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
Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma metabolite.To enhance high-aromatic coconut breeding efforts,it is essential t...Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma metabolite.To enhance high-aromatic coconut breeding efforts,it is essential to deeply understand the hereditary factors governing the production of 2AP.In this study,a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism(SNP)variations from 168 aromatic coconut germplasm resources.Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism.Proteins encoded by these genes are involved in amino acid metabolism,glycolysis,and secondary metabolism.Among these,Asparagine synthetase coding gene ASN1,Gamma-glutamylcysteine synthetase coding gene GSH1,and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504.In particular,the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein,potentially resulting in differences in 2AP content among haplotype populations.Identifying variations in related candidate genes,particularly the gene CnASN1,provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.展开更多
Forensic haplotype analysis of the male Y chromosome is currently used to establish the number of male donors in sexual assaults,the number of male bleeders in blood pattern analysis,and for ancestry correlation to ge...Forensic haplotype analysis of the male Y chromosome is currently used to establish the number of male donors in sexual assaults,the number of male bleeders in blood pattern analysis,and for ancestry correlation to genetic founder populations in biogeographic studies.In forensic laboratory applications,its primary use is for DNA profile generation with trace amounts of male DNA in the presence of excess female DNA(e.g.spermatozoa identification,male component of fingernail scrapings).Our study supports the potential use of the Y chromosome in a"dragnet"approach(most haplotypes are unique)similar to that described by Kayser in 2017 for solving a cold case sex assault and homicide in The Netherlands.Our study also researched the potential for the identification of an ancestral Irish genetic"footprint"linked to surname O'Brien and identified multiple founder group origins in Ireland and England as well as three samples with the Dal Riata(a Gaelic overkingdom)ancestral haplotype.This study indicates correlation to ancestral Irish ancestry by haplotype but not conclusively to the O'Brien surname.展开更多
FLOWERING LOCUS T (FT),a key regulator of photoperiod pathway,plays a pivotal role in modulating flowering time and growth period-related traits in plants.In this study,we identified 10 FT family genes in soybean and ...FLOWERING LOCUS T (FT),a key regulator of photoperiod pathway,plays a pivotal role in modulating flowering time and growth period-related traits in plants.In this study,we identified 10 FT family genes in soybean and examined their functional divergences through sequence alignment analysis.Phylogenetic and amino acid sequence analysis revealed that the 92nd residue and the Segment B domain (sites 129,131,134,135) are the critical determinants of potential functional divergence and activity variation among Gm FT.Using the Soy Omics website,we detected natural variations in the genomic and promoter regions of Gm FTs,along with numerous haplotypes.By correlating these haplotypes with flowering time,we identified 7 potential KASP markers associated with soybean growth period:Gm FT1a-60297360,Gm FT1b-60311669,Gm FT2a-31695562,Gm FT2b-31739433,Gm FT3a-4106476,Gm FT5a-4078626,and Gm FT5b-37490962.All KASP markers exhibited high selection efficiency (97.56%–100.00%) and reliable genotyping accuracy when validated across 82 soybean varieties spanning multiple maturity groups (MGs).This study systematically elucidates the functional divergence of Gm FTs and develops efficient KASP markers,providing essential technological support for photoperiodadaptive breeding and germplasm innovation.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: 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
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
Grain size influences the yield and quality of rice(Oryza sativa L.),and grain length is one of the component traits of grain size.In this study,a near-isogenic line LB3 with long grain size was constructed using japo...Grain size influences the yield and quality of rice(Oryza sativa L.),and grain length is one of the component traits of grain size.In this study,a near-isogenic line LB3 with long grain size was constructed using japonica rice cultivar 02428,with short grain size,as the recipient parent and indica rice cultivar ZYX,with long grain size,as the donor parent,by multi-generation backcrossing and selfing.BSA-seq was used for preliminary QTL mapping and InDel markers were developed to fine map the locus.The major QTL,tentatively named qGL10,for grain length was located in a 128.45 kb region of chromosome 10.Combined with haplotype analysis of rice varieties,expression pattern analysis of candidate genes suggested LOC_Os10g39130(OsMADS56)as a candidate gene.Sequence alignment of OsMADS56 in 02428 and LB3 revealed that there were 15 SNPs in the promoter region and four in the coding region.Further haplotype analysis suggested that SNP9(G/A)located in the TGTCACA motif might account for the different expression levels of OsMADS56 in 02428 and LB3.These results lay a foundation for the application of qGL10 in molecular breeding of new rice varieties.展开更多
Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(...Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.展开更多
Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more e...Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.展开更多
Grain size and weight are closely related traits determining yield in rice(Oryza sativa L.).Since indica and japonica rice varieties differ significantly in multiple traits,a high-generation recombinant inbred line(RI...Grain size and weight are closely related traits determining yield in rice(Oryza sativa L.).Since indica and japonica rice varieties differ significantly in multiple traits,a high-generation recombinant inbred line(RIL)population derived from the crossing LH9(indica)and RPY(japonica)was used to map grainrelated traits in six environments.Pyramiding of the quantitative trait loci(QTL)for thousand-grain weight showed that combinations of multiple QTL significantly increased the phenotypic effect.A novel gene named GSW3.1 controlling grain size and weight was discovered using the major QTL for the colocalization of grain width and thousand-grain weight on chromosome 3.Gene editing revealed that GSW3.1(LOC_Os03g16850)was pleiotropic,positively regulating grain size and weight while affecting several other agronomic traits.Haplotype analysis indicated that some traits,including grain width and weight,were highly correlated with indica-japonica differentiation.展开更多
Increasing wheat yield is a long-term goal for wheat breeders around the world.Exploiting elite genetic resources and dissecting the genetic basis of important agronomic traits in wheat are the necessary methods for h...Increasing wheat yield is a long-term goal for wheat breeders around the world.Exploiting elite genetic resources and dissecting the genetic basis of important agronomic traits in wheat are the necessary methods for high-yield wheat breeding.This study evaluated nine crucial agronomic traits found in a natural population of 156 wheat varieties and77 landraces from Sichuan,China in seven environments over two years.The results of this investigation of agronomic traits showed that the landraces had more tillers and higher kernel numbers per spike (KNS),while the breeding varieties had higher thousand-kernel weight (TKW) and kernel weight per spike (KWS).The generalized heritability (H2) values of the nine agronomic traits varied from 0.74 to 0.95.Structure analysis suggested that the natural population could be divided into three groups using 43 198 single nucleotide polymorphism (SNP) markers from the wheat 55K SNP chip.A total of 67 quantitative trait loci (QTLs) were identified by the genome-wide association study (GWAS) analysis based on the Q+K method of a mixed linear model.Three important QTLs were analyzed in this study.Four haplotypes of QFTN.sicau-7BL.1 for fertile tillers number (FTN),three haplotypes of QKNS.sicau-1AL.2 for KNS,and four haplotypes of QTKW.sicau-3BS.1 for TKW were detected.FTN-Hap2,KNS-Hap1,and TKW-Hap2 were excellent haplotypes for each QTL based on the yield performance of 42 varieties in regional trials from 2002 to 2013.The varieties with all three haplotypes showed the highest yield compared to those with either two haplotypes or one haplotype.In addition,the KASP-AX-108866053 marker of QTL QKNS.sicau-1AL.2 was successfully distinguished between three haplotypes(or alleles) in 63 varieties based on the number of kernels per spike in regional trials between 2018 and 2021.These genetic loci and reliable makers can be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of wheat yield.展开更多
Paw San Hmwe （PSM） rice has been cultivated in many areas of Myanmar for a long time. Strong aroma, good taste and its elongation during cooking are the key characteristics of PSM rice. Thirty-one PSM accessions wer...Paw San Hmwe （PSM） rice has been cultivated in many areas of Myanmar for a long time. Strong aroma, good taste and its elongation during cooking are the key characteristics of PSM rice. Thirty-one PSM accessions were genotypically characterized, and their physical grain and cooking quality traits were studied. We used specific gene markers associated with aroma, apparent amylose content （AAC） and alkali spreading value to determine the alleles carried by different PSM accessions. The results revealed that six PSM accessions （PSM10, PSM12, PSM13, PSM21, PSM22 and PSM30） had a 3-bp insertion in Os2AP gene. Gel consistency （GC） allele was predominant among the PSM accessions for gelatinization temperature （GT）, however, the phenotype observed was between low and intermediate GT because of the combination of the GC allele with the presence of low GT allele at heterozygous state from the other loci of the SSIla gene. Intermediate to high AAC was observed among the PSM accessions corresponding to the haplotype identified for the single nucleotide polymorphism G/T and the （Cm）n repeat in the Wx gene. The characterization and grouping data of PSM accessions posted benefits to Myanmar seed banks, and our results will help in maintaining the integrity of PSM rice variety.展开更多
The SDS-sedimentation volume(SSV)is a critical indicator for assessing wheat gluten quality and is widely used when evaluating wheat processing quality.However,the molecular mechanisms regulating SSV remain poorly und...The SDS-sedimentation volume(SSV)is a critical indicator for assessing wheat gluten quality and is widely used when evaluating wheat processing quality.However,the molecular mechanisms regulating SSV remain poorly understood.In this study,we performed an analysis of quantitative trait loci(QTLs)for SSV using a recombinant inbred line(RIL)population derived from a cross between TAA10 and XX329,and identified four environmentally stable QTLs located on chromosomes 1D,2D,4D,and 6D.Among them,the effects of Qssv.cau-1D and Qssv.cau-6D were likely to be explained by genome variations at the Glu-D1 and Gli-D2 loci.We fine mapped Qssv.cau-2D to the candidate causal gene TaSED,encoding a nucleolar protein.Gene-edited TaSED knockout mutants(tased)had a lower SSV,while TaSED overexpression lines showed a higher SSV.We demonstrated that TaSED interacted with the transcription factor TaSPA to enhance its transcriptional activation activity of glutenin and gliadin,whose expression was downregulated in tased and upregulated in TaSED-OE plants,with corresponding differences in glutenin and gliadin content compared with the wild-type.A molecular marker sedTX was further developed based on a nonsynonymous mutation of the parents in TaSED that could be used to identify haplotypes with high SSV effectively.Our findings elucidate a molecular mechanism governing SSV and reveal valuable variants with promising applications for improving wheat quality.展开更多
Background Our previous research has suggested that genes around D12S1056 in 12q13 may confer susceptibility to ventricular septal defect （VSD） in humans. The present study was to define the chromosome region assign...Background Our previous research has suggested that genes around D12S1056 in 12q13 may confer susceptibility to ventricular septal defect （VSD） in humans. The present study was to define the chromosome region assignment by transmission disequilibrium test （TDT）, and to identify the important candidate gene by family-based association study and haplotype analysis. Methods Surrounding D12S1056, ten microsatellite markers including D12S329, D12S305, D12S1662, D12S1056, D12S1293, D12S334, D12S102, D12S83, D12S1655 and D12S1691 were chosen, and TDT was performed in 62 nuclear family trios each consisting of an affected child and two healty parents. Subsequently, the GLI gene, a positional candidate gene that maps to the target region, was selected for further analysis. Three single nucleotide polymorphisms （SNPs）, G11888C, G11388A, and G11625T, were selected for family-based association study and haplotype analysis. Results VSD was significantly associated with all selected markers except D12S1691 [72.2 centi morgen （cM）] and D12S1700 （75.76 cM）. VSD was also significantly associated with G11888C （X^2 = 5.918, P = 0.015）, G11388A （X^2 = 8.067, P = 0.005）, and G11625T （X^2 = 11.842, P = 0.001）. Haplotype analysis showed a strong linkage disequilibrium between G11888C and G11388A （D＇=0.999）, but in significant （X^2 = 1.035, df = 2, P 〉 0.05）. Conclusions The susceptibility gene of VSD was mapped to 3.56 cM in 12q13 by TDT, and the GLI gene, an important candidate in the target region, was associated with VSD.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 Major Science and Technology Project of Hainan Province(ZDKJ2021012)National Natural Science Foundation of China(32071805)the National Key Research and Development Program of China(2023YFD2200700)。
文摘Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma metabolite.To enhance high-aromatic coconut breeding efforts,it is essential to deeply understand the hereditary factors governing the production of 2AP.In this study,a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism(SNP)variations from 168 aromatic coconut germplasm resources.Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism.Proteins encoded by these genes are involved in amino acid metabolism,glycolysis,and secondary metabolism.Among these,Asparagine synthetase coding gene ASN1,Gamma-glutamylcysteine synthetase coding gene GSH1,and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504.In particular,the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein,potentially resulting in differences in 2AP content among haplotype populations.Identifying variations in related candidate genes,particularly the gene CnASN1,provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.
基金This study was funded by University of New Haven aspart of a Master's thesis in Forensic Science.
文摘Forensic haplotype analysis of the male Y chromosome is currently used to establish the number of male donors in sexual assaults,the number of male bleeders in blood pattern analysis,and for ancestry correlation to genetic founder populations in biogeographic studies.In forensic laboratory applications,its primary use is for DNA profile generation with trace amounts of male DNA in the presence of excess female DNA(e.g.spermatozoa identification,male component of fingernail scrapings).Our study supports the potential use of the Y chromosome in a"dragnet"approach(most haplotypes are unique)similar to that described by Kayser in 2017 for solving a cold case sex assault and homicide in The Netherlands.Our study also researched the potential for the identification of an ancestral Irish genetic"footprint"linked to surname O'Brien and identified multiple founder group origins in Ireland and England as well as three samples with the Dal Riata(a Gaelic overkingdom)ancestral haplotype.This study indicates correlation to ancestral Irish ancestry by haplotype but not conclusively to the O'Brien surname.
基金supported by the National Key R&D Program of China (2023YFD1201300)the Nanfan Special Project of Chinese Academy of Agricultural Sciences (YBXM2428)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences。
文摘FLOWERING LOCUS T (FT),a key regulator of photoperiod pathway,plays a pivotal role in modulating flowering time and growth period-related traits in plants.In this study,we identified 10 FT family genes in soybean and examined their functional divergences through sequence alignment analysis.Phylogenetic and amino acid sequence analysis revealed that the 92nd residue and the Segment B domain (sites 129,131,134,135) are the critical determinants of potential functional divergence and activity variation among Gm FT.Using the Soy Omics website,we detected natural variations in the genomic and promoter regions of Gm FTs,along with numerous haplotypes.By correlating these haplotypes with flowering time,we identified 7 potential KASP markers associated with soybean growth period:Gm FT1a-60297360,Gm FT1b-60311669,Gm FT2a-31695562,Gm FT2b-31739433,Gm FT3a-4106476,Gm FT5a-4078626,and Gm FT5b-37490962.All KASP markers exhibited high selection efficiency (97.56%–100.00%) and reliable genotyping accuracy when validated across 82 soybean varieties spanning multiple maturity groups (MGs).This study systematically elucidates the functional divergence of Gm FTs and develops efficient KASP markers,providing essential technological support for photoperiodadaptive breeding and germplasm innovation.
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 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.
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supported by the Guangdong Provincial Key R&D Program(2021B0707010010)the Key R&D Program of Guangzhou Science and Technology Project(202103000083).
文摘Grain size influences the yield and quality of rice(Oryza sativa L.),and grain length is one of the component traits of grain size.In this study,a near-isogenic line LB3 with long grain size was constructed using japonica rice cultivar 02428,with short grain size,as the recipient parent and indica rice cultivar ZYX,with long grain size,as the donor parent,by multi-generation backcrossing and selfing.BSA-seq was used for preliminary QTL mapping and InDel markers were developed to fine map the locus.The major QTL,tentatively named qGL10,for grain length was located in a 128.45 kb region of chromosome 10.Combined with haplotype analysis of rice varieties,expression pattern analysis of candidate genes suggested LOC_Os10g39130(OsMADS56)as a candidate gene.Sequence alignment of OsMADS56 in 02428 and LB3 revealed that there were 15 SNPs in the promoter region and four in the coding region.Further haplotype analysis suggested that SNP9(G/A)located in the TGTCACA motif might account for the different expression levels of OsMADS56 in 02428 and LB3.These results lay a foundation for the application of qGL10 in molecular breeding of new rice varieties.
基金supported by the Major Program of National Agricultural Science and Technology of China(NK20220607)the West Light Foundation of the Chinese Academy of Sciences(2022XBZG_XBQNXZ_A_001)the Sichuan Science and Technology Program,China(2022ZDZX0014)。
文摘Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.
基金funded by the CGIAR Research Program(CRP)on MAIZEthe USAID through the Accelerating Genetic Gains Supplemental Project(Amend.No.9 MTO 069033),and the One CGIAR Initiative on Accelerated Breeding+1 种基金funding from the governments of Australia,Belgium,Canada,China,France,India,Japan,the Republic of Korea,Mexico,the Netherlands,New Zealand,Norway,Sweden,Switzerland,the United Kingdom,the United States,and the World Banksupported by the China Scholarship Council。
文摘Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.
基金supported by the National Key Research and Development Program of China(2016YFD0100400)the National Special Key Project for Transgenic Breeding(2016ZX08001001)。
文摘Grain size and weight are closely related traits determining yield in rice(Oryza sativa L.).Since indica and japonica rice varieties differ significantly in multiple traits,a high-generation recombinant inbred line(RIL)population derived from the crossing LH9(indica)and RPY(japonica)was used to map grainrelated traits in six environments.Pyramiding of the quantitative trait loci(QTL)for thousand-grain weight showed that combinations of multiple QTL significantly increased the phenotypic effect.A novel gene named GSW3.1 controlling grain size and weight was discovered using the major QTL for the colocalization of grain width and thousand-grain weight on chromosome 3.Gene editing revealed that GSW3.1(LOC_Os03g16850)was pleiotropic,positively regulating grain size and weight while affecting several other agronomic traits.Haplotype analysis indicated that some traits,including grain width and weight,were highly correlated with indica-japonica differentiation.
基金supported by the Sichuan Science and Technology Program , China ( 2022ZDZX0014 and 2021YFYZ0002)the Plan of Tianfu Qingcheng of Sichuan Province, China。
文摘Increasing wheat yield is a long-term goal for wheat breeders around the world.Exploiting elite genetic resources and dissecting the genetic basis of important agronomic traits in wheat are the necessary methods for high-yield wheat breeding.This study evaluated nine crucial agronomic traits found in a natural population of 156 wheat varieties and77 landraces from Sichuan,China in seven environments over two years.The results of this investigation of agronomic traits showed that the landraces had more tillers and higher kernel numbers per spike (KNS),while the breeding varieties had higher thousand-kernel weight (TKW) and kernel weight per spike (KWS).The generalized heritability (H2) values of the nine agronomic traits varied from 0.74 to 0.95.Structure analysis suggested that the natural population could be divided into three groups using 43 198 single nucleotide polymorphism (SNP) markers from the wheat 55K SNP chip.A total of 67 quantitative trait loci (QTLs) were identified by the genome-wide association study (GWAS) analysis based on the Q+K method of a mixed linear model.Three important QTLs were analyzed in this study.Four haplotypes of QFTN.sicau-7BL.1 for fertile tillers number (FTN),three haplotypes of QKNS.sicau-1AL.2 for KNS,and four haplotypes of QTKW.sicau-3BS.1 for TKW were detected.FTN-Hap2,KNS-Hap1,and TKW-Hap2 were excellent haplotypes for each QTL based on the yield performance of 42 varieties in regional trials from 2002 to 2013.The varieties with all three haplotypes showed the highest yield compared to those with either two haplotypes or one haplotype.In addition,the KASP-AX-108866053 marker of QTL QKNS.sicau-1AL.2 was successfully distinguished between three haplotypes(or alleles) in 63 varieties based on the number of kernels per spike in regional trials between 2018 and 2021.These genetic loci and reliable makers can be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of wheat yield.
基金supported by the National Center for Genetic Engineering and Biotechnology,Thailand (Grant No.P1020028)Generation Challenge Program,Mexico (Grant No.P0900835)
文摘Paw San Hmwe （PSM） rice has been cultivated in many areas of Myanmar for a long time. Strong aroma, good taste and its elongation during cooking are the key characteristics of PSM rice. Thirty-one PSM accessions were genotypically characterized, and their physical grain and cooking quality traits were studied. We used specific gene markers associated with aroma, apparent amylose content （AAC） and alkali spreading value to determine the alleles carried by different PSM accessions. The results revealed that six PSM accessions （PSM10, PSM12, PSM13, PSM21, PSM22 and PSM30） had a 3-bp insertion in Os2AP gene. Gel consistency （GC） allele was predominant among the PSM accessions for gelatinization temperature （GT）, however, the phenotype observed was between low and intermediate GT because of the combination of the GC allele with the presence of low GT allele at heterozygous state from the other loci of the SSIla gene. Intermediate to high AAC was observed among the PSM accessions corresponding to the haplotype identified for the single nucleotide polymorphism G/T and the （Cm）n repeat in the Wx gene. The characterization and grouping data of PSM accessions posted benefits to Myanmar seed banks, and our results will help in maintaining the integrity of PSM rice variety.
基金supported financially by STI2030-Major Projects(No.2023ZD0406903)the China Postdoctoral Science Foundation(No.2023M743818)the China Postdoctoral Science Foundation(No.GZC20233050).
文摘The SDS-sedimentation volume(SSV)is a critical indicator for assessing wheat gluten quality and is widely used when evaluating wheat processing quality.However,the molecular mechanisms regulating SSV remain poorly understood.In this study,we performed an analysis of quantitative trait loci(QTLs)for SSV using a recombinant inbred line(RIL)population derived from a cross between TAA10 and XX329,and identified four environmentally stable QTLs located on chromosomes 1D,2D,4D,and 6D.Among them,the effects of Qssv.cau-1D and Qssv.cau-6D were likely to be explained by genome variations at the Glu-D1 and Gli-D2 loci.We fine mapped Qssv.cau-2D to the candidate causal gene TaSED,encoding a nucleolar protein.Gene-edited TaSED knockout mutants(tased)had a lower SSV,while TaSED overexpression lines showed a higher SSV.We demonstrated that TaSED interacted with the transcription factor TaSPA to enhance its transcriptional activation activity of glutenin and gliadin,whose expression was downregulated in tased and upregulated in TaSED-OE plants,with corresponding differences in glutenin and gliadin content compared with the wild-type.A molecular marker sedTX was further developed based on a nonsynonymous mutation of the parents in TaSED that could be used to identify haplotypes with high SSV effectively.Our findings elucidate a molecular mechanism governing SSV and reveal valuable variants with promising applications for improving wheat quality.
基金This work was supported by grants from the National Natural Science Foundation of China (No. 30200305 and No. 30070411) and Educational Department Science Funds of Liaoning Province (No. 202013133 and No. 2004C045).
文摘Background Our previous research has suggested that genes around D12S1056 in 12q13 may confer susceptibility to ventricular septal defect （VSD） in humans. The present study was to define the chromosome region assignment by transmission disequilibrium test （TDT）, and to identify the important candidate gene by family-based association study and haplotype analysis. Methods Surrounding D12S1056, ten microsatellite markers including D12S329, D12S305, D12S1662, D12S1056, D12S1293, D12S334, D12S102, D12S83, D12S1655 and D12S1691 were chosen, and TDT was performed in 62 nuclear family trios each consisting of an affected child and two healty parents. Subsequently, the GLI gene, a positional candidate gene that maps to the target region, was selected for further analysis. Three single nucleotide polymorphisms （SNPs）, G11888C, G11388A, and G11625T, were selected for family-based association study and haplotype analysis. Results VSD was significantly associated with all selected markers except D12S1691 [72.2 centi morgen （cM）] and D12S1700 （75.76 cM）. VSD was also significantly associated with G11888C （X^2 = 5.918, P = 0.015）, G11388A （X^2 = 8.067, P = 0.005）, and G11625T （X^2 = 11.842, P = 0.001）. Haplotype analysis showed a strong linkage disequilibrium between G11888C and G11388A （D＇=0.999）, but in significant （X^2 = 1.035, df = 2, P 〉 0.05）. Conclusions The susceptibility gene of VSD was mapped to 3.56 cM in 12q13 by TDT, and the GLI gene, an important candidate in the target region, was associated with VSD.
