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Genome-wide association with transcriptomics reveals a shade-tolerance gene network in soybean

The Crop Journal 2024年第1期12卷 232-243页

作者： Yanzhu Su Xiaoshuai Hao Weiying Zeng Zhenguang Lai Yongpeng Pan Can Wang Pengfei Guo Zhipeng Zhang Jianbo He Guangnan Xing Wubin Wang Jiaoping Zhang Zudong Sun Junyi Gai Soybean Research Institute/MARA National Center for Soybean improvement MARA key laboratory of Biology and genetic improvement of Soybean/state key laboratory for Crop genetics and Germplasm Enhancement/state Innovation Platform for Integrated production and Education in Soybean Bio-breeding/Jiangsu Collaborative Innovation Center for Modern Crop production Nanjing Agricultural UniversityNanjing 210095JiangsuChina Guangxi Academy of Agricultural Sciences Nanning 530007GuangxiChina

Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade tolerance.An improved GWAS procedure,restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers(GASM-RTM-GWAS),identified 140 genes and their alleles associated with shade-tolerance index(STI),146 with relative pith cell length(RCL),and nine with both.Annotation of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes,of which half were differentially expressed under shading and non-shading conditions as well as at different growth stages.From the identified genes,three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the network.Altogether,both STI and RCL gene systems worked for shade-tolerance with genes interacted each other,this confirmed that shadetolerance is regulated by more than single group of interacted genes,involving multiple biological functions as a gene network.

关键词： Soybean(Glycine max(L.)Merr.) Shade-tolerance Restricted two-stage multi-locus genomewide association study based on gene/allele sequence markers(GASM-RTM-GWAS) Shade-tolerance index(STI) Relative cell length(RCL) Transcriptome

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Single-base editing in IGF2 improves meat production and intramuscular fat deposition in Liang Guang Small Spotted pigs

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Journal of Animal Science and Biotechnology 2024年第1期15卷 108-126页

作者： Tianqi Duo Xiaohong Liu Delin Mo Yu Bian Shufang Cai Min Wang Ruiqiang Li Qi Zhu Xian Tong Ziyun Liang Weilun Jiang Shiyi Chen Yaosheng Chen Zuyong He state key laboratory of Biocontrol School of Life SciencesSun Yat-Sen UniversityGuangzhou 510275GuangdongChina Department of Pharmacology(the state‑Province key Laboratories of Biomedicine‑Pharmaceutics of China Key Laboratory of Cardiovascular ResearchMinistry of Education)College of PharmacyHarbin Medical UniversityHarbin 150081China Hunan Provincial key laboratory for genetic improvement of Domestic Animal College of Animal Science and TechnologyHunan Agricultural UniversityChangsha 410128China

Background Chinese indigenous pigs are popular with consumers for their juiciness,flavour and meat quality,but they have lower meat production.Insulin-like growth factor 2(IGF2) is a maternally imprinted growth factor that promotes skeletal muscle growth by regulating cell proliferation and differentiation.A single nucleotide polymorphism(SNP) within intron 3 of porcine IGF2 disrupts a binding site for the repressor,zinc finger BED-type containing 6(ZBED6),leading to up-regulation of IGF2 and causing major effects on muscle growth,heart size,and backfat thickness.This favorable mutation is common in Western commercial pig populations,but absent in most Chinese indigenous pig breeds.To improve meat production of Chinese indigenous pigs,we used cytosine base editor 3(CBE3)to introduce IGF2 intron3-C3071T mutation into porcine embryonic fibroblasts(PEFs) isolated from a male Liang Guang Small Spotted pig(LGSS),and single-cell clones harboring the desired mutation were selected for somatic cell nuclear transfer(SCNT) to generate the founder line of IGF2^(T/T) pigs.Results We found the heterozygous progeny IGF2^(C/T) pigs exhibited enhanced expression of IGF2,increased lean meat by 18%-36%,enlarged loin muscle area by 3%-17%,improved intramuscular fat(IMF) content by 18%-39%,marbling score by 0.75-1,meat color score by 0.53-1.25,and reduced backfat thickness by 5%-16%.The enhanced accumulation of intramuscular fat in IGF2^(C/T) pigs was identified to be regulated by the PI3K-AKT/AMPK pathway,which activated SREBP1 to promote adipogenesis.Conclusions We demonstrated the introduction of IGF2-intron3-C3071T in Chinese LGSS can improve both meat production and quality,and first identified the regulation of IMF deposition by IGF2 through SREBP1 via the PI3KAKT/AMPK signaling pathways.Our study provides a further understanding of the biological functions of IGF2and an example for improving porcine economic traits through precise base editing.

关键词： CBE3 IGF2 Intramuscular fat Meat production PI3K-AKT/AMPK ZBED6

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Flavonoids from mulberry leaves inhibit fat production and improve fatty acid distribution in adipose tissue in finishing pigs

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Animal Nutrition 2024年第1期16卷 147-157页

作者： Yingying Liu Yinglin Peng Chen Chen Huibo Ren Ji Zhu Yuan Deng Qingming Cui Xionggui Hu Jianhua He Huali Li Xinghui Zhu Yulong Yin Jun He Yi Xiao College of Animal Science and technology Hunan Agricultural University Hunan Institute of Animal and Veterinary Science key laboratory of Conservation and genetic Analysis of Local pig Breed Germplasm Resources College of Information and Intelligence Hunan Agricultural University Institute of Subtropical Agriculture Chinese Academy of Sciences

This study evaluated the effects of flavonoids from mulberry leaves (FML) on plasma biochemical indices,serum activities of lipid metabolism-related enzymes,fat morphology,fatty acid composition,and lipid metabolism in different adipose tissues of finishing pigs.We used 120 Chinese hybrid barrows of Berkshire and Bama mini-pigs with an average initial body weight of 45.11±4.23 kg.The pigs were randomly assigned to five treatment groups and fed a control diet based on corn,soybean meal,and wheat bran or a control diet supplemented with 0.02%,0.04%,0.08%,or 0.16%FML.Each experimental group had six replicates (pens),with four pigs per pen.After a 7-d adaptation period,the feeding trial was conducted for 58 d.Blood and adipose tissue samples were collected from 30 pigs (one pig per pen)at the end of the test.The results showed that FML supplementation significantly decreased the feed intake to body gain ratio,the plasma concentrations of total cholesterol and free fatty acids,and the serum activity of 3-hydroxy-3-methylglutaryl coenzyme A reductase (linear or quadratic effects,Ppigs (linear,P=0.05) and increased the adipocyte area in the visceral adipose tissue (quadratic,Ppigs (Pproduction

关键词： Finishing pig Mulberry leaf Flavonoid Lipid metabolism Fatty acid Lard

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Mechanisms underlying the role of endoplasmic reticulum stress in the placental injury and fetal growth restriction in an ovine gestation model

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Journal of Animal Science and Biotechnology 2024年第1期15卷 201-217页

作者： Hao Zhang Xia Zha Yi Zheng Xiaoyun Liu Mabrouk Elsabagh Hongrong Wang Honghua Jiang Mengzhi Wang laboratory of Metabolic Manipulation of Herbivorous Animal Nutrition College of Animal Science and TechnologyYangzhou UniversityYangzhou 225009P.R.China Joint International Research laboratory of Agriculture and Agri‑Product Safety Ministry of Education of ChinaYangzhou UniversityYangzhou 225009P.R.China Department of Animal production and technology Faculty of Agricultural Sciences and TechnologiesNiğde Omer Halisdemir UniversityNigde 51240Turkey Department of Nutrition and Clinical Nutrition Faculty of Veterinary MedicineKafrelsheikh UniversityKafrelSheikhEgypt Department of Pediatrics Northern Jiangsu People’s HospitalClinical Medical CollegeYangzhou UniversityYangzhou 225001China state key laboratory of Sheep genetic improvement and Healthy production Xinjiang Academy of Agricultural Reclamation ScienceShihezi 832000China

Background Exposure to bisphenol A(BPA),an environmental pollutant known for its endocrine-disrupting properties,during gestation has been reported to increase the risk of fetal growth restriction(FGR)in an ovine model of pregnancy.We hypothesized that the FGR results from the BPA-induced insufficiency and barrier dysfunction of the placenta,oxidative stress,inflammatory responses,autophagy and endoplasmic reticulum stress(ERS).However,precise mechanisms underlying the BPA-induced placental dysfunction,and subsequently,FGR,as well as the potential involvement of placental ERS in these complications,remain to be investigated.Methods In vivo experiment,16 twin-pregnant(from d 40 to 130 of gestation)Hu ewes were randomly distributed into two groups(8 ewes each).One group served as a control and received corn oil once a day,whereas the other group received BPA(5 mg/kg/d as a subcutaneous injection).In vitro study,ovine trophoblast cells(OTCs)were exposed to 4 treatments,6 replicates each.The OTCs were treated with 400μmol/L BPA,400μmol/L BPA+0.5μg/m L tunicamycin(Tm;ERS activator),400μmol/L BPA+1μmol/L 4-phenyl butyric acid(4-PBA;ERS antagonist)and DMEM/F12 complete medium(control),for 24 h.Results In vivo experiments,pregnant Hu ewes receiving the BPA from 40 to 130 days of pregnancy experienced a decrease in placental efficiency,progesterone(P4)level and fetal weight,and an increase in placental estrogen(E2)level,together with barrier dysfunctions,OS,inflammatory responses,autophagy and ERS in type A cotyledons.In vitro experiment,the OTCs exposed to BPA for 24 h showed an increase in the E2 level and related protein and gene expressions of autophagy,ERS,pro-apoptosis and inflammatory response,and a decrease in the P4 level and the related protein and gene expressions of antioxidant,anti-apoptosis and barrier function.Moreover,treating the OTCs with Tm aggravated BPA-induced dysfunction of barrier and endocrine(the increased E2 level and decreased P4 level),OS,inflammatory responses,autophagy,and ERS.However,treati

关键词： Autophagy Bisphenol A Endoplasmic reticulum stress Fetal growth restriction Inflammatory responses Sheep

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OsNAC5 orchestrates OsABI5 to fine-tune cold tolerance in rice

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Journal of Integrative Plant Biology 2024年第4期66卷 660-682页

作者： Ruiqing Li Yue Song Xueqiang Wang Chenfan Zheng Bo Liu Huali Zhang Jian Ke Xuejing Wu Liquan Wu Ruifang Yang Meng Jiang College of Agronomy Anhui Agricultural UniversityHefei 230036China Hainan Institute Yazhou Bay Sci-Tech CityZhejiang UniversitySanya 572025China National key laboratory of Rice Biology Advanced Seed InstituteZhejiang UniversityHangzhou 311225China state key laboratory of Rice Biology and Chinese National Center for Rice improvement China National Rice Research InstituteHangzhou 311401China key laboratory of Germplasm Innovation and genetic improvement of Grain and Oil Crops(Co-Construction by Ministry and Province) Ministry of Agriculture and Rural AffairsCrop Breeding and Cultivation Research InstituteShanghai Academy of Agricultural SciencesShanghai 201106China

Due to its tropical origins,rice(Oryza sativa)is susceptible to cold stress,which poses severe threats to production.OsNAC5,a NAC-type transcription factor,participates in the cold stress response of rice,but the detailed mechanisms remain poorly understood.Here,we demonstrate that OsNAC5 positively regulates cold tolerance at germination and in seedlings by directly activating the expression of ABSCISIC ACID INSENSITIVE 5(OsABI5).Haplotype analysis indicated that single nucleotide polymorphisms in a NAC-binding site in the OsABI5 promoter are strongly associated with cold tolerance.OsNAC5 also enhanced OsABI5 stability,thus regulating the expression of cold-responsive(COR)genes,enabling fine-tuned control of OsABI5 action for rapid,precise plant responses to cold stress.DNA affinity purification sequencing coupled with transcriptome deep sequencing identified several OsABI5 target genes involved in COR expression,including DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR 1A(OsDREB1A),OsMYB20,and PEROXIDASE 70(OsPRX70).In vivo and in vitro analyses suggested that OsABI5 positively regulates COR gene transcription,with marked COR upregulation in OsNAC5-overexpressing lines and downregulation in osnac5 and/or osabi5 knockout mutants.This study extends our understanding of cold tolerance regulation via OsNAC5 through the OsABI5-CORs transcription module,which may be used to ameliorate cold tolerance in rice via advanced breeding.

关键词： ABA signaling ABI5 cold tolerance DREB NAC5 rice

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Characterizing structural variants based on graph-genotyping provides insights into pig domestication and local adaption

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Journal of genetics and Genomics 2024年第4期51卷 394-406页

作者： Xin Li Quan Liu Chong Fu Mengxun Li Changchun Li Xinyun Li Shuhong Zhao Zhuqing Zheng key Lab of Agricultural Animal genetics Breeding and Reproduction of Ministry of Education and Key Laboratory of Swine Genetics and Breeding of Ministry of AgricultureCollege of Animal Science and TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China Institute of Agricultural Biotechnology Jingchu University of TechnologyJingmenHubei 448000China The Cooperative Innovation Center for Sustainable pig production WuhanHubei 430070China Hubei Hongshan laboratory WuhanHubei 430070China

Structural variants(SVs),such as deletions(DELs)and insertions(INSs),contribute substantially to pig genetic diversity and phenotypic variation.Using a library of SVs discovered from long-read primary assemblies and short-read sequenced genomes,we map pig genomic SVs with a graph-based method for re-genotyping SVs in 402 genomes.Our results demonstrate that those SVs harboring specific trait-associated genes may greatly shape pig domestication and local adaptation.Further characterization of SVs reveals that some population-stratified SVs may alter the transcription of genes by affecting regulatory elements.We identify that the genotypes of two DELs(296-bp DEL,chr7:52,172,101e52,172,397;278-bp DEL,chr18:23,840,143 e23,840,421)located in muscle-specific enhancers are associated with the expression of target genes related to meat quality(FSD2)and muscle fiber hypertrophy(LMOD2 and WASL)in pigs.Our results highlight the role of SVs in domestic porcine evolution,and the identified candidate functional genes and SVs are valuable resources for future genomic research and breeding programs in pigs.

关键词： pigs Structural variation Selection signatures Regulatory elements

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Dietary supplementation of laminarin improves the reproductive performance of sows and the growth of suckling piglets

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Journal of Animal Science and Biotechnology 2024年第1期15卷 329-343页

作者： Pengguang Zhang Guoyuan Jiang Chenghong Ma Yubo Wang Enfa Yan Linjuan He Jianxin Guo Xin Zhang Jingdong Yin state key laboratory of Animal Nutrition and Feeding College of Animal Science and TechnologyChina Agricultural UniversityBeijing 100193China

Background Maternal nutrition is essential in keeping a highly efficient production system in the pig industry.Laminarin has been shown to improve antioxidant capacity,reduce the inflammatory response,and favor the homeostasis of intestinal microbiota.However,the effect of dietary supplementation of laminarin on the reproductive performance of sows and the growth of suckling offspring remains unknown.Methods A total of 40 Landrace×Yorkshire multiparous sows on d 85 of gestation,similar in age,body weight(BW),parity and reproductive performance,were randomly divided into four dietary treatments with 10 sows per treatment,receiving a control diet(basal pregnancy or lactating diets)and a basal diet supplemented with 0.025%,0.05%and 0.10%laminarin,respectively.The experiment lasted from d 85 of gestation to d 21 of lactation.Results Laminarin supplementation linearly increased number born alive per litter(P=0.03),average daily feed intake(ADFI,Ppiglets while tending to reduce the culling and death rate before weaning.In addition,alterations to the composition of colostrum and milk,as well as to serum inflammatory cytokines and immunoglobulins of sows were observed.The fecal microbiota profile of sows supported the improvement of reproductive performance in sows and the growth performance in suckling offspring.Conclusions Dietary supplementation of laminarin during late pregnancy and lactation could significantly improve reproductive performance of sows and growth performance of piglets.

关键词： Fecal microbiota Laminarin Milk piglets Reproductive performance Sows

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Mapping short tandem repeats for liver gene expression traits helps prioritize potential causal variants for complex traits in pigs

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Journal of Animal Science and Biotechnology 2022年第3期13卷 707-720页

作者： Zhongzi Wu Huanfa Gong Zhimin Zhou Tao Jiang Ziqi Lin Jing Li Shijun Xiao Bin Yang Lusheng Huang state key laboratory for pig genetic improvement and production technology Jiangxi Agricultural UniversityNanchangChina

Background:Short tandem repeats(STRs)were recently found to have significant impacts on gene expression and diseases in humans,but their roles on gene expression and complex traits in pigs remain unexplored.This study investigates the effects of STRs on gene expression in liver tissues based on the whole-genome sequences and RNA-Seq data of a discovery cohort of 260 F6 individuals and a validation population of 296 F7 individuals from a heterogeneous population generated from crosses among eight pig breeds.Results:We identified 5203 and 5868 significantly expression STRs(eSTRs,FDRpigs,respectively,which were significantly enriched in intron,ATAC peak,compartment A and H3K4me3 regions.We identified 20 fine-mapped STRs located in 100 kb windows upstream and downstream of published complex trait-associated SNPs,which colocalized with epigenetic markers such as H3K27ac and ATAC peaks.These included eSTR of the CLPB,PGLS,PSMD6 and DHDH genes,which are linked with genome-wide association study(GWAS)SNPs for blood-related traits,leg conformation,growth-related traits,and meat quality traits,respectively.Conclusions:This study provides insights into the effects of STRs on gene expression traits.The identified eSTRs are valuable resources for prioritizing causal STRs for complex traits in pigs.

关键词： Cis-eQTL Co-localization Gene expression Liver pig heterogeneous population Short tandem repeats

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Developmental dynamics of the single nucleus regulatory landscape of pig hippocampus

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Science China(Life Sciences) 2023年第11期66卷 2614-2628页

作者： Siyu Yang Dong Chen Lei Xie Xiaoxiao Zou Yanyuan Xiao Lin Rao Tianxiong Yao Qing Zhang Liping Cai Fei Huang Bin Yang Lusheng Huang state key laboratory of pig genetic improvement and production technology Jiangxi Agricultural UniversityNanchang 330045China

The hippocampus is a brain region associated with memory,learning and spatial navigation,its aging-related dysfunction is a common sign of Alzheimer’s disease.pig is a good model for human neurodegenerative disease,but our understanding of the regulatory program of the pig hippocampus and its cross-species conservation in humans remains limited.Here,we profiled chromatin accessibility in 33,409 high-quality nuclei and gene expression in 8,122 high-quality nuclei of the pig hippocampus at four postnatal stages.We identified 510,908 accessible chromatin regions(ACRs)in 12 major cell types,among which progenitor cells such as neuroblasts and oligodendrocyte progenitor cells showed a dynamic decrease from early to later developmental stages.We revealed significant enrichment of transposable elements in cell type-specific ACRs,particularly in neuroblasts.We identified oligodendrocytes as the most prominent cell type with the greatest number of genes that showed significant changes during the development.We identified ACRs and key transcription factors underlying the trajectory of neurogenesis(such as POU3F3 and EGR1)and oligodendrocyte differentiation(RXRA and FOXO6).We examined 27 Alzheimer’s disease-related genes in our data and found that 15 showed cell type-specific activity(TREM2,RIN3 and CLU),and 15 genes displayed age-associated dynamic activity(BIN1,RABEP1 and APOE).We intersected our data with human genome-wide association study results to detect neurological disease-associated cell types.The present study provides a single nucleusaccessible chromatin landscape of the pig hippocampus at different developmental stages and is helpful for the exploration of pigs as a biomedical model in human neurodegenerative diseases.

关键词： hippocampus pig chromatin accessibility gene expression nuclei accessible chromatin regions development

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Construction of a transposase accessible chromatin landscape reveals chromatin state of repeat elements and potential causal variant for complex traits in pigs

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Journal of Animal Science and Biotechnology 2023年第2期14卷 529-545页

作者： Tao Jiang Ziqi Ling Zhimin Zhou Xiaoyun Chen Liqing Chen Sha Liu Yingchun Sun Jiawen Yang Bin Yang Jianzhen Huang Lusheng Huang state key laboratory of pig genetic improvement and production technology Jiangxi Agricultural UniversityNanchang 330045China

Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.Results:Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq,and identified 557,273 merged peaks,which greatly expanded the pig regulatory ele-ment repository.We revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal functions.We identified both positive and negative significant correlations between the regulatory elements and gene transcripts,which showed distinct distributions in terms of their strength and distances from corresponding genes.We investigated the presence of transposable elements(TEs)in open chromatin regions across all tissues,these included identifications of porcine endogenous retroviruses(PERVs)exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements.Furthermore,we prior-itized a potential causal variant for polyunsaturated fatty acid in the muscle.Conclusions:Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions,as well as regula-tory variants of loci associated with complex traits in pigs.

关键词： Chromatin accessibility pig Tissue specific Transcriptome Transposable elements

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