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The Arabidopsis epithiospecifier protein promotes the hydrolysis of glucosinolates to nitriles and influences Trichoplusia ni herbivory.

Glucosinolates are anionic thioglucosides that have become one of the most frequently studied groups of defensive metabolites in plants. When tissue damage occurs, the thioglucoside linkage is hydrolyzed by enzymes known as myrosinases, resulting in the formation of a variety of products that are active against herbivores and pathogens. In an effort to learn more about the molecular genetic and biochemical regulation of glucosinolate hydrolysis product formation, we analyzed leaf samples of 122 Arabidopsis ecotypes. A distinct polymorphism was observed with all ecotypes producing primarily isothiocyanates or primarily nitriles. The ecotypes Columbia (Col) and Landsberg erecta (Ler) differed in their hydrolysis products; therefore, the Col x Ler recombinant inbred lines were used for mapping the genes controlling this polymorphism. The major quantitative trait locus (QTL) affecting nitrile versus isothiocyanate formation was found very close to a gene encoding a homolog of a Brassica napus epithiospecifier protein (ESP), which causes the formation of epithionitriles instead of isothiocyanates during glucosinolate hydrolysis in the seeds of certain Brassicaceae. The heterologously expressed Arabidopsis ESP was able to convert glucosinolates both to epithionitriles and to simple nitriles in the presence of myrosinase, and thus it was more versatile than previously described ESPs. The role of ESP in plant defense is uncertain, because the generalist herbivore Trichoplusia ni (the cabbage looper) was found to feed more readily on nitrile-producing than on isothiocyanate-producing Arabidopsis. However, isothiocyanates are frequently used as recognition cues by specialist herbivores, and so the formation of nitriles instead of isothiocyanates may allow Arabidopsis to be less apparent to specialists.

Amino Acid Sequence↗

Development of a pooled probe method for locating small gene families in a physical map of soybean using stress related paralogues and a BAC minimum tile path.

BACKGROUND: Genome analysis of soybean (Glycine max L.) has been complicated by its paleo-autopolyploid nature and conserved homeologous regions. Landmarks of expressed sequence tags (ESTs) located within a minimum tile path (MTP) of contiguous (contig) bacterial artificial chromosome (BAC) clones or radiation hybrid set can identify stress and defense related gene rich regions in the genome. A physical map of about 2,800 contigs and MTPs of 8,064 BAC clones encompass the soybean genome. That genome is being sequenced by whole genome shotgun methods so that reliable estimates of gene family size and gene locations will provide a useful tool for finishing. The aims here were to develop methods to anchor plant defense- and stress-related gene paralogues on the MTP derived from the soybean physical map, to identify gene rich regions and to correlate those with QTL for disease resistance. RESULTS: The probes included 143 ESTs from a root library selected by subtractive hybridization from a multiply disease resistant soybean cultivar 'Forrest' 14 days after inoculation with Fusarium solani f. sp. glycines (F. virguliforme). Another 166 probes were chosen from a root EST library (Gm-r1021) prepared from a non-inoculated soybean cultivar 'Williams 82' based on their homology to the known defense and stress related genes. Twelve and thirteen pooled EST probes were hybridized to high-density colony arrays of MTP BAC clones from the cv. 'Forrest' genome. The EST pools located 613 paralogues for 201 of the 309 probes used (range 1-13 per functional probe). One hundred BAC clones contained more than one kind of paralogue. Many more BACs (246) contained a single paralogue of one of the 201 probes detectable gene families. ESTs were anchored on soybean linkage groups A1, B1, C2, E, D1a+Q, G, I, M, H, and O. CONCLUSION: Estimates of gene family sizes were more similar to those made by Southern hybridization than by bioinformatics inferences from EST collections. When compared to Arabidopsis thaliana there were more 2 and 4 member paralogue families reflecting the diploidized-tetraploid nature of the soybean genome. However there were fewer families with 5 or more genes and the same number of single genes. Therefore the method can identify evolutionary patterns such as massively extensive selective gene loss or rapid divergence to regenerate the unique genes in some families.

Journal Article↗

Mapping QTLs regulating morpho-physiological traits and yield: case studies, shortcomings and perspectives in drought-stressed maize.

Comparative analysis of a number of studies in drought-stressed maize (Zea mays L.) reporting quantitative trait loci (QTLs) for abscisic acid concentration, root characteristics, other morpho-physiological traits (MPTs) and grain yield (GY) reveals their complex genetic basis and the influence of the genetic background and the environment on QTL effects. Chromosome regions (e.g. near umc11 on chromosome 1 and near csu133 on chromosome 2) with QTLs controlling a number of MPTs and GY across populations and conditions of different water supply have been identified. Examples are presented on the use of QTL information to elucidate the genetic and physiological bases of the association among MPTs and GY. The QTL approach allows us to develop hypotheses accounting for these associations which can be further tested by developing near isogenic lines (NILs) differing for the QTL alleles. NILs also allow for a more accurate assessment of the breeding value of MPTs and, in some cases, may allow for the map-based cloning of the gene(s) underlying the QTL. Although QTL analysis is still time-consuming and resource-demanding, its integration with genomics and post-genomics approaches (e.g. transcriptome, proteome and metabolome analyses) will play an increasingly important role for the identification and validation of candidate genes affecting MPTs and GY.

Abscisic Acid↗

Genetic and biochemical determinants of abnormal monovalent ion transport in primary hypertension.

Data obtained during the last two decades show that spontaneously hypertensive rats, an acceptable experimental model of primary human hypertension, possess increased activity of both ubiquitous and renal cell-specific isoforms of the Na+/H+ exchanger (NHE) and Na+-K+-2Cl- cotransporter. Abnormalities of these ion transporters have been found in patients suffering from essential hypertension. Recent genetic studies demonstrate that genes encoding the beta- and gamma-subunits of ENaC, a renal cell-specific isoform of the Na+-K+-2Cl- cotransporter, and alpha3-, alpha1-, and beta2-subunits of the Na+-K+ pump are localized within quantitative trait loci (QTL) for elevated blood pressure as well as for enhanced heart-to-body weight ratio, proteinuria, phosphate excretion, and stroke latency. On the basis of the homology of genome maps, several other genes encoding these transporters, as well as the Na+/H+ exchanger and Na+-K+-2Cl- cotransporter, can be predicted in QTL related to the pathogenesis of hypertension. However, despite their location within QTL, analysis of cDNA structure did not reveal any mutation in the coding region of the above-listed transporters in primary hypertension, with the exception of G276L substitution in the alpha1-Na+-K+ pump from Dahl salt-sensitive rats and a higher occurrence of T594M mutation of beta-ENaC in the black population with essential hypertension. These results suggest that, in contrast to Mendelian forms of hypertension, the altered activity of monovalent ion transporters in primary hypertension is caused by abnormalities of systems involved in the regulation of their expression and/or function. Further analysis of QTL in F2 hybrids of normotensive and hypertensive rats and in affected sibling pairs will allow mapping of genes causing abnormalities of these regulatory pathways.

Animals↗

Mapping and analysis of quantitative trait loci for grain oil content and agronomic traits using AFLP and SSR in sunflower ( Helianthus annuus L.).

Crosses were made between two inbred lines of sunflower. Parents and 118 F(3) families were planted in the field in a randomized complete block design in two replications. Genetic control for some agronomical traits: grain weight by plant (GWP), 1,000-grain weight (TGW), percentage of oil in grain (POG) and sowing to flowering date (STF) was investigated in F(3) families and their parents. Genetic variability was observed among the 118 F(3) families for all the traits studied. Genetic gain was obtained when the best F(3) family, or the mean of 10% of the selected families was compared with the best parent for GWP, TWG and POG. Heritability was 0.23 for GWP, 0.55 for TGW, 0.57 for POG and 0.32 for STF. A set of 244 F(3) families from the same cross, including the above 118 mentioned families and their two parents, were screened with 276 AFLP and microsatellite markers and a linkage map was constructed based on 170 markers. Two putative QTLs for the GWP trait ( gmp), one QTL for TGW ( tgw), six QTLs for POG ( pog) and two for STF ( stf) were detected. The percentage of phenotypic variance explained by each QTL ranged from 2.6% to 70.9%. The percentage of total phenotypic variance explained was 50.7% for GWP, 5.4% for TGW, 90.4% for POG and 89.3% for STF. Although these regions need to be more-precisely mapped, the information obtained should help in marker-assisted selection.

Chromosome Mapping↗

Congenic strains developed for alcohol- and drug-related phenotypes.

Quantitative trait loci (QTLs) for many alcohol- and drug-related traits have been mapped using well-accepted mapping techniques. The ultimate goal of gene identification necessitates confirmation of the QTL and reduction of the interval surrounding the QTL; both can be accomplished in congenic strains. These strains carry a chromosomal region introgressed from a donor strain onto the genetic background of a second, recipient strain. Multiple generations of backcrossing reduce the unlinked donor genome to less than 0.1%. Then, phenotypic comparisons between mice congenic for the donor region and controls from the recipient strain allow confirmation of the QTL effect. Animals with recombinations in the donor region can be used to generate interval-specific congenic recombinant lines. Numerous congenic strains are currently being developed in which chromosomal regions carrying QTLs for alcohol- and drug-related traits have been transferred from one strain onto a second strain. The purpose of this review is to summarize the chromosomal regions, donor and recipient strains, and results obtained from these congenics. Most researchers developing such strains are willing to share these resources to facilitate localization of the genetic bases of other phenotypes.

Alcoholism↗

Isozyme monitoring of genetic variation in Lycopersicon.

Linkages with isozymic loci facilitate the investigation of certain classes of genetic variation. Due to the mapping of 20 isozymic loci on nine of the 12 chromosomes of the cultivated tomato (Lycopersicon esculentum), much progress has been made in these applications, particularly in the analysis of interspecific hybrids. Isozymes can expedite the selective elimination of inferior wild parent germ plasm in backcross transfer of desired genes to the cultivated parent. Allelic isozyme constitution also aids in identification of lines, particularly in evaluating the purity of F1 hybrid cultivars. Advantages that isozymes impart to such investigations are: (1) unequivocal classification of phenotypes, (2) detection of heterozygotes, (3) lack of epistasis between isozyme loci, (4) lack of effect of allelic isozymes per se on morphology or physiology, (5) prolific source of monogenic markers, and (6) phenotyping at early developmental stages. Each of these attributes can be exploited to great advantage, but collectively they constitute a formidable argument for monitoring genetic variation by means of isozymes. Linkages between isozyme loci and qualitative loci can be exploited as in the monitoring of Mi (gene for root-knot nematode resistance derived from L peruvianum) by the very tightly linked Aps-1(1); in similar fashion, Prx-2(1) serves as a useful marker for ms-10 (male sterility). Asp-1 monitoring in the former is more reliable than testing for nematode resistance per se; codominance of Prx-2 alleles of the latter solves problems incurred by the recessiveness of ms-10; in both instances phenotypes can be ascertained at earlier growth stages for isozymes than for economic traits. In the first backcross of the interspecific hybrid L esculentum x Solanum pennellii to the former, the segregation of four quantitative traits was monitored by allelic isozymes at 12 loci, situated on at least eight chromosomes, covering approximately 60% of the known tomato genome. At least five quantitative trait loci (QTL) were found to determine each of the four traits. Each parent contributes alleles with positive as well as negative effects, the greatest balance for stigma exsertion, the trait also exhibiting the greatest extent of transgressive segregation. Three pairs of linked isozymic loci permitted a crude form of three-point mapping of the associated QTL. interactions between QTL linked with pairs of isozymic genes were tested in all possible combinations; 18 of the 274 comparisons showed significant interactions, indicating epistasis.(ABSTRACT TRUNCATED AT 400 WORDS)

Alleles↗

Mapping of QTLs associated with cytosolic glutamine synthetase and NADH-glutamate synthase in rice (Oryza sativa L.).

Ninety-eight backcross inbred lines (BC1F6) developed between Nipponbare, a japonica rice, and Kasalath, an indica rice were employed to detect putative quantitative trait loci (QTLs) associated with the contents of cytosolic glutamine synthetase (GS1; EC 6.3.1.2) and NADH-glutamate synthase (NADH-GOGAT; EC 1.4.1.14) in leaves. Immunoblotting analyses showed transgressive segregations toward lower or greater contents of these enzyme proteins in these backcross inbred lines. Seven chromosomal QTL regions for GS1 protein content and six for NADH-GOGAT protein content were detected. Some of these QTLs were located in QTL regions for various biochemical and physiological traits affected by nitrogen recycling. These findings suggested that the variation in GS1 and NADH-GOGAT protein contents in this population is related to the changes in the rate of nitrogen recycling from senescing organs to developing organs, leading to changes in these physiological traits. Furthermore, a structural gene for GS1 was mapped between two RFLP markers, C560 and C1408, on chromosome 2 and co-located in the QTL region for one-spikelet weight. A QTL region for NADH-GOGAT protein content was detected at the position mapped for the NADH-GOGAT structural gene on chromosome 1. A QTL region for soluble protein content in developing leaves was also detected in this region. Although fine mapping is required to identify individual genes in the future, QTL analysis could be a useful post-genomic tool to study the gene functions for regulation of nitrogen recycling in rice.

Biological Transport↗

Mapping of selective rat chromosome regions using mouse microsatellite markers.

Four hundred eighty mouse microsatellite markers distributed in discrete regions on five mouse chromosomes were screened for producing PCR products in the rat. Ninety-eight of these markers or 20% give distinctive PCR products. Among these ninety-eight markers, twenty-three are polymorphic between the inbred hypertensive Dahl salt-sensitive (S) rat strain and several normotensive rat strains of interest. Fourteen of these polymorphic markers have been mapped to the homologous chromosome regions of the rat, and have further been utilized to localize quantitative trait loci (QTL) for blood pressure in the S rat.

Animals↗

Major quantitative trait locus for eosinophil count is located on chromosome 2q.

BACKGROUND: Eosinophils are granulocytic white blood cells implicated in asthma and atopic disease. The degree of eosinophilia in the blood of patients with asthma correlates with the severity of asthmatic symptoms. Quantitative trait loci (QTL) linkage analysis of eosinophil count may be a more powerful strategy of mapping genes involved in asthma than linkage analysis using affected relative pairs. OBJECTIVE: To identify QTLs responsible for variation in eosinophil count in adolescent twins. METHODS: We measured eosinophil count longitudinally in 738 pairs of twins at 12, 14, and 16 years of age. We typed 757 highly polymorphic microsatellite markers at an average spacing of approximately 5 centimorgans across the genome. We then used multipoint variance components linkage analysis to test for linkage between marker loci and eosinophil concentrations at each age across the genome. RESULTS: We found highly significant linkage on chromosome 2q33 in 12-year-old twins (logarithm of the odds=4.6; P=.000002) and suggestive evidence of linkage in the same region in 14-year-olds (logarithm of the odds=1.0; P=.016). We also found suggestive evidence of linkage at other areas of the genome, including regions on chromosomes 2, 3, 4, 8, 9, 11, 12, 17, 20, and 22. CONCLUSION: A QTL for eosinophil count is present on chromosome 2q33. This QTL might represent a gene involved in asthma pathophysiology.

Adolescent↗

Molecular mapping of novel genes controlling Fusarium head blight resistance and deoxynivalenol accumulation in spring wheat.

Fusarium head blight of wheat is an extremely damaging disease, causing severe losses in seed yield and quality. The objective of the current study was to examine and characterize alternate sources of resistance to Fusarium head blight (FHB). Ninety-one F1-derived doubled haploid lines from the cross Triticum aestivum 'Wuhan-1' x Triticum aestivum 'Maringa' were examined for disease reaction to Fusarium graminearum by single-floret injection in replicated greenhouse trials and by spray inoculation in replicated field trials. Field and greenhouse experiments were also used to collect agronomic and spike morphology characteristics. Seed samples from field plots were used for deoxynivalenol (DON) determination. A total of 328 polymorphic microsatellite loci were used to construct a genetic linkage map in this population and together these data were used to identify QTL controlling FHB resistance, accumulation of DON, and agronomic and spike morphology traits. The analysis identified QTL for different types of FHB resistance in four intervals on chromosomes 2DL, 3BS, and 4B. The QTLs on 4B and 3BS proximal to the centromere are novel and not reported elsewhere. QTL controlling accumulation of DON independent of FHB resistance were located on chromosomes 2DS and 5AS. Lines carrying FHB resistance alleles on 2DL and 3BS showed a 32% decrease in disease spread after single-floret injection. Lines carrying FHB resistance alleles on 3BS and 4B showed a 27% decrease from the mean in field infection. Finally, lines carrying favourable alleles on 3BS and 5AS, showed a 17% reduction in DON accumulation. The results support a polygenic and quantitative mode of inheritance and report novel FHB resistance loci. The data also suggest that resistance to FHB infection and DON accumulation may be controlled, in part, by independent loci and (or) genes.

Chromosome Mapping↗

Quantitative genetics of vector competence for La Crosse virus and body size in Ochlerotatus hendersoni and Ochlerotatus triseriatus interspecific hybrids.

La Crosse virus is a leading cause of pediatric encephalitis in the United States. The mosquito Ochlerotatus triseriatus is an efficient vector for La Crosse virus, whereas the closely related O. hendersoni transmits only at very low rates. Quantitative trait loci (QTL) affecting the ability to orally transmit this virus and adult body size were identified in 164 F(2) female individuals from interspecific crosses of O. hendersoni females and O. triseriatus males using a combination of composite interval mapping (CIM), interval mapping (IM) for binary traits, and single-marker mapping. For oral transmission (OT), no genome locations exceeded the 95% experimentwise threshold for declaring a QTL using IM, but single-marker analysis identified four independent regions significantly associated with OT that we considered as tentative QTL. With two QTL, an increase in OT was associated with alleles from the refractory vector, O. hendersoni, and likely reflect epistatic interactions between genes that were uncovered by our interspecific crosses. For body size, two QTL were identified using CIM and a third tentative QTL was identified using single-marker analysis. The genome regions associated with body size also contain three QTL controlling OT, suggesting that these regions contain either single genes with pleiotropic effects or multiple linked genes independently determining each trait.

Animals↗

Gene coding variant in Cas1 between the C57BL/6J and DBA/2J inbred mouse strains: linkage to a QTL for ethanol-induced locomotor activation.

BACKGROUND: Among some (e.g., DBA/2J or D2) but not all (C57BL/6J or B6) inbred strains of mice, ethanol has a marked psychostimulant effect. Intercrosses formed from the D2 and B6 strains have been used to detect quantitative trait loci (QTLs) for this phenotype. The major QTL is found at the mid-region of chromosome 2 (Demarest et al., 1999). This QTL has also been detected in heterogeneous stock mice (Demarest et al., 2001). A potential candidate gene in this region is Cas1, which codes for catalase. The current studies were conducted to determine (a) if there was difference in the open reading frame (ORF) of Cas1 between the D2 and B6 strains; (b) if a difference was found, was it likely that the difference had functional effects; and (c) if it could be established that Cas1 meets the criteria for QTL to gene. METHODS: The open reading frame (ORF) of Cas1 was sequenced in both the D2 and B6 mouse strains. A single polymorphism was found between the strains (see below); the strain distribution pattern for this polymorphism was determined in the 36 strains of the B6XD2 (BXD) recombinant inbred (RI) series. These data were used to map the position of Cas1 as described by Cudmore et al. (1999). RESULTS: The only difference between the D2 and B6 strains in the coding region was found at #349, G->A. This will result in a difference in the amino acid sequence between the strains at amino acid #117-alanine is found in the D2 strain while threonine is found in the B6 strain. The RI strain distribution pattern for this polymorphism was used to determine the relative placement of Cas1. The estimate suggests that Cas1 is flanked by D2Mit12 and D2Mit43 and relative to D2Mit94 (which was set at 47 cM), Cas1 is located at approximately 57 cM, confirming previous estimates (see www.jax.org). CONCLUSIONS: Pharmacological data (Correa et al., 2001) strongly support the idea that Cas1 meets the criteria for QTL to gene. However, based on the mapping data, Cas1 is clearly not included in the QTL for heterogeneous stock mice. Finally, other genetic data suggest that the polymorphism is not sufficient to generate the QTL.

Animals↗

[Detection of quantitative trait loci for growth in large white x Meishan intercross].

The development of molecular biology techniques and the application of these techniques to farm animals have progressed rapidly and have opened new vistas for investigators wishing to identify genes that control quantitative traits. Now that a comprehensive map has been developed for the porcine genome, genomic scans to detect quantitative trait loci (QTL) can begin. In order to locate the genetic regions in the swine genome that are responsible for economically important traits, a resource population was developed by intercross with three Large White and seven Meishan pigs. In subsequent generations, 66 F2 offsprings in 2000 were recorded for four growth traits including birth weight (BWT), body weight at 60 day (WT60), average daily gain from birth to 60 day (ADG1) and average daily gain from 60 day to the end of test (ADG2), and genotyped for 48 microsatellite markers spanning six chromosomes. Association analyses were performed using interval mapping by regression under an outbred line-cross model on chromosomes 1, 2, 3, 4, 6 and 7. The F threshold values were determined by permutation. A total of 12 QTL were detected at suggestive level for the four traits evaluated in this study. Of the 12 suggestive QTL, 3 and 1 QTL were significant at the chromosome-wise and genome-wise levels. There was a QTL for ADG2 at genome-wide level on chromosome 4 explained additive variance 2.19%. A chromosome-wide QTL affecting ADG1 and WT60 were detected on chromosomes 2 and 1 explained additive variance 0.01% and 26.01%, respectively.

Animals↗

Exclusion of the acyl CoA:diacylglycerol acyltransferase 1 gene (DGAT1) as a candidate for a fatty acid composition QTL on porcine chromosome 4.

DGAT1 is a microsomal enzyme that catalyses the final step in triglycerides synthesis. DGAT1-deficient mice are viable, lean, fertile and resistant to diet induced obesity. We have previously identified a quantitative trait loci (QTL) on chromosome 4 that affects fatty acid composition in an F2 cross between Iberian x Landrace. The human DGAT1 gene is located on chromosome 8q24.3, this region aligns to porcine chromosome 4, making the pig DGAT1 gene a suggestive positional candidate gene for the QTL. In this study, we sequenced 1679 bp of the mRNA from animals of five pig breeds (Iberian, Landrace, Large White, Piétrian and Meishan) to identify genetic variants. One of the polymorphisms found creates a polymorphic HinfI restriction site and it was genotyped by PCR-RFLP in these five pig breeds. Allele A was not found in the analysed Iberian and Landrace populations, whereas Meishan population presents the highest frequency (35%). The DGAT1 gene was located by radiation hybrid mapping to the porcine chromosome 4, outside the confidence interval for the fatty acid composition QTL and excludes it as a positional candidate gene.

Animals↗

Molecular markers in breeding for virus resistance in barley.

The soil-borne barley yellow mosaic virus disease (BaMMV, BaYMV, BaYMV-2) and the aphid-transmitted barley yellow dwarf virus (BYDV) are serious threats to winter barley cultivation. Resistance to barley yellow mosaic virus disease has been identified in extensive screening programmes and several recessive resistance genes have been mapped, e.g. rym4, rym5, rym9, rym11, rym13. In contrast to barley yellow mosaic virus disease, no complete resistance to BYDV is known in the barley gene pool, but tolerant accessions have been identified and QTL for BYDV-tolerance have been detected on chromosomes 2HL and 3HL. The use of resistance and tolerance in barley breeding can be considerably improved today by molecular markers (RFLPs, RAPDs, AFLPs, SSRs, STSs, SNPs), as they facilitate (i) efficient genotyping and estimation of genetic diversity; (ii) reliable selection on a single plant level independent of symptom expression in the field (iii) acceleration of back crossing procedures; (iv) pyramiding of resistance genes; (v) detection of QTL and marker-based combination of positive alleles; and (vi) isolation of resistance genes via map-based cloning.

Alleles↗

Comparative genetic analysis of quantitative traits in sunflower (Helianthus annuus L.). 2. Characterisation of QTL involved in developmental and agronomic traits.

Seed weight and oil content are important properties of cultivated sunflower under complex genetic and environmental control, and associated with morphological and developmental characteristics such as plant height or flowering dates. Using a genetic map with 290 markers for a cross between two inbred sunflower lines and 2 years of observations on F3 families, QTL controlling seed weight, oil content, plant height, plant lodging, flowering dates, maturity dates and delay from flowering to maturity were detected. QTL detected were compared between the F2 and F3 generations and between the 2 years of testing for the F3 families in 1997 and 1999. Some of the QTL controlling seed weight overlapped with those controlling oil content. Several other co-localisations of QTL controlling developmental or morphological characteristics were observed and the relationships between the traits were also shown by correlation analyses. The relationships between all these traits and with resistance to Sclerotinia sclerotiorum and Diaporthe helianthi are discussed.

Chromosome Mapping↗

Identification of EFHC2 as a quantitative trait locus for fear recognition in Turner syndrome.

One-third of women with Turner syndrome (45,X) have autism-like social and communication difficulties, despite normal verbal IQ. Deletion mapping of the X-chromosome implicated 5 Mb of Xp11.3-4 as critical for recognition of facial fear, a quantitative measure of social cognition. Variability in fear recognition accuracy in Turner syndrome suggested the existence of a quantitative trait locus (QTL) revealed by X-monosomy. We aimed to identify the gene(s) influencing fear recognition by dense mapping of the 5 Mb region. Initial regression-based association mapping of fear recognition in 93 women with Turner syndrome across the critical region was performed, using genotype data at 242 single nucleotide polymorphisms (SNPs). We identified three regions of interest, in which 52 additional SNPs were genotyped. The third region then contained four SNPs associated with fear recognition (0.0030 > P > 0.00046). We obtained an independent sample of 77 Turner syndrome females that we genotyped for 77 SNPs in the initial regions of interest. Region three showed association in the same direction, maximal at SNPs rs7055196 and rs7887763 (P = 0.022 each). Four SNPs in strong linkage disequilibrium (LD), including this pair, span 40 kb within a novel transcript, EF-hand domain containing 2 (EFHC2). In the combined Turner syndrome samples, the most strongly associated SNP (P = 0.00007) has frequency of 8.8% and an estimated effect size accounting for over 13% of the variance in fear recognition. EFHC2 shows genealogy and extended LD consistent with directional selection. This novel QTL may influence social cognition in the general population and in autism.

Chromosome Mapping↗