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GSW3.1,a novel gene controlling grain size and weight in rice

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The Crop Journal 2024年第3期12卷 796-802页

作者： Yifei Jiang Mingao Zhou Simin Ke Xiaoxiao Deng Yangsheng Li State Key Laboratory of Hybrid Rice Key Laboratory for Research and Utilization of Heterosis in Indica RiceMinistry of AgricultureCollege of Life SciencesWuhan UniversityWuhan 430072HubeiChina

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 *** 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 *** editing revealed that GSW3.1(LOC_Os03g16850)was pleiotropic,positively regulating grain size and weight while affecting several other agronomic *** analysis indicated that some traits,including grain width and weight,were highly correlated with indica-japonica differentiation.

关键词： Rice Grain size and weight 3.1(GSW3.1) Quantitative trait locus haplotype analysis

Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

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The Crop Journal 2024年第2期12卷 558-568页

作者： Junqiao Song Angela Pacheco Amos Alakonya Andrea S.Cruz-Morales Carlos Muoz-Zavala Jingtao Qu Chunping Wang Xuecai Zhang Felix San Vicente Thanda Dhliwayo College of Agronomy Henan University of Science and TechnologyLuoyang 471000HenanChina International Maize and Wheat Improvement Center(CIMMYT) El BatanMexico Anyang Academy of Agricultural Sciences Anyang 455000HenanChina CIMMYT-China Specialty Maize Research Center Crop Breedingand Cultivation Research InstituteShanghai Academy of Agricultural SciencesShanghai 201403China

Maize stalk rot reduces grain yield and *** about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the *** prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted *** 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 *** favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred *** genotype-by-environment(G×E)interaction increased genomic prediction accuracy.

关键词： Maize stalk rot Genome-wide association mapping haplotype analysis Genomic prediction G×E interaction

Genetic dissection and validation of a major QTL for grain weight on chromosome 3B in bread wheat(Triticum aestivum L.)

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Journal of Integrative Agriculture 2024年第1期23卷 77-92页

作者： Simin Liao Zhibin Xu Xiaoli Fan Qiang Zhou Xiaofeng Liu Cheng Jiang Liangen Chen Dian Lin Bo Feng Tao Wang Chengdu Institute of Biology Chinese Academy of SciencesChengdu 610041China University of Chinese Academy of Sciences Beijing 100049China The Innovative Academy of Seed Design Chinese Academy of SciencesBeijing 100101China

Grain weight is one of the key components of wheat(Triticum aestivum L.)*** 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 *** major QTLs,***-2D,***-2D,***-3B,***-4B.1,***-2D.1,***-2D.1 and ***-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 *** interactions were detected between the two major TGW QTLs and three major GW *** addition,***-3B.1 and ***-3B were co-located,and the improved TGW at this locus was contributed by *** other loci,***-3B.1/***-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 ***-3B.1/***-3B is likely a novel *** haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and *** to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of ***-3B.1/***-3B was ***,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.

关键词： thousand-grain weight QTL mapping haplotype analysis candidate gene

Fine mapping and candidate gene analysis of qGL10 affecting rice grain length

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The Crop Journal 2023年第2期11卷 540-548页

作者： Tengkui Chen Lixin Luo Zhe Zhao Hui Wang Chun Chen Yongzhu Liu Xinchang Li Tao Guo Wuming Xiao National Plant Space Breeding Engineering Technology Research Center South China Agricultural UniversityGuangzhou 510642GuangdongChina Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology Zhaoqing 526238GuangdongChina

Grain size influences the yield and quality of rice(Oryza sativa L.),and grain length is one of the component traits of grain *** 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 ***-seq was used for preliminary QTL mapping and InDel markers were developed to fine map the *** major QTL,tentatively named qGL10,for grain length was located in a 128.45 kb region of chromosome *** with haplotype analysis of rice varieties,expression pattern analysis of candidate genes suggested LOC_Os10g39130(OsMADS56)as a candidate *** alignment of OsMADS56 in 02428 and LB3 revealed that there were 15 SNPs in the promoter region and four in the coding *** haplotype analysis suggested that SNP9(G/A)located in the TGTCACA motif might account for the different expression levels of OsMADS56 in 02428 and *** results lay a foundation for the application of qGL10 in molecular breeding of new rice varieties.

关键词： Rice Grain length QTL mapping haplotype analysis

Genome-wide association and linkage mapping strategies reveal the genetic loci and candidate genes of important agronomic traits in Sichuan wheat

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Journal of Integrative Agriculture 2023年第11期22卷 3380-3393页

作者： ZHANG Zhi-peng LI Zhen HE Fang Lü Ji-juan XIE Bin YI Xiao-yu LI Jia-min LI Jing SONG Jing-han PU Zhi-en MA Jian PENG Yuan-ying CHEN Guo-yue WEI Yu-ming ZHENG You-liang LI Wei State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Sichuan Agricultural UniversityChengdu 611130P.R.China College of Agronomy Sichuan Agricultural UniversityChengdu 611130P.R.China Triticeae Research Institute Sichuan Agricultural UniversityChengdu 611130P.R.China Sichuan Provincial Seed Station Chengdu 610044P.R.China Huaiyin Institute of Agricultural Sciences of Xuhuai Area in Jiangsu Huai'an 223001P.R.China Beijing Foreign Studies University Beijing 100081P.R.China

Increasing wheat yield is a long-term goal for wheat breeders around the *** elite genetic resources and dissecting the genetic basis of important agronomic traits in wheat are the necessary methods for high-yield wheat *** 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 *** 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 *** 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 *** important QTLs were analyzed in this *** haplotypes of ***-7BL.1 for fertile tillers number (FTN),three haplotypes of ***-1AL.2 for KNS,and four haplotypes of ***-3BS.1 for TKW were ***-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 *** varieties with all three haplotypes showed the highest yield compared to those with either two haplotypes or one *** addition,the KASP-AX-108866053 marker of QTL ***-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 *** genetic loci and reliable makers can be applied in marker-assisted selection or map-based gene cloning for the genetic improvement of wheat yield.

关键词： Sichuan wheat GWAS yield traits haplotype analysis KASP

Glucocorticoid receptor gene haplotype structure and steroid therapy outcome in IBD patients

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World Journal of Gastroenterology 2010年第31期16卷 3888-3896页

作者： Jessica Mwinyi Christa Wenger Jyrki J Eloranta Gerd A Kullak-Ublick Division of Clinical Pharmacology and Toxicol-ogy University Hospital Zurich

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.

关键词： Inflammatory bowel disease Steroid therapy Glucocorticoid receptor Pharmacogenetics haplotype analysis

Characterization of Myanmar Paw San Hmwe Accessions Using Functional Genetic Markers

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Rice science 2015年第2期22卷 53-64页

作者： Kyaw Swar Oo Alisa KONGJAIMUN Srisawat KHANTHONG Myint YI Tin Tin MYINT Siriporn KORINSAK Jonaliza Lanceras SIANGLIW Khin Myo MYINT Apichart VANAVICHIT Chanate MALUMPONG Theerayut TOOJINDA Rice Division Department of Agricultural Research Rice Gene Discovery Unit National Centre for Genetic Engineering and BiotechnologyNational Science and Technology Development AgencyKasetsart University Agronomy Department Faculty of Agriculture at Kamphaeng SaenKasetsart University Center of Excellence on Agricultural Biotechnology Office of Higher Education CommissionMinistry of Education Plant Breeding Faculty of Agriculture at Kamphaeng SaenKasetsart University Plant Biotechnology Center Myanmar Agriculture Service Rice Science Center Kasetsart University

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.

关键词： Paw San Hmwe rice aroma apparent amylose content gel consistency gelatinizationtemperature alkali spreading value functional genetic marker grain quality haplotype analysis

Association of the GLI gene with ventricular septal defect after the susceptibility gene being narrowed to 3.56 cM in 12q13

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Chinese Medical Journal 2006年第4期119卷 267-274页

作者： QIU Guang-rong GONG Li-guo HE Guang XU Xiao-yan XIN Na SUN Gui-feng YUAN Yi-hua SUN Kai-lai Department of Medical Genetics China Medical University Shenyang 110001 China Department of Cardiovascular Surgery First Affiliated Hospital China Medical University Shenyang 110001 China

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.

关键词： ventricular septal defect transmission disequilibrium test GLI gene association study haplotype analysis

Association of A Common haplotype of Hepatocyte Nuclear Factor 1α With Type 2 Diabetes in Chinese Population

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Biomedical and Environmental Sciences 2007年第1期20卷 41-46页

作者： CONG-RONG WANG CHENG HU RONG ZHANG QI-CHEN FANG XIAO-JING MA WEI-PING JIA KUN-SAN XIANG Shanghai Diabetes Institute Department of Endocrinology and Metabolism Shanghai Jiaotong University Affiliated Sixth People＇s Hospital Shanghai 200233China

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.

关键词： Hepatocyte nuclear factor-1α Type2 diabetes SNP haplotype analysis