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candidate genes conferring ethylene-response in cultivated peanuts determined by BSA-seq and fine-mapping

The Crop Journal 2024年第3期12卷 856-865页

作者： Yanyan Tang Zhong Huang Shaohui Xu Wenjie Zhou Jianjun Ren Fuxin Yu Jingshan Wang Wujun Ma Lixian Qiao College of Agronomy Qingdao Agricultural UniversityQingdao 266109ShandongChina Murdoch University Food Futures InstitutePerthWA 6150Australia The Characteristic Laboratory of Crop Germplasm Innovation and Application Provincial Department of EducationCollege of AgronomyQingdao Agricultural UniversityQingdao 266109ShandongChina Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University Dongying 257347ShandongChina

Ethylene plays essential roles in plant growth,development and stress responses.The ethylene signaling pathway and molecular mechanism have been studied extensively in Arabidopsis and rice but limited in peanuts.Here,we established a sand-culture method to screen pingyangmycin mutagenized peanut lines based on their specific response to ethylene(“triple response”).An ethylene-insensitive mutant,inhibition of peanut hypocotyl elongation 1(iph1),was identified that showed reduced sensitivity to ethylene in both hypocotyl elongation and root growth.Through bulked segregant analysis sequencing,a major gene related to iph1,named AhIPH1,was preliminarily mapped at the chromosome Arahy.01,and further narrowed to a 450-kb genomic region through substitution mapping strategy.A total of 7014 genes were differentially expressed among the ACC treatment through RNA-seq analysis,of which only the Arahy.5BLU0Q gene in the candidate mapping interval was differentially expressed between WT and mutant iph1.Integrating sequence variations,functional annotation and transcriptome analysis revealed that a predicated gene,Arahy.5BLU0Q,encoding SNF1 protein kinase,may be the candidate gene for AhIPH1.This gene contained two single-nucleotide polymorphisms at promoter region and was more highly expressed in iph1 than WT.Our findings reveal a novel ethylene-responsive gene,which provides a theoretical foundation and new genetic resources for the mechanism of ethylene signaling in peanuts.

关键词： Ethylene-insensitive Hypocotyl elongation AhIPH1 candidate gene genetic resources

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Meta-QTL analysis for mining of candidate genes and constitutive gene network development for fungal disease resistance in maize(Zea mays L.)

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The Crop Journal 2023年第2期11卷 511-522页

作者： Mamta Gupta Mukesh Choudhary Alla Singh Seema Sheoran Deepak Singla Sujay Rakshit ICAR-Indian Institute of Maize Research LudhianaPunjab 141004India School of Agriculture and Environment The University of Western AustraliaPerthWA 6009Australia The UWA Institute of Agriculture The University of Western AustraliaPerthWA 6009Australia School of Agricultural Biotechnology Punjab Agricultural UniversityLudhianaPunjab 141004India

The development of resistant maize cultivars is the most effective and sustainable approach to combat fungal diseases.Over the last three decades,many quantitative trait loci(QTL)mapping studies reported numerous QTL for fungal disease resistance(FDR)in maize.However,different genetic backgrounds of germplasm and differing QTL analysis algorithms limit the use of identified QTL for comparative studies.The meta-QTL(MQTL)analysis is the meta-analysis of multiple QTL experiments,which entails broader allelic coverage and helps in the combined analysis of diverse QTL mapping studies revealing common genomic regions for target traits.In the present study,128(33.59%)out of 381 reported QTL(from 82 studies)for FDR could be projected on the maize genome through MQTL analysis.It revealed 38 MQTL for FDR(12 diseases)on all chromosomes except chromosome 10.Five MQTL namely 1_4,2_4,3_2,3_4,and 5_4 were linked with multiple FDR.Total of 1910 candidate genes were identified for all the MQTL regions,with protein kinase gene families,TFs,pathogenesis-related,and disease-responsive proteins directly or indirectly associated with FDR.The comparison of physical positions of marker-traits association(MTAs)from genome-wide association studies with genes underlying MQTL interval verified the presence of QTL/candidate genes for particular diseases.The linked markers to MQTL and putative candidate genes underlying identified MQTL can be further validated in the germplasm through marker screening and expression studies.The study also attempted to unravel the underlying mechanism for FDR resistance by analyzing the constitutive gene network,which will be a useful resource to understand the molecular mechanism of defense-response of a particular disease and multiple FDR in maize.

关键词： Meta-QTL Maize genome Fungal disease resistance candidate gene Constitutive genes gene network

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A 1-bp deletion in the MC04g1399 is highly associated with failure to produce fruit wart in bitter gourd

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Horticultural Plant Journal 2024年第1期10卷 171-180页

作者： Jia Liu Junjie Cui Jichi Dong Jian Zhong Chunfeng Zhong Fanchong Yuan Wendong Guan Fang Hu Jiaowen Cheng Kailin Hu College of Horticulture South China Agricultural UniversityGuangzhouGuangdong 510642China Key Laboratory of Biology and genetic Improvement of Horticultural Crops(South China) Ministry of Agriculture and Rural AffairsGuangzhouGuangdong 510642China Guangdong Vegetables Engineering Research Center GuangzhouGuangdong 510642China Department of Horticulture Foshan UniversityFoshanGuangdong 528225China Henry Fok School of Biology and Agricultural Shaoguan UniversityShaoguanGuangdong 512023China

Fruit wart is an important appearance trait influencing consumer preferences of bitter gourd(Momordica charantia L.).The molecular genetic mechanisms underlying fruit wart formation in bitter gourd are largely unknown.In this study,genetic analysis based on four generations showed that fruit wart formation in bitter gourd was controlled by a single dominant locus named as Fwa.The Fwa locus was initially mapped into a 4.82 Mb region on pseudochromosome 4 by BSA-seq analysis and subsequently narrowed down to a 286.30 kb region by linkage analysis.A large F2population consisting of 2360 individuals was used to screen recombinants,and the Fwa locus was finally fine mapped into a 22.70 kb region harboring four protein-coding genes through recombination analysis.MC04g1399,encoding an epidermal patterning factor 2-like protein,was proposed as the best candidate gene for Fwa via sequence variation and expression analysis.In addition,a 1-bp insertion and deletion(InDel)variation within MC04g1399 was converted to a cleaved amplified polymorphic sequence(CAPS)marker that could precisely distinguish between the warty and non-warty types with an accuracy rate of 100%among a wide panel of 126 bitter gourd germplasm resources.Our results not only provide a scientific basis for deciphering the molecular mechanisms underlying fruit wart formation but also provide a powerful tool for efficient genetic improvement of fruit wart via marker-assisted selection.

关键词： Bitter gourd Fruit wart Bulk segregant analysis Fine-mapping candidate gene

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genetic dissection and validation of a major QTL for grain weight on chromosome 3B in bread wheat(Triticum aestivum L.)

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Journal of Integrative Agriculture 2024年第1期23卷 77-92页

作者： Simin Liao Zhibin Xu Xiaoli Fan Qiang Zhou Xiaofeng Liu Cheng Jiang Liangen Chen Dian Lin Bo Feng Tao Wang Chengdu Institute of Biology Chinese Academy of SciencesChengdu 610041China University of Chinese Academy of Sciences Beijing 100049China The Innovative Academy of Seed Design Chinese Academy of SciencesBeijing 100101China

Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.

关键词： thousand-grain weight QTL mapping haplotype analysis candidate gene

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Meta‐analysis and candidate gene mining of low‐phosphorus tolerance in maize

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Journal of Integrative Plant Biology 2014年第3期56卷 262-270页

作者： Hongwei Zhang Mohammed Shalim Uddin Cheng Zou Chuanxiao Xie Yunbi Xu Wen‐Xue Li Institute of Crop Science National Key Facility of Crop Gene Resources and Genetic Improvement the Chinese Academy of Agricultural Sciences Bangladesh Agricultural Research Institute (BARI) International Maize and Wheat Improvement Center (CIMMYT)

Plants with tolerance to low-phosphorus （P） can grow better under Iow-P conditions, and understanding of genetic mechanisms of Iow-P tolerance can not only facilitate identifying relevant genes but also help to develop Iow-P tolerant cultivars. QTL meta-analysis was conducted after a comprehensive review of the reports on O, TL mapping for Iow-P tolerance-related traits in maize. Meta-analysis pro- duced 23 consensus QTL （cQTL）, 17 of which located in similar chromosome regions to those previously reported to influence root traits. Meanwhile, candidate gene mining yielded 215 genes, 22 of which located in the cQTL regions. These 22 genes are homologous to 14 functionally characterized genes that were found to participate in plant Iow-P tolerance, including genes encoding miR399s, Pi transporters and purple acid phosphatases. Four cQTL loci （cQTL2-L cQTLS-3, cQTL6-2, and cQTL10-2） may play important roles for low-P tolerance because each contains more original QTL and has better consistency across previous reports.

关键词： candidate gene consensus QTL low-phosphorustolerance maize meta-analysis

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Construction of SMART cDNA Library of Sheep Ovary and Identification of candidate gene by Homologous Cloning

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Agricultural Sciences in China 2007年第11期6卷 1390-1395页

作者： DU Li-xin LIU Shu-fang ZHU Jin LI Hong-bin LI Shan-gang SONG Xue-mei WANG Ai-hua National Center for Molecular genetics and Breeding of Animal/Institute of Animal Science Chinese Academy of Agricultural Sciences Beijing 100094 P.R.China Laboratory for Sustainable Utilization of Marine Fisheries Resources Ministry of Agriculture/Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Qingdao 266007 P.R.China Center for Experimental Animal Shandong Academy of Medical Sciences Jinan 250001. P.R. China

The cDNA library of an ovary from Small Tail Han sheep before estrus was constructed by switching mechanism at 5＇ end of RNA transcript （SMART） approach. This library had a plaque titer of 1 x 109 pfu mL-1 and a 96% recombinant ratio of which the fragment length of inserted average cDNA sequences was 1.0 kb. Based on bioinformatics analysis of the sequences, we obtained 338 expressed sequence tags （ESTs） from 380 cDNA clones which indicated 191 contigs. These contigs consist of 89 unmatched ESTs, 9 homologous known genes in sheep, and 93 homologous sequences in species of mouse, bovine, and human beings, including 19 sequences expressed in the ovary or follicle and 14 unknown sequences. Several candidate genes associated with sheep reproduction trait such as epidermal growth factor （EGF）, estrogen receptor （ESR）, Inhibin, follicle stimulating hormone receptor （FSHR）, prostaglandin （PG）, and transforming growth factor-β （TGF-β） were identified and the homologous were cloned from this library, which will contribute to compile expression profiles and find the major genes of prolificacy of Small Tail Han sheep.

关键词： candidate gene EST ovary Small Tail Han sheep SMART cDNA library

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Molecular cloning of a candidate gene for hereditary multiple exostoses type II

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Progress in Natural Science:Materials International 1996年第6期 54-61页

作者：邓汉湘范朝红夏家辉徐磊何小轩阮庆国杨毅黄蕾 Changsha 410078. China State Key Laboratory of Medical genetics Hunan Medical University

Hereditary multiple exostoscs (FXT) are an autosomal dominant disorder characterixed by multiple exosloses most commonly arising from the juxtaepiphysial region of the long hones. Three genctie loci have been established by cytogenctic abnormality and molecular linkage analysis at Xq24.1 (EXT1, 11p11(F,XT2) and 19p(FXT3). respectively. A putative tumor suppressor gene at 8q24.1 was cloned and identified to be responsible for FXT1 With positional cloning approach a gene has been cloned which shares striking similarity with FXT1 gene in both DNA and amino acid sequences. This gene is predicted to encode a polypeptide in at least two isoforms, which differ in the middle of the coding region of this gene The isoform isolated from human placenta cDNA library encodes a polypeptide of 728 ammo acids, while the other cloned from human brain cDNA library encodes 718 ammo acids This gene has been mapped by fluorescence in situ hybridization to 11p11, which is the exact region where EXT2 gene is located. The strik

关键词： KXT2 multiple exostoses positional cloning candidate gene tumor suppressor gene.

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New loci for refractive errors and ocular biometric parameters in young Chinese Han adults

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Science China(Life Sciences) 2022年第10期65卷 2050-2061页

作者： Yunyun Sun Zi-Bing Jin Shifei Wei Hongyan Jia Kai Cao Jianping Hu Caixia Lin Wenzai An Jiyuan Guo He LiJing Fu Shi-Ming Li Ningli Wang the Anyang University Students Eye Study Group the Anyang University Students Eye Study Group Beijing Tongren Eye Center Beijing Tongren HospitalCapital Medical UniversityBeijing Ophthalmology&Visual Sciences Key LaboratoryBejing 100730China Beijing Institute of Ophthalmology Bejing 100730China Anyang Eye Hospital Anyang 455000China 不详

Myopia has become a major public health issue with an increasing prevalence.There are still individuals who experience similar environmental risk factors and,yet,remain non-myopic.Thus,there might be genetic factors protecting people from myopia.Considering the opposite ocular characteristics of primary angle closure glaucoma(PACG)to myopia and possible common pathway between them,we propose that certain risk genes for PACG might act as a protective factor for myopia.In this study,2,678 young adults were genotyped for 37 targeted single nucleotide polymorphisms.Compared with emmetropia,rs1401999(allele C:OR=0.795,P=0.03;genotype in dominant model:OR=0.759,P=0.02)and rs1258267(allele A:OR=0.824,P=0.03;genotype in dominant model:OR=0.603,P=0.01)were associated with low to moderate myopia and high myopia,respectively.Genotype under recessive model of rs11024102 was correlated with myopia(OR=1.456,P=0.01),low to moderate myopia(OR=1.443,P=0.02)and high myopia(OR=1.453,P=0.02).However,these associations did not survive Bonferroni correction.Moreover,rs1401999,rs1258267,and rs11024102 showed associations with certain ocular biometric parameters in different groups.Our study suggests that ABCC5,CHAT and PLEKHA7 might be associated with refractive errors by contributing to the regulation of ocular biometry,in terms of uncorrected results and their biological functions.

关键词： candidate gene myopia high myopia ocular biometry primary angle-closure glaucoma

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A significant quantitative trait locus on chromosome Z and its impact on egg production traits in seven maternal lines of meat-type chicken

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Journal of Animal Science and Biotechnology 2023年第1期14卷 47-59页

作者： Jiqiang Ding Fan Ying Qinghe Li Gaomeng Zhang Jin Zhang Ranran Liu Maiqing Zheng Jie Wen Guiping Zhao Institute of Animal Sciences Chinese Academy of Agricultural SciencesBeijingChina. MiLe Xinguang Agricultural and Animal Industrials Corporation MiLeChina.

Background:Egg production is economically important in the meat-type chicken industry.To better understand the molecular genetic mechanism of egg production in meat-type chicken,genetic parameter estimation,genome-wide association analyses combined with meta-analyses,Bayesian analyses,and selective sweep analyses were performed to screen single nucleotide polymorphisms(SNPs)and other genetic loci that were significantly associated with egg number traits in 11,279 chickens from seven material lines.Results:Yellow-feathered meat-type chickens laid 115 eggs at 43 weeks of age and white-feathered chickens laid 143 eggs at 60 weeks of age,with heritability ranging from 0.034–0.258.Based on meta-analyses and selective sweep analyses,one region(10.81–13.05 Mb)on chromosome Z was associated with egg number in all lines.Further analyses using the W2 line was also associated with the same region,and 29 SNPs were identified that significantly affected estimation of breeding value of egg numbers.The 29 SNPs were identified as having a significant effect on the egg number EBV in 3194 birds in line W2.There are 36 genes in the region,with glial cell derived neurotrophic factor,DAB adaptor protein 2,protein kinase AMP-activated catalytic subunit alpha 1,NAD kinase 2,mitochondrial,WD repeat domain 70,leukemia inhibitory factor receptor alpha,complement C6,and complement C7 identified as being potentially affecting to egg number.In addition,three SNPs(rs318154184,rs13769886,and rs313325646)associated with egg number were located on or near the prolactin receptor gene.Conclusion:Our study used genomic information from different chicken lines and populations to identify a genomic region(spanning 2.24 Mb)associated with egg number.Nine genes and 29 SNPs were identified as the most likely candidate genes and variations for egg production.These results contribute to the identification of candidate genes and variants for egg traits in poultry.

关键词： candidate gene Egg production Genome-wide association study Meat-type chicken Selective sweep analysis

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Tagging Blast Resistance gene Pi 1 in Rice (Oryza sativa) Using candidate Resistance genes

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Rice Science 2004年第Z1期 251-254页

作者： Menchu BERNADO Entomology and Plant Pathology Division International Rice Research Institute DAPO P.O. Box 7777.Metro Manila Philippines

An F3 population derived from C101LAC/CO39 containing 90 lines was analyzed for blast resistance with 48 candidate genes developed from resistance gene analogs （RGA） and suppression subtractive library. genetic analysis confirmed that blast resistance of the population was controlled by a single gene Pi 1. One of the candidate genes, R10 was identified as associated with the blast resistance gene on the long arm of chromosome 11 and mapped using a DH population derived from Azucena/IR64. A pair of PCR based primers was designed based on the sequence of R10 for marker-aided selection of the blast resistance gene. The recombination frequency between Pi 1 and the marker was estimated as 1.28%. It suggested that strategy of employing candidate genes is useful for gene identification and mapping. A new RFLP marker and the corresponding PCR marker for tagging of Pi 1 were provided.

关键词： rice candidate gene marker-aided selection blast resistance

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