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Quantitative trait loci detection of E dwardsiella tarda resistance in Japanese flounder Paralichthys olivaceus using bulked segregant analysis

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Chinese Journal of Oceanology and Limnology 2016年第6期34卷 1297-1308页

作者：王晓夏徐文腾刘洋王磊孙何军王磊陈松林 Yellow Sea Fisheries research Institute Chinese Academy of Fishery SciencesFunction Laboratory for Marine Fisheries Science and Food Production ProcessesNational Lab for Ocean Science and TechnologyQingdao 266071China College of Marine Life Science Shanghai Ocean UniversityShanghai 200120China Nanjing Agricultural University Nanjing 210095China College of Fisheries Henan Normal UniversityXinxiang 453007China

In recent years, Edwardsiella tarda has become one of the most deadly pathogens of Japanese fl ounder( Paralichthys olivaceus), causing serious annual losses in commercial production. In contrast to the rapid advances in the aquaculture of P. o livaceus, the study of E. tarda resistance-related markers has lagged behind, hindering the development of a disease-resistant strain. Thus, a marker-trait association analysis was initiated, combining bulked segregant analysis(BSA) and quantitative trait loci(QTL) mapping. Based on 180 microsatellite loci across all chromosomes, 106 individuals from the F1333(♀: F0768 ×♂: F0915)(Nomenclature rule: F+year+family number) were used to detect simple sequence repeats(SSRs) and QTLs associated with E. tarda resistance. After a genomic scan, three markers(Scaffold 404-21589, Scaffold 404-21594 and Scaffold 270-13812) from the same linkage group(LG)-1 exhibited a signifi cant difference between DNA, pooled/bulked from the resistant and susceptible groups( P <0.001). Therefore, 106 individuals were genotyped using all the SSR markers in LG1 by single marker analysis. Two different analytical models were then employed to detect SSR markers with different levels of signifi cance in LG1, where 17 and 18 SSR markers were identifi ed, respectively. Each model found three resistance-related QTLs by composite interval mapping(CIM). These six QTLs, designated q E1–6, explained 16.0%–89.5% of the phenotypic variance. Two of the QTLs, q E-2 and q E-4, were located at the 66.7 c M region, which was considered a major candidate region for E. tarda resistance. This study will provide valuable data for further investigations of E. tarda resistance genes and facilitate the selective breeding of disease-resistant Japanese fl ounder in the future.

关键词： Paralichthys olivaceus Edwardsiella tarda disease resistance simple sequence repeats(SSRs) bulked segregant analysis(BSA) quantitative trait loci(QTL)

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Molecular markers reliably predict post-harvest deterioration of fresh-cut lettuce in modified atmosphere packaging

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Horticulture research 2018年第1期5卷 698-710页

作者： Ivan Simko Ryan J.Hayes Maria-Jose Truco Richard W.Michelmore Rudie Antonise Mark Massoudi u.s.department of agriculture agricultural research serviceu.s.agricultural research stationcrop improvement and protection research unit1636 east alisal streetsalinasca93905usa u.s.department of agriculture national forage seed production research center3450 sw campus waycorvallisor97331usa the genome center and department of plant sciences university of californiadavisca95616usa keygene n.v. p.o.box 2166700 aewageningenthe netherlands ag-biotech 9701 blue larkspur lanesuite amontereyca93940usa

Fresh-cut lettuce is popular,but highly perishable *** studies of two bi-parental populations derived from crossing parents with rapid and slow rates of deterioration showed that the deterioration rate is a heritable trait(broad spectrum heritability,H2 of 0.56–0.87).The major genetic determinant of the deterioration rate in both populations was the quantitative trait locus(QTL),qSL4,located on linkage group *** QTL explained 40–74%of the total phenotypic variation of the trait in the two *** the qSL4 region with single-nucleotide(SNP)markers allowed detection of six haplotypes in a set of 16 lettuce accessions with different rates of *** of the haplotypes were always associated with very rapid rates of deterioration,while the other three haplotypes were associated with slow rates of *** SNPs located 53 bp apart were sufficient to separate the 16 accessions into two groups with different rates of *** accuracy of markers-trait association was subsequently tested on 350 plants from seven F2 families that originated from crossing parents with different rates of *** H2 of deterioration rate in these seven families ranged from 0.64 to *** SNP-based analysis accurately identified individuals with rapid,intermediate,and slow rates of deterioration in each *** rate of deterioration was found in individuals having heterozygous alleles at qSL4,indicating an additive effect of the *** assay can be used for fast,accurate,and reliable identification of deterioration rate after processing for salad.

关键词： deterioration linkage originated

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Genome-wide association study dissecting drought resistance-associated loci based on physiological traits in common bean

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Journal of Integrative Agriculture 2024年第11期23卷 3657-3671页

作者： Lei Wu Yujie Chang Lanfen Wang Shumin Wang Jing Wu Key Laboratory of Agricultural Biosafety and Green production of Upper Yangtze River Ministry of Education/College of Horticulture and Landscape ArchitectureSouthwest UniversityChongqing 400715China Institute of Crop Sciences Chinese Academy of Agricultural SciencesBejing 100081China SXAU-ICS(Shanxi Agricultural University-lnstitute of Crop Sciences)Joint research Center of Minor Crops Shanxi Agricultural UniversityTaiyuan 030031China

Genetic improvement of drought resistance is one of the main breeding goals for common bean,so molecular markers must be identified to facilitate drought resistance *** this study,we evaluated the proline,trehalose,raffinose,and stachyose contents of 210 common bean accessions under two watering conditions and found large variations in all *** coefficients of variation ranged from 21.21%for proline content to 78.69%for stachyose content under well-watered conditions,and from 20.11%for proline content to 50.08%for trehalose content under drought *** to our genome-wide association analysis,32 quantitative trait loci were associated with drought resistance,seven of which overlapped with known *** hotspot regions were identified at Pv01,Pv07 and Pv11.A set of candidate genes was identified,including genes encoding MYB,bZIP,bHLH,ERF,and protein *** these genes,Phvul.001G189400,Phvul.007G273000 and Phvul.008G270500 were annotated as bZIP,ERF and WRKY,*** genes are reportedly involved in drought stress responses in Arabidopsis thaliana and were induced by drought stress in common *** SNPs in six candidate gene regions formed different haplotypes,and phenotypic analysis revealed significant differences among the *** results provide new insight into the genetic basis of drought resistance in common bean and reveal candidate genes and superior natural variations that will be useful for improving common bean.

关键词： common bean drought resistance GWAS physiological trait

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Five years Retrospective Study of Avian Coccidiosis in a Veterinary Clinic Bukuru Plateau State Nigeria

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Journal of Zoological research 2019年第3期1卷 23-27页

作者： Barde,Israel Joshua Ladan,Haruna Bello Shekaro,Audu Ijoma,Sandra Ifynneke Idachaba,Stella Ejura Olabode Victoria Bose Oguche,Moses Ojonugwa Ishaku,Bata Shalangwa National Veterinary research Institute VomPlateau StateNigeria Federal College of Animal Health and production Technology VomPlateau StateNigeria

This study was conducted to evaluate the incidence of avian coccidiosis and its associated various risk factors such as age,type of birds and season in a private veterinary clinic in Bukuru,Plateau State Ngeria.A total of 9406 cases during 2013–2017 were analysed and 1556 of them were positive for *** are several reports on the prevalence of avian coccidiosis by previous researchers;however,in this study we evaluated the prevalence of avian coccidiosis in the study area and its economic *** prevalence of 12.14%in 2013,18.78%in 2014,18.21%in 2015,16.82%in 2016 and 19.07%in 2017 were *** overall prevalence of 85.02%was *** average prevalence of coccidiosis based on this five years study is 17%.The association between coccidiosis and age of the birds was determined and age 5-8 weeks becomes most effective period with wet season having high percentage prevalence of *** on the type of birds,coccidiosis is prevalence almost in equal proportion in both broilers and *** losses caused by avian coccidiosis could be both direct and indirect components which may include the cost of control measures,inadequate good hygiene practices,production losses and lack of prophylaxis *** control of avian coccidiosis can be achieved through good sanitary measures by avoiding water spillage on the pen floor,overcrowded stocking density,the use of prophylaxis-anticoccidials and proper good vaccination practices.

关键词： Avian coccidiosis Plateau state Retrospective study Veterinary clinic

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An imputed whole-genome sequence-based GWAS approach pinpoints causal mutations for complex traits in a specific swine population

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Science China(Life Sciences) 2022年第4期65卷 781-794页

作者： Guorong Yan Xianxian Liu Shijun Xiao Wenshui Xin Wenwu Xu Yiping Li Tao Huang Jiangtao Qin Lei Xie Junwu Ma Zhiyan Zhang Lusheng Huang State Key Laboratory for Pig Genetic Improvement and production Technology Jiangxi Agricultural UniversityNanchang330045China Institute of Photomedicine Shanghai Skin Disease HospitalSchool of MedicineTongji UniversityShanghai200092China

Sequencing-based genome-wide association studies(GWAS) have facilitated the identification of causal associations between genetic variants and traits in diverse species. However, it is cost-prohibitive for the majority of research groups to sequence a large number of samples. Here, we carried out genotype imputation to increase the density of single nucleotide polymorphisms in a large-scale Swine F;population using a reference panel including 117 individuals, followed by a series of GWAS analyses. The imputation accuracies reached 0.89 and 0.86 for allelic concordance and correlation, respectively. A quantitative trait nucleotide(QTN) affecting the chest vertebrate was detected directly, while the investigation of another QTN affecting the residual glucose failed due to the presence of similar haplotypes carrying wild-type and mutant allelesin the reference panel used in this study. A high imputation accuracy was confirmed by Sanger sequencing technology for the most significant loci. Two candidate genes,CPNE5 and MYH3, affecting meat-related traits were proposed. Collectively, we illustrated four scenarios in imputation-based GWAS that may be encountered by researchers, and our results will provide an extensive reference for future genotype imputation-based GWAS analyses in the future.

关键词： genotype imputation GWAS Fine mapping causal mutation pig

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Genetic mapping of quantitative trait loci in crops

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The Crop Journal 2017年第2期5卷 175-184页

作者： Yang Xu Pengcheng Li Zefeng Yang Chenwu Xu Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern production Technology of Grain Crops Key Laboratory of Plant Functional Genomics of Ministry of Education Yangzhou University Yangzhou 225009 China

Dissecting the genetic architecture of complex traits is an ongoing challenge for *** complementary approaches for genetic mapping,linkage mapping and association mapping have led to successful dissection of complex traits in many crop *** of these methods detect quantitative trait loci(QTL) by identifying marker–trait associations,and the only fundamental difference between them is that between mapping populations,which directly determine mapping resolution and *** on this difference,we first summarize in this review the advances and limitations of family-based mapping and natural population-based mapping instead of linkage mapping and association *** then describe statistical methods used for improving detection power and computational speed and outline emerging areas such as large-scale meta-analysis for genetic mapping in *** the era of next-generation sequencing,there has arisen an urgent need for proper population design,advanced statistical strategies,and precision phenotyping to fully exploit high-throughput genotyping.

关键词： Family-based mapping Natural population-based mapping Mixed linear model MAGIC population Meta-analysis Genotyping by sequencing

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Influence of Geographical Regions on Catechin and Caffeine Levels in Tea (Camellia sinensis)

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American Journal of Plant Sciences 2016年第3期7卷 562-571页

作者： Augustine Mutuku John Wanyoko Francis Wachira Samson Kamunya Richard Chalo Samuel Kimutai Kelvin Moseti Stephen Karori Department of Biochemistry Egerton University Egerton Kenya Tea research Institute (TRI) Kericho Kenya association for Strengthening Agricultural research in Eastern and Central Africa Entebbe Uganda Department of Chemistry Egerton University Egerton Kenya

This study aimed at investigating the influence of different growing conditions in two regions, Timbilil and Kangaita, on the levels of catechins and caffeine. Fresh leaf samples of 60 clones cultivated in both sites were obtained, processed and assayed for levels of caffeine, total and individual catechins using Reverse Phase High Performance Liquid Chromatography (RP-HPLC). The obtained data was subjected to analysis of variance using GENSTAT-C statistical software. Safe for a few clones in the Kangaita site had significantly higher total and individual catechins than those grown in the Timbilil site. A mean epigallocatechin gallate (EGCG) content of 7.9% was observed for Kangaita clones compared to 6.7% in Timbilil. A similar trend was observed for the rest of the individual catechin fractions with a mean epicatechin gallate (ECG) of 3.3% in Kangaita and 2.5% in Timbilil, a mean epigallocatechin (EGC) of 5.2% in Kangaita compared to 5.0% in Timbilil and a mean epicatechin (EC) content of 1.5% in Kangaita compared to 1.4% in Timbilil. Similarly in the total catechins analyses, clones in Kangaita had a mean value of 18.7% compared to 16.2% observed for the Timbilil site clones. However, the Timbilil site clones had significantly high caffeine contents (mean, 4.2%) compared to the Kangaita site clones (mean, 3.9%) although with a few exceptions. Significant interactions (P production of tea.

关键词： Camellia sinensis Clonal Variations Regional Variations Catechins Caffeine

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Determination of Residual Catechins, Polyphenolic Contents and Antioxidant Activities of Developed Theaflavin-3,3’-Digallate Rich Black Teas

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Food and Nutrition Sciences 2016年第3期7卷 180-191页

作者： Samuel Kimutai John Wanyoko Thomas Kinyanjui Stephen Karori Augustine Muthiani Francis Wachira KALRO-Tea research Institute Kericho Kenya Department of Chemistry Egerton University Nakuru Kenya Department of Biochemistry Egerton University Nakuru Kenya association for Strengthening Agricultural research in East and Central Africa Entebbe Uganda

This study was carried out to characterize total residual catechins and their fractions, polyphenolic contents and antioxidant activities of black teas enriched with high levels of theaflavin-3,3’-digallate. The made teas were processed from eleven selected cultivars. A comparative study was carried out between the processed teas and those from commercially grown Kenyan cultivars in relation to the above chemical parameters. A correlation matrix analysis was also conducted to find out whether a relationship existed between the antioxidant activities and the said chemical parameters. The total residual catechins were found to range between 3.10% and 8.08%. The total polyphenol levels varied between 19.00% and 28.90%, while the antioxidant activities of the teas ranged from 82.70% to 91.70%. There was a significant p production.

关键词： Total Polyphenols Antioxidant Activity Residual Catechins Theaflavins

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Genomic insights into the genetic basis of cotton breeding in China

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Molecular Plant 2023年第4期16卷 662-677页

作者： Yiqian Li Zhanfeng Si Guoping Wang Zhuolin Shi Jinwen Chen Guoan Qi Shangkun Jin Zegang Han Wenhao Gao Yue Tian Yun Mao Lei Fang Yan Hu Hong Chen Xiefei Zhu Tianzhen Zhang zhejiang Provincial Key Laboratory of Crop Genetic Resources the Advanced Seed InstitutePlant Precision Breeding AcademyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina Xinjang production and Construction Corps Seventh Division Agricultural research Institute KuintunChina state Key Laboratory of Crop Genetics and Germplasm Enhancement Nanjing Agricutural UniversityNanjingChina College of Biotechnology Jiangsu University of Science and TechnologyZhenjiangChina Key Laboratory of China Northwestern Inland Region Ministry of AgricultureCotton Research InstituteXinjiang Academy of Agricultural and Reclamation ScienceShiheziChina

The excellent Upland cotton(Gossypium hirsutum)cultivars developed since 1949 have made a huge contribution to cotton production in China,the world's largest producer and consumer of ***,the genetic and genomic basis for the improvements of these cotton cultivars remains largely *** this study,we selected 16 Upland cotton cultivars with important historical status in Chinese cotton breeding and constructed a multiparent,advanced generation,intercross(MAGiC)population comprising 920 recombinant inbred lines.A genome-wide association study using the MAGIC population identified 54 genomic loci associated with lint yield and fiber *** them,25(46.30%)pleiotropic genomic loci cause simultaneous changes of lint yield and/or fiber quality traits,revealing complex trade-offs and linkage drags in Upland cotton agronomic *** sequencing data of 11 introduced ancestor cultivars and publicly available resequencing datasets of 839 cultivars developed in China during the past 70 years were integrated to explore the historical distribution and origin of the elite or selected ***,85%oftheseelitealleles were selectedandfixed fromdifferent Americanancestors,consistentwithcotton breeding practices in ***,seven elite alleles of native origin that are responsible for Fusarium wilt resistance,early maturing,good-quality fiber,and other characteristics were not found in American an-cestors but have greatly contributed to Chinese cotton breeding and wide *** together,these results provide a genetic basis for further improving cotton cultivars and reveal that the genetic composition of Chinese cotton cultivars is narrow and mainly derived from early introduced American varieties.

关键词： cotton MAGiC population GWAS whole-genome sequencing pleiotropic loci breeding history

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Melatonin alters the secondary metabolite profile of grape berry skin by promoting VvMYB14-mediated ethylene biosynthesis

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Horticulture research 2021年第1期8卷 628-642页

作者： Wanyun Ma Lili Xu Shiwei Gao Xingning Lyu Xiaolei Cao Yuxin Yao State Key Laboratory of Crop Biology Collaborative Innovation Center of Fruit&Vegetable Quality and Efficient ProductionCollege of Horticulture Science and EngineeringShandong Agricultural UniversityTai-AnShandong 271018China

The interplay between melatonin and ethylene in the regulation of fruit metabolism and the underlying molecular mechanism of this interplay remain largely ***,widely targeted metabolomics analysis revealed a total of 464 metabolites present in berry *** them,27 significantly differentially accumulated metabolites(DAMs)were produced in response to melatonin treatment in the presence or absence of *** of the DAMs were secondary metabolites,including flavonoids,phenolic acids,stilbenes,and ***,the accumulation of 25 DAMs was regulated by melatonin via ***-seq analysis indicated that melatonin primarily regulated the pathways of plant hormone signal transduction and secondary metabolite biosynthesis via ***-metabolite association analysis showed that melatonin regulated the expression of the VvSTS1,VvF3H,VvLAR2,and VvDFR genes,suggesting that these genes may play key roles in regulating secondary metabolites in the skin;additionally,VvMYB14 and VvACS1 were suggested to be involved in the regulation of secondary *** experiments revealed that melatonin induced the expression of VvMYB14 and that VvMYB14 increased ethylene production by transcriptionally activating VvACS1,thereby affecting the accumulation of secondary ***,melatonin promotes ethylene biosynthesis and alters secondary metabolite accumulation through the regulation of VvACS1 by VvMYB14.

关键词： thereby phenolic metabolism

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