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candidate genes for mastitis resistance in dairy cattle:a data integration approach

Journal of Animal Science and Biotechnology 2023年第3期14卷 966-979页

作者： Zala Brajnik Jernej Ogorevc Biotechnical Faculty Department of Animal ScienceUniversity of LjubljanaGroblje 3Domzale SI‑1230Slovenia

Background Inflammation of the mammary tissue(mastitis)is one of the most detrimental health conditions in dairy ruminants and is considered the most economically important infectious disease of the dairy sector.Improving mastitis resistance is becoming an important goal in dairy ruminant breeding programmes.However,mastitis resistance is a complex trait and identification of mastitis-associated alleles in livestock is difficult.Currently,the only applicable approach to identify candidate loci for complex traits in large farm animals is to combine different information that supports the functionality of the identified genomic regions with respect to a complex trait.Methods To identify the most promising candidate loci for mastitis resistance we integrated heterogeneous data from multiple sources and compiled the information into a comprehensive database of mastitis-associated candidate loci.Mastitis-associated candidate genes reported in association,expression,and mouse model studies were collected by searching the relevant literature and databases.The collected data were integrated into a single database,screened for overlaps,and used for gene set enrichment analysis.Results The database contains candidate genes from association and expression studies and relevant transgenic mouse models.The 2448 collected candidate loci are evenly distributed across bovine chromosomes.Data integration and analysis revealed overlaps between different studies and/or with mastitis-associated QTL,revealing promising candidate genes for mastitis resistance.Conclusion Mastitis resistance is a complex trait influenced by numerous alleles.Based on the number of independent studies,we were able to prioritise candidate genes and propose a list of the 22 most promising.To our knowledge this is the most comprehensive database of mastitis associated candidate genes and could be helpful in selecting genes for functional validation studies.

关键词： Association study candidate genes Epigenetics Mammary gland Mastitis Quantitative trait loci

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Identifying candidate genes involved in trichome formation on carrot stems by transcriptome profiling and resequencing

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Journal of Integrative Agriculture 2022年第12期21卷 3589-3599页

作者： WU Zhe YANG Xuan ZHAO Yu-xuan JIA Li College of Horticulture Shanxi Agricultural UniversityTaigu 030801P.R.China Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop of Anhui Province Institute of HorticultureAnhui Academy of Agricultural SciencesHefei 230001P.R.China

Trichomes are specialized structures developed from epidermal cells and can protect plants against biotic and abiotic stresses.Trichomes cover carrots during the generative phase.However,the morphology of the carrot trichomes and candidate genes controlling the formation of trichomes are still unclear.This study found that carrot trichomes were nonglandular and unbranched hairs distributed on the stem,leaf,petiole,pedicel,and seed of carrot.Resequencing analysis of a trichome mutant with sparse and short trichomes(sst)and a wild type(wt)with long and dense trichomes on carrot stems was conducted.A total of 15396 genes containing nonsynonymous mutations in sst were obtained,including 42 trichomerelated genes.We also analyzed the transcriptome of the trichomes on secondary branches when these secondary branches were 10 cm long between wt and sst and obtained 6576 differentially expressed genes(DEGs),including 24 trichome-related genes.qRT-PCR validation exhibited three significantly up-regulated DEGs,20 significantly downregulated,and one with no difference.We considered both the resequencing and transcriptome sequencing analyses and found that 12 trichome-related genes that were grouped into five transcription factor families containing nonsynonymous mutations and significantly down-regulated in sst.Therefore,these genes are potentially promising candidate genes whose nonsynonymous mutations and down-regulation may result in scarce and short trichomes mutation on carrot stems in sst.

关键词： carrot trichome resequencing transcriptome candidate genes

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Identification of novel genes associated with atherosclerosis in Bama miniature pig

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Animal Models and Experimental Medicine 2024年第3期7卷 377-387页

作者： Dengfeng Ding Yuqiong Zhao Yunxiao Jia Miaomiao Niu Xuezhuang Li Xinou Zheng Hua Chen Laboratory Animal Center Chinese PLA General HospitalBeijingChina

Background:Atherosclerosis is a chronic cardiovascular disease of great concern.However,it is difficult to establish a direct connection between conventional small animal models and clinical practice.The pig's genome,physiology,and anatomy reflect human biology better than other laboratory animals,which is crucial for studying the pathogenesis of atherosclerosis.Methods:We used whole-genome sequencing data from nine Bama minipigs to perform a genome-wide linkage analysis,and further used bioinformatic tools to filter and identify underlying candidate genes.candidate gene function prediction was performed using the online prediction tool STRING 12.0.Immunohistochemistry and immunofluorescence were used to detect the expression of proteins encoded by candidate genes.Results:We mapped differential single nucleotide polymorphisms(SNPs)to genes and obtained a total of 102 differential genes,then we used GO and KEGG pathway enrichment analysis to identify four candidate genes,including SLA-1,SLA-2,SLA-3,and TAP2.nsSNPs cause changes in the primary and tertiary structures of SLA-I and TAP2 proteins,the primary structures of these two proteins have undergone amino acid changes,and the tertiary structures also show slight changes.In addition,immunohistochemistry and immunofluorescence results showed that the expression changes of TAP2 protein in coronary arteries showed a trend of increasing from the middle layer to the inner layer.Conclusions:We have identified SLA-I and TAP2 as potential susceptibility genes of atherosclerosis,highlighting the importance of antigen processing and immune response in atherogenesis.

关键词： atherosclerosis candidate genes genome-wide linkage analysis major histocompatibility complex whole genome sequencing

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Fine mapping and transcriptome sequencing reveal candidate genes conferring all-stage resistance to stripe rust on chromosome arm 1AL in Chinese wheat landrace AS1676

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作物学报:英文版 2023年第5期11卷 1501-1511页

作者： Xiu Yang Yunfeng Jiang Xianghai Yu Haipeng Zhang Yuqi Wang Fangnian Guan Li Long Hao Li Wei Li Qiantao Jiang Jirui Wang Yuming Wei Jian Ma Houyang Kang Pengfei Qi Qiang Xu Meng Deng Yazhou Zhang Youliang Zheng Yonghong Zhou Guoyue Chen State Key Laboratory of Crop Gene Exploitation and Utilization in Southwest China WenjiangChengdu 611130SichuanChina Triticeae Research Institute Sichuan Agricultural UniversityWenjiangChengdu 611130SichuanChina College of Agronomy Sichuan Agricultural UniversityWenjiangChengdu 611130SichuanChina

Stripe rust, caused by Puccinia striiformis f. sp. tritici(Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against Pst race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F7recombinant inbred line(RIL) population lacking the Yr18 gene, a near-isogenic line(NIL) population was developed to map the resistance gene. An allstage resistance gene, YrAS1676, was identified on chromosome arm 1AL via bulked-segregant exomecapture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between KA1A_485.36 and KA1A_490.13, spanning 485.36–490.13 Mb on1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to Pst race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of YrAS1676. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with Pst challenge,the YrAS1676 genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that YrAS1676 has potential use in wheat stripe rust resistance breeding.

关键词： Stripe rust All-stage resistance(ASR) BSE-Seq Transcriptome analyses candidate genes

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Genome-wide association and linkage mapping strategies reveal genetic loci and candidate genes of phosphorus utilization in soybean

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Journal of Integrative Agriculture 2022年第9期21卷 2521-2537页

作者： ZHANG Hua WU Hai-yan TIAN Rui KONG You-bin CHU Jia-hao XING Xin-zhu DU Hui JIN Yuan LI Xi-huan ZHANG Cai-ying State Key Laboratory of North China Crop Improvement and Regulation/Hebei Agricultural University Baoding 071001P.R.China

Insufficient available phosphorus in soil has become an important limiting factor for the improvement of yield and quality in soybean. The mining of QTLs and candidate genes controlling soybean phosphorus utilization related traits is a necessary strategy to solve this problem. In this study, 11 phosphorus utilization related traits of a natural population of 281 typical soybean germplasms and a recombinant inbred line(RIL) population of 270 lines were evaluated under different phosphorus conditions at two critical stages: the four-leaf stage as the seedling critical stage was designated as the Tstage, and the six-leaf stage as the flowering critical stage was designated as the Tstage. In total, 200 single nucleotide polymorphism(SNP) loci associated with phosphorus utilization related traits were identified in the natural population, including 91 detected at the Tstage, and 109 detected at the Tstage. Among these SNP loci, one SNP cluster(s715611375, ss715611377, ss715611379 and ss715611380) on Gm12 was shown to be significantly associated with plant height under the low phosphorus condition at the Tstage, and the elite haplotype showed significantly greater plant height than the others. Meanwhile, one pleiotropic SNP cluster(ss715606501, ss715606506 and ss715606543) on Gm10 was found to be significantly associated with the ratio of root/shoot, root and total dry weights under the low phosphorus condition at the Tstage, and the elite haplotype also presented significantly higher values for related characteristics under the phosphorus starvation condition. Furthermore, four co-associated SNP loci(ss715597964, ss715607012, ss715622173 and ss715602331) were identified under the low phosphorus condition at both the Tand Tstages, and 12 QTLs were found to be consistent with these genetic loci in the RIL population. More importantly, 14 candidate genes, including MYB transcription factor, purple acid phosphatase, sugar transporter and HSP20-like chaperones superfamily genes, etc., showed differential expression levels

关键词： soybean phosphorus utilization GWAS linkage mapping genetic loci candidate genes

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Genome-wide association study reveals candidate genes for gummy stem blight resistance in cucumber

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Horticultural Plant Journal 2023年第2期9卷 261-272页

作者： Jianan Han Shaoyun Dong Yanxia Shi Zhuonan Dai Han Miao Baoju Li Xingfang Gu Shengping Zhang Institute of Vegetables and Flowers Chinese Academy of Agricultural SciencesBeijing 100081China

Gummy stem blight(GSB),caused by Didymella bryoniae,is a serious fungal disease that leads to decline in cucumber yield and quality.The molecular mechanism of GSB resistance in cucumber remains unclear.Here,we investigated the GSB resistance of cucumber core germplasms from four geographic groups at the seedling and adult stages.A total of 9 SNPs related to GSB resistance at the seedling stage and 26 SNPs at the adult stage were identified,of which some are co-localized to previously mapped Quantitative trait loci(QTLs)for GSB resistance(gsb3.2/gsb3.3,gsb5.1,and gsb-s6.2).Based on haplotype analysis and expression levels after inoculation,four candidate genes were identified within the region identified by both Genome-wide association study(GWAS)and previous identified QTL mapping,including Csa3G129470 for gsb3.2/gsb3.3,Csa5G606820 and Csa5G606850 for gsb5.1,and Csa6G079730 for gsb-s6.2.The novel GSB resistant accessions,significant SNPs,and candidate genes facilitate the breeding of GSB resistant cucumber cultivars and provide a novel idea for understanding GSB resistance mechanism in cucumber.

关键词： Cucumber(Cucumis sativus L.) GSB GWAS Quantitative trait loci QTL candidate genes

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Genome-wide association study identifies novel candidate loci or genes affecting stalk strength in maize

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The Crop Journal 2023年第1期11卷 220-227页

作者： Shuhui Xu Xiao Tang Xiaomin Zhang Houmiao Wang Weidong Ji Chenwu Xu Zefeng Yang Pengcheng Li Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding Yangzhou UniversityYangzhou 225009JiangsuChina Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops Yangzhou UniversityYangzhou 225009JiangsuChina National Maize Improvement Center of China China Agricultural UniversityBeijing 100193China State Key Laboratory of Crop Stress Adaptation and Improvement Key Laboratory of Plant Stress BiologySchool of Life SciencesHenan UniversityKaifeng 475001HenanChina

Stalk strength increases resistance to stalk lodging,which causes maize(Zea mays L.)production losses worldwide.The genetic mechanisms regulating stalk strength remain unclear.In this study,three stalk strength-related traits(rind penetrometer resistance,stalk crushing strength,and stalk bending strength)and four plant architecture traits(plant height,ear height,stem diameter,stem length)were measured in three field trials.Substantial phenotypic variation was detected for these traits.A genome-wide association study(GWAS)was conducted using general and mixed linear models and 372,331 single-nucleotide polymorphisms(SNPs).A total of 94 quantitative trait loci including 241 SNPs were detected.By combining the GWAS data with public gene expression data,56 candidate genes within 50 kb of the significant SNPs were identified,including genes encoding flavonol synthase(GRMZM2G069298,ZmFLS2),nitrate reductase(GRMZM5G878558,ZmNR2),glucose-1-phosphate adenylyltransferase(GRMZM2G027955),and laccase(GRMZM2G447271).Resequencing GRMZM2G069298 and GRMZM5G878558 in all tested lines revealed respectively 47 and 2 variants associated with RPR.Comparison of the RPR of the zmnr2EMS mutant and the wild-type plant under high-and low-nitrogen conditions verified the GRMZM5G878558 function.These findings may be useful for clarifying the genetic basis of stalk strength.The identified candidate genes and variants may be useful for the genetic improvement of maize lodging resistance.

关键词： Stalk strength Maize GWAS candidate genes Lodging resistance

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Assessment of molecular markers and marker-assisted selection for drought tolerance in barley(Hordeum vulgare L.)

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Journal of Integrative Agriculture 2024年第1期23卷 20-38页

作者： Akmaral Baidyussen Gulmira Khassanova Maral Utebayev Satyvaldy Jatayev Rystay Kushanova Sholpan Khalbayeva Aigul Amangeldiyeva Raushan Yerzhebayeva KulpashBulatova Carly Schramm Peter Anderson Colin L.D.Jenkins Kathleen LSoole Yuri Shavrukov Faculty of Agronomy S.Seifullin Kazakh AgroTechnical Research UniversityAstana 010000Kazakhstan A.I.Barayev Research and Production Centre of Grain Farming Shortandy 021601Kazakhstan Kazakh Research Institute of Agriculture and Plant Growing AlmalybakAlmaty District 040909Kazakhstan College of Science and Engineering Biological SciencesFlinders UniversityAdelaideSA 5042Australia

This review updates the present status of the field of molecular markers and marker-assisted selection(MAS),using the example of drought tolerance in barley.The accuracy of selected quantitative trait loci(QTLs),candidate genes and suggested markers was assessed in the barley genome cv.Morex.Six common strategies are described for molecular marker development,candidate gene identification and verification,and their possible applications in MAS to improve the grain yield and yield components in barley under drought stress.These strategies are based on the following five principles:(1)Molecular markers are designated as genomic‘tags’,and their‘prediction’is strongly dependent on their distance from a candidate gene on genetic or physical maps;(2)plants react differently under favourable and stressful conditions or depending on their stage of development;(3)each candidate gene must be verified by confirming its expression in the relevant conditions,e.g.,drought;(4)the molecular marker identified must be validated for MAS for tolerance to drought stress and improved grain yield;and(5)the small number of molecular markers realized for MAS in breeding,from among the many studies targeting candidate genes,can be explained by the complex nature of drought stress,and multiple stress-responsive genes in each barley genotype that are expressed differentially depending on many other factors.

关键词： barley candidate genes drought tolerance gene verification via expression grain yield marker-assisted selection(MAS) molecular markers quantitative trait loci(QTLs) strategy for MAS

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Fine‑mapping and association analysis of candidate genes for papilla number in sea cucumber,Apostichopus japonicus

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Marine Life Science & Technology 2022年第3期4卷 343-355页

作者： Xinghai Zhu Ping Ni Marc Sturrock Yangfan Wang Jun Ding Yaqing Chang Jingjie Hu Zhenmin Bao Ministry of Education Key Laboratory of Marine Genetics and Breeding College of Marine Life SciencesOcean University of ChinaQingdao 266003China Department of Physiology and Medical Physics Royal College of Surgeons in IrelandDublin D02 YN77Ireland College of Fisheries and Life Science Dalian Ocean UniversityDalian 116023China Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering Sanya Oceanographic InstitutionOcean University of ChinaSanya 572000China

The papilla number is one of the most economically important traits of sea cucumber in the China marketing trade.However,the genetic basis for papilla number diversity in holothurians is still scarce.In the present study,we conducted genomewide association studies(GWAS)for the trait papilla number of sea cucumbers utilizing a set of 400,186 high-quality SNPs derived from 200 sea cucumbers.Two significant trait-associated SNPs that passed Bonferroni correction(Pgenes related to papilla formation and cellular activity,including PPP2R3C,GBP1,and BCAS3.Potential SNPs with Pcandidate genes PATS1,PPP2R3C,and EIF4G that near or cover the two lead SNPs was conducted in papilla tissue of TG(Top papilla number group)and BG(Bottom papilla number group)by qRT-PCR.We found the significantly higher expression profile of PATS1(3.34-fold),PPP2R3C(4.90-fold),and EIF4G(4.23-fold)in TG,implying their potential function in papilla polymorphism.The present results provide valuable information to decipher the phenotype differences of the papilla trait and will provide a scientific basis for selective breeding in sea cucumbers.

关键词： Genome-wide association study Apostichopus japonicus Molecular breeding candidate genes Papilla number

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QTL mapping by whole genome re-sequencing and analysis of candidate genes for salt tolerance in linseed(Linum usitatissmum L.)

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Oil Crop Science 2022年第2期7卷 80-85页

作者： Wei Zhao Yanping Zhang Jianping Zhang Yanni Qi Limin Wang Zhao Dang Yaping Xie Wenjuan Li Li Zhao Crop Institute Gansu Academy of Agricultural SciencesLanzhou730070China Gansu Provincial Academy of Agricultural Sciences Institute of Biotechnology Lanzhou730070China

Soil salinization is detrimental to the growth and development of flax and ultimately leads to a decrease in yield.However,the molecular mechanism of linseed response to salt stress is still unclear.In this study,a salt-tolerant(ST)linseed variety STS and a salt-sensitive(SS)variety DYM were selected as experiment materials.Bulk segregation analysis and whole-genome resequencing technologies were performed to map salt tolerance quantitative trait loci(QTL).A total of 38,625 QTL loci were identified.Fifteen genes(which were not annotated in the reference genome)were identified within a 2.597 Mb region in chromosome 1.Two salt tolerance candidate genes Lus.***.m.scaffold91.141 and Lus.o.m.Scaffold1.14 encoding WD40 and cytochrome P450 were identified by predicting protein functions.Previous studies showed that WD40 and cytochrome P450 could significantly improve plant salt stress tolerance.In this paper,results showed that Lus.***.m.scaffold91.141 and Lus.o.m.Scaffold1.14 might be involved in response to salt stress in lineseed.The fine mapping and functional analysis of these genes provide a molecular breeding basis for the genetic improvement of high salt-tolerant linseed varieties.

关键词： Linseed Salt-tolerant Whole-genome re-sequencing QTL candidate genes

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