A linked SNP marker to genotype Fr-B2 in wheat
H. A. Eagles![https://orcid.org/0000-0003-1023-5738](/media/client/orcid_16x16.png)
A CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia.
B Mailing address: 3 Tacoma Boulevard, Pasadena, SA 5042, Australia.
C Department of Economic Development, Jobs, Transport and Resources, PB260, Horsham, Vic. 3401, Australia.
D Mailing address: 18 Pindari Drive, Mt Clear, Vic. 3350, Australia.
E Department of Economic Development, Jobs, Transport and Resources, Agriculture Victoria Research, Agribio Centre, La Trobe Research and Development Park, Bundoora, Vic. 3083, Australia.
F School of Applied Biology, La Trobe University, Bundoora, Vic. 2086, Australia.
G Corresponding author. Email: jessica.hyles@csiro.au
Crop and Pasture Science 69(9) 859-863 https://doi.org/10.1071/CP18248
Submitted: 01 June 2018 Accepted: 18 July 2018 Published: 24 August 2018
Abstract
Fr-B2 is a complex locus on chromosome 5B that affects frost tolerance, days to heading, grain yield and probably other traits of commercial importance in wheat (Triticum aestivum L.). It interacts epistatically with other major genes, especially VRN1. There are two known alleles of Fr-B2: an intact, wild-type allele, and an allele with a large deletion. Published methods for identifying these alleles are slow and expensive, making the development of a high-throughput, co-dominant SNP (single-nucleotide polymorphism) marker highly desirable, especially for commercial wheat breeding.
A diverse panel of cultivars and breeding lines was characterised for SNPs and alleles of Fr-B2. Four SNP markers co-segregated as a haplotype block with Fr-B2 across unrelated cultivars and related backcrosses differing for alleles of Fr-B2. A robust KASP (Kompetitive allele-specific PCR) assay was developed for one of the SNPs, KASP_IWB26333, which should facilitate the inclusion of Fr-B2 on genotyping platforms for breeding and research.
Additional keywords: marker-assisted breeding, pleiotropy, SNP–gene co-segregation.
References
Badawi M, Danyluk J, Boucho B, Houde M, Sarhan F (2007) The CBF gene family in hexaploid wheat and its relationship to the phylogenetic complexity of cereal CBFs. Molecular Genetics and Genomics 277, 533–554.| The CBF gene family in hexaploid wheat and its relationship to the phylogenetic complexity of cereal CBFs.Crossref | GoogleScholarGoogle Scholar |
Boer R, Campbell LC, Fletcher DJ (1993) Characteristics of frost in a major wheat-growing region of Australia. Australian Journal of Agricultural Research 44, 1731–1743.
| Characteristics of frost in a major wheat-growing region of Australia.Crossref | GoogleScholarGoogle Scholar |
Cane K, Spackman M, Eagles HA (2004) Puroindoline genes and their effects on grain quality traits in southern Australian wheat cultivars. Australian Journal of Agricultural Research 55, 89–98.
| Puroindoline genes and their effects on grain quality traits in southern Australian wheat cultivars.Crossref | GoogleScholarGoogle Scholar |
Cane K, Eagles HA, Laurie DA, Trevaskis B, Vallance N, Eastwood RF, Gororo NN, Kuchel H, Martin PJ (2013) Ppd-B1 and Ppd-D1 and their effects in southern Australian wheat. Crop & Pasture Science 64, 100–114.
| Ppd-B1 and Ppd-D1 and their effects in southern Australian wheat.Crossref | GoogleScholarGoogle Scholar |
Chhetri M, Bariana H, Wong D, Sohail Y, Hayden M, Bansal U (2017) Development of robust molecular markers for marker-assisted selection of leaf rust resistance gene Lr23 in common and durum wheat breeding programs. Molecular Breeding 37, 21
| Development of robust molecular markers for marker-assisted selection of leaf rust resistance gene Lr23 in common and durum wheat breeding programs.Crossref | GoogleScholarGoogle Scholar |
Cromey MG, Wright DSC, Boddington HJ (1998) Effects of frost during grain filling on wheat yield and grain structure. New Zealand Journal of Crop and Horticultural Science 26, 279–290.
| Effects of frost during grain filling on wheat yield and grain structure.Crossref | GoogleScholarGoogle Scholar |
Eagles HA, Cane K, Trevaskis B, Vallance N, Eastwood RF, Gororo NN, Kuchel H, Martin PJ (2014) Ppd1, Vrn1, ALMT1 and Rht genes and their effects on grain yield in lower rainfall environments in southern Australia. Crop & Pasture Science 65, 159–170.
| Ppd1, Vrn1, ALMT1 and Rht genes and their effects on grain yield in lower rainfall environments in southern Australia.Crossref | GoogleScholarGoogle Scholar |
Eagles HA, Wilson J, Cane K, Vallance N, Eastwood RF, Kuchel H, Martin PJ, Trevaskis B (2016) Frost-tolerance genes Fr-A2 and Fr-B2 in Australian wheat and their effects on days to heading and grain yield in lower rainfall environments in southern Australia. Crop & Pasture Science 67, 119–127.
| Frost-tolerance genes Fr-A2 and Fr-B2 in Australian wheat and their effects on days to heading and grain yield in lower rainfall environments in southern Australia.Crossref | GoogleScholarGoogle Scholar |
Flohr BM, Hunt JR, Kirkegaard JA, Evans JR (2017) Water and temperature stress define the optimal flowering period for wheat in south-eastern Australia. Field Crops Research 209, 108–119.
| Water and temperature stress define the optimal flowering period for wheat in south-eastern Australia.Crossref | GoogleScholarGoogle Scholar |
Hanocq E, Niarquin M, Heumez E, Rousset M, Le Gouis L (2004) Detection and mapping of QTL for earliness components in a bread wheat recombinant inbred lines population. Theoretical and Applied Genetics 110, 106–115.
| Detection and mapping of QTL for earliness components in a bread wheat recombinant inbred lines population.Crossref | GoogleScholarGoogle Scholar |
Harris FAJ, Eagles HA, Virgona JM, Martin PJ, Condon JR, Angus JF (2017) Effect of VRN1 and PPD1 genes on anthesis date and wheat growth. Crop & Pasture Science 68, 195–201.
| Effect of VRN1 and PPD1 genes on anthesis date and wheat growth.Crossref | GoogleScholarGoogle Scholar |
Heyne EG (1959) Registration of improved wheat varieties, XX111. Agronomy Journal 51, 689–692.
| Registration of improved wheat varieties, XX111.Crossref | GoogleScholarGoogle Scholar |
International Wheat Genome Sequencing Consortium (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345,
| A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.Crossref | GoogleScholarGoogle Scholar |
Kohn GD, Storrier RR (1970) Time of sowing and wheat production in southern New South Wales. Australian Journal of Experimental Agriculture and Animal Husbandry 10, 604–609.
| Time of sowing and wheat production in southern New South Wales.Crossref | GoogleScholarGoogle Scholar |
Pearce S, Zhu J, Boldizsár Á, Vágújfalvi A, Burke A, Garland-Campbell K, Galiba G, Dubcovsky J (2013) Large deletions in the CBF gene cluster at the Fr-B2 locus are associated with reduced frost tolerance in wheat. Theoretical and Applied Genetics 126, 2683–2697.
| Large deletions in the CBF gene cluster at the Fr-B2 locus are associated with reduced frost tolerance in wheat.Crossref | GoogleScholarGoogle Scholar |
Perry EM, Nuttall JG, Wallace AJ, Fitzgerald GJ (2017) In-field methods for rapid detection of frost damage in Australian dryland wheat during the reproductive and grain-filling phase. Crop & Pasture Science 68, 516–526.
| In-field methods for rapid detection of frost damage in Australian dryland wheat during the reproductive and grain-filling phase.Crossref | GoogleScholarGoogle Scholar |
Ramirez-Gonzalez RH, Uauy C, Caccamo M (2015) PolyMarker: A fast polyploid primer design pipeline. Bioinformatics 31, 2038–2039.
| PolyMarker: A fast polyploid primer design pipeline.Crossref | GoogleScholarGoogle Scholar |
Rasheed A, Wen W, Gao F, Zhai S, Jin H, Liu J, Guo Q, Zhang Y, Dreisigacker S, Xia X, He Z (2016) Development and validation of KASP assays for genes underpinning key economic traits in bread wheat. Theoretical and Applied Genetics 129, 1843–1860.
| Development and validation of KASP assays for genes underpinning key economic traits in bread wheat.Crossref | GoogleScholarGoogle Scholar |
Rasheed A, Hao Y, Xia X, Khan A, Xu Y, Varshney RK, He Z (2017) Crop breeding chips and genotyping platforms: Progress, challenges, and perspectives. Molecular Plant 10, 1047–1064.
| Crop breeding chips and genotyping platforms: Progress, challenges, and perspectives.Crossref | GoogleScholarGoogle Scholar |
Reynolds M, Langridge P (2016) Physiological breeding. Current Opinion in Plant Biology 31, 162–171.
| Physiological breeding.Crossref | GoogleScholarGoogle Scholar |
Single WV (1961) Studies on frost injury to wheat. 1. Laboratory freezing tests in relation to the behaviour of varieties in the field. Australian Journal of Agricultural Research 12, 767–782.
| Studies on frost injury to wheat. 1. Laboratory freezing tests in relation to the behaviour of varieties in the field.Crossref | GoogleScholarGoogle Scholar |
Tóth B, Galiba G, Fehér E, Sutka J, Snape JW (2003) Mapping genes affecting flowering time and frost resistance on chromosome 5B of wheat. Theoretical and Applied Genetics 107, 509–514.
| Mapping genes affecting flowering time and frost resistance on chromosome 5B of wheat.Crossref | GoogleScholarGoogle Scholar |
Voss-Fels KP, Robinson H, Mudge SR, Richard C, Newman S, Wittkop B, Stahl A, Friedt W, Frisch M, Gabur I, Miller-Cooper A, Campbell BC, Kelly A, Fox G, Christopher J, Christopher M, Chenu K, Franckowiak J, Mace ES, Borrell AK, Eagles H, Jordan DR, Botella JR, Hammer G, Godwin ID, Trevaskis B, Snowdon RJ, Hickey LT (2018) VERNALIZATION1 modulates root system architecture in wheat and barley. Molecular Plant 11, 226–229.
| VERNALIZATION1 modulates root system architecture in wheat and barley.Crossref | GoogleScholarGoogle Scholar |
Wang J, Eagles HA, Trethowan R, van Ginkel M (2005) Using computer simulation of the selection process and known gene information to assist in parental selection in wheat quality breeding. Australian Journal of Agricultural Research 56, 465–473.
| Using computer simulation of the selection process and known gene information to assist in parental selection in wheat quality breeding.Crossref | GoogleScholarGoogle Scholar |
Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo M-C, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E (2014) Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array. Plant Biotechnology Journal 12, 787–796.
| Characterization of polyploid wheat genomic diversity using a high-density 90000 single nucleotide polymorphism array.Crossref | GoogleScholarGoogle Scholar |
Würschum T, Longin CFH, Hahn V, Tucker MR, Leiser WL (2017) Copy number variations of CBF genes at the Fr-A2 locus are essential components of winter hardiness in wheat. The Plant Journal 89, 764–773.
| Copy number variations of CBF genes at the Fr-A2 locus are essential components of winter hardiness in wheat.Crossref | GoogleScholarGoogle Scholar |
Zheng B, Chapman SC, Christopher JT, Frederiks TM, Chenu K (2015) Frost trends and their estimated impact on yield in the Australian wheatbelt. Journal of Experimental Botany 66, 3611–3623.
| Frost trends and their estimated impact on yield in the Australian wheatbelt.Crossref | GoogleScholarGoogle Scholar |
Zhu J, Pearce S, Burke A, See DR, Skinner DZ, Dubcovsky J, Garland-Campbell K (2014) Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat. Theoretical and Applied Genetics 127, 1183–1197.
| Copy number and haplotype variation at the VRN-A1 and central FR-A2 loci are associated with frost tolerance in hexaploid wheat.Crossref | GoogleScholarGoogle Scholar |