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Precision Phenotyping Reveals Novel Loci for Quantitative Resistance to Septoria Tritici Blotch

Plant Phenomics 2019年第1期1卷 58-68页

作者： Steven Yates Alexey Mikaberidze Simon GKrattinger Michael Abrouk Andreas Hund Kang Yu bruno studer Simone Fouche Lukas Meile Danilo Pereira Petteri Karisto Bruce A.McDonald Molecular Plant Breeding Institute of Agricultural SciencesETH ZurichZurichSwitzerland Plant Pathology Institute of Integrative BiologyETH ZurichZurichSwitzerland Biological and Environmental Science and Engineering Division King Abdullah University of Science and Technology(KAUST)ThuwalSaudi Arabia Crop Science Institute of Agricultural SciencesETH ZurichZurichSwitzerland

Accurate,high-throughput phenotyping for quantitative traits is a limiting factor for progress in plant *** developed an automated image analysis to measure quantitative resistance to septoria tritici blotch(STB),a globally important wheat disease,enabling identification of small chromosome intervals containing plausible candidate genes for STB resistance.335 winter wheat cultivars were included in a replicated field experiment that experienced natural epidemic development by a highly diverse but fungicide-resistant pathogen *** than 5.4 million automatically generated phenotypes were associated with 13,648 SNP markers to perform the *** identified 26 chromosome intervals explaining 1.9-10.6%of the variance associated with four independent resistance *** of the intervals overlapped with known STB resistance intervals,suggesting that our phenotyping approach can identify simultaneously(i.e.,in a single experiment)many previously defined STB resistance *** of the intervals were less than 5 Mbp in size and encoded only 173 genes,including many genes associated with disease *** intervals contained four or fewer genes,providing high priority targets for functional *** chromosome intervals were not previously associated with STB resistance,perhaps representing resistance to pathogen strains that had not been tested in earlier *** SNP markers associated with these chromosome intervals can be used to recombine different forms of quantitative STB resistance that are likely to be more durable than pyramids of major resistance *** experiment illustrates how high-throughput automated phenotyping can accelerate breeding for quantitative disease resistance.

关键词： resistance limiting globally

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Auxin Binding Protein 1 Reinforces Resistance to Sugarcane Mosaic Virus in Maize

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Molecular Plant 2017年第10期10卷 1357-1360页

作者： Pengfei Leng Qing Ji Torben Asp Ursula K. Frei Christina R. Ingvardsen Yongzhong Xing bruno studer Margaret Redinbaugh Mark Jones Priyanka Gajjar Sisi Liu Fei Li Guangtang Pan Mingliang Xu Thomas Lǖbberstedt National Maize Improvement Center China Agricultural University Beijing 100193 China Department of Agronomy Iowa State University Ames IA 50011 USA Department of Molecular Biology and Genetics Aarhus University Forsegsvej 14200 Slagelse Denmark National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University Wuhan 430070 China Institute of Agricultural Sciences Molecular Plant Breeding ETH Zurich Universitaetstrasse 2 8092 Zurich Switzerland USDA Agricultural Research Service Corn Soybean and Wheat Quality Research Unit and Department of Plant Pathology Ohio State University Wooster OH 44691 USA Maize Research Institute Sichuan Agricultural University Chengdu 611130 China School of Life Sciences Guizhou Normal University Laboratory of Plant Physiology and Developmental Regulation Guiyang 550000 China

Dear Editor,Sugarcane mosaic virus （SCMV） causes severe viral diseases in maize worldwide （Fuchs and Gruntzig, 1995）, resulting in significant losses in grain and forage yield in susceptible cultivars of maize and related crops. The most promising solution is to cultivate resistant varieties, which contribute to sustainable crop production. Two epistatically interacting major SCMV resistance loci （Scmvl and Scmv2） are required to confer complete resistance against SCMV in the resistant nearisogenic line F7RPJRR （the letters left of the slash refer to the genotype at Scmv2 on chromosome 3 and those on the right refer to the genotype at Scmvl on chromosome 6, with R indicating a resistance allele and S a susceptibility allele）（Xing et al., 2006）.

关键词： Auxin Binding Protein 1 Reinforces Resistance Sugarcane Mosaic Virus Maize

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Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility

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Molecular Plant 2023年第9期16卷 1427-1444页

作者： Kaixuan Zhang Yuqi He Xiang Lu Yaliang Shi Hui Zhao Xiaobo Li Jinlong Li Yang Liu Yinan Ouyang Yu Tang Xue Ren Xuemei Zhang Weifei Yang Zhaoxia Sun Chunhua Zhang Muriel Quinet Zlata Luthar Mateja Germ Ivan Kreft Dagmar Janovska Vladimir Meglic Barbara Pipan Milen I.Georgiev bruno studer Mark A.Chapman Meiliang Zhou Institute of Crop Sciences Chinese Academy of Agricultural SciencesNational Crop Genebank BuildingZhongguancun South Street No.12Haidian DistrictBeijing 100081China College of Agronomy Sichuan Agricultural UniversityChengdu 611130China Annoroad Gene Technology(Beijing)Co. LtdBeijing 100176China College of Agriculture Institute of Agricultural BioengineeringShanxi Agricultural UniversityTaigu 030801ShanxiChina Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding Shanxi Agricultural UniversityTaiyuan 030031ShanxiChina Tongliao Institute Agricultural and Animal Husbandry Sciences Tongliao 028015Inner MongoliaChina Groupe de Recherche en Physiologie Ve´ge´tale(GRPV) Earth and Life Institute-Agronomy(ELI-A)Universite´Catholique de LouvainCroix du Sud 4-5bo^ıte L7.07.13B-1348Louvain-la-NeuveBelgium Biotechnical Faculty University of Ljubljana1000 LjubljanaSlovenia Nutrition Institute Trzaska 401000 LjubljanaSlovenia Gene Bank Crop Research InstituteDrnovska´507Prague 6Czech Republic Agricultural Institute of Slovenia Hacquetova ulicaLjubljanaSlovenia Laboratory of Metabolomics Institute of MicrobiologyBulgarian Academy of SciencesPlovdivBulgaria Center of Plant Systems Biology and Biotechnology PlovdivBulgaria Molecular Plant Breeding Institute of Agricultural SciencesETH ZurichUniversitaetstrasse 28092 ZurichSwitzerland Biological Sciences University of SouthamptonLife Sciences Building 85Highfield CampusSouthampton SO171BJUK

Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide *** to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly important throughout the *** availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat,but the high heterozygosity due to the outcrossing nature has greatly hindered the genome *** we report the assembly of a chromosome-scale high-quality reference genome of *** ***,a homozygous self-pollinating variant of common *** genomics revealed that two cultivated buckwheat species,common buckwheat(***)and Tartary buckwheat(***),underwent metabolomic divergence and ecotype *** expansion of several gene families in common buckwheat,including FhFAR genes,is associated with its wider distribution than Tartary *** number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary ***,we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common *** and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated ***-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period,a key agronomic trait controlling the yield of outcrossing crops,and that Fh06G015130 is a crucial gene underlying flavor-associated ***,we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common ***,our results elucidate the genetic basis of spe

关键词： buckwheat genomics natural variation adaptation flavonoids Fagopyrum

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The apple REFPOP—a reference population for genomics-assisted breeding in apple

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Horticulture Research 2020年第1期7卷 364-379页

作者： Michaela Jung Morgane Roth Maria JoséAranzana Annemarie Auwerkerken Marco Bink Caroline Denancé Christian Dujak Charles-Eric Durel Carolina Font i Forcada Celia M.Cantin Walter Guerra Nicholas P.Howard Beat Keller Mariusz Lewandowski Matthew Ordidge Marijn Rymenants Nadia Sanin bruno studer Edward Zurawicz François Laurens Andrea Patocchi Hélène Muranty Molecular Plant Breeding Institute of Agricultural SciencesETH Zurich8092 ZurichSwitzerland Breeding Research group Agroscope 8820 WädenswilSwitzerland IRTA(Institut de Recerca i Tecnologia Agroalimentàries) 08140 Caldes de MontbuiBarcelonaSpain Centre for Research in Agricultural Genomics(CRAG)CSIC-IRTA-UAB-UB Campus UAB08193 BellaterraBarcelonaSpain Better3fruit N.V. 3202 RillaarBelgium Biometris Wageningen University and Research6708 PB WageningenThe Netherlands Hendrix Genetics Research Technology and Services B.V.PO Box 1145830AC BoxmeerThe Netherlands IRHS Universitéd’AngersINRAEInstitut AgroSFR 4207 QuaSaV49071 BeaucouzéFrance ARAID(Fundación Aragonesa para la Investigación y el Desarrollo) 50018 ZaragozaSpain Research Centre Laimburg 39040 AuerItaly Department of Horticultural Science University of MinnesotaSt.PaulMN 55108USA Institute of Biology and Environmental Sciences University of Oldenburg26129 OldenburgGermany Research Institute of Horticulture 96-100 SkierniewicePoland School of Agriculture Policy and DevelopmentUniversity of ReadingWhiteknights RG66AR ReadingUK Laboratory for Plant Genetics and Crop Improvement KU Leuven B-3001 LeuvenBelgium GAFL INRAE84140 MontfavetFrance

Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection ***-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs,and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic *** we present an apple reference population:the apple REFPOP,a large collection formed of 534 genotypes planted in six European countries,as a unique tool to accelerate apple *** population consisted of 269 accessions and 265 progeny from 27 parental combinations,representing the diversity in cultivated apple and current European breeding material,respectively.A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of *** on the genotypic data,linkage disequilibrium was low and population structure was *** well-studied phenological traits of horticultural importance were *** found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date,*** decreasing SNP density,the detection of significant marker–trait associations varied depending on trait *** of the trait,10,000 SNPs sufficed to maximize genomic prediction *** confirm the suitability of the apple REFPOP design for genomics-assisted breeding,especially for breeding programs using related germplasm,and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.

关键词： breeding planted utilize

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