Logarithm Of The Odds Research Articles

Fine Mapping of 6q23.1 Identifies TULP4 as Contributing to Clefts

Objective : The aim of this work was to fine-map the region 6q23.1, which obtained suggestive linkage signal (logarithm of the odds [LOD] score = 2.22 under a recessive model) to cleft lip with or without cleft palate (CL±P) in our previous genome-wide linkage scan to identify possible genetic variants that may contribute to CL±P. Design : We used densely spaced markers spanning the entire 6q23.1 region to test for association with CL±P in a family cohort sample. Setting : Clinical information and DNA samples were obtained from families in the Philippines at their homes or primary health care clinics. Participants : The study sample consisted of 477 subjects (224 females and 253 males), segregating isolated CL±P, from 72 living in the same area in the Philippines. Main Outcome Measure : Overtransmission of alleles to persons born with CL±P. Results : We found statistical evidence of association between a marker of TULP4 (rs651333) with CL±P (P = .00007). Conclusions : Our results further support the linkage results for the chromosome 6q region and reveal a novel candidate gene for CL±P.

Genome-wide significant linkage to IgG subclass responses against Plasmodium falciparum antigens on chromosomes 8p22-p21, 9q34 and 20q13.

A genome-wide scan was conducted for the levels of total immunoglobulin G (IgG) and IgG subclasses directed against Plasmodium falciparum antigens in an urban population living in Burkina Faso. Non-parametric multipoint linkage analysis provided three chromosomal regions with genome-wide significant evidence (logarithm of the odds (LOD) score >3.6), and five chromosomal regions with genome-wide suggestive evidence (LOD score >2.2). IgG3 levels were significantly linked to chromosomes 8p22-p21 and 20q13, whereas IgG4 levels were significantly linked to chromosome 9q34. In addition, we detected suggestive linkage of IgG1 levels to chromosomes 18p11-q12 and 18q12-q21, IgG4 levels to chromosomes 1p31 and 12q24 and IgG levels to chromosome 6p24-p21. Moreover, we genotyped genetic markers located within the regions of interest in a rural population living in Burkina Faso. We detected genome-wide significant and suggestive linkage results when combining the two study populations for chromosomes 1p31, 6p24-p21, 8p22-p21, 9q34, 12q24 and 20q13. Because high anti-parasite IgG3 and low anti-parasite IgG4 levels were associated with malaria resistance, the chromosomal regions linked to IgG3 and IgG4 levels are of special interest. Although the results should be confirmed in an independent population, they may provide new insights in understanding both the genetic control of IgG production and malaria resistance.

The value of ADC, T2 signal intensity, and a combination of both parameters to assess Gleason score and primary Gleason grades in patients with known prostate cancer.

The ability to non-invasively analyze tumor aggressiveness is an important predictor for individual treatment stratification and patient outcome in prostate cancer (PCA). To evaluate: (i) whether apparent diffusion coefficient (ADC), the T2 signal intensity (SI), and a combination of both parameters allow for an improved discrimination of Gleason Score (GS) ≥7 (intermediate and high risk) and GS <7 (low risk) in PCA; and (ii) whether ADC may distinguish between 3 + 4 and 4 + 3 PCA (primary Gleason grades [pGG]). Prostatectomy specimens of 66 patients (mean age, 63 ± 5.6 years; 104 PCA foci) with a preceding multiparametric 1.5 T endorectal coil magnetic resonance imaging (MRI) were included. ADC (b values = 0, 100, 400, 800 s/mm(2)), standardized T2 (T2s), and the ADC/T2s ratio were tested for correlation with GS applying multivariate analysis. ADC cutoff values were calculated for prediction of GS and pGG, and logarithm of the odds (LOGIT) was used to express the probability for GS and pGG. Diagnostic accuracy was assessed by ROC analysis. We found an almost linear negative relationship of ADC for GS ≥7 (P = 0.002). The effect of ADC for GS ≥7 (adjusted odds ratio = 0.995) was almost identical for peripheral and transition zone PCA (P = 0.013 and P < 0.001, respectively). ADC showed an AUC of 78.9% for discrimination between GS <7 and GS ≥7. An ADC cutoff of <1.005 × 10(-3 )mm(2)/s indicated a GS ≥7 (90.5% sensitivity, 62.5% specificity). Within the group of GS = 7 PCA, an ADC > 0.762 × 10(-3 )mm(2)/s indicated a pGG of3 (AUC = 69.6%). T2s and the ADC/T2s ratio do not provide additional information regarding prediction of GS. ADC values have a good discriminatory power to distinguish tumors with GS ≥7 from GS <7 and to predict pGG in GS = 7 PCA.

Dual-trait selection for ethanol consumption and withdrawal: genetic and transcriptional network effects.

Data from C57BL/6J (B6)×DBA/2J (D2) F2 intercrosses (B6xD2F2 ), standard and recombinant inbred strains, and heterogeneous stock mice indicate that a reciprocal (or inverse) genetic relationship exists between alcohol consumption and withdrawal severity. Furthermore, some genetic studies have detected reciprocal quantitative trait loci (QTLs) for these traits. We used a novel mouse model developed by simultaneous selection for both high alcohol consumption/low withdrawal and low alcohol consumption/high withdrawal and analyzed the gene expression and genome-wide genotypic differences. Randomly chosen third selected generation (S3 ) mice (N=24/sex/line), bred from a B6xD2F2 , were genotyped using the Mouse Universal Genotyping Array, which provided 2,760 informative markers. QTL analysis used a marker-by-marker strategy with the threshold for a significant log of the odds (LOD) set at 10. Gene expression in the ventral striatum was measured using the Illumina Mouse 8.2 array. Differential gene expression and the weighted gene co-expression network analysis (WGCNA) were implemented. Significant QTLs for consumption/withdrawal were detected on chromosomes (Chr) 2, 4, 9, and 12. A suggestive QTL mapped to Chr 6. Some of the QTLs overlapped with known QTLs mapped for 1 of the traits individually. One thousand seven hundred and forty-five transcripts were detected as being differentially expressed between the lines; there was some overlap with known withdrawal genes (e.g., Mpdz) located within QTL regions. WGCNA revealed several modules of co-expressed genes showing significant effects in both differential expression and intramodular connectivity; a module richly annotated with kinase-related annotations was most affected. Marked effects of selection on expression and network structure were detected. QTLs overlapping with differentially expressed genes on Chr 2 (distal) and 4 suggest that these are cis-eQTLs (Chr 2: Kif3b, Kcnq2; Chr 4: Mpdz, Snapc3). Other QTLs identified were on Chr 2 (proximal), 9, and 12. Network results point to involvement of kinase-related mechanisms and outline the need for further efforts such as interrogation of noncoding RNAs.

A missense mutation in the splicing factor gene DHX38 is associated with early-onset retinitis pigmentosa with macular coloboma

BackgroundRetinitis pigmentosa (RP) is the most frequent inherited retinal disease, which shows a relatively high incidence of the autosomal-recessive form in Pakistan.MethodsGenome-wide high-density single-nucleotide polymorphism (SNP) microarrays were used to...

Quantitative Trait Loci Mapping for Seed Calcium Content of Soybean

ABSTRACTCalcium content is one of the determining characteristics of seed texture affecting soyfood quality. Seed with higher calcium content tends to have harder texture, which is not desirable for certain soyfood such as natto. Molecular markers and quantitative trait loci (QTL) for seed calcium will facilitate the development of elite cultivars with desired calcium content through marker assisted selection (MAS). The objectives of this study were to (i) identify new QTL and associated markers and (ii) confirm previously reported QTL for calcium content. A high calcium parent, PI 407818 B, was crossed with two low calcium parents, KS4303sp and PI 408052 C, creating two mapping populations with 120 and 124 progeny each. Mapping populations were screened with simple sequence repeat (SSR) markers and tested for calcium content. The F2:4 and F2:5 lines from the two populations were grown in a randomized complete block design (RCBD) with two replications, at two Arkansas locations in 2 yr. Composite interval mapping (CIM) for SSR markers revealed a novel QTL Ca5 for seed calcium content that is located approximately at 13cM and linked to Sat_290 and Satt115 on chromosome 18 with a logarithm of the odds (LOD) score of 2.7. Single marker analysis revealed 13 markers for seed calcium content that are stable across environments on chromosomes 1, 2, 5, 7, 8, 18, and 20. Previously reported markers linked to QTL Ca1 (chr. 8), Ca3, and Ca4 (chr. 7) were confirmed in both populations, while Ca2 (chr. 20) was confirmed only in the population derived from KS4303sp × PI 407818 B. These confirmed and newly identified QTL with associated markers offer a potential tool for MAS for calcium content.

Autosomal dominant partial epilepsy with auditory features: A new locus on chromosome 19q13.11–q13.31

To clinically and genetically characterize a large Brazilian family with autosomal dominant partial epilepsy with auditory features (ADPEAF) not related to leucine-rich, glioma-inactivated 1 (LGI1) gene. Seventy family members (four married-ins) participating in the study were assessed by a detailed clinical interview and a complete neurologic examination. Genetic mapping was conducted through autosome-wide single nucleotide polymorphism (SNP) genotyping and subsequent linkage analysis on 16 and haplotype analysis on 25 subjects, respectively. The pedigree comprised 15 affected members, of whom 11 were included in the study (male/female: 6/5; mean age 39.5 years). All but two (III:22 and IV:92) had focal seizures with auditory aura followed by secondary generalization in 44.4%. The mean age at onset of epilepsy seizures was 13.7 years. Initial autosome-wide SNP linkage analysis conducted on 12 subjects (8 affected) pointed to a single genomic region on chromosome 19 with a maximum multipoint logarithm of the odds (LOD) score of 2.60. Further refinement of this region through SNP and microsatellite genotyping on 16 subjects (11 affected) increased the LOD score to 3.41, thereby establishing 19q13.11-q13.31 as a novel ADPEAF locus. Haplotype analysis indicated that the underlying mutation is most likely located in a 9.74 Mb interval between markers D19S416 and D19S420. Sequence analysis of the most prominent candidate genes within this critical interval (SCN1B, LGI4, KCNK6, and LRFN1) did not reveal any mutation. This study disclosed a novel ADPEAF locus on chromosome 19q13.11-q13.31, contributing to future identification of a second dominant gene for this epileptic syndrome. A PowerPoint slide summarizing this article is available for download in the Supporting Information section here.

Evidence for linkage of migraine in Rolandic epilepsy to known 1q23 FHM2 and novel 17q22 genetic loci

Migraine headaches are a common comorbidity in Rolandic epilepsy (RE) and familial aggregation of migraine in RE families suggests a genetic basis not mediated by seizures. We performed a genome-wide linkage analysis of the migraine phenotype in 38 families with RE to localize potential genetic contribution, with a follow-up in an additional 21 families at linked loci. We used two-point and multipoint LOD (logarithm of the odds) score methods for linkage, maximized over genetic models. We found evidence of linkage to migraine at chromosome 17q12-22 [multipoint HLOD (heterogeneity LOD) 4.40, recessive, 99% penetrance], replicated in the second dataset (HLOD 2.61), and suggestive evidence at 1q23.1-23.2, centering over the FHM2 locus (two-point LOD 3.00 and MP HLOD 2.52). Sanger sequencing in 14 migraine-affected individuals found no coding mutations in the FHM2 gene ATP1A2. There was no evidence of pleiotropy for migraine and either reading or speech disorder, or the electroencephalographic endophenotype of RE when the affected definition was redefined as those with migraine or the comorbid phenotype, and pedigrees were reanalyzed for linkage. In summary, we report a novel migraine susceptibility locus at 17q12-22, and a second locus that may contribute to migraine in the general population at 1q23.1-23.2. Comorbid migraine in RE appears genetically influenced, but we did not obtain evidence that the identified susceptibility loci are consistent with pleiotropic effects on other comorbidities in RE. Loci identified here should be fine-mapped in individuals from RE families with migraine, and prioritized for analysis in other types of epilepsy-associated migraine.

Resistance to Oculimacula yallundae and Oculimacula acuformis is conferred by Pch2 in wheat

The recent report of a differential response of wheat lines containing the Pch2 gene to infection with the eyespot pathogens Oculimacula yallundae and O. acuformis has prompted this re‐examination of the response to these fungi by the recombinant lines used to map Pch2. Homozygous recombinant substitution lines (RSL) derived from the hybridization of Chinese Spring (CS) and the CS chromosome substitution line Cappelle Desprez 7A (CS/CD7A), previously evaluated for response to glucuronidase (GUS)‐transformed O. yallundae, were evaluated for response to infection with GUS‐transformed O. acuformis. Based on visual scores and on GUS expression level, which reflects fungal colonization of seedling plants, evidence of a quantitative trait locus (QTL) conferring resistance to O. acuformis was found in two separate growth chamber experiments (logarithm of the odds, LOD, = 2·7 and 6·7 at 305 and 289 cM, respectively) that was equivalent in location to that for resistance to O. yallundae (LOD = 13·2 and 11·4 at 289 and 304 cM, respectively). These results confirm that Pch2 confers some degree of resistance against both O. yallundae and O. acuformis under these conditions.

A novel genetic locus modulates infarct volume independently of the extent of collateral circulation

In the mouse model of permanent, middle cerebral artery occlusion, infarct volume varies widely across inbred strains but generally is inversely correlated with collateral vessel number. However, we also observed certain mouse strains that share similar collateral vessel anatomy but exhibit significantly different infarct volume. To identify genetic factors determining infarct volume in a collateral vessel-independent manner, we performed quantitative trait locus analysis on a F2 cross between C57BL/6J and C3H/HeJ strains. We mapped four novel loci (Civq4 through Civq7) that modulate infarct volume. Civq4, on chromosome 8, is the strongest locus (logarithm of the odds 9.8) that contributes 21% of the phenotypic variance of infarct volume in the cross. The Civq4 and Civq6 loci represent transgressive B6 alleles that render animals susceptible to larger infarcts. Based on genomic sequence and microarray analyses, we propose candidate genes for the Civq4 locus. By selecting inbred strains with similar collateral vessel anatomy but that vary significantly in infarct volume, we have mapped four loci determining infarct volume in a mouse model of ischemic stroke. Two of the loci appear to modulate infarct volume through a collateral vessel-independent mechanism. Based on strain-specific sequence variants and differences in transcript levels, Msr1 and Mtmr7 appear to be strong candidate genes for Civq4. Identifying the underlying genetic factors of these loci will elucidate the genetic architecture response to cerebral ischemia, shed new light on disease mechanisms of ischemic stroke, and identify potential therapeutic targets for clinical applications.

Susceptibility to lethal cerebral malaria is regulated by epistatic interaction between chromosome 4 (Berr6) and chromosome 1 (Berr7) loci in mice

In humans, cerebral malaria is a rare but often lethal complication of infection with Plasmodium parasites, the occurrence of which is influenced by complex genetic factors of the host. We used a mouse model of experimental cerebral malaria (ECM) with Plasmodium berghei ANKA to study genetic factors regulating appearance of neurological symptoms and associated lethality. In a genome-wide screen of N-ethyl-N-nitrosourea-mutagenized mice derived from C57BL/6J (B6) and 129S1/SvImJ (129) mouse strains, we detected a strong interaction between the genetic backgrounds of these strains, which modulates ECM resistance. We have mapped a major gene locus to central chromosome 4 (log of the odds (LOD) 6.7; 79.6-97.3 Mb), which we designate Berr8. [corrected]. B6 alleles at Berr6 are associated with resistance, and are inherited in a co-dominant fashion. In mice heterozygous for Berr6 B6/129 alleles, resistance to ECM is strongly modulated by a second locus, Berr7, that maps to the proximal portion of chromosome 1 (LOD 4.03; 41.4 Mb). 129 alleles at Berr7 are associated with ECM resistance in a dosage-dependent fashion. Results are discussed in view of the possible role of this two-locus system in susceptibility to unrelated inflammatory conditions in mice and humans.

Molecular polymorphism and linkage analysis in sweet passion fruit, an outcrossing species

AbstractOne of the current challenges of tropical fruit crop improvement is to incorporate molecular marker‐based approaches into conventional breeding programmes. This study was designed to build an integrated genetic map of the sweet passion fruit (Passiflora alata), a diploid (2n = 18) outcrossing species which is greatly appreciated forin naturaconsumption, and reported to inspire cosmetic and pharmaceutical companies to create plant‐derived compounds. With this in mind, a full‐sib family of 180 individuals was genotyped using different molecular marker types, such as amplified fragment length polymorphisms (AFLP), microsatellite‐AFLP (M‐AFLP), simple sequence repeats (SSR), resistance gene analogues (RGA) and target region amplification polymorphism (TRAP). On average, the rate of polymorphism between the parental genotypes was 20.3%. We also searched for single nucleotide polymorphisms (SNPs) in someAFLPbands and in seven gene fragments, and found oneSNPevery 87 bp. AllSNPswere biallelic and occurred most frequently in putative gene fragments (81.5%) rather than inAFLPbands (60.0%) analyzed. Excellent gel profiles were obtained allowing the recognition of all types of segregation expected for a progeny of an outcrossing species. Multipoint linkage analysis was performed usingOneMapsoftware, with logarithm of the odds (LOD) score ≥ 5.6 and recombination fraction &lt;0.5. The resulting integrated map consists of 549 markers, 2.0% of which fit a segregation ratio of 1:1:1:1, 1.3% a ratio of 1:2:1, 27.3% a ratio of 3:1 and 69.4% a ratio of 1:1. The map spanned a total of 2073.0 cM, with an average distance between adjacent markers of 3.8 cM. This is the first linkage study on sweet passion fruit and should prove useful for quantitative trait loci mapping.

A New Genetic Linkage Map of the Zygomycete Fungus Phycomyces blakesleeanus

Phycomyces blakesleeanus is a member of the subphylum Mucoromycotina. A genetic map was constructed from 121 progeny of a cross between two wild type isolates of P. blakesleeanus with 134 markers. The markers were mostly PCR-RFLPs. Markers were located on 46 scaffolds of the genome sequence, covering more than 97% of the genome. Analysis of the alleles in the progeny revealed nine or 12 linkage groups, depending on the log of the odds (LOD) score, across 1583.4 cM at LOD 5. The linkage groups were overlaid on previous mapping data from crosses between mutants, aided by new identification of the mutations in primary metabolism mutant strains. The molecular marker map, the phenotype map and the genome sequence are overall congruent, with some exceptions. The new genetic map provides a genome-wide estimate for recombination, with the average of 33.2 kb per cM. This frequency is one piece of evidence for meiosis during zygospore development in Mucoromycotina species. At the same time as meiosis, transmission of non-recombinant chromosomes is also evident in the mating process in Phycomyces. The new map provides scaffold ordering for the genome sequence and a platform upon which to identify the genes in mutants that are affected in traits of interest, such as carotene biosynthesis, phototropism or gravitropism, using positional cloning.

Quantitative trait loci associated to agronomic traits and yield components in a &amp;lt;i&amp;gt;Sorghum bicolor&amp;lt;/i&amp;gt; L. Moench RIL population cultivated under pre-flowering drought and well-watered conditions

The present study aims to identify QTL influencing agronomic traits and yield components under well-watered and pre-flowering drought stress conditions. One hundred F5 recombinant inbred lines (RIL) and the parental lines of a cross between a drought-tolerant and a susceptible line in a field experiment were carried out at Nong Lam University of Ho Chi Minh City, Vietnam. Drought stress was induced by withholding irrigation water from the plants at four weeks after sowing to flowering. Leaf area of the third leaf, stem diameter, plant height, days to heading, anthesis and maturity, panicle length, number of seeds per plant, hundred kernel weight and grain yield were measured. Plants were genotyped with 117 Diversity Arrays Technology (DArT) and eight expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers. Composite interval mapping was carried out on the traits and significant QTL were claimed at a logarithm of the odds (LOD) score >2.5. A total of 50 QTL were detected on nine chromosomes or 13 linkage groups, respectively. Six promising QTL regions with seven QTL for yield and agronomic traits especially related to pre-flowering drought tolerance were identified on chromosomes SBI-01, SBI-03, SBI-04, SBI-05 and SBI-07.

A variable age of onset segregation model for linkage analysis, with correction for ascertainment, applied to glioma.

We propose a 2-step model-based approach, with correction for ascertainment, to linkage analysis of a binary trait with variable age of onset and apply it to a set of multiplex pedigrees segregating for adult glioma. First, we fit segregation models by formulating the likelihood for a person to have a bivariate phenotype, affection status and age of onset, along with other covariates, and from these we estimate population trait allele frequencies and penetrance parameters as a function of age (N = 281 multiplex glioma pedigrees). Second, the best fitting models are used as trait models in multipoint linkage analysis (N = 74 informative multiplex glioma pedigrees). To correct for ascertainment, a prevalence constraint is used in the likelihood of the segregation models for all 281 pedigrees. Then the trait allele frequencies are reestimated for the pedigree founders of the subset of 74 pedigrees chosen for linkage analysis. Using the best-fitting segregation models in model-based multipoint linkage analysis, we identified 2 separate peaks on chromosome 17; the first agreed with a region identified by Shete and colleagues who used model-free affected-only linkage analysis, but with a narrowed peak: and the second agreed with a second region they found but had a larger maximum log of the odds (LOD). Our approach was able to narrow the linkage peak previously published for glioma. We provide a practical solution to model-based linkage analysis for disease affection status with variable age of onset for the kinds of pedigree data often collected for linkage analysis.

Genome-wide Linkage and Positional Association Study of Blood Pressure Response to Dietary Sodium Intervention

The authors conducted a genome-wide linkage scan and positional association analysis to identify the genetic determinants of salt sensitivity of blood pressure (BP) in a large family-based, dietary-feeding study. The dietary intervention was conducted among 1,906 participants in rural China (2003-2005). A 7-day low-sodium intervention was followed by a 7-day high-sodium intervention. Salt sensitivity was defined as BP responses to low- and high-sodium interventions. Signals of the logarithm of the odds to the base 10 (LOD ≥ 3) were detected at 33-42 centimorgans of chromosome 2 (2p24.3-2p24.1), with a maximum LOD score of 3.33 for diastolic blood pressure responses to high-sodium intervention. LOD scores were 2.35-2.91 for mean arterial pressure (MAP) and 0.80-1.49 for systolic blood pressure responses in this region, respectively. Correcting for multiple tests, single nucleotide polymorphism (SNP) rs11674786 (2.7 kilobases upstream of the family with sequence similarity 84, member A, gene (FAM84A)) in the linkage region was significantly associated with diastolic blood pressure (P = 0.0007) and MAP responses (P = 0.0007), and SNP rs16983422 (2.8 kilobases upstream of the visinin-like 1 gene (VSNL1)) was marginally associated with diastolic blood pressure (P = 0.005) and MAP responses (P = 0.005). An additive interaction between SNPs rs11674786 and rs16983422 was observed, with P = 7.00 × 10(-5) and P = 7.23 × 10(-5) for diastolic blood pressure and MAP responses, respectively. The authors concluded that genetic region 2p24.3-2p24.1 might harbor functional variants for the salt sensitivity of BP.

Identification of renin signaling as a blood pressure modifying mechanism in soluble guanylate cyclase α1-deficient mice

Male mice deficient in the α 1 subunit of soluble guanylate cyclase, a nitric oxide (NO) receptor, are hypertensive when on a 129S6 (S6) background (sGC α 1 - / - S 6 ) but not when on a C57BL/6 (B6) background (sGC α 1 - / - B 6 ) , suggesting that hypertension associated with sGCα 1 -deficiency is modulated by genetic factors. Genetic linkage analyses in 284 male F2 offspring from an sGC α 1 - / - S 6 X sGC α 1 - / - B 6 intercross (sGC α 1 - / - F 2 ) revealed a quantitative trait locus (QTL) on chromosome 1 that was linked to mean arterial pressure (MAP) with a maximal logarithm of the odds (LOD) score of 6.3. This region is syntenic with previously identified blood pressure-related QTLs in the human and rat genome and contains the genes coding for renin. Hypertension was associated with increased activity of the renin-angiotensin-aldosterone system (RAAS): plasma angiotensin II levels were higher in S6 mice than in B6 mice (of either genotype), and plasma aldosterone levels were greater in sGC α 1 - / - S 6 than in WT S6 mice. Renal function, as assessed by glomerular filtration rate, urinary volume and blood urea nitrogen, was similar in sGC α 1 - / - S 6 mice and in WT S6 mice. Inhibiting the RAAS normalized MAP and improved endothelium-dependent vasorelaxation in sGC α 1 - / - S 6 mice. These data identify the RAAS as a blood pressure-modifying signaling pathway in a setting of impaired NO-cGMP signaling. The finding that NO-cGMP and RAAS signaling (established pathways in the regulation of blood pressure) interact to regulate blood pressure, has great potential to advance our understanding of the etiology of human hypertension, and may help define genetically distinct subgroups of men and women with essential hypertension.

Mapping quantitative trait loci for kernel composition in almond

BackgroundAlmond breeding is increasingly taking into account kernel quality as a breeding objective. Information on the parameters to be considered in evaluating almond quality, such as protein and oil content, as well as oleic acid and tocopherol concentration, has been recently compiled. The genetic control of these traits has not yet been studied in almond, although this information would improve the efficiency of almond breeding programs.ResultsA map with 56 simple sequence repeat or microsatellite (SSR) markers was constructed for an almond population showing a wide range of variability for the chemical components of the almond kernel. A total of 12 putative quantitative trait loci (QTL) controlling these chemical traits have been detected in this analysis, corresponding to seven genomic regions of the eight almond linkage groups (LG). Some QTL were clustered in the same region or shared the same molecular markers, according to the correlations already found between the chemical traits. The logarithm of the odds (LOD) values for any given trait ranged from 2.12 to 4.87, explaining from 11.0 to 33.1 % of the phenotypic variance of the trait.ConclusionsThe results produced in the study offer the opportunity to include the new genetic information in almond breeding programs. Increases in the positive traits of kernel quality may be looked for simultaneously whenever they are genetically independent, even if they are negatively correlated. We have provided the first genetic framework for the chemical components of the almond kernel, with twelve QTL in agreement with the large number of genes controlling their metabolism.

Linkage analysis and mutation screening of candidate gene in a Han Nationality family with autosomal dominant retinitis pigmentosa

Background Retinitis pigmentosa (RP) has the genetic and phenotype heterogeneity.To determine the disease-causing gene is a foundation of gene therapy. Objective This study was to localize the pathogenic gene and screen the gene mutation associated with Han Nationality autosomal dominant retinitis pigmentosa (ADRP) in a Chinese family. Methods Twenty-one families enrolled this study,including 12 patients with ADRP and 9 individuals with normal phenotype.Perimetry,fundus examination,electrooculogram ( EOG ) and electroretinogram (ERG) were performed in 12 patients.Genetic linkage analysis was performed on the subjects in all known genetic loci related to ADRP with a panel of microsatellite markers.Subsequently,the mutation screening of rhodopsin gene was screened by direct DNA sequencing.This study was approved by Ethic Committee of Zhongnan Hospital of Wuhan University.Informed consent was obtained from each subject. Results The fundus appearance of the proband was in accordance with the ADRP,and the EOG and ERG showed undetectable.Contractive visual field also was exhibited in the proband.Linkage analysis showed that the maximum logarithm of the odds(LOD) score reached 3.6671 at marker D3S1292 at recombination fraction θ =0.0.The results of direct DNA sequencing revealed a C→ G transversion mutation at codon 53 in exon 1 of rhodopsin gene,which resulted in a proline to arginine change (Pro53Arg) in 12 patients.However,no similar mutation was found in the unaffected members of this family.Conclusions The missence mutation Pro53Arg in rhodopsin gene cosegregate with the RP disease.It is determined to be a pathogenic factor of this ADRP family. Key words: Retinitis pigmentosa; Inheritance; Linkage analysis; Cene mutation; Rhodopsin

Consensus Mapping and Identification of Markers for Marker‐Assisted Selection of Wsm2 in Wheat

ABSTRACTA recently identified Wheat streak mosaic virus (WSMV) resistance gene Wsm2 confers a high level of resistance. Objective of this study was to identify closely linked DNA markers for Wsm2 for use in marker‐assisted selection (MAS) in wheat (Triticum aestivum L.). Two segregating populations (CO960293‐2 × ‘TAM 111’ and CO960293‐2 × ‘Yuma’) of F2:3 families were evaluated for response to WSMV infection in growth chamber experiments. Forty‐eight simple sequence repeat (SSR) or sequence‐tagged site (STS) markers were screened for polymorphism between the parents of both populations. In the CO960293‐2 × TAM 111 population, five markers were mapped to the region of Wsm2 with XSTS3B‐55 being the closest marker (5.2 cM distal to Wsm2). In the CO960293‐2 × Yuma population, eight markers were linked to Wsm2 with the closest marker Xbarc102 linked at 3.9 cM proximal to Wsm2. Results from consensus mapping of the two populations suggested that Xbarc102 was distal to Wsm2. The marker Xbarc102 was associated with Wsm2 in all 22 wheat lines derived from crosses between susceptible parents and either CO960293‐2 or ‘RonL’ (also carrying Wsm2). The marker allele Xbarc102‐219‐bp present in CO960293‐2 was amplified in polymerase chain reaction (PCR) from Wsm2‐carrying genotypes CO960293‐w133, RonL, and ‘Snowmass’ but not from the resistant line KS96HW10‐3 (carrying Wsm1) or the susceptible genotypes ‘Karl 92’, ‘TAM 107’, and ‘N96L9970’. Therefore, this marker should be useful for MAS of Wsm2 in breeding programs.