Genome-Wide Association Mapping of Barley Yellow Dwarf Virus Tolerance in Spring Oat (Avena Sativa L.)

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2016 May 14

PMID 27175781

Citations 12

Authors

Bradley J Foresman

Rebekah E Oliver

Eric W Jackson

Shiaoman Chao

Marcio P Arruda

Frederic L Kolb

Affiliations

Soon will be listed here.

Abstract

Barley yellow dwarf viruses (BYDVs) are responsible for the disease barley yellow dwarf (BYD) and affect many cereals including oat (Avena sativa L.). Until recently, the molecular marker technology in oat has not allowed for many marker-trait association studies to determine the genetic mechanisms for tolerance. A genome-wide association study (GWAS) was performed on 428 spring oat lines using a recently developed high-density oat single nucleotide polymorphism (SNP) array as well as a SNP-based consensus map. Marker-trait associations were performed using a Q-K mixed model approach to control for population structure and relatedness. Six significant SNP-trait associations representing two QTL were found on chromosomes 3C (Mrg17) and 18D (Mrg04). This is the first report of BYDV tolerance QTL on chromosome 3C (Mrg17) and 18D (Mrg04). Haplotypes using the two QTL were evaluated and distinct classes for tolerance were identified based on the number of favorable alleles. A large number of lines carrying both favorable alleles were observed in the panel.

Citing Articles

Recovery from virus infection: plant's armory in action.

Malavika M, Prakash V, Chakraborty S Planta. 2023; 257(6):103.

PMID: 37115475 DOI: 10.1007/s00425-023-04137-9.

Archetypes of inflorescence: genome-wide association networks of panicle morphometric, growth, and disease variables in a multiparent oat population.

Carlson C, Fiedler J, Naraghi S, Nazareno E, Ardayfio N, McMullen M Genetics. 2022; 223(2).

PMID: 36106985 PMC: 9910404. DOI: 10.1093/genetics/iyac128.

Identification and Validation of Quantitative Trait Loci for Resistance in Wheat ( spp.).

Pfrieme A, Ruckwied B, Habekuss A, Will T, Stahl A, Pillen K Front Plant Sci. 2022; 13:828639.

PMID: 35498699 PMC: 9047360. DOI: 10.3389/fpls.2022.828639.

Applied phenomics and genomics for improving barley yellow dwarf resistance in winter wheat.

Silva P, Evers B, Kieffaber A, Wang X, Brown R, Gao L G3 (Bethesda). 2022; 12(7).

PMID: 35353191 PMC: 9258586. DOI: 10.1093/g3journal/jkac064.

Deciphering the Genetic Architecture of Plant Virus Resistance by GWAS, State of the Art and Potential Advances.

Monnot S, Desaint H, Mary-Huard T, Moreau L, Schurdi-Levraud V, Boissot N Cells. 2021; 10(11).

PMID: 34831303 PMC: 8625838. DOI: 10.3390/cells10113080.

References

Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M . AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 1995; 23(21):4407-14. PMC: 307397. DOI: 10.1093/nar/23.21.4407. View

Stich B, Mohring J, Piepho H, Heckenberger M, Buckler E, Melchinger A . Comparison of mixed-model approaches for association mapping. Genetics. 2008; 178(3):1745-54. PMC: 2278052. DOI: 10.1534/genetics.107.079707. View

Oliver R, Obert D, Hu G, Bonman J, OLeary-Jepsen E, Jackson E . Development of oat-based markers from barley and wheat microsatellites. Genome. 2010; 53(6):458-71. DOI: 10.1139/g10-021. View

Jin H, Domier L, Kolb F, Brown C . Identification of quantitative Loci for tolerance to barley yellow dwarf virus in oat. Phytopathology. 2008; 88(5):410-5. DOI: 10.1094/PHYTO.1998.88.5.410. View

Carlson C, Eberle M, Rieder M, Yi Q, Kruglyak L, Nickerson D . Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium. Am J Hum Genet. 2003; 74(1):106-20. PMC: 1181897. DOI: 10.1086/381000. View

Chaffin A, Huang Y, Smith S, Bekele W, Babiker E, Gnanesh B . A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement. Plant Genome. 2016; 9(2). DOI: 10.3835/plantgenome2015.10.0102. View

G Williams J, Kubelik A, Livak K, Rafalski J, Tingey S . DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 1990; 18(22):6531-5. PMC: 332606. DOI: 10.1093/nar/18.22.6531. View

Oliver R, Tinker N, Lazo G, Chao S, Jellen E, Carson M . SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS One. 2013; 8(3):e58068. PMC: 3606164. DOI: 10.1371/journal.pone.0058068. View

Oliver R, Lazo G, Lutz J, Rubenfield M, Tinker N, Anderson J . Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. BMC Genomics. 2011; 12:77. PMC: 3041746. DOI: 10.1186/1471-2164-12-77. View

10.

Niks R, Habekuss A, Bekele B, Ordon F . A novel major gene on chromosome 6H for resistance of barley against the barley yellow dwarf virus. Theor Appl Genet. 2004; 109(7):1536-43. DOI: 10.1007/s00122-004-1777-7. View

11.

DArcy C, Mayo M . Proposals for changes in luteovirus taxonomy and nomenclature. Arch Virol. 1997; 142(6):1285-7. View

12.

Tinker N, Kilian A, Wight C, Heller-Uszynska K, Wenzl P, Rines H . New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genomics. 2009; 10:39. PMC: 2661094. DOI: 10.1186/1471-2164-10-39. View

13.

Scholz M, Ruge-Wehling B, Habekuss A, Schrader O, Pendinen G, Fischer K . Ryd4 (Hb): a novel resistance gene introgressed from Hordeum bulbosum into barley and conferring complete and dominant resistance to the barley yellow dwarf virus. Theor Appl Genet. 2009; 119(5):837-49. DOI: 10.1007/s00122-009-1093-3. View

14.

Yu J, Pressoir G, Briggs W, Vroh Bi I, Yamasaki M, Doebley J . A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 2005; 38(2):203-8. DOI: 10.1038/ng1702. View

15.

Moon J, Allen R, Domier L, Hewings A . Molecular and Biological Characterization of a Trackable Illinois Isolate of Barley yellow dwarf virus-PAV. Plant Dis. 2019; 84(4):483-486. DOI: 10.1094/PDIS.2000.84.4.483. View

16.

Huang Y, Poland J, Wight C, Jackson E, Tinker N . Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PLoS One. 2014; 9(7):e102448. PMC: 4105502. DOI: 10.1371/journal.pone.0102448. View

17.

Newell M, Asoro F, Scott M, White P, Beavis W, Jannink J . Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin. Theor Appl Genet. 2012; 125(8):1687-96. DOI: 10.1007/s00122-012-1945-0. View

18.

McKirdy S, Jones R, Nutter Jr F . Quantification of Yield Losses Caused by Barley yellow dwarf virus in Wheat and Oats. Plant Dis. 2019; 86(7):769-773. DOI: 10.1094/PDIS.2002.86.7.769. View

19.

Zhu S, Kolb F, Kaeppler H . Molecular mapping of genomic regions underlying barley yellow dwarf tolerance in cultivated oat (Avena sativa L.). Theor Appl Genet. 2003; 106(7):1300-6. DOI: 10.1007/s00122-003-1198-z. View

20.

Perry K, Kolb F, Sammons B, Lawson C, Cisar G, Ohm H . Yield Effects of Barley yellow dwarf virus in Soft Red Winter Wheat. Phytopathology. 2008; 90(9):1043-8. DOI: 10.1094/PHYTO.2000.90.9.1043. View