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Lin Y, Gnanesh BN, Chong J, Chen G, Beattie AD, Mitchell Fetch JW, Kutcher HR, Eckstein PE, Menzies JG, Jackson EW, McCartney CA. A major quantitative trait locus conferring adult plant partial resistance to crown rust in oat. BMC PLANT BIOLOGY 2014; 14:250. [PMID: 25260759 PMCID: PMC4181729 DOI: 10.1186/s12870-014-0250-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/18/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND Crown rust, caused by Puccinia coronata f. sp. avenae, is the most important disease of oat worldwide. Adult plant resistance (APR), based upon partial resistance, has proven to be a durable rust management strategy in other cereal rust pathosystems. The crown rust APR in the oat line MN841801 has been effective for more than 30 years. The genetic basis of this APR was studied under field conditions in three recombinant inbred line (RIL) populations: 1) AC Assiniboia/MN841801, 2) AC Medallion/MN841801, and 3) Makuru/MN841801. The populations were evaluated for crown rust resistance with the crown rust isolate CR251 (race BRBB) in multiple environments. The 6 K oat and 90 K wheat Illumina Infinium single nucleotide polymorphism (SNP) arrays were used for genotyping the AC Assiniboia/MN841801 population. KASP assays were designed for selected SNPs and genotyped on the other two populations. RESULTS This study reports a high density genetic linkage map constructed with oat and wheat SNP markers in the AC Assiniboia/MN841801 RIL population. Most wheat SNPs were monomorphic in the oat population. However the polymorphic wheat SNPs could be scored accurately and integrated well into the linkage map. A major quantitative trait locus (QTL) on oat chromosome 14D, designated QPc.crc-14D, explained up to 76% of the APR phenotypic variance. This QTL is flanked by two SNP markers, GMI_GBS_90753 and GMI_ES14_c1439_83. QPc.crc-14D was validated in the populations AC Medallion/MN841801 and Makuru/MN841801. CONCLUSIONS We report the first APR QTL in oat with a large and consistent effect. QPc.crc-14D was statistically significant in all environments tested in each of the three oat populations. QPc.crc-14D is a suitable candidate for use in marker-assisted breeding and also an excellent target for map-based cloning. This is also the first study to use the 90 K wheat Infinium SNP array on oat for marker development and comparative mapping. The Infinium SNP array is a useful tool for saturating oat maps with markers. Synteny with wheat suggests that QPc.crc-14D is orthologous with the stripe rust APR gene Yr16 in wheat.
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Affiliation(s)
- Yang Lin
- />Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Belaghihalli N Gnanesh
- />Agriculture and Agri-Food Canada, Cereal Research Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - James Chong
- />Agriculture and Agri-Food Canada, Cereal Research Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - Gang Chen
- />Agriculture and Agri-Food Canada, Cereal Research Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - Aaron D Beattie
- />Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Jennifer W Mitchell Fetch
- />Agriculture and Agri-Food Canada, Cereal Research Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - H Randy Kutcher
- />Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Peter E Eckstein
- />Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8 Canada
| | - Jim G Menzies
- />Agriculture and Agri-Food Canada, Cereal Research Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
| | - Eric W Jackson
- />General Mills Agriculture Research, 150 N. Research Campus Dr, Kannapolis, NC 28081 USA
| | - Curt A McCartney
- />Agriculture and Agri-Food Canada, Cereal Research Centre, 101 Route 100, Morden, MB R6M 1Y5 Canada
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He J, Zhao X, Laroche A, Lu ZX, Liu H, Li Z. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. FRONTIERS IN PLANT SCIENCE 2014; 5:484. [PMID: 25324846 PMCID: PMC4179701 DOI: 10.3389/fpls.2014.00484] [Citation(s) in RCA: 271] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/02/2014] [Indexed: 05/05/2023]
Abstract
Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.
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Affiliation(s)
- Jiangfeng He
- Inner Mongolia Academy of Agriculture and Husbandry ScienceHohhot, China
- Lethbridge Research Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agriculture and Husbandry ScienceHohhot, China
| | - André Laroche
- Lethbridge Research Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Zhen-Xiang Lu
- Lethbridge Research Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - HongKui Liu
- Inner Mongolia Academy of Agriculture and Husbandry ScienceHohhot, China
- *Correspondence: Hongkui Liu and Ziqin Li, Inner Mongolia Academy of Agriculture and Husbandry Science, Zhaojun Road 22, Hohhot, Inner Mongolia 010031, China e-mail: ;
| | - Ziqin Li
- Inner Mongolia Academy of Agriculture and Husbandry ScienceHohhot, China
- *Correspondence: Hongkui Liu and Ziqin Li, Inner Mongolia Academy of Agriculture and Husbandry Science, Zhaojun Road 22, Hohhot, Inner Mongolia 010031, China e-mail: ;
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