Extensive Diversity of the ADRB3 Gene in Chinese Sheep Identified by PCR-SSCP

The β₃-adrenergic receptor (ADRB3) is the main mediator of the lipolytic and thermogenic effects of high catecholamine concentrations. Polymorphism in the ovine ADRB3 gene has been reported to be associated with birth weight, growth rate, carcass composition, and cold survival. Eight alleles have been identified in New Zealand sheep, but to date, breeds from other countries have not been studied in detail. In this study, we employed PCR-SSCP to detect ADRB3 polymorphism in the Hu, Tan, small-tailed Han, and Tibet breeds of Chinese sheep. Thirteen SSCP patterns were observed, including the eight previously reported and five new patterns. The newly identified SSCP patterns represent five novel sequences, increasing the reported number of alleles of ADRB3 from 8 to 13. In these Chinese sheep, the most common allele was the previously reported allele C (49.0%); the A allele was the next most common (22.0%). These results suggest that Chinese sheep have more diversity in ADRB3 than New Zealand sheep and therefore have possibly been selected either naturally or via breeding for different traits.     

Allelic variation in ovine fatty acid-binding protein (FABP4) gene

The fatty acid-binding protein 4 (FABP4) plays a role in lipid metabolism and has been implicated in intra-cellular lipid transport. While FABP4 variation has been reported in some species, variation in the coding sequence has not been reported in sheep. In this study two regions of ovine FABP4 were analysed using PCR-SSCP and sequencing. Five different PCR-SSCP patterns, representing five specific sequences (A ₁ –E ₁ ) were detected in region 1 (exon 2–intron 2) with sequence analysis revealing three nucleotide substitutions and one deletion in the intron. In region 2 (exon 3–intron 3), four different PCR-SSCP patterns (A ₂ –D ₂ ) were observed and four nucleotide substitutions were revealed. In total, fourteen haplotypes through both regions were defined. There was a difference (P?<?0.001) in allele frequencies between two selection lines of Coopworth sheep that have been bred over many generations to be lean or fat. In region 1, A ₁ and B ₁ were most common (at a frequency of 50 and 30?% respectively) in the fat line, whereas these two variants were absent or rare in the lean line in which C ₁ predominated (89?%). In region 2, C ₂ was the most common variant (59?%) in the lean line but was absent in the fat line, whereas B ₂ was predominant (83?%) in the fat line but was rare (3?%) in the lean line. These results indicate that ovine FABP4 is polymorphic and suggest further analysis is required to see if the variation detected affects fat deposition in sheep.     

ADRB2 Haplotype Is Associated With Glucose Tolerance and Insulin Sensitivity in Obese Postmenopausal Women

The β₂‐adrenergic receptor (ADRB2) mediates obesity, cardiorespiratory fitness, and insulin resistance. We examined the hypothesis that ADRB2 Arg16Gly‐Gln27Glu haplotype is associated with body composition, glucose tolerance, and insulin sensitivity in obese, postmenopausal women. Obese (>35% body fat), postmenopausal (age 45–75 years) women (n = 123) underwent genotyping, dual‐energy X‐ray absorptiometry, and computed tomography scans, exercise testing (VO_2max), 2‐h oral glucose tolerance tests (OGTTs), and hyperinsulinemic‐euglycemic clamps (80 mU/m²/min). Analysis of covariance (ANCOVA) tested for differences among haplotypes, with race, % body fat, and VO_2max as covariates. We found that ADRB2 haplotype was independently associated with % body fat, abdominal fat distribution, VO_2max, insulin sensitivity (M/ΔInsulin), and glucose tolerance (ANOVA, P < 0.05 for all). Women homozygous for Gly16–Gln27 haplotype had the highest % body fat (52.7 ± 1.9%), high abdominal fat, low M/ΔInsulin (0.49 ± 0.08 mg/kg/min/pmol/l/10²), and impaired glucose tolerance (IGT) during an OGTT (G₁₂₀ = 10.2 ± 0.9 mmol/l). Women homozygous for Gly16–Glu27 haplotype also had low M/ΔInsulin (0.51 ± 0.05 mg/kg/min/pmol/l/10²) and IGT (G₁₂₀ = 8.2 ± 0.7 mmol/l). Subjects with Arg16–Gln27/Gly16–Gln27 haplotype combination had the highest VO_2max (1.84 ± 0.07 l/min) and M/ΔInsulin (0.7 ± 0.04 mg/kg/min/pmol/l/10²), and normal glucose tolerance (G₁₂₀ = 6.4 ± 0.4 mmol/l), despite being obese. These data show associations of the ADRB2 Arg16Gly‐Gln27Glu haplotype with VO_2max and body composition, and an independent association with glucose metabolism, which persists after controlling for body composition and fitness. This suggests that ADRB2 haplotypes may mediate insulin action, glucose tolerance, and potentially risk for type 2 diabetes mellitus (T2DM) in obese, postmenopausal women.     

Diversity of the glycine/tyrosine-rich keratin-associated protein 6 gene (<Emphasis Type="Italic">KAP6</Emphasis>) family in sheep

Keratin-associated proteins (KAPs) are structural components of wool and variation in them may affect wool characteristics. In this study, we used PCR-SSCP to analyse the ovine KAP6 family which encodes glycine and tyrosine-rich KAPs. Five unique PCR-SSCP patterns were detected in the 250 sheep investigated. Between two and five patterns were observed in individual sheep and none with only one pattern was detected. This suggests the amplicons were heterogeneous and derived from more than one locus. To analyse these heterogeneous PCR amplicons, a sequencing approach using SSCP to separate individual amplified sequences, was developed. Using this approach, five DNA sequences (A–E) representing five unique PCR-SSCP patterns were obtained. D was identical to a published ovine KAP6-1 sequence (GenBank accession no. M95719), whereas the others were novel, but the closest homology was with KAP6 sequences from human, sheep, goats and cattle. The five ovine KAP6 sequences could be assigned into three distinct groups. B and D were identical to each other, with the exception of a 57-bp deletion/insertion and a single nucleotide polymorphism (SNP) in the 3′-UTR region. These appear to be allelic variants of ovine KAP6-1. A and C could form another group, as they were similar to each other (with only one synonymous SNP), but different to the other sequences. This group appears to be related to a sheep KAP6 amino acid sequence, and represent allelic variation at another KAP6 locus (designated KAP6-2). The remaining sequence E did not show high sequence homology with either the KAP6-1 or KAP6-2 sequences, but exhibited homology with a bovine KAP6-3 sequence, with the exception of a deletion/insertion of 30 nucleotides. This suggests that E represents ovine KAP6-3. This sequence was detected in only 11% of the sheep investigated, suggesting either a KAP6-3 null allele, or failure to amplify allleles. These results suggest that ovine KAP6 is a complex gene family, that is not only comprised multiple loci, but that is also polymorphic.     

Detection of Bovine Central Nervous System Tissue as Bovine Spongiform Encephalopathy Risk Material by Real-Time Reverse Transcriptase-PCR in Raw and Cooked Beef Products

PCR-SSCP and DNA sequencing methods were applied to reveal single nucleotide polymorphisms (SNPs) in the bovine VEGF-B gene in 675 samples belonging to three native Chinese cattle breeds. We found 3 SNPs and a duplication NC_007330.5: g. [782 A>G p. (Gly112 =) (;) 1000-1001dup CT (;) 1079 C>T (;) 2129 G>A p. (Arg184Gln)]. We also observed a statistically significant association of the polymorphism (1000-1001dup CT) in intron 3 of the VEGF-B gene with the body weight of the Nanyang cattle (p < 0.05). This polymorphisms of VEGF-B gene need to be verified among a larger cattle population before it can be identified as a marker for bovine body weight.     

Effect of β2-adrenergic receptor gene (ADRB2) 3′ untranslated region polymorphisms on inhaled corticosteroid/long-acting β2-adrenergic agonist response

Background

Evidence suggests that variation in the length of the poly-C repeat in the 3′ untranslated region (3′UTR) of the β₂-adrenergic receptor gene (ADRB2) may contribute to interindividual variation in β-agonist response. However, methodology in previous studies limited the assessment of the effect of sequence variation in the context of poly-C repeat length. The objectives of this study were to design a novel genotyping method to fully characterize sequence variation in the ADRB2 3′UTR poly-C repeat in asthma patients treated with inhaled corticosteroid and long-acting β₂-adrenergic agonist (ICS/LABA) combination therapy, and to analyze the effect of the poly-C repeat polymorphism on clinical response.

Methods

In 2,250 asthma patients randomized to treatment with budesonide/formoterol or fluticasone/salmeterol in a six-month study (AstraZeneca study code: SD-039-0735), sequence diversity in the ADRB2 poly-C repeat region was determined using a novel sequencing-based genotyping method. The relationship between the poly-C repeat polymorphism and the incidence of severe asthma exacerbations, and changes in pulmonary function and asthma symptoms from baseline to the average during the treatment period, were analyzed.

Results

Poly-C repeat genotypes were assigned in 97% (2,192/2,250) of patients. Of the 13 different poly-C repeat alleles identified, six alleles occurred at a frequency of >5% in one or more population in this study. The repeat length of these six common alleles ranged from 10 to 14 nucleotides. Twelve poly-C repeat genotypes were observed at a frequency of >1%. No evidence of an association between poly-C repeat genotype and the incidence of severe asthma exacerbations was observed. Patients’ pulmonary function measurements improved and asthma symptoms declined when treated with ICS/LABA combination therapy regardless of poly-C repeat genotype.

Conclusions

The extensive sequence diversity present in the poly-C repeat region of the ADRB2 3′UTR did not predict therapeutic response to ICS/LABA therapy.     

No Consistent Effect of ADRB2 Haplotypes on Obesity,Hypertension and Quantitative Traits of Body Fatness and Blood Pressure among 6,514 Adult Danes

Background

Evidence regarding the association of variation within ADRB2, the gene encoding the beta-adrenergic receptor 2 (ADRB2) with obesity and hypertension is exceedingly ambiguous. Despite negative reports, functional impacts of individual genetic variants have been reported. Also, functional haplotypes as well as haplotype combinations affecting expression levels in vivo of ADRB2 mRNA and protein as well as receptor sensitivity have been reported. The aim of the present study was therefore to evaluate if variations within ADRB2 as haplotypes or as haplotype combinations confer an increased prevalence of obesity and hypertension among adults.

Methodology/Principal Findings

We genotyped five variants required to capture common variation in a region including the ADRB2 locus in a population-based study of 6,514 unrelated, middle-aged Danes. Phases of the genotypes were estimated in silico. The variations were then investigated for their combined association with obesity, hypertension and related quantitative traits. The present study did not find consistent evidence for an association of ADRB2 variants with either obesity or hypertension when variations were analysed in a case-control study. The same lack of impact was also seen in the quantitative trait analyses, apart from nominal differences on waist-to-hip ratio and systolic blood pressure between specific haplotype combinations.

Conclusions/Significance

In a population-based sample of 6,514 Danes we found no consistent associations between five common variants which tag the ADRB2 locus and prevalence of obesity or hypertension neither when analysed as individual haplotypes nor as haplotype pairs.     

Role ofADRB2 gene polymorphism in asthma and response to β2-agonists in Polish children

The aims of this study were: (1) to find associations of asthma with single-nucleotide polymorphisms (SNPs) within theADRB2 gene: Arg16Gly, Gln27Glu, −1023 G/A, −367 T/C, −47 C/T ; (2) to define linkage disequilibrium in the gene region, basing on the analyzed SNPs; and (3) to analyze the importance ofADRB2 polymorphism for response to bronchodilator drugs in children diagnosed with bronchial asthma. We compared 113 asthmatic children and 123 healthy subjects from the Polish population. Genotyping was performed by PCR-RFLP. We found an association of the A allele of −1023A/GADRB2 polymorphism with asthma (P = 0.024). No significant associations with other SNPs were detected. Moderate linkage was found between Gln27Glu and −47C/T polymorphisms in linkage disequilibrium analysis (D’ = 0.85,r ² = 0.429, LOD = 31.97). No significant differences were found in haplotype frequencies in comparison to the control group, implicating that they are not associated with susceptibility to asthma in the analyzed population. There was no significant correlation between the analyzed SNPs of theADRB2 gene and the response to β₂-agonists. This is the first report providing suggestive evidence for association of —1023A/GADRB2 polymorphism with an increased risk of asthma. The analyzed SNPs may not play a major role in response to β₂-agonists in asthmatic children.     

Functional analysis of guinea pig β1-adrenoceptor

Although similarity of pharmacological responses to certain stimuli between guinea pigs and humans has been reported, this has been poorly defined by a molecular biological approach. In this study, we cloned the gene of guinea pig β1-adrenoceptor (ADRB1). The deduced amino acid sequence of guinea pig ADRB1 (467-aa) showed 91% and 92% identity with the human and rat ADRB1 sequences, respectively. Using HEK293T cells expressing guinea pig, human and rat ADRB1s independently, we elucidated the functional characteristics of each ADRB1. The ligand-binding profiles and the concentration-response relationships for isoprenaline-induced cyclic adenosine monophosphate (cAMP) production were similar among the three ADRB1s. Isoprenaline also induced phosphorylation of extracellular-signal related kinases (ERK) through ADRB1s in a concentration-dependent manner. The minimum effective concentration of isoprenaline for phosphorylation of ERK, through guinea pig ADRB1 was the same as through human ADRB1, but markedly lower than that of through rat ADRB1. ERK phosphorylation through guinea pig ADRB1 was sensitive to pertussis toxin, a dominant-negative ras and PD98059, indicating that a G_i-mediated pathway is involved in the ADRB1/ERK signaling loop. These results suggest that the G_i-coupling efficacy of guinea pig and human ADRB1s may be higher than that of rat ADRB1.     

Polymorphism at the ovine beta3-adrenergic receptor locus: associations with birth weight,growth rate,carcass composition and cold survival

The beta3-adrenergic receptors (ADRB3s) are predominantly found on the surface of adipocytes and are the major mediators of the lipolytic and thermogenic effects of high catecholamine concentrations. Polymerase chain reaction-single strand conformational polymorphism (PCR-SSCP) analysis of part of the ovine beta3-adrenergic receptor gene (ADRB3) intron was used to screen 12 large Merino half-sib families for sequence variation. Six different alleles that segregated in a Mendelian fashion were observed. The genetic basis for the allelic differences were identified by sequencing the ADRB3 (coding and non-coding regions) from animals that were homozygous for each of the alleles. Five sire lines (two Merino x Merino, two Merino x Coopworth, one Dorset Down x Coopworth) provided phenotypic and genotypic data used to ascertain the effects of allelic variation at the ADRB3 locus on birth weight, weaning weight, growth rate (up until weaning), carcass composition at 63 days post-weaning and cold survival. Statistical analyses within each half-sib family showed that in some sire lines (S13, S15, and S17) the inheritance of a particular allele was associated with increased birth weights and/or increased growth rates up until weaning. The inheritance of a particular sire allele was associated with fatter carcasses in sire line S16. Chi-squared analysis revealed the association of the E allele with cold survival and the D allele with cold-related mortality in sire line S14. Such associations support the hypothesis that ADRB3s are involved in energy homeostasis. With more research, the variation detected at the ADRB3 locus may assist in the genetic selection for desirable animal production traits.     

Association of BMI with the β3‐Adrenergic Receptor Gene Polymorphism in Japanese: Meta‐Analysis

Objective: To assess the effect of the Trp64Arg polymorphism in the β3‐adrenergic receptor gene (ADRB3) on body mass index (BMI) in the Japanese population. Research Methods and Procedures: We selected studies that evaluated the association between BMI and ADRB3 polymorphism among Japanese, using MEDLINE and PubMed. After data collection, an extension of ANOVA was performed to assess the differences according to the genotype. Results: In a total of 35 subgroups including 2316 subjects with the Trp64Arg variant and 4266 subjects without this variant, the weighted mean difference in BMI was 0.26 kg/m² (95% confidence interval: 0.18 to 0.42; p < 0.01), indicating that variant carriers exhibited higher BMI than did normal homozygous subjects. Discussion: Although it is known that the allele frequency of the ADRB3 polymorphism differs among races, this study focuses on the Japanese population, which has a high allele frequency of ADRB3 polymorphism. We assumed that statistical errors would be prevented due to the sufficient number of subjects. In conclusion, the results support the hypothesis that ADRB3 gene polymorphism is associated with BMI.     

A Single Nucleotide Polymorphism and Sequence Analysis of CSN1S1 Gene Promoter Region in Chinese BOS Grunniens (YAK)

The aim of this study was to investigate the polymorphism of the CSN1S1 gene promoter region in 4 Chinese yak breeds, and compare the yak CSN1S1 gene promoter region sequences with other ruminants. A Polymerase Chain Reaction-Single Strand Conformation Polymorphism protocol was developed for rapid genotyping of the yak CSN1S1 gene. One hundred fifty-eight animals from 4 Chinese yak breeds were genotyped at the CSN1S1 locus using the protocol developed. A single nucleotide polymorphism of the CSN1S1 gene promoter region has been identified in all yak breeds investigated. The polymorphism consists of a single nucleotide substitution G→A at position 386 of the CSN1S1 gene promoter region, resulting in two alleles named, respectively, G₃₈₆ and A₃₈₆, based on the nucleotide at position 386. The allele G₃₈₆ was found to be more common in the animals investigated. The corresponding nucleotide sequences in GenBank of yak (having the same nucleotides as allele G₃₈₆ in this study), bovine, water buffalo, sheep, and goat had similarity of 99.68%, 99.35%, 97.42%, 95.14%, and 94.19%, respectively, with the yak allele A_386.     

Novel SNPs in <Emphasis Type="Italic">HSP70A1A</Emphasis> gene and the association of polymorphisms with thermo tolerance traits and tissue specific expression in Chinese Holstein cattle

Heat stress induces heat shock proteins (HSPs) expression and HSP70 family is one of them that have been reported to involve in cellular protection against heat stress. But whether there is any association of genetic variation in the HSP70A1A gene with thermo tolerance is unknown. PCR-SSCP and DNA sequencing were used to detect possible SNPs in HSP70A1A gene in 890 Chinese Holstein cattle. Three fragments were amplified and five novel mutations were found in HSP70A1A gene in Chinese Holstein cattle. G/A mutation was found at nucleotide 1524 in coding region that resulting two genotypes of AA and AB. T/C mutation was found at nucleotide 3494 in 3′-UTR resulting three genotypes of CC, CD and DD. The other three point mutations, G/C at nucleotide 6400, C/T at nucleotide 6600 and G/A at nucleotide 6601 were also found in 3′-UTR resulting six genotypes of EE, EF, FF, EG, FG and GG. Linkage disequilibrium (LD) analysis showed that the nucleotide 6400, 6600 and 6601 were in strong LD (D > 0.75). Association analysis indicated that AB, DD and FF genotype were the thermo tolerance genotype. SBYE Green I was used to quantify HSP70A1A mRNA expression in different tissues through quantitative real-time PCR assay. The results of the real-time PCR showed that the expression of HSP70A1A mRNA in the heart was significantly higher than that in the other tissues (P < 0.05). We presume that these mutations could be used in marker assisted selection for anti-heat stress cows in our breeding program.     

Halplotypes of the ovine ADRB3 gene (ADRB3) and their association with post-weaning growth in New Zealand Suffolk sheep

The β₃-adrenergic receptor (ADRB3) regulates thermogenesis and lipolysis in brown and white adipose tissue. Previously, sixteen ovine ADRB3 haplotypes have been defined. In this study, the relationship between these ADRB3 haplotypes and variation in post-weaning growth was investigated in 797 New Zealand Suffolk lambs from 38 sire lines and eight studs, using PCR-SSCP and General Linear Mixed-effects Models. Seven haplotypes were found in these sheep and they comprised five previously reported intron sequences and four previously reported 3′UT sequences. The frequencies of the various diplotypes ranged from 0.1 to 17.6 % and individual haplotypes from 0.8 to 32.5 %. The presence of haplotype A-b was associated with a decreased weaning-weight (P = 0.001). Sheep with the B-c/F-e diplotype had a higher mean weaning-weight than those with A-b/B-c or A-b/E-e (P < 0.05). The presence of C-a was found to be associated with increased post-weaning growth (P = 0.008), while the presence of B-c was associated with decreased post-weaning growth (P = 0.005). Sheep with A-b/C-a had higher mean post-weaning growth than those with A-b/A-b, A-b/B-c, B-c/B-c, B-c/E-e or B-c/F-e (P < 0.05). Sheep with B-c/B-c had lower mean post-weaning growth than those with A-b/C-a or B-c/C-a (P < 0.05). Additive effects for the different forms of the B-c haplotypes on post-weaning growth were identified. The effects of the ovine ADRB3 haplotypes on weaning-weight and post-weaning growth confirm that they could be used as a candidate gene-marker for improving sheep growth.     

β3 Adrenergic Receptor Polymorphism and Obesity‐Related Phenotypes in Hypertensive Patients

Objectives: Obesity is a complex trait that is affected by both environmental and genetic risk factors. The β₃ adrenergic receptor (ADRB3) is expressed in adipose tissue and plays a role in energy metabolism. A missense mutation on codon 64 of this gene (W64R) is associated with receptor malfunction. Previous studies examining the relation between this polymorphism and obesity produced inconsistent findings. The current study assessed the association between the W64R genotype and obesity‐related phenotypes, including body weight, BMI, and serum triglycerides, cholesterol, and glucose. Research Methods and Procedures: We determined the ADRB3 W64R genotypes and fasting serum lipid and glucose concentrations for 695 hypertensive adults (336 men, 359 women) from a rural county in Anhui Province, China. Multivariate linear regression models were fit to detect associations between the genetic polymorphism and obesity‐related phenotypes. Results: The ADRB3 W64R polymorphism was significantly associated with body weight and BMI in men but not in women. After controlling for potential confounding variables, men who were homozygous for the R64 allele were 11.8 kg heavier (p < 0.001) and had a BMI that was 3.7 kg/m² greater (p = 0.001) than men who were homozygous for the W64 allele. Serum concentrations of lipids and glucose were found not associated with the genetic polymorphism. Discussion: The ADRB3 R64 allele was associated with increased body weight and BMI in men but not in women. The genetic association was not modified by triglyceride, cholesterol, blood glucose, or blood pressure levels of the subjects.     

A candidate gene for lignin composition in Eucalyptus: cinnamoyl-CoA reductase (CCR)

Lignin content and composition are considered as mandatory traits of eucalyptus breeding programs, especially for pulp, paper, and bioenergy production. In this article, we used 33 Eucalyptus urophylla full-sib families of an 8 × 8 factorial design to provide estimates of genetic parameters for lignin- and growth-related traits. Secondly, from the sequencing of the 16 unrelated founders, we described the nucleotide and haplotype variability of cinnamoyl-CoA reductase (CCR), a candidate gene for lignin-related traits encoding the cinnamoyl-CoA reductase. Finally, we tested the association between CCR polymorphisms and trait variation using a mixed linear model. A high value of narrow sense heritability was obtained for lignin content (h2 = 0.85) and S/G ratio (h2 = 0.62) indicating that these traits are under strong genetic control. High levels of nucleotide (θ_π = 0.0131) and haplotype (Hd = 0.958) diversity were detected for CCR. From an initial set of 152 biallelic single nucleotide polymorphisms (SNPs), a subset of 65 nonredundant loci was selected. Three intronic SNPs were found to be associated to the variation of S/G ratio after multiple testing correction. In the line of what has been obtained in forest trees, these SNPs explained between 2.45% and 2.87% of the genetic variance of the trait. This study demonstrates the interest of the candidate gene approach for quantitative trait nucleotide detection in Eucalyptus and paves the way to gene assisted selection of lignin composition in E. urophylla.     

Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.)

The characteristics of starch, such as gelatinization temperature (GT), apparent amylose content (AAC), pasting temperature (PT) and other physicochemical properties, determine the quality of various products of rice, e.g., eating, cooking and processing qualities. The GT of rice flour is controlled by the alk locus, which has been co-mapped to the starch synthase IIa (SSIIa) locus. In this study, we sequenced a 2,051 bp DNA fragment spanning part of intron 6, exon 7, intron 7, exon 8 and part of 3′ untranslated region of SSIIa for 30 rice varieties with diverse geographical distribution and variation in starch physicochemical properties. A total of 24 single nucleotide polymorphisms (SNPs) and one insertion/deletion (InDel) were identified, which could be classified into nine haplotypes. The mean pairwise nucleotide diversity π was 0.00292, and Watterson’s estimator θ was 0.00296 in this collection of rice germplasm. Tajima’s D test for selection showed no significant deviation from the neutral expectation (D = − 0.04612, P > 0.10). However, significant associations were found between seven of the SNPs and peak GT (T _p) at P < 0.05, of which two contiguous SNPs (GC/TT) showed a very strong association with T _p (P < 0.0001). With some rare exception, this GC/TT polymorphism alone can differentiate rice varieties with high or intermediate GT (possessing the GC allele) from those with low GT (possessing the TT allele). In contrast, none of these SNPs or InDel was significantly associated with amylose content. A further 509 rice varieties with known physicochemical properties (e.g., AAC and PT) and known alleles of other starch synthesizing genes were genotyped for the SSIIa GC/TT alleles. Association analysis indicated that 82% of the total variation of AAC in these samples could be explained by a (CT)n simple sequence repeat (SSR) and a G/T SNP of Waxy gene (Wx), and 62.4% of the total variation of PT could be explained by the GC/TT polymorphism. An additional association analysis was performed between these molecular markers and the thermal and retrogradation properties for a subset of 245 samples from the 509 rice varieties. The SSIIa GC/TT polymorphism explained more than 60% of the total variation in thermal properties, whereas the SSR and SNP of Wx gene explained as much as the SSIIa GC/TT of the total variation in retrogradation properties. Our study provides further support for the utilization of the GC/TT polymorphism in SSIIa. As shown in our study of 509 rice varieties, the GC/TT SNP could differentiate rice with high or intermediate GT from those with low GT in about 90% of cases. Using four primers in a single PCR reaction, the GC/TT polymorphism can be surveyed on a large scale. Thus, this SNP polymorphism can be very useful in marker-assisted selection for the improvement of GT and other physicochemical properties of rice.     

Strategy for fluorescent labeling of human acidic fibroblast growth factor without impairment of mitogenic activity: a bona fide tracer

A deuterium reagent, 1-(d5) phenyl-3-methyl-5-pyrazolone (d5-PMP), has been synthesized and used for relative quantitative analysis of oligosaccharides by mass spectrometry (MS) using d0/d5-PMP stable isotopic labeling. Previously reported permethylation-based isotopic labels generate variable mass differences, and reductive amination-based isotopic labels cause a loss of some acid-labile groups in carbohydrates. In contrast, d0/d5-PMP stable isotopic labeling is performed at the reducing end of glycans under basic conditions without desialylation, and the mass difference (Δm = 10 Da) between the heavy form (d5-PMP derivative) and light form (d0-PMP derivative) of each glycan is invariable. When the two derivative forms of a glycan are mixed in equimolar amounts, a pair of peaks with a 10-Da mass differences is observed in the MS profile. The difference at relative intensity between the d0- and d5-PMP derivatives reflects the difference in quantity of glycans in two samples, making it possible to carry out both qualitative and relative quantitative analyses of glycans in glycomic studies. Application of this method on DP₂ to DP₆ maltodextrin oligosaccharides and N-linked glycans released from ribonuclease B and bovine fetuin demonstrates a 10-fold relative quantitative dynamic range, a satisfying reproducibility (coefficient of variation [CV] ? 8.34%), and good accuracy (relative error [RE] ? 5.1%) of the method. The suggested technique has been successfully applied for comparative quantitative analysis of free oligosaccharides in human and bovine milk.     

Cloning of bovine LYST gene and identification of a missense mutation associated with Chediak-Higashi syndrome of cattle

An inheritable bleeding disorder with light coat color caused by an autosomal recessive gene has been reported in a population of Japanese black cattle. The disease has been diagnosed as Chediak-Higashi Syndrome (CHS) of cattle which correspond to a human inheritable disorder caused by mutation in LYST gene. To characterize the molecular lesion causing CHS in cattle, cDNAs encoding bovine LYST were isolated from a bovine brain cDNA library. The nucleotide and deduced amino acid sequences of bovine LYST had 89.6 and 90.2% identity with those of the human LYST gene, respectively. In order to identify the mutation within the LYST gene causing CHS in cattle, cDNA fragments of the LYST gene were amplified from an affected animal by RT-PCR and their nucleotide sequences were completely determined. Notably, a nucleotide substitution of A to G transition, resulting in an amino acid substitution of histidine to arginine (H2015R) was identified in the affected animal. The presence of the substitution was completely corresponding with the occurrence of the CHS phenotype among 105 members of pedigrees of the Japanese black cattle and no cattle of other populations had this substitution. These findings strongly suggested that H2015R is the causative mutation in CHS of Japanese black cattle. Received: 25 May 1999 / Accepted: 26 July 1999