Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into a...Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.展开更多
Understanding the genetic diversity–area relationship(GAR)is essential for comprehending how species adapt to environmental changes,as genetic diversity is an indicator of a species’adaptive potential.Variation in e...Understanding the genetic diversity–area relationship(GAR)is essential for comprehending how species adapt to environmental changes,as genetic diversity is an indicator of a species’adaptive potential.Variation in environmental adaptation capacity exists among species and animal taxa with different distribution areas,highlighting the importance of understanding the GAR.To obtain a more comprehensive understanding of the GAR in terrestrial vertebrates,we assessed both haplotype diversity–area and nucleotide diversity–area relationships using 25,453 cytochrome c oxidase subunit I(COI)sequences from 142 amphibian species,574 bird species,and 342 mammal species.We found that both measures of genetic diversity increased with species range size across major animal groups.Nevertheless,the GAR did not differ among animal groups,while haplotype diversity performed better than nucleotide diversity in profiling the GAR,as indicated by higher R2 values.The difference in the modeling fit may stem from the distinct biological and mathematical significance of nucleotide diversity and haplotype diversity.These results suggest that the GAR follows similar rules among different animal taxa.Furthermore,haplotype diversity may serve as a more reliable indicator for assessing the potential effects of area size changes on animal populations and provide better guidance for conserving genetic diversity.展开更多
In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values w...In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large numberof samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study withhigh efficiency. The platform has been well evaluated by several sets of real data.展开更多
AIM： Prostaglandin G/H synthase 2 （PTGS2 or COX2） is one of the key factors in the cellular response to inflammation. PTGS2 is expressed in the affected intestinal segments of patients with inflammatory bowel disea...AIM： Prostaglandin G/H synthase 2 （PTGS2 or COX2） is one of the key factors in the cellular response to inflammation. PTGS2 is expressed in the affected intestinal segments of patients with inflammatory bowel diseases （IBD）. In IBD patients, non-steroidal anti-inflammatory drugs, which have been shown to reduce both the production and activity of PTGS2, may activate IBD and aggravate the symptoms. We aimed at examining genetic variants of PTGS2 that may be risk factors for IBD. METHODS： We genotyped 291 individuals diagnosed with IBD and 367 controls from the Dutch population for the five most frequent polymorphisms of the PTG52 gene. Clinical data were collected on all patients. DNA was extracted via normal laboratory methods. Genotyping was carried out using multiplex PCR followed by the Invader Assay and the 5＇ exonuclease assay （TaqMan）. New polymorphism screening was performed by pre-screening with denaturing high-performance liquid chromatography, followed by fluorescent sequencing. RESULTS： Allele 5209G was weakly associated with Crohn＇s disease （odds ratio [OR] 1.63, 95% confidence interval [CI] 1.03-2.57）, and allele 8473T with ulcerativecolitis （OR 1.50, 95%CI 1.00-2.27）. The haplotype including both alleles showed a strong association with IBD （OR 13.15, 95%CI 3.17-116.15）. This haplotype, while rare （-0.3%） in the general population, is found more frequently in patients （3.5%）. CONCLUSION： Our data suggest that this haplotype of PTGS2 contributes to the susceptibility of IBD.展开更多
Most modern wheat cultivars were selected on the basis of yield-related indices measured under optimal fertilizer and irrigation inputs.With climate change,land degradation and salinity caused by sea water encroachmen...Most modern wheat cultivars were selected on the basis of yield-related indices measured under optimal fertilizer and irrigation inputs.With climate change,land degradation and salinity caused by sea water encroachment,wheat is increasingly subjected to environmental stress.Moreover,expanding urbanization increasingly encroaches upon prime agricultural land in countries like China,and alternative cropping areas must be found.Some of these areas have moderate constraining factors,such as salinity.Therefore,it is important to investigate whether current genetic materials and breeding procedures are maintaining adequate variability to address future problems caused by abiotic stress.In this study,a panel of 307 wheat accessions,including local landraces,exotic cultivars used in Chinese breeding programs and Chinese cultivars released during different periods since1940,were subjected to a genome-wide association study to dissect the genetic basis of salinity tolerance.Both marker-based and pedigree-based kinship analyses revealed that favorable haplotypes were introduced in some exotic cultivars as well as a limited number of Chinese landraces from the 1940 s.However,improvements in salinity tolerance during modern breeding are not as obvious as that of yield.To broaden genetic diversity for increasing salt tolerance,there is a need to refocus attention on local landraces that have high degrees of salinity tolerance and carry rare favorable alleles that have not been exploited in breeding.展开更多
AIM:To evaluate the association between the geneticpolymorphisms and haplotypes of the ITGA1 gene and the risk of gastric cancer.METHODS:The study subjects were 477 age-and sex-matched case-control pairs.Genotyping wa...AIM:To evaluate the association between the geneticpolymorphisms and haplotypes of the ITGA1 gene and the risk of gastric cancer.METHODS:The study subjects were 477 age-and sex-matched case-control pairs.Genotyping was performed for 15 single nucleotide polymorphisms(SNPs)in ITGA1.The associations between gastric cancer and these SNPs and haplotypes were analyzed with multivariate conditional logistic regression models.Multiple testing corrections were carried out following methodology for controlling the false discovery rate.Gene-based association tests were performed using the versatile gene-based association study(VEGAS)method.RESULTS:In the codominant model,the ORs for SNPs rs2432143(1.517;95%CI:1.144-2.011)and rs2447867(1.258;95%CI:1.051-1.505)were statistically significant.In the dominant model,polymorphisms of rs1862610 and rs2447867 were found to be significant risk factors,with ORs of 1.337(95%CI:1.029-1.737)and 1.412(95%CI:1.061-1.881),respectively.In the recessive model,only the rs2432143 polymorphism was significant(OR=1.559,95%CI:1.150-2.114).The C-C type of ITGA1 haplotype block 2 was a significant protective factor against gastric cancer in the both codominant model(OR=0.602,95%CI:0.212-0.709,P=0.021)and the dominant model(OR=0.653,95%CI:0.483-0.884).The ITGA1 gene showed a significant gene-based association with gastric cancer in the VEGAS test.In the dominant model,the A-T type of ITGA1 haplotype block 2 was a significant risk factor(OR=1.341,95%CI:1.034-1.741).SNP rs2447867 might be related to the severity of gastric epithelial injury due to inflammation and,thus,to the risk of developing gastric cancer.CONCLUSION:ITGA1 gene SNPs rs1862610,rs2432143,and rs2447867 and the ITGA1 haplotype block that includes SNPs rs1862610 and rs2432143 were significantly associated with gastric cancer.展开更多
AIM： To determine the distribution and frequencies of the genotypes and haplotypes of the genes encoding for the glucocorticoid receptor （GR）, the tumor necrosis factor （TNF）-α and the interleukin （IL）-10 in c...AIM： To determine the distribution and frequencies of the genotypes and haplotypes of the genes encoding for the glucocorticoid receptor （GR）, the tumor necrosis factor （TNF）-α and the interleukin （IL）-10 in childhood Crohn＇s disease （CD） and to assess the impact of the corresponding DNA variants on clinical and disease phenotypes.METHODS： Ten variants in GR, TNF-a and IL-10 were genotyped in 113 childhood CD cases and 95 healthy subjects, both of French-Canadian origin.RESULTS： For the GR polymorphisms （R23K and N363S） and IL-10 variants in the 5＇flanking region （-1082 G 〉 A, -819 T 〉 C and -592 A 〉 C）, no difference was observed in allele and genotype frequencies between CD patients and controls. At the haplotype level, we found three IL-10 haplotypes previously described in Caucasians （GCC, ACC and ATA） and three novel haplotypes only present in IBD patients. When we analyzed the haplotype distribution with the anatomical location of the disease, the GCC haplotype was associated with the colonic and the ACC haplotype with the terminal ileum location, respectively. The genotyping of five polymorphisms in the promoter region of the TNF-α gene （-1031 T 〉 C, -863 A 〉 C, -857 T 〉 C, -308 A 〉 G and -238 A 〉 G） revealed a significant overrepresentation of homozygous -1031 CC among CD patients （OR = 9.9） and an association with the colonic location. For TNF-α, eleven haplotypes were inferred, including two frequent ones, TCCGG and CACGG, which were significantly observed more frequently in controls and cases, respectively.CONCLUSION： This is one of the first studies investigating the association between haplotype structure and disease location in a CD pediatric cohort. Our results will help to increase our understanding of the genetic determinants of childhood CD.展开更多
The paternally inherited Y chromosome has been widely used in forensics for personal identification, in anthropology and population genetics to understand origin and migration of human populations, and also in medical...The paternally inherited Y chromosome has been widely used in forensics for personal identification, in anthropology and population genetics to understand origin and migration of human populations, and also in medical and clinical studies （Wang and Li, 2013; Wang et al., 2014）. There are two kinds of extremely useful markers in Y chromosome, single nucle- otide polymorphism （SNP） and short tandem repeats （STRs）. With a very low mutation rate on the order of 3.0 x 10-8 mutations/nucleotide/generation （Xue et al., 2009）, SNP markers have been used in constructing a robust phylogeny tree linking all the Y chromosome lineages from world pop- ulations （Karafet et al., 2008）. Those lineages determined by the pattern of SNPs are called haplogroups. That is to say, we have to genotype an appropriate number of SNPs in order to assign a given Y chromosome to a haplogroup. Compared with SNPs, the mutation rates of STR markers are about four to five orders of magnitude higher （Gusmgo et al., 2005; Ballantyne et al., 2010）. Typing STR has advantages of saving time and cost compared with typing SNPs in phylogenetic assignment of a Y chromosome （Wang et al., 2010）. A set of STR values for an individual is called a haplotype. Because of the disparity in mutation rates between SNP and STR, one SNP haplogroup could actually comprise many STR haplotypes （Wang et al., 2010）. It is most interesting that STR variability is clustered more by haplogroups than by populations （Bosch et al., 1999; Behar et al., 2004）, which indicates that STR haplotypes could be used to infer the haplogroup information of a given Y chromosome. There has been increasing interest in this cost- effective strategy for predicting the haplogroup from a given STR haplotype when SNP data are unavailable. For instance, Vadim Urasin＇s YPredictor （http：//predictor.ydna.ru/）, Whit Atheys＇ haplogroup predictor （http：//www.hprg.com/hapest5/） （Athey, 2005, 2006）, and haplogroup classifier of Arizona University （Schlecht et al., 2008） have been widely employed in previous studies for haplogroup prediction （Larmuseau et al., 2010; Bembea et al., 2011; Larmuseau et al., 2012; Tarlykov et al., 2013）.展开更多
Reconstructed embryos derived from intersubspecies somatic cell nuclear transfer （SCNT） have poorer developmental potential than those from intrasubspecies SCNT. Based on our previous study that Holstein dairy bovi...Reconstructed embryos derived from intersubspecies somatic cell nuclear transfer （SCNT） have poorer developmental potential than those from intrasubspecies SCNT. Based on our previous study that Holstein dairy bovine （HD） mitochondrial DNA （mtDNA） haplotype compatibility between donor karyoplast and recipient cytoplast is crucial for SCNT embryo development, we performed intersubspecies SCNT using HD as donor karyoplast and Luxi yellow heifer （LY） as recipient cytoplast according to mtDNA haplotypes determined by polymerase chain reaction- restriction fragment length polymorphism （PCR-RFLP） analysis. The results demonstrated that intersubspecies mtDNA homotype SCNT embryos had higher pre- and post-implantation developmental competence than intrasubspecies mtDNA heterotype embryos as well as improved blastocyst reprogramming status, including normal H3K9 dimethylation pattern and promoter hypomethylation of pluripotent genes such as Oct4 and Sox2, suggesting that intersubspecies SCNT using LY oocytes maintains HD cloning efficiency and may reprogram HD nuclei to develop into a normal cloned animal ultimately. Our results indicated that karyoplast-cytoplast interactions and mtDNA haplotype compatibility may affect bovine intersubspecies SCNT efficiency. This study on bovine intersubspecies SCNT is valuable for understanding the mechanisms of mtDNA haplotype compatibility between karyoplast and cytoplast impacting the bovine SCNT efficiency, and provides an alternative and economic resource for HD cloning.展开更多
The laying quail is a worldwide breed which exhibits high economic value. In our current study, the vas- oactive intestinal peptide receptor-1 （VIPR-1） was selected as the candidate gene for identifying traits of eg...The laying quail is a worldwide breed which exhibits high economic value. In our current study, the vas- oactive intestinal peptide receptor-1 （VIPR-1） was selected as the candidate gene for identifying traits of egg produc- tion. A single nucleotide polymorphism （SNP） detection was performed in 443 individual quails, including 196 quails from the H line, 202 quails from the L line, and 45 wild quails. The SNPs were genotyped using a polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP）. Two mutations （G373T, A313G） were detected in all the tested quail populations. The associated analysis showed that the SNP genotypes of the VIPR-1 gene were sig- nificantly linked with the egg weight of G373T and A313G in 398 quails. The quails with the genotype GG always exhibited the largest egg weight for the two mutations in the H and L lines. Linkage disequilibrium （LD） analysis in- dicated that G373T and A313G loci showed the weakest LD. Seven main diplotypes from the four main reconstructed haplotypes were observed, indicating a significant association of diplotypes with egg weight. Quails with the hlh2 （GGGT） diplotype always exhibited the smallest egg weight and largest egg number at 20 weeks of age. The overall results suggest that the alterations in quails may be linked with potential major loci or genes affecting reproductive traits.展开更多
AIM: To study whether the glucocorticoid receptor (GR/ NR3C1) gene haplotypes influence the steroid therapy outcome in inflammatory bowel disease (IBD). METHODS: We sequenced all coding exons and flanking intronic seq...AIM: To study whether the glucocorticoid receptor (GR/ NR3C1) gene haplotypes influence the steroid therapy outcome in inflammatory bowel disease (IBD). METHODS: We sequenced all coding exons and flanking intronic sequences of the NR3C1 gene in 181 IBD patients, determined the single nucleotide polymorphisms, and predicted the NR3C1 haplotypes. Furthermore, we investigated whether certain NR3C1 haplotypes are significantly associated with steroid therapy outcomes. RESULTS: We detected 13 NR3C1 variants, which led to the formation of 17 different haplotypes with a certainty of > 95% in 173 individuals. The three most commonly occurring haplotypes were included in the association analysis of the influence of haplotype on steroid therapy outcome or IBD activity. None of the NR3C1 haplotypes showed statistically signifi cant association with glucocorticoid therapy success. CONCLUSION: NR3C1 haplotypes are not related to steroid therapy outcome.展开更多
Whether the 370-371insACA, 494T〉C, and 1423C〉T haplotype in ubiquitin-specific protease 26 （USP26） gene is associated with male infertility is controversial. To clarify this issue, we conducted a meta-analysis bas...Whether the 370-371insACA, 494T〉C, and 1423C〉T haplotype in ubiquitin-specific protease 26 （USP26） gene is associated with male infertility is controversial. To clarify this issue, we conducted a meta-analysis based on the most recent studies. Eligible studies were screened by using PubMed and Embase. Pooled odd ratio （OR） with 95% confidence interval （CI） was calculated with fixed effect models. Ten studies with 1603 patients and 2505 controls were included, Overall, the results indicated that there was an association between the haplotype and male infertile risk （OR = 1.74, 95% CI： 1.09-2.77）. The OR calculated based on the five studies in Asia and three in Europe was 1.96 （95% CI： 1,05-3.67） and 1.54 （95% Ch 0.75-3.16） respectively, however, the OR was 0.86 （95% Ch 0.05-15,29） based on the two investigations in America. In addition, the data from the patients with azoospermia （AZO） showed an increased pooled OR of 2.35 （95% Cl： 1.22-4.50）. In contrast, the studies with oligoasthenoteratozoospermia （OAT） exhibited that the pooled OR was 0,97 （95% Ch 0.43-2.16）. Our analyses indicate that there is an association of alteration in USP26 with male infertility, especially in AZO and Asian population.展开更多
The present study was aimed to analyze the frequencies of human leukocyte antigen （HLA）-A, -B, and -DRB1 alleles and A-B-DRBI, A-B, A-DRB1 and B-DRB1 haplotypes in inhabitants of Guizhou province, China. All samples...The present study was aimed to analyze the frequencies of human leukocyte antigen （HLA）-A, -B, and -DRB1 alleles and A-B-DRBI, A-B, A-DRB1 and B-DRB1 haplotypes in inhabitants of Guizhou province, China. All samples were typed in the HLA-A,-B, and -DRB1 loci using the polymerase chain reaction-reverse sequence spe- cific oligonucleotide probe （PCR-rSSOP） method and HLA polymorphisms were analyzed. A total of 18 HLA-A, 31 HLA-B, and 13 HLA-DRB1 alleles were found in the Guizhou population. The first two frequent alleles in the HLA-A, -B, and -DRB1 loci were A＊1 1（30.72%） and A＊02（30.65%）, B＊40（16.27%） and B＊46（16.27%）, and DRBl＊09（15.91%） and DRBl＊15（13.51%）, respectively. The most common haplotype was A＊02-B＊46- DRBl＊09（5.59%） in A-B-DRB1, A＊02-B＊46（I 1.73%） in A-B, B＊46-DRBl＊09（7.49%） in B-DRB1, and A＊02- DRBl＊09（8.08%） in A-DRB1. Some baplotypes with strong linkage disequilibrium （LD） were found not only in the common haplotypes, such as A＊33-B＊58, B＊30-DRB1＊07, and B＊33-DRB1＊03, but also in the rare haplotypes, such as A＊01-B＊37, B＊37-DRB1＊10, and A＊01-DRB1＊10. Guizhou inhabitants shared some characteristics of the Southern Chinese population but also had their own unique features. Overall, HLA polymorphism in Guizhou population was more consistent with that of Chengdu population than that of other populations in China.展开更多
Objective: To investigate the distributions of human leukocyte antigen (HLA)-A and-B alleles and HLA-A-B haplotypes in the Yi ethnic minority of the Yunnan Province, situated in southwestern China. Methods: DNA typing...Objective: To investigate the distributions of human leukocyte antigen (HLA)-A and-B alleles and HLA-A-B haplotypes in the Yi ethnic minority of the Yunnan Province, situated in southwestern China. Methods: DNA typing for HLA-A and-B loci was performed using the polymerase chain reaction-sequence-based typing (PCR-SBT) method on 114 randomly selected healthy individuals of the Yi population. The allelic frequencies of HLA-A and-B loci were calculated by direct counting and HLA-A-B haplotypes were estimated using the expectation maximization algorithm. Results: A total of 17 HLA-A and 38 HLA-B alleles were found in the Yi population. The most frequent alleles were A2402 (32.46%), A1101 (26.32%), and A0203 (10.09%) at the HLA-A locus and B4601 (12.28%), B1525 (10.09%), B4001 (8.77%), and B3802 (7.89%) at the HLA-B locus. The predominant HLA-A-B haplotypes were A2402-B1525 (7.86%) and A0203-B3802 (5.64%), followed by A1101-B4001 (4.69%). Phylogenetic analysis indicates that the Yi population in the Honghe, Yunnan Province of China basically belongs to groups of southeastern Asian origin, but shares some characteristics with northeastern Asian groups. Conclusion: The present study may add to the understanding of HLA polymorphism in the Yi ethnic group that was poorly defined previously, and provide useful information for bone marrow transplantation, anthropological research, and forensic sciences as well as for disease-association studies.展开更多
Objective To analyze the association of variants of hepatocyte nuclear factor-1α （HNF-1α） gene with type 2 diabetes in Chinese population. Methods In 152 unrelated type 2 diabetes patients and 93 unrelated control...Objective To analyze the association of variants of hepatocyte nuclear factor-1α （HNF-1α） gene with type 2 diabetes in Chinese population. Methods In 152 unrelated type 2 diabetes patients and 93 unrelated controls, eleven single nucleotide polymorphisms （SNPs） were identified and genotyped. Statistical analyses were performed to investigate whether these SNPs were associated with diabetes status in our samples. Results In the individual SNP study, no SNP differed significantly in frequency between type 2 diabetes patients and controls. In the haplotype analysis, two haplotype blocks were identified. In haplotype block 1, no evidence was found between common HNF-1α haplotypes and type 2 diabetes. However, in haplotype block 2, a common haplotype GCGC formed by four tagging SNPs （tSNPs） was found to be associated with decreased risk of type 2 diabetes （odds ratio [OR] 0.6011, 95% confidence interval [CI] 0.4138-0.8732, P=0.0073, empirical P=0.0511, permutation test）. A similar trend was also observed in the diplotype analysis, indicating that the increasing copy number of the haplotype GCGC was associated with the decreased frequency of diabetes （P=0.0193）. Conclusion The results of this study provide evidence that the haplotype of HNF-1α decreases the risk of type 2 diabetes in Chinese individuals.展开更多
The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2...The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2,were identified in the Chinese wheat breeding line Shaanmai 155.QYr SM155.1 was mapped to a 3.0-c M interval between the single-nucleotide polymorphism(SNP)markers AX-109583610 and AX-110907562 on chromosome arm 2 BL.QYr SM155.2 was mapped to a 2.1-c M interval flanked by the SNP markers AX-110378556 and AX-86173526 on chromosome arm 7 AS.A genome-wide association study was used to identify markers associated with APR in a panel of 411 spring wheat lines.Thirteen and 11 SNPs were significantly associated with QYr SM155.1 and QYr SM155.2,respectively,corresponding to physical intervals of 653.75–655.52 Mb on 2 BL and 81.63–83.93 Mb on7 AS.To characterize the haplotype variation and the distribution of these QTL,haplotype analysis was performed based on these SNPs in an independent panel of 1101 worldwide wheat accessions.Three major haplotypes(2 B_h1,2 B_h2,and 2 B_h3)for QYr SM155.1 and four major haplotypes(7 A_h1,7 A_h2,7 A_h3,and 7 A_h4)for QYr SM155.2 were identified.Accessions individually harboring QYr SM155.1_h1 and QYr SM155.2_h1 haplotypes and their combination displayed resistance.Additional assays of 1306 current Chinese cultivars and breeding lines using markers flanking QYr SM155.1 and QYr SM155.2 indicated that the resistance haplotypes of the two QTL were present in respectively 1.45%and 14.16%of lines.Increasing resistance haplotype frequencies at these two loci using marker-assisted selection should benefit wheat production in China.展开更多
The associations of polymorphic Alu insertions （POALINs） with major histocompatibility complex （MHC） class I genes enable us to better identify origins and evolution of MHC class I region haplotypes in different p...The associations of polymorphic Alu insertions （POALINs） with major histocompatibility complex （MHC） class I genes enable us to better identify origins and evolution of MHC class I region haplotypes in different populations. For further studying origins and evolution of MHC class I region haplotypes in Han and Jinuo populations in Yunnan Province, we investigated frequencies of five POALINs, their associations with HLA-A and -B, the three-loci POALINs haplotype frequencies and HLA/POALIN four-loci haplotype frequencies within the alpha block of MHC class I region. We found that a strong positive association between AluHG and HLA-A＊02 is in Jinuo, but not in Yunnan Han. These results suggest that MHC class I region haplotypes of the two studied populations might derive from different progenitor haplotypes and MHC I-POALINs are informative genetic markers for investigating origins and evolution of MHC class I region haplotypes in different populations.展开更多
Pre-harvest sprouting(PHS)poses a significant global challenge to cereal production,impacting both yield and quality.In this study,we employed genome-wide association studies(GWAS)on diverse rice accessions to identif...Pre-harvest sprouting(PHS)poses a significant global challenge to cereal production,impacting both yield and quality.In this study,we employed genome-wide association studies(GWAS)on diverse rice accessions to identify novel PHS-associated haplotypes.An assessment of 127 cultivated accessions for panicle germination(PHS)and detached grain germination(germination rate of detached grains at the 14th day(D14))revealed considerable phenotypic variation among rice ecotypes.GWAS analysis identified 91 significant signals at–log10(P-value)>5,including 15SNPs for PHS and 76 SNPs for D14.A subsequent linkage disequilibrium(LD)block-based GWAS analysis detected 227 significant SNPs for both traits,consisting of 18 nonsynonymous substitutions located on the coding regions of nine genes.Further haplotype analysis identified 32 haplotypes,with 10 specific to cultivated accessions,19 specific to the wild type,and three shared between them.A phenotypic assessment of major haplotypes revealed significant differences between resistant(Hap1 and Hap2)and susceptible haplotypes(Hap5,Hap27,and Hap28),distinguished by a G/A SNP within a novel gene,Os04g0545200.The identified haplotypes offer promising prospects for haplotypebased breeding aimed at enhancing PHS resistance in rice.展开更多
基金supported by the Shenzhen Science and Technology Program,China(Grant No.KCXFZ20211020163808012)the Nanfan Special Project,Chinese Academy of Agricultural Sciences,China(Grant No.YBXM2426).
文摘Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.
基金supported by the National Natural Science Foundation of China(32130013,32070434)the National Key Research and Development Program of China(2022YFC2601601)+1 种基金the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK05010112,2019QZKK0304-02)Hainan Tropical Rainforest Conservation Research Project,ZDYF2023RDYL01(supported by the Hainan Institute of National Park,HINP,KY-24ZK02).
文摘Understanding the genetic diversity–area relationship(GAR)is essential for comprehending how species adapt to environmental changes,as genetic diversity is an indicator of a species’adaptive potential.Variation in environmental adaptation capacity exists among species and animal taxa with different distribution areas,highlighting the importance of understanding the GAR.To obtain a more comprehensive understanding of the GAR in terrestrial vertebrates,we assessed both haplotype diversity–area and nucleotide diversity–area relationships using 25,453 cytochrome c oxidase subunit I(COI)sequences from 142 amphibian species,574 bird species,and 342 mammal species.We found that both measures of genetic diversity increased with species range size across major animal groups.Nevertheless,the GAR did not differ among animal groups,while haplotype diversity performed better than nucleotide diversity in profiling the GAR,as indicated by higher R2 values.The difference in the modeling fit may stem from the distinct biological and mathematical significance of nucleotide diversity and haplotype diversity.These results suggest that the GAR follows similar rules among different animal taxa.Furthermore,haplotype diversity may serve as a more reliable indicator for assessing the potential effects of area size changes on animal populations and provide better guidance for conserving genetic diversity.
基金This work was supported by the Major State Basic Research Development program of Chinathe National High Technology Research and Development Program of China.
文摘In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large numberof samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study withhigh efficiency. The platform has been well evaluated by several sets of real data.
基金Supported by The Grants from the International Agency for Research on Cancer (Special Training Award to DGC)the French Association for Research on Cancer (grant #7478)the Crohn's and Colitis Foundation of America (to ASP)
文摘AIM： Prostaglandin G/H synthase 2 （PTGS2 or COX2） is one of the key factors in the cellular response to inflammation. PTGS2 is expressed in the affected intestinal segments of patients with inflammatory bowel diseases （IBD）. In IBD patients, non-steroidal anti-inflammatory drugs, which have been shown to reduce both the production and activity of PTGS2, may activate IBD and aggravate the symptoms. We aimed at examining genetic variants of PTGS2 that may be risk factors for IBD. METHODS： We genotyped 291 individuals diagnosed with IBD and 367 controls from the Dutch population for the five most frequent polymorphisms of the PTG52 gene. Clinical data were collected on all patients. DNA was extracted via normal laboratory methods. Genotyping was carried out using multiplex PCR followed by the Invader Assay and the 5＇ exonuclease assay （TaqMan）. New polymorphism screening was performed by pre-screening with denaturing high-performance liquid chromatography, followed by fluorescent sequencing. RESULTS： Allele 5209G was weakly associated with Crohn＇s disease （odds ratio [OR] 1.63, 95% confidence interval [CI] 1.03-2.57）, and allele 8473T with ulcerativecolitis （OR 1.50, 95%CI 1.00-2.27）. The haplotype including both alleles showed a strong association with IBD （OR 13.15, 95%CI 3.17-116.15）. This haplotype, while rare （-0.3%） in the general population, is found more frequently in patients （3.5%）. CONCLUSION： Our data suggest that this haplotype of PTGS2 contributes to the susceptibility of IBD.
基金financially supported by the National Youth Foundation of China(31901494,31601306,and 31901869)the National Natural Science Foundation of China(31971890)+1 种基金supported by Young Elite Scientists Sponsorship Program of China Association for Science and Technology(2017QNRC001)the Natural Science Fund of Jiangsu Province,China(BK20161092)。
文摘Most modern wheat cultivars were selected on the basis of yield-related indices measured under optimal fertilizer and irrigation inputs.With climate change,land degradation and salinity caused by sea water encroachment,wheat is increasingly subjected to environmental stress.Moreover,expanding urbanization increasingly encroaches upon prime agricultural land in countries like China,and alternative cropping areas must be found.Some of these areas have moderate constraining factors,such as salinity.Therefore,it is important to investigate whether current genetic materials and breeding procedures are maintaining adequate variability to address future problems caused by abiotic stress.In this study,a panel of 307 wheat accessions,including local landraces,exotic cultivars used in Chinese breeding programs and Chinese cultivars released during different periods since1940,were subjected to a genome-wide association study to dissect the genetic basis of salinity tolerance.Both marker-based and pedigree-based kinship analyses revealed that favorable haplotypes were introduced in some exotic cultivars as well as a limited number of Chinese landraces from the 1940 s.However,improvements in salinity tolerance during modern breeding are not as obvious as that of yield.To broaden genetic diversity for increasing salt tolerance,there is a need to refocus attention on local landraces that have high degrees of salinity tolerance and carry rare favorable alleles that have not been exploited in breeding.
基金Supported by The National R and D Program for Cancer ControlMinistry of Health and Welfare+1 种基金South KoreaNo.1120330
文摘AIM:To evaluate the association between the geneticpolymorphisms and haplotypes of the ITGA1 gene and the risk of gastric cancer.METHODS:The study subjects were 477 age-and sex-matched case-control pairs.Genotyping was performed for 15 single nucleotide polymorphisms(SNPs)in ITGA1.The associations between gastric cancer and these SNPs and haplotypes were analyzed with multivariate conditional logistic regression models.Multiple testing corrections were carried out following methodology for controlling the false discovery rate.Gene-based association tests were performed using the versatile gene-based association study(VEGAS)method.RESULTS:In the codominant model,the ORs for SNPs rs2432143(1.517;95%CI:1.144-2.011)and rs2447867(1.258;95%CI:1.051-1.505)were statistically significant.In the dominant model,polymorphisms of rs1862610 and rs2447867 were found to be significant risk factors,with ORs of 1.337(95%CI:1.029-1.737)and 1.412(95%CI:1.061-1.881),respectively.In the recessive model,only the rs2432143 polymorphism was significant(OR=1.559,95%CI:1.150-2.114).The C-C type of ITGA1 haplotype block 2 was a significant protective factor against gastric cancer in the both codominant model(OR=0.602,95%CI:0.212-0.709,P=0.021)and the dominant model(OR=0.653,95%CI:0.483-0.884).The ITGA1 gene showed a significant gene-based association with gastric cancer in the VEGAS test.In the dominant model,the A-T type of ITGA1 haplotype block 2 was a significant risk factor(OR=1.341,95%CI:1.034-1.741).SNP rs2447867 might be related to the severity of gastric epithelial injury due to inflammation and,thus,to the risk of developing gastric cancer.CONCLUSION:ITGA1 gene SNPs rs1862610,rs2432143,and rs2447867 and the ITGA1 haplotype block that includes SNPs rs1862610 and rs2432143 were significantly associated with gastric cancer.
基金Supported by Crohn’s and Colitis Foundation of Canada and Valorisation Recherche Quebec
文摘AIM： To determine the distribution and frequencies of the genotypes and haplotypes of the genes encoding for the glucocorticoid receptor （GR）, the tumor necrosis factor （TNF）-α and the interleukin （IL）-10 in childhood Crohn＇s disease （CD） and to assess the impact of the corresponding DNA variants on clinical and disease phenotypes.METHODS： Ten variants in GR, TNF-a and IL-10 were genotyped in 113 childhood CD cases and 95 healthy subjects, both of French-Canadian origin.RESULTS： For the GR polymorphisms （R23K and N363S） and IL-10 variants in the 5＇flanking region （-1082 G 〉 A, -819 T 〉 C and -592 A 〉 C）, no difference was observed in allele and genotype frequencies between CD patients and controls. At the haplotype level, we found three IL-10 haplotypes previously described in Caucasians （GCC, ACC and ATA） and three novel haplotypes only present in IBD patients. When we analyzed the haplotype distribution with the anatomical location of the disease, the GCC haplotype was associated with the colonic and the ACC haplotype with the terminal ileum location, respectively. The genotyping of five polymorphisms in the promoter region of the TNF-α gene （-1031 T 〉 C, -863 A 〉 C, -857 T 〉 C, -308 A 〉 G and -238 A 〉 G） revealed a significant overrepresentation of homozygous -1031 CC among CD patients （OR = 9.9） and an association with the colonic location. For TNF-α, eleven haplotypes were inferred, including two frequent ones, TCCGG and CACGG, which were significantly observed more frequently in controls and cases, respectively.CONCLUSION： This is one of the first studies investigating the association between haplotype structure and disease location in a CD pediatric cohort. Our results will help to increase our understanding of the genetic determinants of childhood CD.
基金supported by the National Excellent Youth Science Foundation of China(No.31222030)the National Natural Science Foundation of China(No.91131002)+3 种基金the Shanghai Rising-Star Program(No.12QA1400300)the China Ministry of Education Scientific Research Major Project(Nos. 311016 and 113022A)the MOE University Doctoral Research Supervisor's Funds(No.20120071110021)the Shanghai Professional Development Funding(No.2010001)
文摘The paternally inherited Y chromosome has been widely used in forensics for personal identification, in anthropology and population genetics to understand origin and migration of human populations, and also in medical and clinical studies （Wang and Li, 2013; Wang et al., 2014）. There are two kinds of extremely useful markers in Y chromosome, single nucle- otide polymorphism （SNP） and short tandem repeats （STRs）. With a very low mutation rate on the order of 3.0 x 10-8 mutations/nucleotide/generation （Xue et al., 2009）, SNP markers have been used in constructing a robust phylogeny tree linking all the Y chromosome lineages from world pop- ulations （Karafet et al., 2008）. Those lineages determined by the pattern of SNPs are called haplogroups. That is to say, we have to genotype an appropriate number of SNPs in order to assign a given Y chromosome to a haplogroup. Compared with SNPs, the mutation rates of STR markers are about four to five orders of magnitude higher （Gusmgo et al., 2005; Ballantyne et al., 2010）. Typing STR has advantages of saving time and cost compared with typing SNPs in phylogenetic assignment of a Y chromosome （Wang et al., 2010）. A set of STR values for an individual is called a haplotype. Because of the disparity in mutation rates between SNP and STR, one SNP haplogroup could actually comprise many STR haplotypes （Wang et al., 2010）. It is most interesting that STR variability is clustered more by haplogroups than by populations （Bosch et al., 1999; Behar et al., 2004）, which indicates that STR haplotypes could be used to infer the haplogroup information of a given Y chromosome. There has been increasing interest in this cost- effective strategy for predicting the haplogroup from a given STR haplotype when SNP data are unavailable. For instance, Vadim Urasin＇s YPredictor （http：//predictor.ydna.ru/）, Whit Atheys＇ haplogroup predictor （http：//www.hprg.com/hapest5/） （Athey, 2005, 2006）, and haplogroup classifier of Arizona University （Schlecht et al., 2008） have been widely employed in previous studies for haplogroup prediction （Larmuseau et al., 2010; Bembea et al., 2011; Larmuseau et al., 2012; Tarlykov et al., 2013）.
基金This work was supported by the grants from the National High-Tech R&D Program of China(No.2007AA100502)the National Science and Technology Major Project of China (No.2008ZX08007-004)the National Natural Science Foundation of China(No.30770242)
文摘Reconstructed embryos derived from intersubspecies somatic cell nuclear transfer （SCNT） have poorer developmental potential than those from intrasubspecies SCNT. Based on our previous study that Holstein dairy bovine （HD） mitochondrial DNA （mtDNA） haplotype compatibility between donor karyoplast and recipient cytoplast is crucial for SCNT embryo development, we performed intersubspecies SCNT using HD as donor karyoplast and Luxi yellow heifer （LY） as recipient cytoplast according to mtDNA haplotypes determined by polymerase chain reaction- restriction fragment length polymorphism （PCR-RFLP） analysis. The results demonstrated that intersubspecies mtDNA homotype SCNT embryos had higher pre- and post-implantation developmental competence than intrasubspecies mtDNA heterotype embryos as well as improved blastocyst reprogramming status, including normal H3K9 dimethylation pattern and promoter hypomethylation of pluripotent genes such as Oct4 and Sox2, suggesting that intersubspecies SCNT using LY oocytes maintains HD cloning efficiency and may reprogram HD nuclei to develop into a normal cloned animal ultimately. Our results indicated that karyoplast-cytoplast interactions and mtDNA haplotype compatibility may affect bovine intersubspecies SCNT efficiency. This study on bovine intersubspecies SCNT is valuable for understanding the mechanisms of mtDNA haplotype compatibility between karyoplast and cytoplast impacting the bovine SCNT efficiency, and provides an alternative and economic resource for HD cloning.
基金supported by the Open Project of Hubei Key Laboratory of Animal Embryo and Molecular Breeding(No.2015ZD146),China
文摘The laying quail is a worldwide breed which exhibits high economic value. In our current study, the vas- oactive intestinal peptide receptor-1 （VIPR-1） was selected as the candidate gene for identifying traits of egg produc- tion. A single nucleotide polymorphism （SNP） detection was performed in 443 individual quails, including 196 quails from the H line, 202 quails from the L line, and 45 wild quails. The SNPs were genotyped using a polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP）. Two mutations （G373T, A313G） were detected in all the tested quail populations. The associated analysis showed that the SNP genotypes of the VIPR-1 gene were sig- nificantly linked with the egg weight of G373T and A313G in 398 quails. The quails with the genotype GG always exhibited the largest egg weight for the two mutations in the H and L lines. Linkage disequilibrium （LD） analysis in- dicated that G373T and A313G loci showed the weakest LD. Seven main diplotypes from the four main reconstructed haplotypes were observed, indicating a significant association of diplotypes with egg weight. Quails with the hlh2 （GGGT） diplotype always exhibited the smallest egg weight and largest egg number at 20 weeks of age. The overall results suggest that the alterations in quails may be linked with potential major loci or genes affecting reproductive traits.
基金Supported by The Swiss IBD Cohort Study (SNF Grant 33CSC0-108792)the Swiss National Science Foundation (Grant 32-120463/1)+2 种基金the Zurich University Research Priority Pro-gramme "Integrative Human Physiology" (ZIHP)the Center of Clinical Research at the University Hospital Zurichthe Novartis Foundation for Biomedical Research
文摘AIM: To study whether the glucocorticoid receptor (GR/ NR3C1) gene haplotypes influence the steroid therapy outcome in inflammatory bowel disease (IBD). METHODS: We sequenced all coding exons and flanking intronic sequences of the NR3C1 gene in 181 IBD patients, determined the single nucleotide polymorphisms, and predicted the NR3C1 haplotypes. Furthermore, we investigated whether certain NR3C1 haplotypes are significantly associated with steroid therapy outcomes. RESULTS: We detected 13 NR3C1 variants, which led to the formation of 17 different haplotypes with a certainty of > 95% in 173 individuals. The three most commonly occurring haplotypes were included in the association analysis of the influence of haplotype on steroid therapy outcome or IBD activity. None of the NR3C1 haplotypes showed statistically signifi cant association with glucocorticoid therapy success. CONCLUSION: NR3C1 haplotypes are not related to steroid therapy outcome.
文摘Whether the 370-371insACA, 494T〉C, and 1423C〉T haplotype in ubiquitin-specific protease 26 （USP26） gene is associated with male infertility is controversial. To clarify this issue, we conducted a meta-analysis based on the most recent studies. Eligible studies were screened by using PubMed and Embase. Pooled odd ratio （OR） with 95% confidence interval （CI） was calculated with fixed effect models. Ten studies with 1603 patients and 2505 controls were included, Overall, the results indicated that there was an association between the haplotype and male infertile risk （OR = 1.74, 95% CI： 1.09-2.77）. The OR calculated based on the five studies in Asia and three in Europe was 1.96 （95% CI： 1,05-3.67） and 1.54 （95% Ch 0.75-3.16） respectively, however, the OR was 0.86 （95% Ch 0.05-15,29） based on the two investigations in America. In addition, the data from the patients with azoospermia （AZO） showed an increased pooled OR of 2.35 （95% Cl： 1.22-4.50）. In contrast, the studies with oligoasthenoteratozoospermia （OAT） exhibited that the pooled OR was 0,97 （95% Ch 0.43-2.16）. Our analyses indicate that there is an association of alteration in USP26 with male infertility, especially in AZO and Asian population.
基金supported by the Chinese Marrow Donor Program(CMDP),CMDP Guizhou Registry
文摘The present study was aimed to analyze the frequencies of human leukocyte antigen （HLA）-A, -B, and -DRB1 alleles and A-B-DRBI, A-B, A-DRB1 and B-DRB1 haplotypes in inhabitants of Guizhou province, China. All samples were typed in the HLA-A,-B, and -DRB1 loci using the polymerase chain reaction-reverse sequence spe- cific oligonucleotide probe （PCR-rSSOP） method and HLA polymorphisms were analyzed. A total of 18 HLA-A, 31 HLA-B, and 13 HLA-DRB1 alleles were found in the Guizhou population. The first two frequent alleles in the HLA-A, -B, and -DRB1 loci were A＊1 1（30.72%） and A＊02（30.65%）, B＊40（16.27%） and B＊46（16.27%）, and DRBl＊09（15.91%） and DRBl＊15（13.51%）, respectively. The most common haplotype was A＊02-B＊46- DRBl＊09（5.59%） in A-B-DRB1, A＊02-B＊46（I 1.73%） in A-B, B＊46-DRBl＊09（7.49%） in B-DRB1, and A＊02- DRBl＊09（8.08%） in A-DRB1. Some baplotypes with strong linkage disequilibrium （LD） were found not only in the common haplotypes, such as A＊33-B＊58, B＊30-DRB1＊07, and B＊33-DRB1＊03, but also in the rare haplotypes, such as A＊01-B＊37, B＊37-DRB1＊10, and A＊01-DRB1＊10. Guizhou inhabitants shared some characteristics of the Southern Chinese population but also had their own unique features. Overall, HLA polymorphism in Guizhou population was more consistent with that of Chengdu population than that of other populations in China.
基金Project supported by the National Natural Science Foundation of China (Nos. 30700470 and 30871348)the Shaan’xi Provincial Science and Technology Research and Development Project Fund (No. 2008K09-02), China
文摘Objective: To investigate the distributions of human leukocyte antigen (HLA)-A and-B alleles and HLA-A-B haplotypes in the Yi ethnic minority of the Yunnan Province, situated in southwestern China. Methods: DNA typing for HLA-A and-B loci was performed using the polymerase chain reaction-sequence-based typing (PCR-SBT) method on 114 randomly selected healthy individuals of the Yi population. The allelic frequencies of HLA-A and-B loci were calculated by direct counting and HLA-A-B haplotypes were estimated using the expectation maximization algorithm. Results: A total of 17 HLA-A and 38 HLA-B alleles were found in the Yi population. The most frequent alleles were A2402 (32.46%), A1101 (26.32%), and A0203 (10.09%) at the HLA-A locus and B4601 (12.28%), B1525 (10.09%), B4001 (8.77%), and B3802 (7.89%) at the HLA-B locus. The predominant HLA-A-B haplotypes were A2402-B1525 (7.86%) and A0203-B3802 (5.64%), followed by A1101-B4001 (4.69%). Phylogenetic analysis indicates that the Yi population in the Honghe, Yunnan Province of China basically belongs to groups of southeastern Asian origin, but shares some characteristics with northeastern Asian groups. Conclusion: The present study may add to the understanding of HLA polymorphism in the Yi ethnic group that was poorly defined previously, and provide useful information for bone marrow transplantation, anthropological research, and forensic sciences as well as for disease-association studies.
基金This research was supported by the National 973 Program (2006 CB503901) the Major Project of Shanghai Science and Technology Development Foundation (02DJ14052-I)+1 种基金the Science and Technology Development Foundation of Shanghai Municipal Health Bureau (034043) the Young Doctor Training Project of Shanghai Municipal Health Bureau
文摘Objective To analyze the association of variants of hepatocyte nuclear factor-1α （HNF-1α） gene with type 2 diabetes in Chinese population. Methods In 152 unrelated type 2 diabetes patients and 93 unrelated controls, eleven single nucleotide polymorphisms （SNPs） were identified and genotyped. Statistical analyses were performed to investigate whether these SNPs were associated with diabetes status in our samples. Results In the individual SNP study, no SNP differed significantly in frequency between type 2 diabetes patients and controls. In the haplotype analysis, two haplotype blocks were identified. In haplotype block 1, no evidence was found between common HNF-1α haplotypes and type 2 diabetes. However, in haplotype block 2, a common haplotype GCGC formed by four tagging SNPs （tSNPs） was found to be associated with decreased risk of type 2 diabetes （odds ratio [OR] 0.6011, 95% confidence interval [CI] 0.4138-0.8732, P=0.0073, empirical P=0.0511, permutation test）. A similar trend was also observed in the diplotype analysis, indicating that the increasing copy number of the haplotype GCGC was associated with the decreased frequency of diabetes （P=0.0193）. Conclusion The results of this study provide evidence that the haplotype of HNF-1α decreases the risk of type 2 diabetes in Chinese individuals.
基金financially the National Natural Science Foundation of China(31871611 and31971890)the National Science Foundation for Young Scientistsin China(31901494 and 31901869)+1 种基金International Cooperation and Exchange of the National Natural Science Foundation of China(31961143019)the Integrated Extension Project of Agricultural Science and Technology Innovation in Shaanxi Province(NYKJ-2021-YL(XN)15)。
文摘The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust.In the present study,two loci for adult plant resistance(APR),QYr SM155.1 and QYr SM155.2,were identified in the Chinese wheat breeding line Shaanmai 155.QYr SM155.1 was mapped to a 3.0-c M interval between the single-nucleotide polymorphism(SNP)markers AX-109583610 and AX-110907562 on chromosome arm 2 BL.QYr SM155.2 was mapped to a 2.1-c M interval flanked by the SNP markers AX-110378556 and AX-86173526 on chromosome arm 7 AS.A genome-wide association study was used to identify markers associated with APR in a panel of 411 spring wheat lines.Thirteen and 11 SNPs were significantly associated with QYr SM155.1 and QYr SM155.2,respectively,corresponding to physical intervals of 653.75–655.52 Mb on 2 BL and 81.63–83.93 Mb on7 AS.To characterize the haplotype variation and the distribution of these QTL,haplotype analysis was performed based on these SNPs in an independent panel of 1101 worldwide wheat accessions.Three major haplotypes(2 B_h1,2 B_h2,and 2 B_h3)for QYr SM155.1 and four major haplotypes(7 A_h1,7 A_h2,7 A_h3,and 7 A_h4)for QYr SM155.2 were identified.Accessions individually harboring QYr SM155.1_h1 and QYr SM155.2_h1 haplotypes and their combination displayed resistance.Additional assays of 1306 current Chinese cultivars and breeding lines using markers flanking QYr SM155.1 and QYr SM155.2 indicated that the resistance haplotypes of the two QTL were present in respectively 1.45%and 14.16%of lines.Increasing resistance haplotype frequencies at these two loci using marker-assisted selection should benefit wheat production in China.
文摘The associations of polymorphic Alu insertions （POALINs） with major histocompatibility complex （MHC） class I genes enable us to better identify origins and evolution of MHC class I region haplotypes in different populations. For further studying origins and evolution of MHC class I region haplotypes in Han and Jinuo populations in Yunnan Province, we investigated frequencies of five POALINs, their associations with HLA-A and -B, the three-loci POALINs haplotype frequencies and HLA/POALIN four-loci haplotype frequencies within the alpha block of MHC class I region. We found that a strong positive association between AluHG and HLA-A＊02 is in Jinuo, but not in Yunnan Han. These results suggest that MHC class I region haplotypes of the two studied populations might derive from different progenitor haplotypes and MHC I-POALINs are informative genetic markers for investigating origins and evolution of MHC class I region haplotypes in different populations.
基金supported by the National Research Foundation of Korea(NRF)grants funded by the Ministry of Science and Information and Communication Technology(MSIT),Republic of Korea(NRF2022R1A4A1030348 and 2023R1A2C1004432)the Korea Institute of Planning and Evaluation for Technology in Food,Agriculture and Forestry(IPET)through the Digital Breeding Transformation Technology Development Program,funded by the Ministry of Agriculture,Food and Rural Affairs(MAFRA),Republic of Korea(322060031HD020)the Cooperative Research Program for Agriculture Science and Technology Development,Rural Development Administration,Republic of Korea(RS-2023-00222739)。
文摘Pre-harvest sprouting(PHS)poses a significant global challenge to cereal production,impacting both yield and quality.In this study,we employed genome-wide association studies(GWAS)on diverse rice accessions to identify novel PHS-associated haplotypes.An assessment of 127 cultivated accessions for panicle germination(PHS)and detached grain germination(germination rate of detached grains at the 14th day(D14))revealed considerable phenotypic variation among rice ecotypes.GWAS analysis identified 91 significant signals at–log10(P-value)>5,including 15SNPs for PHS and 76 SNPs for D14.A subsequent linkage disequilibrium(LD)block-based GWAS analysis detected 227 significant SNPs for both traits,consisting of 18 nonsynonymous substitutions located on the coding regions of nine genes.Further haplotype analysis identified 32 haplotypes,with 10 specific to cultivated accessions,19 specific to the wild type,and three shared between them.A phenotypic assessment of major haplotypes revealed significant differences between resistant(Hap1 and Hap2)and susceptible haplotypes(Hap5,Hap27,and Hap28),distinguished by a G/A SNP within a novel gene,Os04g0545200.The identified haplotypes offer promising prospects for haplotypebased breeding aimed at enhancing PHS resistance in rice.
