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Creation and judicious application of a wheat resistance gene atlas

Molecular Plant 2021年第7期14卷 1053-1070页

作者： Amber N.Hafeez Sanu Arora Sreya Ghosh David Gilbert Robert L.Bowden Brande B.H.Wulff John Innes Centre Norwich Research ParkNorwichUK usda-ars Hard Winter Wheat Genetics Research UnitManhattanKS 66506USA

Disease-resistance(R)gene cloning in wheat(Triticum aestivum)has been accelerated by the recent surge of genomic resources,facilitated by advances in sequencing technologies and ***,with the challenges of population growth and climate change,it is vital not only to clone and functionally characterize a few handfuls of R genes,but also to do so at a scale that would facilitate the breeding and deployment of crops that can recognize the wide range of pathogen effectors that threaten *** populations are continually changing,and breeders must have tools and resources available to rapidly respond to those changes if we are to safeguard our daily *** meet this challenge,we propose the creation of a wheat R-gene atlas by an international community of researchers and *** atlas would consist of an online directory from which sources of resistance could be identified and deployed to achieve more durable resistance to the major wheat pathogens,such as wheat rusts,blotch diseases,powdery mildew,and wheat *** present a costed proposal detailing how the inter-acting molecular components governing disease resistance could be captured from both the host and the pathogen through biparental mapping,mutational genomics,and whole-genome association *** explore options for the configuration and genotyping of diversity panels of hexaploid and tetraploid wheat,as well as their wild relatives and major pathogens,and discuss how the atlas could inform a dynamic,durable approach to R-gene *** against the current magnitude of wheat yield losses worldwide,recently estimated at 21%,this endeavor presents one route for bringing R genes from the lab to the field at a considerable speed and quantity.

关键词： wheat Triticum aestivum disease resistance R genes association genetics gene stewardship durable resistance

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Indirect plant defense against insect herbivores： a review

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Insect Science 2018年第1期25卷 2-23页

作者： Zainab Aljbory Ming-Shun Chen Department of Entomology Kansas State University Manhattan Kansas USA hard winter wheat genetics research unit USDA-ARS Kansas State University Manhattan Kansas USA

Plants respond to herbivore attack by launching 2 types of defenses： direct defense and indirect defense. Direct defense includes all plant traits that increase the resistance of host plants to insect herbivores by affecting the physiology and/or be- havior of the attackers. Indirect defense includes all traits that by themselves do not have significant direct impact on the attacking herbivores, but can attract natural en- emies of the herbivores and thus reduce plant loss. When plants recognize herbivore- associated elicitors, they produce and release a blend of volatiles that can attract preda- tors, parasites, and other natural enemies. Known herbivore-associated elicitors include fatty acid-amino acid conjugates, sulfur-containing fatty acids, fragments of cell walls, peptides, esters, and enzymes. Identified plant volatiles include terpenes, nitrogenous compounds, and indoles. In addition, constitive traits including extrafloral nectars, food bodies, and domatia can be further induced to higher levels and attract natural enemies as well as provide food and shelter to carnivores. A better understanding of indirect plant defense at global and componential levels via advanced high throughput technolo- gies may lead to utilization of indirect defense in suppression of herbivore damage to plants.

关键词： elicitor indirect plant defense natural enemies volatile

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Characterization of Rsg2.a3:A new greenbug resistance allele at the Rsg2 locus from wild barley(Hordeum vulgare ***)

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The Crop Journal 2022年第6期10卷 1727-1732页

作者： Xiangyang Xu Dolores Mornhinweg Amy Bernardo Genqiao Li Ruolin Bian Brian J.Steffenson Guihua Bai usda-ars wheat Peanutand Other Field Crop Research UnitStillwaterOK 74075USA usda-ars hard winter wheat genetics research unit ManhattanKS 66506USA Department of Plant Pathology Kansas State UniversityManhattanKS 66506USA Department of Plant Pathology University of MinnesotaSt.PaulMN 55108USA

Greenbug(Schizaphis graminum Rondani)is a destructive insect pest that not only damages plants,but also serves as a vector for many *** plant resistance is the preferred strategy for managing *** greenbug resistance genes,Rsg1 and Rsg2,have been reported in *** breed cultivars with effective resistance against various greenbug biotypes,additional resistance genes are urgently needed to sustain barley *** barley accession WBDC053(PI 681777)was previously found to be resistant to several greenbug *** this study,a recombinant inbred line(RIL)population derived from Weskan×WBDC053 was evaluated for response to two greenbug biotypes(E and TX1)and genotyped using genotyping by sequencing(GBS).A set of 3347 high quality GBS-derived single nucleotide polymorphisms(SNPs)were then used to map the greenbug resistance gene in this wild barley *** analysis placed the greenbug resistance gene in a 2.35 Mb interval(0-2,354,645 bp)in the terminal region of the short arm of chromosome *** interval harbors 15 genes with leucine-rich-repeat(LRR)protein *** allelism test indicated that the greenbug resistance gene in WBDC053,designated Rsg2.a3,is likely allelic or closely linked to ***-SNPs 2H_1318811and 2H_1839499 co-segregating with Rsg2.a3 in the RIL population were converted to Kompetitive allele specific PCR(KASP)markers KASP-Rsg2.a3-1 and KASP-Rsg2.a3-2,*** two KASP markers can be used to select Rsg2.a3 and have the potential to tag Rsg2 in barley improvement programs.

关键词： Barley Greenbug resistance gene KASP markers Genotyping by sequencing Linkage mapping

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Genomic location of Gb1, a unique gene conferring wheat resistance to greenbug biotype F

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作物学报:英文版 2023年第5期11卷 1595-1599页

作者： Xiangyang Xu Genqiao Li Guihua Bai Brett FCarver Ruolin Bian Amy Bernardo JScott Armstrong usda-ars wheat Peanutand Other Field Crop Research UnitStillwaterOK 74075USA usda-ars hard winter wheat genetics research unit ManhattanKS 66506USA Department of Agronomy Kansas State UniversityManhattanKS 66506USA Department of Plant and Soil Sciences Oklahoma State UniversityStillwaterOK 74078USA

Greenbug(Schizaphis graminum, Rondani) is a serious insect pest in many wheat growing regions and has been infesting cereal crops in the USA for over a century. Continuous occurrence of new greenbug biotypes makes it essential to explore all greenbug resistant sources available to manage this pest. Gb1, a recessive greenbug resistance gene in DS28A, confers resistance to several economically important greenbug biotypes and is the only gene found to be resistant to greenbug biotype F. A set of 174 F_(2:3)lines from the cross DS28A × Custer was evaluated for resistance to greenbug biotype F in 2020 and 2022. Selective genotyping of the corresponding F_(2) population using single nucleotide polymorphism(SNP) markers generated by genotyping-by-sequencing(GBS) led to the identification of a candidate genomic region for Gb1. Thus, SSR markers previously mapped in this region were used to genotype the entire F2population,and kompetitive allele specific PCR(KASP) markers were also developed from SNPs in the target ***1 was placed in the terminal region of the short arm of chromosome 1A, and its location was confirmed in a second population derived from the cross DS28A × PI 697274. The combined data analysis from the two mapping populations delimited Gb1 to a < 1 Mb interval between 13,328,200 and 14,241,426 bp on1AS.

关键词： wheat Greenbug resistance gene Gb1 KASP markers Linkage analysis Genotyping-by-sequencing

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Single nucleotide polymorphisms linked to quantitative trait loci for grain quality traits in wheat

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The Crop Journal 2016年第1期4卷 1-11页

作者： Chunlian Li Guihua Bai Shiaoman Chao Brett Carver Zhonghua Wang College of Agronomy Northwest A&F University State Key Laboratory of Crop Stress Biology for Arid Areas Northwest A&F University Agronomy Department Kansas State University hard winter wheat genetics research unit USDA-ARS Cereal Crops research unit USDA-ARS Department of Plant and Soil Science Oklahoma State University

wheat(Triticum aestivum L.) grain quality traits that are controlled by quantitative traits loci(QTL) define suitable growing areas and potential end-use products of a wheat cultivar. To dissect QTL for these traits including protein content(GPC); test weight(TW); single kernel characterization system(SKCS)-estimated kernel weight(SKW); kernel diameter(KD);kernel hardness measured by near-infrared reflectance spectroscopy(NIRS) hardness index(NHI); and SKCS-hardness index(SHI), a high-density genetic map with single nucleotide polymorphism(SNP) and simple sequence repeat(SSR) markers was developed using recombinant inbred lines(RILs) derived from Ning7840 × Clark. The RILs were evaluated for these quality traits in seven Oklahoma environments from 2001 to 2003. A total of 41 QTL with additive effects on different traits were mapped on most wheat chromosomes,excluding 1A, 2A, 3D, 4D, 6D, and 7B. Seven chromosome regions showed either tightly linked QTL or QTL with pleiotropic effects on two to four traits. Ten pairs of QTL showed additive × additive effects(AA), four QTL were involved in additive × environment(AE)effects, and one was involved in AAE effects. Two to eleven QTL for each of the six traits and139 tightly linked markers to these QTL were identified. The findings shed light on the inheritance of wheat grain quality traits and provide DNA markers for manipulating these important traits to improve quality of new wheat cultivars.

关键词： Triticum aestivum Epistasis Grain quality traits QTL×environments interaction SNP

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Identification of powdery mildew resistance loci in wheat by integrating genome-wide association study(GWAS) and linkage mapping

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The Crop Journal 2019年第3期7卷 294-306页

作者： Genqiao Li Xiangyang Xu Chengcheng Tan Brett F.Carver Guihua Bai Xuewen Wang J.Michael Bonman Yanqi Wu Robert Hunger Christina Cowger wheat Peanut and Other Field Crops Research UnitUSDA-ARSStillwaterOK 74075USA Plant and Soil Science Department Oklahoma State UniversityStillwaterOK 74078USA hard winter wheat genetics research unit USDA-ARSManhattanKS 66506USA Department of genetics University of GeorgiaAthensGA 30602USA Small Grains and Potato Germplasm research unit USDA-ARSAberdeenID 83210USA Entomology and Pathology Department Oklahoma State UniversityStillwaterOK 74078USA Plant Science research unit USDA-ARSRaleighNC 27695USA

wheat powdery mildew(Blumeria graminis ***, Bgt) is a disease of increasing importance globally due to the adoption of high yielding varieties and modern sustainable farming *** resistant cultivars is a preferred approach to managing this disease, and novel powdery mildew resistance genes are urgently needed for new cultivar development.A genome-wide association study was performed on a panel of 1292 wheat landraces and historical cultivars using 5011 single nucleotide polymorphism(SNP)*** association panel was evaluated for reactions to three Bgt inoculants, OKS(14)-B-3-1, OKS(14)-C-2-1, and *** disequilibrum(LD) analysis indicated that genome-wide LD decayed to 0.1 at 23 Mb, and population structure analysis revealed seven subgroups in the *** analysis using a mixed linear model(MLM) identified three loci for powdery mildew resistance on chromosome 2 B, designated ***-2BL1,***-2BL2, and *** evaluate the efficacy of GWAS in gene discovery,***-2BL2 was validated using F2 and F2:3 populations derived from PI420646 × *** analysis delimited the powdery mildew resistance gene in PI 420646 to an interval where ***-2BL2 was located, lending credence to the GWAS ***-2BL1 and ***-2BL3, which were associated with four SNPs located at 457.7–461.7 Mb and two SNPs located at 696.6–715.9 Mb in the Chinese Spring reference IWGSC RefSeq v1.0, respectively, are likely novel loci for powdery mildew resistance and can be used in wheat breeding to improve powdery mildew resistance.

关键词： wheat Powdery mildew GWAS Linkage mapping Genome-wide linkage disequilibrium

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Leveraging the potential of big genomic and phenotypic data for genome-wide association mapping in wheat

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The Crop Journal 2024年第3期12卷 803-813页

作者： Moritz Lell Yusheng Zhao Jochen C.Reif Leibniz Institute of Plant genetics and Crop Plant research(IPK) Corrensstraße 3D-06466 SeelandGermany

Genome-wide association mapping studies(GWAS)based on Big Data are a potential approach to improve marker-assisted selection in plant *** number of available phenotypic and genomic data sets in which medium-sized populations of several hundred individuals have been studied is rapidly *** these data and using them in GWAS could increase both the power of QTL discovery and the accuracy of estimation of underlying genetic effects,but is hindered by data heterogeneity and lack of *** this study,we used genomic and phenotypic data sets,focusing on Central European winter wheat populations evaluated for heading *** explored strategies for integrating these data and subsequently the resulting potential for *** interoperability between data sets was greatly aided by some overlapping genotypes and a linear relationship between the different phenotyping protocols,resulting in high quality integrated phenotypic *** this context,genomic prediction proved to be a suitable tool to study relevance of interactions between genotypes and experimental series,which was low in our *** to expectations,fewer associations between markers and traits were found in the larger combined data than in the individual experimental ***,the predictive power based on the marker-trait associations of the integrated data set was higher across data ***,the results show that the integration of medium-sized to Big Data is an approach to increase the power to detect QTL in *** results encourage further efforts to standardize and share data in the plant breeding community.

关键词： Big Data Genome-wide association study Data integration Genomic prediction wheat

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A combination of leaf rust resistance gene Lr34 and lesion mimic gene lm significantly enhances adult plant resistance to Puccinia triticina in wheat

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Chinese Science Bulletin 2012年第17期57卷 2113-2119页

作者： LI Tao BAI GuiHua GU ShiLiang Jiangsu Provincial Key Laboratory of Crop genetics and Physiology Key Laboratory of Plant Functional Genomics of Ministry of EducationYangzhou UniversityYangzhou 225009China Department of Plant Pathology Kansas State UniversityManhattanKS 66506USA usda-ars hard winter wheat genetics research unit ManhattanKS 66506USA

Leaf rust caused by Puccinia triticina is an economically-important disease in wheat worldwide.A combination of different types of resistance genes may significantly enhance rust resistance under rust-favorable *** investigate the interactions between the rust resistance gene Lr34 and the lesion mimic gene lm on 1BL in Ning 7840,a segregating F8-10 population of 180 recombinant inbred lines was developed from Ning 7840/Chokwang and evaluated for both lesion mimic expression and leaf rust response at the adult plant stage in a greenhouse.A major quantitative trait locus(QTL),derived from Sumai 3,was co-localized with Lr34 on chromosome 7D and explained 41.5% of phenotypic variations for rust severity and 22.1% for leaf tip necrosis(LTN).The presence of Lr34 was confirmed by Lr34-specific markers cssfr1 and cssfr2 in Ning 7840 and Sumai *** Lr34,lm conditioned a spontaneous lesion mimic phenotype and had a significant effect on reducing uredinial size,and a smaller effect on *** effects were observed between lm and Lr34 for severity and LTN,and an epistatic effect was observed for infection *** marker analysis also identified several other QTL with minor effects on severity,infection type,or LTN.

关键词：抗叶锈病基因小麦叶锈菌抗条锈病成株期病变模仿单标记分析数量性状位点

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Quantitative trait loci for Fusarium head blight resistance in wheat cultivars Yangmai 158 and Zhengmai 9023

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The Crop Journal 2021年第1期9卷 143-153页

作者： Pingping Zhang Chenjin Guo Zhao Liu Amy Bernardo Hongxiang Maa Hongxiang Ma Peng Jiang Guicheng Song Guihua Bai Jiangsu Academy of Agricultural Sciences Jiangsu Collaborative Innovation Center for Modern Crop ProductionNanjing 210014JiangsuChina Department of Agronomy Kansas State UniversityManhattanKS 66506USA Hebei Agricultural University Baoding 071001HebeiChina usda-ars Hard Winter Wheat Genetics Research UnitManhattanKS 66506USA

Fusarium head blight(FHB)is one of the prevalent fungal diseases of wheat *** new FHB resistance quantitative trait loci(QTL)in adapted wheat cultivars is a critical step for breeding new FHB-resistant *** this study,we developed a population of 236 F5:7 recombinant inbred lines(RILs)using two popular Chinese wheat cultivars,Yangmai 158 and Zhengmai 9023,with moderate FHB resistance to identify the QTL for FHB type II *** population was evaluated for percentage of symptomatic spikelets per spike(PSS)using single floret injection in repeated greenhouse *** PSSs were 33.2%for Yangmai 158 and 30.3%for Zhengmai 9023.A genetic linkage map of 1002 single nucleotide polymorphisms(SNPs)generated by genotyping-by-sequencing(GBS)was constructed for the RIL *** QTL were identified for FHB resistance,and three of them were repeatable in the both *** 9023 contributed the resistance allele at one repeatable QTL,designated as Qfhb.7D,whereas Yangmai 158 contributed the resistance alleles at the other two repeatable QTL,Qfhb.3AL and *** additional QTL,Qfhb.4AS was significant in the mean PSS,and Qfhb.2DL and Qfhb.7AS were significant in only one *** of each allele individually at the three repeatable QTL significantly changed ***.3AL,Qfhb.2DS,and Qfhb.7D explained 8.35%to 9.89%,5.13%to 7.43%,and 6.15%to 9.32%of the phenotypic variations,*** three repeatable QTL contributed by the two parents were additive and stacking the resistance alleles from all the three repeatable QTL showed the highest level of resistance in the current RIL *** SNPs in the QTL regions of Qfhb.3AL,Qfhb.2DS,and Qfhb.7D were converted into KBioscience competitive allele-specific PCR(KASP)*** KASP marker for Qfhb.3AL was validated in a panel of wheat cultivars from *** of these KASP markers could be useful for marker-assisted selection to stack these QTL.

关键词： QTL mapping FHB Yangmai 158 Zhengmai 9023 KASP

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genetics-inspired data-driven approaches explain and predict crop performance fluctuations attributed to changing climatic conditions

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Molecular Plant 2022年第2期15卷 203-206页

作者： Xianran Li Tingting Guo Guihua Bai Zhiwu Zhang Deven See Juliet Marshall Kimberly A.Garland-Campbell Jianming Yu usda Agricultural Research ServiceWheat HealthGeneticsand Quality Research UnitPullmanWA 99164USA Department of Agronomy Iowa State UniversityAmesIA 50011USA usda Agricultural Research ServiceHard Winter Wheat Genetics Research UnitManhattanKS 66506USA Department of Crop and Soil Sciences Washington State UniversityPullmanWA 99164USA Department of Plant Sciences University of Idaho Research and ExtensionIdaho FallsID 83402USA

Dear Editor,genetics-focused approaches have been widely used to uncover major genetic variants associated with performance ***,manipulating,and editing genetic variants significantly improve crop ***,the genetic component explains a portion of performance variation,and the environ-mental component contributes to the remaining,often large,portion(Laidig et al.,2017;Bonecke et al.,2020;Li et al.,2021).To ensure superior and robust performance,elite varieties are extensively tested across multiple years and *** extensive performance records,coupled with climatic profiles,could be leveraged to understand climate's impact on agriculture through approaches parallel to quantitative genetics approaches(Figure 1A).

关键词： performance attributed Figure

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