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Long-read sequencing reveals novel genetic polymorphisms in the major histocompatibility complex region and their impacts on the Han Chinese population

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Science China Life Sciences 2025年

作者： Cong Zhou Tingting Gong Shuhang Li Li Jin Shaohua Fan State Key laboratory of Genetic Engineering Lab for Evolutionary Synthesis School of Life Sciences Human Phenome Institute Fudan University Research Unit of Dissecting the population genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058) Chinese Academy of Medical Sciences

Human leukocyte antigen(HLA) genes in the major histocompatibility complex(MHC) region are crucial for immunity and are associated with numerous diseases and phenotypes. The MHC region's complexity and high genetic diversity make it challenging to analyze using short-read sequencing(SRS) technology. We sequence the MHC region of 100 Han Chinese individuals using both long-read sequencing(LRS) and SRS platforms at approximately 30X coverage to study genetic alterations and their potential functional impacts. LRS provides significantly greater coverage of the MHC region and eight classical HLA genes, particularly at the HLA-DRB1 locus, compared with SRS. We detect 78,249 single nucleotide polymorphisms(SNPs) using LRS, with 26.0% undetectable by SRS. Based on SNP and inferred HLA allele types, we construct an LRS-based MHC reference panel for the Han Chinese, containing approximately 2.6 times more genetic variants than the SRS-based Han-MHC reference panel. A phenome-wide association study assessing 26,024 phenotypes across 15 categories identifies significant associations for 7,879 independent variants(including 809 LRS-specific SNPs) with 409 phenotypes in nine categories. This analysis reveals 24 unreported HLA allele associations in the bioelectric and cellular categories. The conditional analysis identifies 530independent signals across the 409 phenotypes, including 28 previously unreported signals of eight classical HLA genes associated with 33phenotypes. Of the top-associated SNPs, 191 are detected by LRS only. Fine-mapping identifies 126 independent candidate causal SNPs for three immune-related cellular phenotypes, with 17 detected exclusively by LRS. Our study reveals previously unreported variants and their functional impacts in the MHC region, enhancing our understanding of genetic diversity and its potential biological implications in the Han Chinese population.

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A population genetics model of linkage disequilibrium in admixed populations

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Chinese Science Bulletin 2001年第3期46卷 193-197页

作者： Shiheng Tao Rongmei Zhang Jianhua Chu Xiaoming Liu Liping Du Qingyuan Qi Zewei Luo laboratory of population and Quantitative genetics Institute of Genetics School of Life Science Fudan University Shanghai China

Understanding linkage disequilibrium (LD) created in admixed population and the rate of decay in the disequilibrium over evolution is an important subject in population genetics theory and in disease gene mapping in human populations. The present study represents the theoretical investigation of effects of gene frequencies, levels of LD and admixture proportions of donor populations on the evolutionary dynamics of the LD of the admixed population. We examined the conditions under which the admixed population reached linkage equilibrium or the peak level of the LD. The study reveals the inappropriateness in approximating the dynamics of the LD generated by population admixture by the commonly used formula in literature. An appropriate equation for the dynamics isproposed. The distinct feature of the newly suggested formula is that the value of the nonlinear component of the LD remains constant in the first generation of the population evolution. Comparison between the predicted disequilibrium dynamics

关键词： linkage disequilibrium admixture population error analysis.

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A novel Rad gene polymorphism combined with obesity increases risk for type 2 diabetes mellitus

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Chinese Medical Journal 2004年第5期117卷 770-771页

作者：王国英牛天华陈常忠李琼芳徐希平 Department of Endocrinology Program for population genetics

The ras-associated diabetes (Rad) was initially identified by subtraction cloning from the skeletal muscle of humans with non-insulin dependent diabetes mellitus (type 2 DM).1 Rad mRNA expression is markedly increased... 详细信息

关键词： Rad gene·obesity · polymorphism·type 2 diabetes mellitus

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Fine-tuning the spatial allocation of phytohormones for smart canopy, smart breeding, and smart agriculture

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Science China Life Sciences 2025年第1期 309-310页

作者： Tao Zhou Lin Li National Key laboratory of Crop Genetic Improvement Huazhong Agricultural University HuBei HongShan laboratory

The dual challenges of global climate change and population growth have increased demand for higher crop yields per unit area. The innovative technology of smart agriculture aims to synergize breeding, cultivation, and production through the application of biological and informatics technologies. Historically, the “Green Revolution” introduced semidwarf varieties of certain key crops by utilizing mutations affecting gibberellin pathways, which significantly increased planting densities and yields.

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Dietary carbohydrate intake and risk of type 2 diabetes:a 16-year prospective cohort study

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Science China Life Sciences 2025年

作者： Lu Gan Yi Yang Bin Zhao Kai Yu Kehua Guo Fang Fang Zhiguang Zhou Demetrius Albanes Jiaqi Huang Key laboratory of Diabetes Immunology Ministry of Education and Department of Metabolism and Endocrinology The Second Xiangya Hospital of Central South University CSU-Sinocare Research Center for Nutrition and Metabolic Health Xiangya School of Public Health Central South UniversityFurong Laboratory Division of Cancer Epidemiology and genetics National Cancer Institute NIH Department of Health and Human Services School of Computer Science and Engineering Central South University Institute of Environmental Medicine Karolinska Institute National Clinical Research Center for Metabolic Diseases Key Laboratory of Diabetes Immunology Ministry of Education and Department of Metabolism and Endocrinology The Second Xiangya Hospital of Central South University

Despite considerable research underscoring the importance of carbohydrate intake in relation to the risk of type 2 diabetes(T2D), a comprehensive assessment of this relationship is currently lacking. We aimed to examine the associations of various types and food sources of dietary carbohydrate intake with the risk of T2D, to evaluate potential effect modification by other factors, including genetic susceptibility,and to explore the potential mediators for such associations. The present study included 161,872 participants of the UK Biobank who were free of prevalent cancer, cardiovascular disease, or diabetes, and had at least one validated 24-h dietary recall assessment. Multivariableadjusted age-stratified Cox proportional hazard regression models were applied to estimate hazard ratios(HRs) and 95% confidence intervals(CI) for the associations of various types and food sources of dietary carbohydrate intake with risk of T2D. During a median follow-up of13.6 years, 4,176 incident cases of T2D were identified. In the multivariable-adjusted models, a greater intake of fiber, carbohydrates from whole grains, and carbohydrates from non-starchy vegetables was significantly associated with a lower risk of T2D(highest vs. lowest quantile, HR [95% CI]=0.70 [0.62–0.79], 0.74 [0.67–0.82], and 0.83 [0.75–0.92], respectively, all P for trend population subgroups, including individuals with different genetic susceptibility to T2D. Mediation analyses of the inverse association between T

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The F-box protein HAWAIIAN SKIRT is required for mimicry target-induced microRNA degradation in Arabidopsis

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Journal of Integrative Plant Biology 2019年第11期61卷 1121-1127页

作者： Jun Mei Ning Jiang Guodong Ren State Key laboratory of Genetic Engineering and Ministry of Education Key laboratory for Biodiversity Science and Ecological Engineering School of Life SciencesFudan UniversityShanghai 200438China laboratory of population&Quantitative genetics Institute of Genetics and BiostatisticsSchool of Life SciencesFudan UniversityShanghai 200438China

Mimicry target-directed micro RNA degradation is widespread and highly conserved among eukaryotes. However, little is known about its mechanism of action. In this letter, by using STTM160(target mimic of mi R160) as a reporter, we show that dysfunction of HAWAIIAN SKIRT(HWS) suppresses the pleiotropic phenotype of STTM160. Small RNA sequencing and Northern blot analyses suggested that HWS only affects a subset of micro RNAs. Intriguingly,we identified a stable coexistence of mi R160/mi R399 and their mimicry targets within the AGO1 complex when HWS is compromised, pointing to a possible role of HWS in the clearance of RNA-induced silencing complexes associated with mimicry target.

关键词： mimicry letter HAWAII

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To be or not to be:The host genetic factor and beyond in Helicobacter pylori mediated gastro-duodenal diseases

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World Journal of Gastroenterology 2015年第10期21卷 2883-2895页

作者： Dipanjana Datta De Susanta Roychoudhury R and D Division (genetics) School of Human Genetics and Population Health Cancer Biology and Inflammatory Disease Division Indian Institute of Chemical Biology

Helicobacter pylori(***)have long been associated with a spectrum of disease outcomes in the gastroduodenal *** in bacterial virulence factors or strains is not enough to explain the divergent disease phenotypes manifested by the *** review focuses on host genetic factors that are involved during infection and eventually are thought to influence the disease *** have summarizedthe different host genes that have been investigated for association studies in *** mediated duodenal ulcer or gastric *** discuss that as the bacteria co-evolved with the host;these host gene also show much variation across different ethnic *** illustrate the allelic distribution of interleukin-1B,across different population which is one of the most popular candidate gene studied with respect to *** ***,we highlight that several polymorphisms in the pathway gene can by itself or collectively affect the acid secretion pathway axis(gastrin:somatostatin)thereby resulting in a spectrum of disease

关键词： Helicobacter pylori Gastric cancer Duodenal ulcer

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Whole-genome resequencing infers genomic basis of giant phenotype in Siamese fighting fish(Betta splendens)

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Zoological Research 2022年第1期43卷 78-80页

作者： Le Wang Fei Sun May Lee Gen-Hua Yue Molecular population genetics&Breeding Group Temasek Life Sciences LaboratorySingapore 117604Singapore Department of Biological Sciences National University of SingaporeSingapore 117543Singapore

Understanding the genetic basis of phenotypes is of importance in evolutionary biology and for genetic improvement of economically valuable *** giant phenotype of the fighting fish,Betta splendens,provides a unique opportunity to explore the genetic architecture of overgrowth in body *** such,we re-sequenced and analyzed the genomes of 54 fighting ***-wide FST and selective sweep analyses using 3582429 DNA variants revealed three genomic regions at chr1,chr9,and chr11 that were associated with the giant *** a total length of~3.5 Mb,these regions showed high divergence between the giant and non-giant *** contrast,no signature of selection was detected in the wild-type *** analysis of brain and muscle samples from giant and normal bettas identified 14 candidate genes that were likely responsible for the giant ***,our data provide novel insights into the genetic basis of body size *** genome sequences,transcriptome sequences,DNA sequence variants,and candidate genes for body size provide valuable resources for further biological and evolutionary studies,as well as for rapid improvement in growth-related traits.

关键词： fighting Whole giant

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

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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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