

Seed longevity is a crucial issue for germplasm conservation and seed marketing. This trait is determined not only by environmental conditions, but also by genetic factors. Molecular mapping of responsible loci has been performed with several crops, but not with tobacco (Nicotianatabacum L.). In the present study, we investigate 122 recombinant inbred lines derived from a cross between the cultivars Florida 301 and Hicks. Four germination-related traits were studied by examining seeds either untreated or after controlled deterioration (CD): total germination (TG, %), normal germination (%), time to reach 50 % of TG (h), and the area under the curve after 200 h of germination. Whereas Hicks exhibited high germination percentage and speed in untreated (fresh) seeds, Florida 301 seems to withstand the CD treatment better, having increased seed longevity. In total, four genomic regions located on four different linkage groups (LGs) were identified to be associated with the selected traits. Positive alleles for the individual traits were contributed by both parents. A major quantitative trait locus (QTL) for high percentage TG located on LG 8/18 appeared in both control and deteriorated seeds and was contributed by Hicks. In contrast, Florida 301 donated a favorable allele for germination speed on LG seven after CD only. The position of this locus compared well with a QTL detected in the same population, in a former study examining resistance against the black shank disease caused by Phytophthora nicotianae). The effects of environmental growing conditions of the mother plants on seed longevity are discussed.

FLT3 and NPM1 mutations in acute myeloid leukemia (AML) with double trisomy of chromosomes 8 and 21

Aim Characterisation of AML by cytogenetics and molecular genetics. Patient history A 60-year-old female with previous melanoma and squamous cell carcinoma presented with 60% blasts in peripheral blood and > 70% blasts in bone marrow. Flow cytometry was positive for CD13, CD33, CD117 and HLA-DR, but lacked CD34 and aberrant CD7 expression. These results are consistent with AML. Methods Karyotyping, fluorescence in situ hybridisation (FISH) and mutation analysis of FLT3 and NPM1. Results and discussion A 48, XX,+ 8,+ 21 karyotype was found and FISH confirmed. NPM-1 was positive and FLT3-ITD mutant allele burden 31.7%. The significance of double trisomy 8 and 21 in AML with FLT3-ITD and NPM1 mutations is unclear. However, trisomy 8 or 21 as sole abnormalities is associated with intermediate to poor prognosis and adversely affected by age. NPM1 mutations usually have favourable outcome, however the poor prognosis of FLT3-ITD overrides NPM1 risk status. Overall these findings appear to indicate an unfavourable outcome.

Quantitative trait loci underlying the adhesion of Azospirillum brasilense cells to wheat roots

The capacity to adhere Azospirillum brasilense cells on the seedling root is a variable trait in wheat varieties (Triticum aestivum L.). The parents of a CIMMYT bread wheat mapping population derived from the cross cv. Opata × synthetic hexaploid line WSHD67.2 (257) contrasted for this trait, providing an opportunity to determine its genetic basis. The capacity to adhere effectively was shown by 32 % of the mapping population individuals. A genetic map was constructed using 157 informative microsatellite loci and 1,356 SNP loci. The resulting quantitative trait loci (QTL) analysis identified four chromosomes as harboring loci associated with adhesion. Chromosome 1A was the site of both a major (LOD >3) and a minor (LOD 2–3) QTL, while the remaining four minor loci mapped to chromosomes 2D, 5A and 6B (two loci). QAdh.uabcs-1A.2 explained 8.6 % of the phenotypic variance and the full set of QTL explained 23.1 %. The source of the positive allele of QAdh.uabcs-1A.2 was cv. Opata. The recognition that adherence has a genetic component has consequences for the use of biofertilizers, and opens the way for breeding for improved levels of A. brasilense adherence.

Genomic regions associated with grain yield under drought stress in wheat (Triticum aestivum L.)

Water deficit stress (WDS) is a serious constraint to wheat productivity in rain-fed and limited irrigation environments. Identifying genomic regions responsible for grain yield (GY) under WDS will aid in understanding the genetics of drought tolerance (DT) and development of DT cultivars. A population of 206 recombinant inbred lines derived from WL711/C306 was phenotyped for GY and related traits under water deficit and irrigated conditions in seven different environments to identify genomic regions associated with eleven yield related traits. Both the parents contributed positive alleles for the traits studied. A novel genomic region for GY under WDS, qGYWD.3B.1 was detected on chromosome 3BS of wheat. The yield enhancing allele under drought stress at this locus was contributed by DT parent C306. This genomic region explained 18.7 % of phenotypic variation for GY under WDS and co-located with genomic regions for GY components. Another novel, consistent genomic region for GY under WDS, qGYWD.3B.2 explained 19.6 % of phenotypic variation with positive allele coming from drought susceptible parent WL711. A novel genomic region for drought susceptibility index for GY, qDSIGY.4A.1 was consistently detected in six of seven environments explaining 15.6 % of phenotypic variation. Other important genomic regions for GY and biomass under WDS were mapped on chromosomes 7BL and 6AS, respectively. Fine mapping of the major QTLs on chromosome 3BS will enable identification of robust markers and candidate genes for marker-assisted breeding for DT in wheat.

IMPROVEMENT OF EARLY MATURITY IN RICE VARIETY BY MARKER ASSISTED BACKCROSS BREEDING OF Hd2 GENE

Early-maturing and high-yielding rice variety is very useful for increasing rice production in Indonesia. The aim of this research was to develop new lines of Indonesian rice containing Hd2 gene using Code variety as a recipient parent and Nipponbare variety as a donor parent through targetted MAB approach using RM1362 and RM7601 in chromosom 7 for foreground selection. After two generations of backcrossing, the positive alleles of Hd2 gene from Nipponbare had successfully trans-ferred into Code. The plant number CdNp_29 in BC2F2 popula-tion had the highest genome recovery of 82.7%. The twelve BC2F3 plants were selected for self-pollination to generate BC2F4. These selected lines that carried the Hd2 gene were screened in the greenhouse for the evaluation of heading date and agronomic traits. All improved lines had Hd2 gene similar to the donor parent Nipponbare. The heading date of the breeding lines ranged from 73 to 89 days (Code 85 days) or fill the third criterion of rice maturity that is 103-104 days compared to Code of 116-119 days, whereas their agronomic performances were similar with that of Code. Application of MABc for im-proving rice early maturity has accelerated the development and selection in early generation of superior lines having genetic background of Code. It is expected that the newly developed lines of Code will be utilized to increase rice production in Indonesia.

IMPROVEMENT OF EARLY MATURITY IN RICE VARIETY BY MARKER ASSISTED BACKCROSS BREEDING OF Hd2 GENE

Early-maturing and high-yielding rice variety is very useful for increasing rice production in Indonesia. The aim of this research was to develop new lines of Indonesian rice containing Hd2 gene using Code variety as a recipient parent and Nipponbare variety as a donor parent through targetted MAB approach using RM1362 and RM7601 in chromosom 7 for foreground selection. After two generations of backcrossing, the positive alleles of Hd2 gene from Nipponbare had successfully trans-ferred into Code. The plant number CdNp_29 in BC2F2 popula-tion had the highest genome recovery of 82.7%. The twelve BC2F3 plants were selected for self-pollination to generate BC2F4. These selected lines that carried the Hd2 gene were screened in the greenhouse for the evaluation of heading date and agronomic traits. All improved lines had Hd2 gene similar to the donor parent Nipponbare. The heading date of the breeding lines ranged from 73 to 89 days (Code 85 days) or fill the third criterion of rice maturity that is 103-104 days compared to Code of 116-119 days, whereas their agronomic performances were similar with that of Code. Application of MABc for im-proving rice early maturity has accelerated the development and selection in early generation of superior lines having genetic background of Code. It is expected that the newly developed lines of Code will be utilized to increase rice production in Indonesia.

Identification of QTLs Underlying Folate Content in Milled Rice

Understanding the genetic mechanism underlying folate biosynthesis and accumulation in rice would be beneficial for breeding high folate content varieties as a cost-effective approach to addressing widespread folate deficiency in developing countries. In this study, the inheritance of rice grain folate content was investigated in the Lemont/Teqing recombinant inbred lines and the Koshihikari/Kasalath//Koshihikari backcross inbred lines. 264 F12 recombinant inbred lines (RILs) and 182 BC1F10 backcross inbred lines (BILs) with their parents planted in randomized complete blocks with two replicates in 2010, and RILs harvested in 2008 were used for QTL detection using inclusive composite interval mapping (ICIM) method. In the RIL population, two QTLs, denoted by qQTF-3-1 and qQTF-3-2 (QTF, quantitative total folate), explaining 7.8% and 11.1-15.8% of the folate content variation were detected in one or two years, respectively. In the BIL population, a QTL, denoted by qQTF-3-3, was detected, explaining 25.3% of the variation in folate content. All the positive alleles for higher folate content were from the high-folate parents, i.e., Teqing and Kasalath. The known putative folate biosynthesis genes do not underlie the QTLs detected in this study and therefore may be novel loci affecting folate content in milled rice. QTLs identified in this study have potential value for marker assisted breeding for high-folate rice variety.

Genetic interactions matter more in less-optimal environments: a Focused Review of "Phenotype uniformity in combined-stress environments has a different genetic architecture than in single-stress treatments" (Makumburage and Stapleton, 2011).

An increase in the distribution of data points indicates the presence of genetic or environmental modifiers. Mapping of the genetic control of the spread of points, the uniformity, allows us to allocate genetic difference in point distribution to adjacent, cis effects or to independently segregating, trans genetic effects. Our genetic architecture-mapping experiment elucidated the “environmental context specificity” of modifiers, the number and effect size of positive and negative alleles important for uniformity in single and combined stress, and the extent of additivity in estimated allele effects in combined stress environments. We found no alleles for low uniformity in combined stress treatments in the maize mapping population we examined. The major advances in this research area since early 2011 have been in improved methods for modeling of distributions and means and detection of important loci. Double hierarchical general linear models and, more recently, a likelihood ratio formulation have been developed to better model and estimate the genetic and environmental effects in populations. These new methods have been applied to real data sets by the method authors and we now encourage additional development of the software and wider application of the methods. We also propose that simulations of genetic regulatory network models to examine differences in uniformity and systematic exploration of models using shared simulations across communities of researchers would be constructive avenues for developing further insight into the genetic mechanisms of variation control.

Haplotype Analysis on Chromosome 6p of Tumor Necrosis Factor Alpha, Vascular Endothelial Growth Factor A, and Interleukin-17F Alleles Associated With Corneal Transplant Rejection

ObjectiveThe aim of this work was to investigate single-nucleotide polymorphisms (SNPs) in multiple genes on chromosome 6p in corneal transplant recipients known to be at increased risk of failure through immunologic rejection (ie, “high-risk” corneal transplants). Tumor necrosis factor alpha (TNF-α) is a key immunoregulatory cytokine in the ocular environment, interacting with a variety of factors in a synergistic way and playing a crucial role in many stages of the inflammatory response. Vascular endothelial growth factor (VEGF) is one of the most important angiogenic factors, supporting both hemangiogenesis and lymphangiogenesis, both key in transplant tolerance and rejection. Interleukin-17 (IL-17) is a multifunctional cytokine produced by T-helper 17 cells, exerting specific effector functions during an immune response. Association of SNPs in all 3 genes with corneal transplant outcome was therefore investigated. MethodsThree hundred five corneal transplant recipients were followed for 3 years, and episodes of allograft rejection were recorded. With the use of patient DNA, 6 SNPs of 3 different genes on chromosome 6p were investigated. The TNF-α promoter SNP −308 G/A (rs1800629) was analyzed with the use of induced heteroduplex generation; 2 VEGF-A functional variants were analyzed, −2578 (rs699947) C/A and −1154 (rs1570360) G/A, with the use of Taqman genotyping assays; and 3 nonsynonymous IL-17F SNPs in exon 3 (negative strand), (rs2397084) A/G, (rs11465553) G/A, and (rs763780) A/G, were investigated with the use of direct sequencing. Haplotypes were inferred with the use of PHASE using positive strand alleles, and exact measures of association were determined with the use of Mid-P exact chi-square. ResultsSix common haplotypes were inferred, with the haplotype TNF-α (rs1800629), VEGF-A (rs699947), (rs1570360), IL-17F (rs763780), (rs11465553), and (rs2397084) ACGTCT having a significant association with corneal transplant rejection (odds ratio, 1.78; 95% confidence interval, 1.01–3.11; P = .04). ConclusionsThe results suggest that patients carrying a combination of SNPs for TNF-α, VEGF-A, and IL-17F of ACGTCT haplotype may have an increased risk of corneal allograft rejection compared with patients carrying other haplotypes.