The ability of wheat to adapt to a wide range of environmental conditions is determined mostly by allelic diversity among genes regulating vernalization requirement.Vrn-1 is a major regulator of this requirement.In th...The ability of wheat to adapt to a wide range of environmental conditions is determined mostly by allelic diversity among genes regulating vernalization requirement.Vrn-1 is a major regulator of this requirement.In this study,two novel alleles of Vrn-A1 were discovered in Chinese cultivars:vrn-A1n was identified in two landraces,Jiunong 2 and Ganchun 16,and Vrn-A1o was detected in Duanhongmangmai.Both novel alleles showed a linked duplication in the promoter region.The common copy of these two alleles was identical to the recessive allele vrn-A1.Compared with the recessive allele vrn-A1,the other copy of vrn-A1n contained a 54-bp deletion in the promoter region and the distinct copy of Vrn-A1o contained an11-bp deletion in the promoter region.In segregating populations in the greenhouse under nonvernalizing(20–25°C)and long-day(16 h light)conditions,plants with the novel vrn-A1n allele did not head earlier than those with the recessive vrn-A1 allele.However,plants that were either homozygous or heterozygous for the novel Vrn-A1o allele headed earlier than those with the recessive vrn-A1 allele.To identify the novel allele with the small-sized product and facilitate screening,a DNA marker for the novel dominant allele Vrn-A1o was designed.Analysis of the novel-allele distribution showed that two cultivars carrying the vrn-A1n allele were dispersed in the northwestern spring wheat zone,and 12 cultivars carrying the dominant Vrn-A1o allele were widely distributed in the northwestern spring wheat zone,Xinjiang winter and spring wheat zone,Yellow and Huai River valley winter wheat zone,and QinghaiTibetan Plateau spring and winter wheat zone.Our study identifies useful germplasm and a DNA marker for wheat breeding.展开更多
Chrysanthemums are sensitive to waterlogging stress,and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breedin...Chrysanthemums are sensitive to waterlogging stress,and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding.To understand the genetic basis of waterlogging tolerance(WT)in chrysanthemums,we performed a genome-wide association study(GWAS)using 92,811 single nucleotide polymorphisms(SNPs)in a panel of 88 chrysanthemum accessions,including 64 spray cut and 24 disbud chrysanthemums.The results showed that the average MFVW(membership function value of waterlogging)of the disbud type(0.65)was significantly higher than that of the spray type(0.55)at P<0.05,and the MFVW of the Asian accessions(0.65)was significantly higher than that of the European accessions(0.48)at P<0.01.The GWAS performed using the general linear model(GLM)and mixed linear model(MLM)identified 137 and 14 SNP loci related to WT,respectively,and 11 associations were commonly predicted.By calculating the phenotypic effect values for 11 common SNP loci,six highly favorable SNP alleles that explained 12.85—21.85%of the phenotypic variations were identified.Furthermore,the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified(r2=0.45;P<0.01).A major SNP locus(Marker6619-75)was converted into a derived cleaved amplified polymorphic sequence(dCAPS)marker that cosegregated with WT with an average efficiency of 78.9%.Finally,four putative candidate genes in the WT were identified via quantitative real-time PCR(qRT-PCR).The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection(MAS)in chrysanthemum WT breeding programs.展开更多
Semi-dwarfing improves the lodging resistance and yield of rice,and the vast majority of modern rice varieties harbor the sd1 allele to decrease plant height,resulting in reduced genetic diversity and negative agronom...Semi-dwarfing improves the lodging resistance and yield of rice,and the vast majority of modern rice varieties harbor the sd1 allele to decrease plant height,resulting in reduced genetic diversity and negative agronomic traits.Thus,exploring alternative sources of dwarfism is imperative for rice breeding.Here,we identified a novel RGA1 allele,d1-w,from a local indica variety Xiaolixiang(XLX)using a map-based cloning approach.Compared with other rice varieties,RGA1 in XLX contained a unique single nucleotide polymorphism that resulted in an additional transcript and reduced functional RGA1 transcript level.The RGA1 from Nipponbare was introduced into XLX to estimate the value of d1-w in rice breeding.Compared with transgenic XLX plants(XLX^(D1)),XLX exhibited reduced plant height,increased stem strength,lower reactive oxygen species accumulation,delayed senescence,stronger photosynthesis,higher grain yield and quality(including external,milling and nutritional qualities),and enhanced resistance to drought and Rhizoctonia solani.Therefore,we proposed that the d1-w allele has potential as an excellent dwarfism resource for rice breeding.展开更多
Self-incompatibility(SI)to self-compatibility(SC)transition is one of the most frequent and prevalent evolutionary shifts in flowering plants.Prunus L.(Rosaceae)is a genus of over 200 species most of which exhibit a G...Self-incompatibility(SI)to self-compatibility(SC)transition is one of the most frequent and prevalent evolutionary shifts in flowering plants.Prunus L.(Rosaceae)is a genus of over 200 species most of which exhibit a Gametophytic SI system.Peach[Prunus persica(L.)Batsch;2n=16]is one of the few exceptions in the genus known to be a fully selfcompatible species.However,the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and,in order to fill that gap,in this study 24 peach accessions were analyzed.Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes.The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant(P>0.05),except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus.Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additionalα-helices at the C-termini.Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2,while the SFB1 seemed to evolve neutrally.Thus,our results show that the SFB2 allele diversified after P.persica and P.dulcis(almond)divergence,a period which is characterized by an important bottleneck,while SFB1 diversified at a transition time between the bottleneck and population expansion.展开更多
Polymorphisms in promoter regions of inflammatory cytokines have been widely studied,and potentially functional polymorphisms have been discovered.Conflicting results from meta-analyses of interleukin(IL)-1B and IL-10...Polymorphisms in promoter regions of inflammatory cytokines have been widely studied,and potentially functional polymorphisms have been discovered.Conflicting results from meta-analyses of interleukin(IL)-1B and IL-10 polymorphisms show differences in gastric cancer susceptibilities between Caucasian and Asian populations.In particular,we note the suggestion of an allele flip in IL-1B and IL-10 gene polymorphisms.In Asian populations,the IL-1B-1464G/-511C/-31T haplotype indicates risk for gastric cancer,while the opposite haplotype,IL-1B-1464C/-511T/-31C is the risk-related allele in Caucasians.Furthermore,while IL-10-1082G/-819C/-592C is associated with gastric cancer in Asians,IL-10-1082A/-819T/-592T is linked to gastric cancer risk in Caucasians.These seemingly contradictory results may be attributed to distinct carcinogenic mechanisms underlying the different gastric cancer subtypes.The allele flip observed in IL-10 and gastric cancer appears to reflect allelic heterogeneity,similar to that observed in IL-1B.In this review,we focus on the allele flip phenomenon observed between different ethnic groups in an effort to resolve certain controversial results from recent studies on interleukin polymorphism.In addition,we re-emphasize the importance of stratifying gastric cancer subtypes based on anatomical site and Lauren classification to prevent false associations arising through dilution of true ones.展开更多
Waxy maize is one of the main fresh-eating maize types,and a mutation of the waxy gene causes the waxy character of maize grains.China is rich in waxy maize landraces,and Yunnan and its surrounding areas,are the place...Waxy maize is one of the main fresh-eating maize types,and a mutation of the waxy gene causes the waxy character of maize grains.China is rich in waxy maize landraces,and Yunnan and its surrounding areas,are the place of origin and genetic diversity center of Chinese waxy maize.The six known waxy alleles of Chinese waxy maize are wx-D7,wx-D10,wx-Cin4,wx-124,wx-Reina,and wx-Xuanwei.The mutation sites of these alleles all occur in the coding region of the waxy gene,however,the mechanism by which the waxy characteristic is caused by the mutation in the regulatory region has only been reported rarely in maize.In this study,405 waxy maize landraces from Yunnan were used as materials to identify the insertion and deletion of a large sequence fragment in the upstream~3.5 kb regulatory region of the waxy gene by molecular marker detection.Three different waxy alleles were identifed in this study:wx-PIF/Harbinger,wx-hAT and wxElote2.These three types of mutations all represented transposons inserted into the regulatory region of the waxy gene.Wx-PIF/Harbinger was a 304-bp MITE class transposon insertion belonging to the PIF/Harbinger family,while wx-hAT was a 560-bp MITE class transposon insertion belonging to the hAT family,and wx-Elote2 was a 6560-bp LTR-like transposon insertion.In this study,the alleles were identifed for more than 70%of the waxy maize landraces in Yunnan,which provids a basis for the utilization of these waxy maize landraces.展开更多
Blast,a disease caused by Magnaporthe oryzae,is a major constraint for rice production worldwide.Introgression of durable blast resistance genes into high-yielding rice cultivars has been considered a priority to cont...Blast,a disease caused by Magnaporthe oryzae,is a major constraint for rice production worldwide.Introgression of durable blast resistance genes into high-yielding rice cultivars has been considered a priority to control the disease.The blast resistance Pik locus,located on chromosome 11,contains at least six important resistance genes,but these genes have not been widely employed in resistance breeding since existing markers hardly satisfy current breeding needs due to their limited scope of application.In this study,two PCR-based markers,Pikp-Del and Pi1-In,were developed to target the specific In Del(insertion/deletion)of the Pik-p and Pi-1 genes,respectively.The two markers precisely distinguished Pik-p,Pi-1,and the K-type alleles at the Pik locus,which is a necessary element for functional genes from rice varieties.Results also revealed that only several old varieties contain the two genes,of which nearly half carry the K-type alleles.Therefore,these identified varieties can serve as new gene sources for developing blast resistant rice.The two newly developed markers will be highly useful for the use of Pik-p,Pi-1 and other resistance genes at the Pik locus in markerassisted selection(MAS)breeding programs.展开更多
Strawberry(Fragaria spp.)is a member of the Rosoideae subfamily in the family Rosaceae.The self-incompatibility(SI)of some diploid species is a key agronomic trait that acts as a basic pollination barrier;however,the ...Strawberry(Fragaria spp.)is a member of the Rosoideae subfamily in the family Rosaceae.The self-incompatibility(SI)of some diploid species is a key agronomic trait that acts as a basic pollination barrier;however,the genetic mechanism underlying SI control in strawberry remains unclear.Two candidate S-RNases(S a-and S^-RNase)identi fi ed in the transcriptome of the styles of the self-incompatible Fragaria viridis 42 were con fi rmed to be SI determinants at the S locus following genotype identi fi cation and intraspeci fi c hybridization using sel fi ng progenies.Whole-genome collinearity and RNase T2 family analysis revealed that only an S locus exists in Fragaria;however,none of the compatible species contained S-RNase.Although the results of interspeci fi c hybridization experiments showed that F.viridis(SI)styles could accept pollen from F.mandshurica(self-compatible),the reciprocal cross was incompatible.S a and S b-RNase contain large introns,and their noncoding sequences(promotors and introns)can be transcribed into long noncoding RNAs(lncRNAs).Overall,the genus Fragaria exhibits S-RNase-based gametophytic SI,and S-RNase loss occurs at the S locus of compatible germplasms.In addition,a type of SI-independent unilateral incompatibility exists between compatible and incompatible Fragaria species.Furthermore,the large introns and neighboring lncRNAs in S-RNase in Fragaria could offer clues about S-RNase expression strategies.展开更多
ebisu dwarf (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived f...ebisu dwarf (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived from a Nippon- bare mutant library (d2-3, d2-4, and d2-6) produced more severe dwarf phenotypes than the previously characterized null allele from a Taichung 65 mutant library, d2-1. Linkage analysis and a complementation test clearly indicated that the mutant phenotypes in d2-6 were caused by defects in CYP90D2/D2, and exogenous treatment with brassinolide, a bioactive brassinosteroid, rescued the dwarf phenotype of three Nipponbare-derived d2 mutants. However, the content of endogenous bioactive brassinosteroid, castasterone, and the expression of brassinosteroid-response genes indicated that partial suppression of the brassinosteroid response in addition to a brassinosteroid deficiency has occurred in the Nipponbare-derived d2 mutants. Based on these results, we discuss the possibility that wild-type Nipponbare has some defects in an unknown factor or factors related to the brassinosteroid response in rice.展开更多
A 32bp deletion in the chemokine receptor 5 (CCR5) gene (CMKBR5) was shown to be linked to HIV resistance. Bone marrow transplantation from the homozygous CCR5-del32 donor to a CDC Stage 2 HIV-positive recipient was d...A 32bp deletion in the chemokine receptor 5 (CCR5) gene (CMKBR5) was shown to be linked to HIV resistance. Bone marrow transplantation from the homozygous CCR5-del32 donor to a CDC Stage 2 HIV-positive recipient was demonstrated to confer a HIV resistance, resulting in discontinuation of antiretroviral therapy. In search for an unlimited source of CCR5-del32 cells for transplantation purposes, we tested 137 human embryonic stem cell (hESC) lines from the Reproductive Genetics Institute’s hESC lines collection, and report here the finding of 12 hESC lines with the CCR5-del32 allele, one of which represents a unique partenogenetic ESC line containing two copies of this deletion and may be studied for utility in stem cell transplantation treatment of HIV.展开更多
The genus Solenopsis includes more than 100 species in the New World. When introduced, some species cause serious harm to the native wildlife and agriculture. Two forms of social organization are known in the genus, n...The genus Solenopsis includes more than 100 species in the New World. When introduced, some species cause serious harm to the native wildlife and agriculture. Two forms of social organization are known in the genus, namely, monogyne and polygyne. Here, we present the genetic profile of a Solenopsis invicta Buren 1972 colony recorded in the central region of the city of São Paulo, São Paulo state, Brazil (23°33'37.18"S;46°42'48.66"W) to describe allele diversity. Eight microsatellite loci were used for the analysis of 30 worker ants. The results show the presence of seven alleles genotyped at the same microsatellite locus. Because this is an unusual finding, all of the alleles were sequenced, and surprisingly, an eighth allele was identified. These data suggest that the intracolonial genetic profile of fire ants must be investigated more frequently because there may be unexpected, albeit unknown, genetic patterns for S. invicta that can help inform better control and management programs.展开更多
Cerebrovascular endothelial dysfunction is involved in the progression of leukoaraiosis. Asymmetric dimethylarginine is a competitive inhibitor of nitric oxide, which is highly expressed in patients with leukoaraiosis...Cerebrovascular endothelial dysfunction is involved in the progression of leukoaraiosis. Asymmetric dimethylarginine is a competitive inhibitor of nitric oxide, which is highly expressed in patients with leukoaraiosis. Dimethylarginine dimethylaminohydrolase(DDAH) is a hydrolytic enzyme that is primarily responsible for eliminating asymmetric dimethylarginine, and it plays a role in the pathogenesis of cardiovascular and cerebrovascular diseases. The DDAH2 subtype is expressed in organs rich in induced nitric oxide synthase, including the heart, the placenta, and the cerebral endothelium during cerebral ischemia, in the stress state, or under neurotoxicity. Overexpression of the DDAH2 gene can inhibit asymmetric dimethylarginine-induced peripheral circulating endothelial cell dysfunction. However, it is unknown whether this polymorphism regulates plasma asymmetric dimethylarginine levels in patients with leukoaraiosis. In this doubleblind study, we recruited 46 patients with leukoaraiosis and 46 healthy, matched controls. Plasma asymmetric dimethylarginine levels were determined using enzyme-linked immunoassays. Genomic DNA was isolated from whole blood samples, and polymerase chain reaction, Sma I restriction enzyme digestion, restriction fragment length polymorphisms, and agarose electrophoresis were used to detect DDAH2(-449 G/C) gene polymorphisms. The results revealed that 95.65% of leukoaraiosis patients had recessive genetic models(GG and CG), while 89.13% of healthy control subjects had dominant genetic models(CC and CG). There was a significant difference in the genotype composition ratio between leukoaraiosis patients and healthy controls(P = 0.0002). The frequency of G alleles in the leukoaraiosis patients(71.74%) was significantly higher than in healthy controls, whereas the frequency of C alleles was lower(χ~2 = 13.9580, P = 0.0002). Furthermore, asymmetric dimethylarginine concentrations in subjects with the GG genotype were significantly higher than in subjects with the CG and CC genotypes(Kruskal–Wallis H = 24.5955, P < 0.0001). In addition, the GG genotype of DDAH2(-449 G/C) was more common in patients with leukoaraiosis. These findings suggest that the G allele of DDAH2(-449 G/C) is a risk factor for leukoaraiosis morbidity and is correlated with high levels of asymmetric dimethylarginine. This study was approved by the Institutional Ethics Committee of the 2~(nd) Affiliated Hospital of Harbin Medical University of China(approval No. KY2016-177) on July 28, 2016.展开更多
The Green Revolution gene sd1 has been used extensively in modern rice breeding,especially in indica cultivars.However,elite sd1 alleles and related germplasm resources used for japonica rice breeding have not been id...The Green Revolution gene sd1 has been used extensively in modern rice breeding,especially in indica cultivars.However,elite sd1 alleles and related germplasm resources used for japonica rice breeding have not been identified,and extensive efforts are needed for japonica rice breeding to obtain new dwarfing sources.Data from MBKbase-Rice revealed seven sd1 haplotypes in indica and four in japonica rice.Two new sd1 alleles were identified in indica rice.In 295 japonica accessions from northeast Asia,except for the weak functional allele SD1-EQ,sd1-r was the major allele,reducing plant height in comparison with SD1-EQ.Japonica germplasm resources carrying reported sd1 alleles were identified by genotype searching and further verified by literature search,genealogical analysis,and d Caps markers.Pedigrees and geographic distribution showed that sd1-r is an excellent allele widely used in northern China and Tohoku in Japan,and sd1-j is commonly used in east China and Kyushu in Japan.Dongnong-and Xiushui-series cultivars carrying sd1-r and sd1-j,respectively,are essential branches of the backbone parents of Chinese japonica rice,Akihikari and Ce21,with the largest number of descendants and derived generations.In semi-dwarf japonica rice breeding,sd1-d was introgressed into Daohuaxiang 2(DHX2).Dwarf and semi-dwarf lines carrying sd1-d were selected and designated as 1279 and 1280,respectively,after withstanding typhoon-induced strong winds and heavy rains in 2020,and are anticipated to become useful intermediate materials for future genetic research and breeding.This work will facilitate the introduction,parental selection,and marker-assisted breeding,and provide a material basis for the next step in identifying favorable genes that selected together with the sd1 alleles in japonica backbone parents.展开更多
A new, improved version of the catalog of 182 alleles at the six Gli loci of common wheat(T.aestivum L.) shown in electrophoregrams of 128 standard genotypes was used for analysis of1060 cultivars and lines bred in th...A new, improved version of the catalog of 182 alleles at the six Gli loci of common wheat(T.aestivum L.) shown in electrophoregrams of 128 standard genotypes was used for analysis of1060 cultivars and lines bred in the 20 th century. The most frequent alleles in the studied germplasm occurred with frequencies of 18%–40%, with 30 unique alleles, one in each cultivar. Extremely high genetic diversity was found(average H for the six main Gli loci was0.870 ± 0.046), nearly identical in winter(H = 0.831) and spring(H = 0.856) wheats but differing among 28 groups of cultivars released in 22 countries. Each country or region was characterized by its own specific set of the most frequent Gli alleles, and the 28 cultivar groups formed five main relationship clusters if polymorphism at the six Gli loci was considered. However, different levels of similarity between groups of cultivars were found if polymorphism of the A, B, or D genomes of common wheat was tested separately. In general, the 20 th century germplasm of common wheat was differentiated and structured by country or region and cultivar type(spring or winter). Each elemental genome(in particular, A and D) contributed to the structure of the polymorphism studied. We propose that the structure of the wheat germplasm was a result of natural selection under the ecoclimatic conditions of cultivation specific to each country or region. As many as 27.4% of cultivars studied violated the requirement of the DUS rules for uniformity, being represented by mixtures of two or more closely related genotypes. However, the composition of a cultivar as a set of related but different genotypes may contribute to its adaptivity, and thereby to the known high plasticity of common wheat.展开更多
Objective:To compare the genotype frequencies of HLA class-ⅡDRB1 alleles in Giardia(G.)lamblia-infected children.Methods:A total of 490 Egyptian children aged 2-16 years were subjected to microscopic stool examinatio...Objective:To compare the genotype frequencies of HLA class-ⅡDRB1 alleles in Giardia(G.)lamblia-infected children.Methods:A total of 490 Egyptian children aged 2-16 years were subjected to microscopic stool examination to detect G.lamblia infection,and to exclude other intestinal pathogens.On the basis of their microscopic findings,a group of 80 children were chosen as giardiasis cases,another 80 children were confirmed as Giardia free control group by immunochromatographic test,and the remaining children were excluded.Both giardiasis and control groups were then subjected to blood examination to identify their genetic type of HLA-DRB1 alleles.Results:HLA class-ⅡDRB1*03:01 and DRB1*13:01 alleles were significantly associated with G.lamblia infection(P<0.001 for each variable).On the other hand,HLA class-ⅡDRB1*04:02,DRB1*10:01,DRB1*14:01 and DRB1*15:01 alleles were significantly demonstrated in Giardia free children.However,other HLA-DRB1 alleles did not show any significant association with giardiasis.Conclusions:HLA class-ⅡDRB1*03,DRB1*13,DRB1*04,DRB1*10,DRB1*14 and DRB1*15 alleles may be involved in the establishment of host immune response to G.lamblia infection.展开更多
DEAR EDITOR,Understanding the different immune responses of wild and domestic caprid species is critical for addressing certain zoonotic diseases.In this study,we generated blood transcriptomes of 13 Siberian ibex and...DEAR EDITOR,Understanding the different immune responses of wild and domestic caprid species is critical for addressing certain zoonotic diseases.In this study,we generated blood transcriptomes of 13 Siberian ibex and domestic goat hybrids and performed allele-specific expression and splicing analyses.Results showed that genes exhibiting significant imbalance between the ibex and goat were highly related to the Toll-like receptor(TLR),antigen recognition,and immune activation pathways.Comparative genomic analysis of the species revealed that immune function-related genes were under strong selection pressure in the domestic goat.展开更多
This study investigated distribution of HLA alleles (HLADRB1*01, *03, *04, *07, HLA-DQB1*0201, *0301/4) in 34 healthy controls and 57 rheumatoid arthritis (RA) patients in a Bangladeshi population and correlated the g...This study investigated distribution of HLA alleles (HLADRB1*01, *03, *04, *07, HLA-DQB1*0201, *0301/4) in 34 healthy controls and 57 rheumatoid arthritis (RA) patients in a Bangladeshi population and correlated the genotypic frequencies with clinical parameters. Frequency distribution of HLA-DRB1*04 (34%) and HLA-DRB1*01 (32%) were the highest followed by HLA-DQB1*0301/4 (29%) and HLA-DQB1*0201 (26%) in RA patients while HLA-DRB1*03 (12%) had lowest frequency. Plasma level of anti-CCP and rheumatoid factor antibodies confirmed diagnosis of RA patients that varied significantly between patients and healthy controls. Likewise, plasma levels of C-reactive protein, triglycerides, cholesterol, HDL-cholesterol and activities of AST and ALT exhibited significant variation between the two groups. In contrast, the levels of glucose, total protein, uric acid, LDL-cholesterol and plasma activity of ALP in RA patients had no significant deviations from healthy controls. Relationship between HLA genotype frequency and clinical parameters revealed that the mean levels of anti-CCP and rheumatoid factor antibodies were highest in the patients harboring HLA-DRB1*04 allele. These findings underpin the correlation between HLA genotype with clinical markers of RA which are indicative of disease severity. The positive correlation of these markers with certain HLA genes may be used to identify susceptible individuals who are likely to have RA in Bangladeshi population.展开更多
Background: In Iranian patients with opticospinal multiple sclerosis (OSMS), a paucity of brain lesions and short spinal cord lesions extending less than three spinal segments are characteristic findings on magnetic r...Background: In Iranian patients with opticospinal multiple sclerosis (OSMS), a paucity of brain lesions and short spinal cord lesions extending less than three spinal segments are characteristic findings on magnetic resonance imaging (MRI). It also shows a relatively benign course with negative CSF oligo-coonal bands. Objective: We aimed to clarify the possible relationship between clinical phenotype and MRI features of OSMS and human leucocyte antigen (HLA) system in Iran. Methods: Genotyping of HLA class II allele frequencies in 20 patients with OSMS were done, using polymerase chain reaction sequence-specific primer amplification method. Blood samples were extracted and typed for HLA-DRB, DQA, and DQB loci and compared with 100 controls. Results: Significant positive association was observed in DRB1*03, DQA1*0201, DQA1*03, DQB1*0201, and DQB1*0611, while DQB1*0602 was absent in our patients. Conclusion: These finding suggest that HLA-DRB association pattern in OSMS is different from conventional MS in Iran which is mostly associated with DRB1*1501 and from similar Japanese OSMS who are negative for brain lesions fulfilling the Barkhof criteria and negative for the presence of longitudinally extensive spinal cord lesions who carries the DRB*0405 allele. OSMS is immunogenetically heterogeneous. Also absence of DQB1*0602 allele may negatively be associated with the absence of Barkhof brain lesion.展开更多
Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objec...Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objective of this study was to estimate the degree of additive genetic variance explained by single nucleotide polymorphism (SNP) marker groups with different levels of minor allele frequency (MAF) for marbling score and carcass weight in Japanese Black cattle. Phenotypic data on 872 fattened steers with the genotype information about 40,000 autosomal SNPs were analyzed using two different statistical models: one considering only SNPs selected based on MAF (model 1) and the other also considering all remaining SNPs as the different term (model 2). All available SNPs were classified into 10 groups based on their MAFs. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2. For carcass weight, relatively high values of the proportion of the additive genetic variance were estimated when using SNPs with MAFs which were in the ranges of 0.20 to 0.25 and 0.25 to 0.30, which may be partly due to the three previously-reported quantitative trait loci candidate regions. The results could have provided some information on the genetic architecture for the carcass traits in Japanese Black cattle, although its validity may be limited, mainly due to the sample size and the use of simpler statistical models in this study.展开更多
基金funded by the National Key Research and Development Program of China(2016YFD0101802)the Key Research and Development Project of Shaanxi Province(2019ZDLNY04-05)+1 种基金the National Basic Research Program of China(2014CB138102)the National Natural Science Foundation of China(30971770 and 31671693)。
文摘The ability of wheat to adapt to a wide range of environmental conditions is determined mostly by allelic diversity among genes regulating vernalization requirement.Vrn-1 is a major regulator of this requirement.In this study,two novel alleles of Vrn-A1 were discovered in Chinese cultivars:vrn-A1n was identified in two landraces,Jiunong 2 and Ganchun 16,and Vrn-A1o was detected in Duanhongmangmai.Both novel alleles showed a linked duplication in the promoter region.The common copy of these two alleles was identical to the recessive allele vrn-A1.Compared with the recessive allele vrn-A1,the other copy of vrn-A1n contained a 54-bp deletion in the promoter region and the distinct copy of Vrn-A1o contained an11-bp deletion in the promoter region.In segregating populations in the greenhouse under nonvernalizing(20–25°C)and long-day(16 h light)conditions,plants with the novel vrn-A1n allele did not head earlier than those with the recessive vrn-A1 allele.However,plants that were either homozygous or heterozygous for the novel Vrn-A1o allele headed earlier than those with the recessive vrn-A1 allele.To identify the novel allele with the small-sized product and facilitate screening,a DNA marker for the novel dominant allele Vrn-A1o was designed.Analysis of the novel-allele distribution showed that two cultivars carrying the vrn-A1n allele were dispersed in the northwestern spring wheat zone,and 12 cultivars carrying the dominant Vrn-A1o allele were widely distributed in the northwestern spring wheat zone,Xinjiang winter and spring wheat zone,Yellow and Huai River valley winter wheat zone,and QinghaiTibetan Plateau spring and winter wheat zone.Our study identifies useful germplasm and a DNA marker for wheat breeding.
基金supported by the National Natural Science Foundation of China(31730081)the National Science Fund for Distinguished Young Scholars(31425022)+2 种基金the National Natural Science Foundation of China(31572152)the National Science Fund of Jiangsu Province(BK20151429)the Fundamental Research Funds for the Central Universities(KYRC201601).
文摘Chrysanthemums are sensitive to waterlogging stress,and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding.To understand the genetic basis of waterlogging tolerance(WT)in chrysanthemums,we performed a genome-wide association study(GWAS)using 92,811 single nucleotide polymorphisms(SNPs)in a panel of 88 chrysanthemum accessions,including 64 spray cut and 24 disbud chrysanthemums.The results showed that the average MFVW(membership function value of waterlogging)of the disbud type(0.65)was significantly higher than that of the spray type(0.55)at P<0.05,and the MFVW of the Asian accessions(0.65)was significantly higher than that of the European accessions(0.48)at P<0.01.The GWAS performed using the general linear model(GLM)and mixed linear model(MLM)identified 137 and 14 SNP loci related to WT,respectively,and 11 associations were commonly predicted.By calculating the phenotypic effect values for 11 common SNP loci,six highly favorable SNP alleles that explained 12.85—21.85%of the phenotypic variations were identified.Furthermore,the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified(r2=0.45;P<0.01).A major SNP locus(Marker6619-75)was converted into a derived cleaved amplified polymorphic sequence(dCAPS)marker that cosegregated with WT with an average efficiency of 78.9%.Finally,four putative candidate genes in the WT were identified via quantitative real-time PCR(qRT-PCR).The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection(MAS)in chrysanthemum WT breeding programs.
基金supported by grants from the National Natural Science Foundation of China (Grant Nos. 31960403 and 31501286)Jiangxi Natural Science Foundation-Outstanding Youth Science Fund Project,China (Grant No. 20212ACB215003)
文摘Semi-dwarfing improves the lodging resistance and yield of rice,and the vast majority of modern rice varieties harbor the sd1 allele to decrease plant height,resulting in reduced genetic diversity and negative agronomic traits.Thus,exploring alternative sources of dwarfism is imperative for rice breeding.Here,we identified a novel RGA1 allele,d1-w,from a local indica variety Xiaolixiang(XLX)using a map-based cloning approach.Compared with other rice varieties,RGA1 in XLX contained a unique single nucleotide polymorphism that resulted in an additional transcript and reduced functional RGA1 transcript level.The RGA1 from Nipponbare was introduced into XLX to estimate the value of d1-w in rice breeding.Compared with transgenic XLX plants(XLX^(D1)),XLX exhibited reduced plant height,increased stem strength,lower reactive oxygen species accumulation,delayed senescence,stronger photosynthesis,higher grain yield and quality(including external,milling and nutritional qualities),and enhanced resistance to drought and Rhizoctonia solani.Therefore,we proposed that the d1-w allele has potential as an excellent dwarfism resource for rice breeding.
基金supported by the Tunisian“Ministère de l’Enseignement Supérieur et de la Recherche Scientifique”and“Ministerio de Economía y Competitividad-European Regional Development Fund,European Union”(AGL2016-77267-R and PID2019-109566RB-I00)The authors would like to gratefully thank“Sodon collection”(Bou-Selem,Tunisia)and Tunisian farmers for kindly providing plant material.
文摘Self-incompatibility(SI)to self-compatibility(SC)transition is one of the most frequent and prevalent evolutionary shifts in flowering plants.Prunus L.(Rosaceae)is a genus of over 200 species most of which exhibit a Gametophytic SI system.Peach[Prunus persica(L.)Batsch;2n=16]is one of the few exceptions in the genus known to be a fully selfcompatible species.However,the evolutionary process of the complete and irreversible loss of SI in peach is not well understood and,in order to fill that gap,in this study 24 peach accessions were analyzed.Pollen tube growth was controlled in self-pollinated flowers to verify their self-compatible phenotypes.The linkage disequilibrium association between alleles at the S-locus and linked markers at the end of the sixth linkage group was not significant(P>0.05),except with the closest markers suggesting the absence of a signature of negative frequency dependent selection at the S-locus.Analysis of SFB1 and SFB2 protein sequences allowed identifying the absence of some variable and hypervariable domains and the presence of additionalα-helices at the C-termini.Molecular and evolutionary analysis of SFB nucleotide sequences showed a signature of purifying selection in SFB2,while the SFB1 seemed to evolve neutrally.Thus,our results show that the SFB2 allele diversified after P.persica and P.dulcis(almond)divergence,a period which is characterized by an important bottleneck,while SFB1 diversified at a transition time between the bottleneck and population expansion.
文摘Polymorphisms in promoter regions of inflammatory cytokines have been widely studied,and potentially functional polymorphisms have been discovered.Conflicting results from meta-analyses of interleukin(IL)-1B and IL-10 polymorphisms show differences in gastric cancer susceptibilities between Caucasian and Asian populations.In particular,we note the suggestion of an allele flip in IL-1B and IL-10 gene polymorphisms.In Asian populations,the IL-1B-1464G/-511C/-31T haplotype indicates risk for gastric cancer,while the opposite haplotype,IL-1B-1464C/-511T/-31C is the risk-related allele in Caucasians.Furthermore,while IL-10-1082G/-819C/-592C is associated with gastric cancer in Asians,IL-10-1082A/-819T/-592T is linked to gastric cancer risk in Caucasians.These seemingly contradictory results may be attributed to distinct carcinogenic mechanisms underlying the different gastric cancer subtypes.The allele flip observed in IL-10 and gastric cancer appears to reflect allelic heterogeneity,similar to that observed in IL-1B.In this review,we focus on the allele flip phenomenon observed between different ethnic groups in an effort to resolve certain controversial results from recent studies on interleukin polymorphism.In addition,we re-emphasize the importance of stratifying gastric cancer subtypes based on anatomical site and Lauren classification to prevent false associations arising through dilution of true ones.
基金supported by the National Crop Sharing and Service Platform-Yunnan sub Platform,China(NICGR2018-030)the Post-doctoral Targeted Funding of Yunnan Province,China(YRST 2018[168])。
文摘Waxy maize is one of the main fresh-eating maize types,and a mutation of the waxy gene causes the waxy character of maize grains.China is rich in waxy maize landraces,and Yunnan and its surrounding areas,are the place of origin and genetic diversity center of Chinese waxy maize.The six known waxy alleles of Chinese waxy maize are wx-D7,wx-D10,wx-Cin4,wx-124,wx-Reina,and wx-Xuanwei.The mutation sites of these alleles all occur in the coding region of the waxy gene,however,the mechanism by which the waxy characteristic is caused by the mutation in the regulatory region has only been reported rarely in maize.In this study,405 waxy maize landraces from Yunnan were used as materials to identify the insertion and deletion of a large sequence fragment in the upstream~3.5 kb regulatory region of the waxy gene by molecular marker detection.Three different waxy alleles were identifed in this study:wx-PIF/Harbinger,wx-hAT and wxElote2.These three types of mutations all represented transposons inserted into the regulatory region of the waxy gene.Wx-PIF/Harbinger was a 304-bp MITE class transposon insertion belonging to the PIF/Harbinger family,while wx-hAT was a 560-bp MITE class transposon insertion belonging to the hAT family,and wx-Elote2 was a 6560-bp LTR-like transposon insertion.In this study,the alleles were identifed for more than 70%of the waxy maize landraces in Yunnan,which provids a basis for the utilization of these waxy maize landraces.
基金the National Natural Science Foundation of China(31640006)the China Postdocotral Science Foundation(2019M662219)+1 种基金the Youngth Program of Fujian Academy of Agricultural Sciences(YC2019004)the Projection of Public Welfare of Fujian Province(2017R1019-10)。
文摘Blast,a disease caused by Magnaporthe oryzae,is a major constraint for rice production worldwide.Introgression of durable blast resistance genes into high-yielding rice cultivars has been considered a priority to control the disease.The blast resistance Pik locus,located on chromosome 11,contains at least six important resistance genes,but these genes have not been widely employed in resistance breeding since existing markers hardly satisfy current breeding needs due to their limited scope of application.In this study,two PCR-based markers,Pikp-Del and Pi1-In,were developed to target the specific In Del(insertion/deletion)of the Pik-p and Pi-1 genes,respectively.The two markers precisely distinguished Pik-p,Pi-1,and the K-type alleles at the Pik locus,which is a necessary element for functional genes from rice varieties.Results also revealed that only several old varieties contain the two genes,of which nearly half carry the K-type alleles.Therefore,these identified varieties can serve as new gene sources for developing blast resistant rice.The two newly developed markers will be highly useful for the use of Pik-p,Pi-1 and other resistance genes at the Pik locus in markerassisted selection(MAS)breeding programs.
基金This work was supported by the National Natural Science Foundation of Chi na(Gr ant no.32072540,31872056)the Fun dame ntal Research Fun ds for the Central Universities(Grant no.KYZZ2021002)a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD).
文摘Strawberry(Fragaria spp.)is a member of the Rosoideae subfamily in the family Rosaceae.The self-incompatibility(SI)of some diploid species is a key agronomic trait that acts as a basic pollination barrier;however,the genetic mechanism underlying SI control in strawberry remains unclear.Two candidate S-RNases(S a-and S^-RNase)identi fi ed in the transcriptome of the styles of the self-incompatible Fragaria viridis 42 were con fi rmed to be SI determinants at the S locus following genotype identi fi cation and intraspeci fi c hybridization using sel fi ng progenies.Whole-genome collinearity and RNase T2 family analysis revealed that only an S locus exists in Fragaria;however,none of the compatible species contained S-RNase.Although the results of interspeci fi c hybridization experiments showed that F.viridis(SI)styles could accept pollen from F.mandshurica(self-compatible),the reciprocal cross was incompatible.S a and S b-RNase contain large introns,and their noncoding sequences(promotors and introns)can be transcribed into long noncoding RNAs(lncRNAs).Overall,the genus Fragaria exhibits S-RNase-based gametophytic SI,and S-RNase loss occurs at the S locus of compatible germplasms.In addition,a type of SI-independent unilateral incompatibility exists between compatible and incompatible Fragaria species.Furthermore,the large introns and neighboring lncRNAs in S-RNase in Fragaria could offer clues about S-RNase expression strategies.
文摘ebisu dwarf (d2) is a mutant caused by mutation in a rice brassinosteroid biosynthetic enzyme gene, CYP90D2/D2, thereby conferring a brassinosteroid-deficient dwarf phenotype. Three newly isolated d2 alleles derived from a Nippon- bare mutant library (d2-3, d2-4, and d2-6) produced more severe dwarf phenotypes than the previously characterized null allele from a Taichung 65 mutant library, d2-1. Linkage analysis and a complementation test clearly indicated that the mutant phenotypes in d2-6 were caused by defects in CYP90D2/D2, and exogenous treatment with brassinolide, a bioactive brassinosteroid, rescued the dwarf phenotype of three Nipponbare-derived d2 mutants. However, the content of endogenous bioactive brassinosteroid, castasterone, and the expression of brassinosteroid-response genes indicated that partial suppression of the brassinosteroid response in addition to a brassinosteroid deficiency has occurred in the Nipponbare-derived d2 mutants. Based on these results, we discuss the possibility that wild-type Nipponbare has some defects in an unknown factor or factors related to the brassinosteroid response in rice.
文摘A 32bp deletion in the chemokine receptor 5 (CCR5) gene (CMKBR5) was shown to be linked to HIV resistance. Bone marrow transplantation from the homozygous CCR5-del32 donor to a CDC Stage 2 HIV-positive recipient was demonstrated to confer a HIV resistance, resulting in discontinuation of antiretroviral therapy. In search for an unlimited source of CCR5-del32 cells for transplantation purposes, we tested 137 human embryonic stem cell (hESC) lines from the Reproductive Genetics Institute’s hESC lines collection, and report here the finding of 12 hESC lines with the CCR5-del32 allele, one of which represents a unique partenogenetic ESC line containing two copies of this deletion and may be studied for utility in stem cell transplantation treatment of HIV.
文摘The genus Solenopsis includes more than 100 species in the New World. When introduced, some species cause serious harm to the native wildlife and agriculture. Two forms of social organization are known in the genus, namely, monogyne and polygyne. Here, we present the genetic profile of a Solenopsis invicta Buren 1972 colony recorded in the central region of the city of São Paulo, São Paulo state, Brazil (23°33'37.18"S;46°42'48.66"W) to describe allele diversity. Eight microsatellite loci were used for the analysis of 30 worker ants. The results show the presence of seven alleles genotyped at the same microsatellite locus. Because this is an unusual finding, all of the alleles were sequenced, and surprisingly, an eighth allele was identified. These data suggest that the intracolonial genetic profile of fire ants must be investigated more frequently because there may be unexpected, albeit unknown, genetic patterns for S. invicta that can help inform better control and management programs.
基金supported by the Foundation of Harbin Science Technology Bureau of China,No. 2014RFQGJ042 (to YF)Harbin Medical University Scientific Research Innovation Fund of China,No. 2016LCZX06 (to QG)the Natural Science Foundation of Heilongjiang of China,No. H2016027 (to QG)。
文摘Cerebrovascular endothelial dysfunction is involved in the progression of leukoaraiosis. Asymmetric dimethylarginine is a competitive inhibitor of nitric oxide, which is highly expressed in patients with leukoaraiosis. Dimethylarginine dimethylaminohydrolase(DDAH) is a hydrolytic enzyme that is primarily responsible for eliminating asymmetric dimethylarginine, and it plays a role in the pathogenesis of cardiovascular and cerebrovascular diseases. The DDAH2 subtype is expressed in organs rich in induced nitric oxide synthase, including the heart, the placenta, and the cerebral endothelium during cerebral ischemia, in the stress state, or under neurotoxicity. Overexpression of the DDAH2 gene can inhibit asymmetric dimethylarginine-induced peripheral circulating endothelial cell dysfunction. However, it is unknown whether this polymorphism regulates plasma asymmetric dimethylarginine levels in patients with leukoaraiosis. In this doubleblind study, we recruited 46 patients with leukoaraiosis and 46 healthy, matched controls. Plasma asymmetric dimethylarginine levels were determined using enzyme-linked immunoassays. Genomic DNA was isolated from whole blood samples, and polymerase chain reaction, Sma I restriction enzyme digestion, restriction fragment length polymorphisms, and agarose electrophoresis were used to detect DDAH2(-449 G/C) gene polymorphisms. The results revealed that 95.65% of leukoaraiosis patients had recessive genetic models(GG and CG), while 89.13% of healthy control subjects had dominant genetic models(CC and CG). There was a significant difference in the genotype composition ratio between leukoaraiosis patients and healthy controls(P = 0.0002). The frequency of G alleles in the leukoaraiosis patients(71.74%) was significantly higher than in healthy controls, whereas the frequency of C alleles was lower(χ~2 = 13.9580, P = 0.0002). Furthermore, asymmetric dimethylarginine concentrations in subjects with the GG genotype were significantly higher than in subjects with the CG and CC genotypes(Kruskal–Wallis H = 24.5955, P < 0.0001). In addition, the GG genotype of DDAH2(-449 G/C) was more common in patients with leukoaraiosis. These findings suggest that the G allele of DDAH2(-449 G/C) is a risk factor for leukoaraiosis morbidity and is correlated with high levels of asymmetric dimethylarginine. This study was approved by the Institutional Ethics Committee of the 2~(nd) Affiliated Hospital of Harbin Medical University of China(approval No. KY2016-177) on July 28, 2016.
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA24020301)Young Scientists Fund(CN)(31900423)+1 种基金Excellent Youth Foundation for Heilongjiang Scientific Committee(JC2017009)Cooperative Innovation Extension System of Rice Modern Agricultural Industrial Technology in Heilongjiang province。
文摘The Green Revolution gene sd1 has been used extensively in modern rice breeding,especially in indica cultivars.However,elite sd1 alleles and related germplasm resources used for japonica rice breeding have not been identified,and extensive efforts are needed for japonica rice breeding to obtain new dwarfing sources.Data from MBKbase-Rice revealed seven sd1 haplotypes in indica and four in japonica rice.Two new sd1 alleles were identified in indica rice.In 295 japonica accessions from northeast Asia,except for the weak functional allele SD1-EQ,sd1-r was the major allele,reducing plant height in comparison with SD1-EQ.Japonica germplasm resources carrying reported sd1 alleles were identified by genotype searching and further verified by literature search,genealogical analysis,and d Caps markers.Pedigrees and geographic distribution showed that sd1-r is an excellent allele widely used in northern China and Tohoku in Japan,and sd1-j is commonly used in east China and Kyushu in Japan.Dongnong-and Xiushui-series cultivars carrying sd1-r and sd1-j,respectively,are essential branches of the backbone parents of Chinese japonica rice,Akihikari and Ce21,with the largest number of descendants and derived generations.In semi-dwarf japonica rice breeding,sd1-d was introgressed into Daohuaxiang 2(DHX2).Dwarf and semi-dwarf lines carrying sd1-d were selected and designated as 1279 and 1280,respectively,after withstanding typhoon-induced strong winds and heavy rains in 2020,and are anticipated to become useful intermediate materials for future genetic research and breeding.This work will facilitate the introduction,parental selection,and marker-assisted breeding,and provide a material basis for the next step in identifying favorable genes that selected together with the sd1 alleles in japonica backbone parents.
文摘A new, improved version of the catalog of 182 alleles at the six Gli loci of common wheat(T.aestivum L.) shown in electrophoregrams of 128 standard genotypes was used for analysis of1060 cultivars and lines bred in the 20 th century. The most frequent alleles in the studied germplasm occurred with frequencies of 18%–40%, with 30 unique alleles, one in each cultivar. Extremely high genetic diversity was found(average H for the six main Gli loci was0.870 ± 0.046), nearly identical in winter(H = 0.831) and spring(H = 0.856) wheats but differing among 28 groups of cultivars released in 22 countries. Each country or region was characterized by its own specific set of the most frequent Gli alleles, and the 28 cultivar groups formed five main relationship clusters if polymorphism at the six Gli loci was considered. However, different levels of similarity between groups of cultivars were found if polymorphism of the A, B, or D genomes of common wheat was tested separately. In general, the 20 th century germplasm of common wheat was differentiated and structured by country or region and cultivar type(spring or winter). Each elemental genome(in particular, A and D) contributed to the structure of the polymorphism studied. We propose that the structure of the wheat germplasm was a result of natural selection under the ecoclimatic conditions of cultivation specific to each country or region. As many as 27.4% of cultivars studied violated the requirement of the DUS rules for uniformity, being represented by mixtures of two or more closely related genotypes. However, the composition of a cultivar as a set of related but different genotypes may contribute to its adaptivity, and thereby to the known high plasticity of common wheat.
文摘Objective:To compare the genotype frequencies of HLA class-ⅡDRB1 alleles in Giardia(G.)lamblia-infected children.Methods:A total of 490 Egyptian children aged 2-16 years were subjected to microscopic stool examination to detect G.lamblia infection,and to exclude other intestinal pathogens.On the basis of their microscopic findings,a group of 80 children were chosen as giardiasis cases,another 80 children were confirmed as Giardia free control group by immunochromatographic test,and the remaining children were excluded.Both giardiasis and control groups were then subjected to blood examination to identify their genetic type of HLA-DRB1 alleles.Results:HLA class-ⅡDRB1*03:01 and DRB1*13:01 alleles were significantly associated with G.lamblia infection(P<0.001 for each variable).On the other hand,HLA class-ⅡDRB1*04:02,DRB1*10:01,DRB1*14:01 and DRB1*15:01 alleles were significantly demonstrated in Giardia free children.However,other HLA-DRB1 alleles did not show any significant association with giardiasis.Conclusions:HLA class-ⅡDRB1*03,DRB1*13,DRB1*04,DRB1*10,DRB1*14 and DRB1*15 alleles may be involved in the establishment of host immune response to G.lamblia infection.
基金supported by the National Natural Science Foundation of China(32002140,32050410304)China Agriculture Research System of MOF and MARA(CARS-39-21)+3 种基金Natural Science Basic Research Program of Shaanxi(2021JCW-11)Natural Science Basic Research Program of Xinjiang(2022 XJRMY-01)Special Fund for Animal Husbandry of Shaanxi(K3030821073)China Postdoctoral Science Foundation(2020M682446)。
文摘DEAR EDITOR,Understanding the different immune responses of wild and domestic caprid species is critical for addressing certain zoonotic diseases.In this study,we generated blood transcriptomes of 13 Siberian ibex and domestic goat hybrids and performed allele-specific expression and splicing analyses.Results showed that genes exhibiting significant imbalance between the ibex and goat were highly related to the Toll-like receptor(TLR),antigen recognition,and immune activation pathways.Comparative genomic analysis of the species revealed that immune function-related genes were under strong selection pressure in the domestic goat.
文摘This study investigated distribution of HLA alleles (HLADRB1*01, *03, *04, *07, HLA-DQB1*0201, *0301/4) in 34 healthy controls and 57 rheumatoid arthritis (RA) patients in a Bangladeshi population and correlated the genotypic frequencies with clinical parameters. Frequency distribution of HLA-DRB1*04 (34%) and HLA-DRB1*01 (32%) were the highest followed by HLA-DQB1*0301/4 (29%) and HLA-DQB1*0201 (26%) in RA patients while HLA-DRB1*03 (12%) had lowest frequency. Plasma level of anti-CCP and rheumatoid factor antibodies confirmed diagnosis of RA patients that varied significantly between patients and healthy controls. Likewise, plasma levels of C-reactive protein, triglycerides, cholesterol, HDL-cholesterol and activities of AST and ALT exhibited significant variation between the two groups. In contrast, the levels of glucose, total protein, uric acid, LDL-cholesterol and plasma activity of ALP in RA patients had no significant deviations from healthy controls. Relationship between HLA genotype frequency and clinical parameters revealed that the mean levels of anti-CCP and rheumatoid factor antibodies were highest in the patients harboring HLA-DRB1*04 allele. These findings underpin the correlation between HLA genotype with clinical markers of RA which are indicative of disease severity. The positive correlation of these markers with certain HLA genes may be used to identify susceptible individuals who are likely to have RA in Bangladeshi population.
文摘Background: In Iranian patients with opticospinal multiple sclerosis (OSMS), a paucity of brain lesions and short spinal cord lesions extending less than three spinal segments are characteristic findings on magnetic resonance imaging (MRI). It also shows a relatively benign course with negative CSF oligo-coonal bands. Objective: We aimed to clarify the possible relationship between clinical phenotype and MRI features of OSMS and human leucocyte antigen (HLA) system in Iran. Methods: Genotyping of HLA class II allele frequencies in 20 patients with OSMS were done, using polymerase chain reaction sequence-specific primer amplification method. Blood samples were extracted and typed for HLA-DRB, DQA, and DQB loci and compared with 100 controls. Results: Significant positive association was observed in DRB1*03, DQA1*0201, DQA1*03, DQB1*0201, and DQB1*0611, while DQB1*0602 was absent in our patients. Conclusion: These finding suggest that HLA-DRB association pattern in OSMS is different from conventional MS in Iran which is mostly associated with DRB1*1501 and from similar Japanese OSMS who are negative for brain lesions fulfilling the Barkhof criteria and negative for the presence of longitudinally extensive spinal cord lesions who carries the DRB*0405 allele. OSMS is immunogenetically heterogeneous. Also absence of DQB1*0602 allele may negatively be associated with the absence of Barkhof brain lesion.
文摘Japanese Black cattle are a beef breed and well known to excel in carcass quality, but the details of genetic architectures for carcass traits in beef breeds including this breed are still poorly understood. The objective of this study was to estimate the degree of additive genetic variance explained by single nucleotide polymorphism (SNP) marker groups with different levels of minor allele frequency (MAF) for marbling score and carcass weight in Japanese Black cattle. Phenotypic data on 872 fattened steers with the genotype information about 40,000 autosomal SNPs were analyzed using two different statistical models: one considering only SNPs selected based on MAF (model 1) and the other also considering all remaining SNPs as the different term (model 2). All available SNPs were classified into 10 groups based on their MAFs. For both traits, the estimated proportions of additive genetic variance explained by SNPs selected based on their MAFs using model 1 were always higher than the estimated ones using model 2. For carcass weight, relatively high values of the proportion of the additive genetic variance were estimated when using SNPs with MAFs which were in the ranges of 0.20 to 0.25 and 0.25 to 0.30, which may be partly due to the three previously-reported quantitative trait loci candidate regions. The results could have provided some information on the genetic architecture for the carcass traits in Japanese Black cattle, although its validity may be limited, mainly due to the sample size and the use of simpler statistical models in this study.
