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Co-location of QTL for Sclerotinia stem rot resistance and flowering time in Brassica napus

The Crop Journal 2019年第2期7卷 227-237页

作者： Jian Wu Peipei Chen Qing Zhao Guangqin Cai Yue Hu Yang Xiang Qingyong Yang Youping Wang Yongming Zhou Jiangsu Provincial Key laboratory of Crop genetics and Physiology Yangzhou University National Key laboratory of Crop Genetic Improvement Huazhong Agricultural University Agricultural Bioinformatics Key laboratory of Hubei Province College of Informatics Huazhong Agricultural University Guizhou Rapeseed Institute Guizhou Academy of Agricultural Sciences

Sclerotinia stem rot(SSR) caused by Sclerotinia sclerotiorum(Lib.) de Bary is one of the most devastating diseases of Brassica napus worldwide. Both SSR resistance and flowering time(FT) adaptation are major breeding goals in B. napus. However, early maturing rapeseed varieties, which are important for rice-rapeseed rotation in China, are often highly susceptible to SSR. Here, we found that SSR resistance was significantly negatively correlated with FT in a natural population containing 521 rapeseed inbred lines and a double haploid(DH) population with 150 individual lines, both of which had great variation in FT. Four chromosomal regions on A2, A6, C2, and C8 affecting both SSR resistance and FT were identified using quantitative trait loci(QTL) mapping after constructing a high-density genetic map based on single nucleotide polymorphism markers in the DH ***, we aligned QTL for the two traits identified in the present and previous studies to the B. napus reference genome, and identified four colocalized QTL hotspots of SSR resistance and FT on A2(0–7.7 Mb), A3(0.8–7.5 Mb), C2(0–15.2 Mb), and C6(20.2–36.6 Mb). Our results revealed a genetic link between SSR resistance and FT in ***, which should facilitate the development of effective strategies in both early maturing and SSR resistance breeding and in map-based cloning of SSR resistance QTL.

关键词： Sclerotinia stem rot Brassica napus QTL mapping Flowering time SNP array

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Mapping QTLs Affecting Economic Traits on BTA3 in Chinese Holstein with Microsatellite Markers

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Journal of Integrative Agriculture 2014年第9期13卷 1999-2004页

作者： QIN Chun-hua CHU Qin CHU Gui-yan ZHANG Yi ZHANG Qin ZHANG Sheng-li SUN Dong-xiao College of Animal Science and Technology/Key laboratory of Animal genetics and Breeding Ministry of Agriculture/National Engineering Laboratory of Animal Genetics China Agricultural University

It had been demonstrated that the strong and highly significant quantitative trait locus（QTL） can affect protein percentage on Bos Taurus Autosome 3（BTA3） at the position 52 cM, near the microsatellite DIK4353, with the 95% confidence interval spanning from 25 to 57 cM in Chinese Holstein population using QTL-express, MQREML, and GRIDQTL softwares. This study herein focused on such region of fine mapping QTLs for milk production and functional traits with 16 microsatellite markers with coverage of 33 cM between the markers BMS2904 and MB099 on BTA3 in a daughter-designed Chinese Holstein population. A total of 1 298 Holstein cows and 7 sires were genotyped for 16 microsatellites with ABI 3700 DNA sequencer. The variance components QTL linkage analysis（LA） and linkage-disequilibrium（LD） analysis（LA/LD） was performed to map QTLs for 7 traits, i.e., 305-d milk yield, fat yield, protein yield, fat percentage, protein percentage, somatic cell score and persistency of milk yield. Four strong and highly significant QTLs were detected for fat yield, fat percentage, protein percentage and somatic cell score at the position 40, 30, 27 and 26 cM, respectively. Two minor QTLs for milk yield and persistency of milk yield were identified at 42 and 46 cM, respectively. These findings provided a general idea for the fine mapping of the causal mutation for milk production and functional traits on BTA3 in the future.

关键词： QTL mapping economic traits microsatellite markers BTA3 Chinese Holstein

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Fine Mapping QTLs Affecting Milk Production Traits on BTA6 in Chinese Holstein with SNP Markers

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Journal of Integrative Agriculture 2013年第1期12卷 110-117页

作者： LIU Rui SUN Dong-xiao WANG Ya-chun YU Ying ZHANG Yi CHEN Hui-yong ZHANG Qin ZHANG Sheng-li ZHANG Yuan College of Animal Science and Technology/Key laboratory of Animal genetics and Breeding Ministry of Agriculture/National Engineering Laboratory of Animal Genetics/China Agricultural University Sichuan Animal Science Academy

Our previous studies demonstrated that the region around markers BMS470 and BMS1242 on BTA6 showed a linkage to 305-d milk yield and composition traits in the Chinese Holstein population. We herein focused on such narrow region to fine map milk production QTLs with 15 SNPs across 25 Mb with each SNP in 1 Mb within most regions in a Chinese Holstein population with daughter design. 1 449 Holstein cows and 11 sires were genotyped for such SNPs by using TaqMan probe and RFLP assays. Multipoint linkage analysis across family revealed a QTL affecting milk yield between PPARGC1A C4075T and SLC34A2 T1713C. Meanwhile, within family analysis found three milk yield QTLs （two in CR T60984131G-CEP135 C501T and one in PDLIM5 A106C-OPN T3907, a fat yield QTLin UGDH T1670C-CR T60984131G region, and two protein yield QTLs in TBC1D1 G501C-UGDH T1670C and PPARGC1A C4075T-SLC34A2 T1713C, respectively. Associations between aforementioned significant SNP markers and milk production traits were further implemented. We found significant associations of PPARGC1A C4075T, SLC34A2 T1713C with milk yield （P0.05, P0.01, P0.01）, UGDH T1670C, and CR T60984131G with fat yield （P0.01, P0.01）, and PPARGC1A C4075T, SLC34A2 T1713C, UGDH T1670C and OPN T3907 with protein yield （P0.01, P0.01, P0.01, P0.01）. Our findings implied that QTLs affecting milk production traits on BTA6 were pleictropism or multigenic effect and PPARGC1A and OPN may be the causal mutations behind milk production QTLs on BTA6 in the Chinese Holstein population.

关键词： fine mapping milk production trait SNP BTA6 Chinese Holstein

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Statistical recovering of incomplete genotypic information of DNA molecular markers

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Science China(Life Sciences) 1998年第4期41卷 442-448页

作者： JIANG Changjian MO Huidong laboratory of Quantitative genetics Agricultural Collego University of YangzhouYangzhou 225009China

Genetic information provided by a dominant marker about the genotype is partial or incomplete,and a missing marker provides no information at *** the present study,based on some basic genetic and statistical principles,a general algorithm is proposed to systematically recover the genotypic information of all dominant and missing markers on a genome for individuals from an F_(2)*** recovered information can then increase the efficiency and precision in mapping quantitative trait loci(QTL)and marker assisted selection(MAS).The derived method can be easily extended to other populations consisting of all 3 genotypes on each marker locus,such as populations derived from an F_(2)by selfing or random mating.

关键词： dominant marker missing marker genotypic information statistical recovering conditional probablility

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Analysis of DNA Methylation of Gracilariopsis lemaneiformis Under Temperature Stress Using the Methylation Sensitive Amplification Polymorphism(MSAP) Technique

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Journal of Ocean University of China 2018年第3期17卷 623-631页

作者： PENG Chong SUI Zhenghong ZHOU Wei HU Yiyi MI Ping JIANG Minjie LI Xiaodong RUAN Xudong Key laboratory of Marine genetics and Breeding of Ministry of Education Ocean University of China

Gracilariopsis lemaneiformis is an economically important agarophyte, which contains high quality gel and shows a high growth rate. Wild population of G. lemaneiformis displayed resident divergence, though with a low genetic diversity as was revealed by amplified fragment length polymorphism(AFLP) and simple sequence repeat(SSR) analyses. In addition, different strains of G. lemaneiformis are diverse in morphology. The highly inconsistence between genetic background and physiological characteristics recommends strongly to the regulation at epigenetic level. In this study, the DNA methylation change in G. lemaneiformis among different generation branches and under different temperature stresses was assessed using methylation sensitive amplified polymorphism(MSAP) technique. It was shown that DNA methylation level among different generation branches was diverse. The full and total methylated DNA level was the lowest in the second generation branch and the highest in the third generation. The total methylation level was 61.11%, 60.88% and 64.12% at 15℃, 22℃ and 26℃, respectively. Compared with the control group(22℃), the fully methylated and totally methylated ratios were increased in both experiment groups(15℃ and 26℃). All of the cytosine methylation/demethylation transform(CMDT) was further analyzed. High temperature treatment could induce more CMDT than low temperature treatment did.

关键词： DNA methylation/demethylation epigenetics Gracilariopsis lemaneiformis MSAP temperature stress

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BnlR:A multi-omics database with various tools for Brassica napus research and breeding

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Molecular Plant 2023年第4期16卷 775-789页

作者： Zhiquan Yang Shengbo Wang Lulu Wei Yiming Huang Dongxu Liu Yupeng Jia Chengfang Luo Yuchen Lin Congyuan Liang Yue Hu Cheng Dai Liang Guo Yongming Zhou Qing-Yong Yang National Key laboratory of Crop Genetic Improvement Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China Hubei Key laboratory of Agricultural Bioinformatics College of InformaticsHuazhong Agricultural UniversityWuhan 430070China Innovative Center of Molecular genetics and Evolution School of Life SciencesGuangzhou UniversityGuangzhou 510405China

In the post-genome-wide association study era,multi-omics techniques have shown great power and poten-tial for candidate gene mining and functional genomics ***,due to the lack of effective data integration and multi-omics analysis platforms,such techniques have not still been applied widely in rape-seed,an important oil crop ***,we report a rapeseed multi-omics database(BnlR;http:/l ***/BnlR),which provides datasets of six omics including genomics,transcriptomics,variomics,epigenetics,phenomics,and metabolomics,as well as numerous"variation-gene expression-phenotype"associations by using multiple statistical *** addition,a series of multi-omics search and analysis tools are integrated to facilitate the browsing and application of these *** is the most comprehensive multi-omics database for rapeseed so far,and two case studies demonstrated its power to mine candidate genes associated with specific traits and analyze their potential regulatory mechanisms.

关键词： Brassica napus multi-omics database candidate gene mining functional genomics

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FHA domain of AGGF1 is essential for its nucleocytoplasmic transport and angiogenesis

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Science China(Life Sciences) 2021年第11期64卷 1884-1894页

作者： Cui-Fang Zhang Han-Ming Wang Andong Wu Yang Li Xiao-Li Tian Department of Human population genetics Institute of Molecular MedicinePeking UniversityBeijing 100871China Aging and Vascular Diseases Human Aging Research Institute and School of Life ScienceNanchang Universityand Jiangxi Key Laboratory of Human AgingNanchang 330031China

Angiogenic factor with G-patch and FHA domains 1(AGGF1) exhibits a dynamic distribution from the nucleus to the cytoplasm in endothelial cells during angiogenesis, but the biological significance and underlying mechanism of this nucleocytoplasmic transport remains unknown. Here, we demonstrate that the dynamic distribution is essential for AGGF1 to execute its angiogenic function. To search the structural bases for this nucleocytoplasmic transport, we characterized three potential nuclear localization regions, one potential nuclear export region, forkhead-associated(FHA), and G-patch domains to determine their effects on nucleocytoplasmic transport and angiogenesis, and we show that AGGF1 remains intact during the dynamic subcellular distribution and the region from 260 to 288 amino acids acts as a signal for its nuclear localization. The distribution of AGGF1 in cytoplasm needs both FHA domain and 14-3-3α/β. Binding of AGGF1 via FHA domain to 14-3-3α/β is required to complete the transport. Thus, we for the first time established structural bases for the nucleocytoplasmic transport of AGGF1 and revealed that the FHA domain of AGGF1 is essential for its nucleocytoplasmic transport and angiogenesis.

关键词： AGGF1 nucleocytoplasmic transport angiogenesis FHA domain 14-3-3α/β

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Transcriptomic basis of neutrophil ratio variation induced by poly I:C stimulation in porcine peripheral blood

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Frontiers of Agricultural Science and Engineering 2017年第3期4卷 342-352页

作者： Haiyan WANG Qiaoxia ZHANG Lilin YIN Xiangdong LIU Shuhong ZHAO Mengjin ZHU Changchun LI Key laboratory of Agricultural Animal genetics Breeding and Reproduction of Ministry of Education & Key Laboratory of Swine Genetics and BreedingMinistry of AgricultureHuazhong Agricultural University The Cooperative Innovation Center for Sustainable Pig Production Huazhong Agricultural University College of informatics Huazhong Agricultural University

Neutrophils are vital components of defense mechanisms against invading pathogens and are closely linked with the individual antiviral capacity of pigs and other mammals. Neutrophilia is a well-known clinical characteristic of viral and bacterial infections. Using Affymetrix porcine genome microarrays, we investigated the gene expression profiles associated with neutrophil variation in porcine peripheral blood before and after polyriboinosinic-polyribocytidylic acid stimulation. Transcriptomic analysis showed 796 differentially expressed genes(DEGs) in extreme response(ER) pigs and 192 DEGs in moderate response(MR) pigs. Most DEGs were related to immune responses, included MXD1, CXCR4,CREG1, My D88, CD14, TLR2, TLR4, IRF3 and *** ontology analysis indicated that the DEGs of both ER and MR pigs were involved in common biological processes, such as cell proliferation, growth regulation,immune response, inflammatory response and cell activation. The ER and MR groups also showed differences in DEGs involved in biological processes. DEGs involved in cell division and cell cycle were specifically found in the ER pigs, whereas DEGs involved in cell migration were specifically found in the MR pigs. The study provides a basic understanding of the molecular basis for the antiviral capacity of pigs and other mammals.

关键词： neutrophil peripheral blood pig poly I:C transcriptome

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Haplotype Data of 23 Y-chromosome Markers in Minnan Han Chinese and Comparison with Those of 12 Y-chromosome Markers

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Journal of Huazhong University of Science and Technology(Medical Sciences) 2015年第3期35卷 456-463页

作者：尚杰胡盛平 Molecular Biology and Forensic genetics laboratory Shantou University Medical College

We genotyped 23 Y-STR loci（DYS576, DYS389 I, DYS448, DYS389 II, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458, DYS385a/b, DYS456, and GATA-H4） in a sample of 109 unrelated male Chinese people residing in Minnan area and compared the results with those from our previous study on 12 Y-STR. The haplotype diversity and the discrimination capacity of the 23 Y-STR reached 0.9903 and 0.9725, respectively, and the genetic diversity for each locus ranged from 0.321（DYS391） to 0.955（DYS385）. Besides, we observed a strong correlation between the number of Y-STR markers and the substantial improvement of forensic parameters used to discriminate between individuals. The results indicated that these highly polymorphic Y-STR markers were useful for human identification in forensic cases and paternity tests within the Minnan Han Chinese population.

关键词： Y-STR Minnan Han Chinese comparison off-ladder

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Genetic mapping of telomere-associated sequences in soybean (Glycine max)

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Progress in Natural Science:Materials International 2001年第5期11卷 33-39页

作者：刘峰张德水张劲松陈受宜 Beijing 100101 China Chinese Academy of Sciences Institute of genetics Plant Biotechnology laboratory

Two telomere-associated sequences (TAS), named STAS8 and STAS10, were cloned from soybean genomic DNA using polymerase chain reaction (PCR) amplification. Southern analysis showed that they were sequences with moderate copy number in soybean genome. Sequence analysis demonstrated that STAS10 had tandemly arrayed consensus sequences of TTTAGGG and TTAGGG . The mapping of these two TAS was performed with a population of F8 re-combinant inbred line using restriction fragment length polymorphisms( RFLP). Seven out of nine polymorphic fragments were mapped to the most distal position of five linkage groups, Dla, F, G2, H and Q of soybean, and the other two loci were closely linked and mapped to two interstitial positions within linkage group Dla. The mapping of TAS in soybean is essential for completeness of a molecular genetic map of soybean.

关键词： soybean (Glycine max) telomere-associated sequence (TAS) genetic mapping.

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