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Nazareno ES, Fiedler JD, Ardayfio NK, Miller ME, Figueroa M, Kianian SF. Genetic Analysis and Physical Mapping of Oat Adult Plant Resistance Loci Against Puccinia coronata f. sp. avenae. PHYTOPATHOLOGY 2023; 113:1307-1316. [PMID: 36721375 DOI: 10.1094/phyto-10-22-0395-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Six quantitative trait loci (QTLs) for adult plant resistance against oat crown rust (Puccinia coronata f. sp. avenae) were identified from mapping three recombinant inbred populations. Using genotyping-by-sequencing with markers called against the OT3098 v1 reference genome, the QTLs were mapped on six different chromosomes: Chr1D, Chr4D, Chr5A, Chr5D, Chr7A, and Chr7C. Composite interval mapping with marker cofactor selection showed that the phenotypic variance explained by all identified QTLs for coefficient of infection range from 12.2 to 46.9%, whereas heritability estimates ranged from 0.11 to 0.38. The significant regions were narrowed down to intervals of 3.9 to 25 cM, equivalent to physical distances of 11 to 133 Mb. At least two flanking single-nucleotide polymorphism markers were identified within 10 cM of each QTL that could be used in marker-assisted introgression, pyramiding, and selection. The additive effects of the QTLs in each population were determined using single-nucleotide polymorphism haplotype data, which showed a significantly lower coefficient of infection in lines homozygous for the resistant alleles. Analysis of pairwise linkage disequilibrium also revealed high correlation of markers and presence of linkage blocks in the significant regions. To further facilitate marker-assisted breeding, polymerase chain reaction allelic competitive extension (PACE) markers for the adult plant resistance loci were developed. Putative candidate genes were also identified in each of the significant regions, which include resistance gene analogs that encode for kinases, ligases, and predicted receptors of avirulence proteins from pathogens.
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Affiliation(s)
- Eric S Nazareno
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
| | - Jason D Fiedler
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, U.S.A
| | - Naa Korkoi Ardayfio
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Crops Research Unit, Fargo, ND, U.S.A
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, U.S.A
- Pairwise Plants, LLC, 807 East Main Street, Suite 4-100, Durham, NC, U.S.A
| | - Melania Figueroa
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Shahryar F Kianian
- U.S. Department of Agriculture-Agricultural Research Service, Cereal Disease Laboratory, St. Paul, MN, U.S.A
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Brodführer S, Mohler V, Stadlmeier M, Okoń S, Beuch S, Mascher M, Tinker NA, Bekele WA, Hackauf B, Herrmann MH. Genetic mapping of the powdery mildew resistance gene Pm7 on oat chromosome 5D. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:53. [PMID: 36913008 PMCID: PMC10011287 DOI: 10.1007/s00122-023-04288-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Three independent experiments with different genetic backgrounds mapped the resistance gene Pm7 in the oat genome to the distal part of the long arm of chromosome 5D. Resistance of oat to Blumeria graminis DC. f. sp. avenae is an important breeding goal in Central and Western Europe. In this study, the position of the effective and widely used resistance gene Pm7 in the oat genome was determined based on three independent experiments with different genetic backgrounds: genome-wide association mapping in a diverse set of inbred oat lines and binary phenotype mapping in two bi-parental populations. Powdery mildew resistance was assessed in the field as well as by detached leaf tests in the laboratory. Genotyping-by-sequencing was conducted to establish comprehensive genetic fingerprints for subsequent genetic mapping experiments. All three mapping approaches located the gene to the distal part of the long arm of chromosome 5D in the hexaploid oat genome sequences of OT3098 and 'Sang.' Markers from this region were homologous to a region of chromosome 2Ce of the C-genome species, Avena eriantha, the donor of Pm7, which appears to be the ancestral source of a translocated region on the hexaploid chromosome 5D.
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Affiliation(s)
- Sophie Brodführer
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Julius Kuehn Institute (JKI), Rudolf-Schick-Platz 3a, OT Gross Lüsewitz, 18190, Sanitz, Germany
- I.G. Saatzucht GmbH & Co KG, Am Park 3, 18276, Gülzow-Prüzen OT Boldebuck, Germany
| | - Volker Mohler
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 6, 85354, Freising, Germany
| | - Melanie Stadlmeier
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Am Gereuth 6, 85354, Freising, Germany
| | - Sylwia Okoń
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Steffen Beuch
- Nordsaat Saatzucht GmbH, Saatzucht Granskevitz, Granskevitz 3, 18569, Schaprode, Germany
| | - Martin Mascher
- Research Group Domestication Genomics, Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstraße 3, Stadt Seeland OT, 06466, Gatersleben, Germany
| | - Nicholas A Tinker
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Wubishet A Bekele
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Bernd Hackauf
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Julius Kuehn Institute (JKI), Rudolf-Schick-Platz 3a, OT Gross Lüsewitz, 18190, Sanitz, Germany
| | - Matthias Heinrich Herrmann
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Julius Kuehn Institute (JKI), Rudolf-Schick-Platz 3a, OT Gross Lüsewitz, 18190, Sanitz, Germany.
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3
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Zane SN, Pupo JA. What Predicts Out-of-Home Placement in Juvenile Court Dispositions? A Systematic Review and Meta-Analysis. J Youth Adolesc 2023; 52:229-244. [PMID: 36261614 DOI: 10.1007/s10964-022-01686-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/29/2022] [Indexed: 01/12/2023]
Abstract
Research suggests that juvenile court dispositions are influenced by legal factors, such as offense severity and prior record, as well as extralegal factors, such as race/ethnicity, sex, and age. To date, however, no research has reviewed whether legal or extralegal factors are more predictive of juvenile court dispositions across extant research. To address this gap, the present study reports on a systematic review and meta-analysis of predictors of residential placement in the juvenile justice system. A total of 40 independent samples were analyzed from 33 studies that met the criteria for inclusion in the review. Meta-analytic techniques were used to examine the average effects of offense characteristics, prior record, age, preadjudication detention status, race and ethnicity, sex, and contextual factors on odds of placement. The findings suggest that legal factors are more strongly associated with juvenile court dispositions than extralegal or contextual factors. Additionally, the strongest predictor of placement was whether the juvenile defendant had been detained at intake, illustrating the influential role of early case assessment in juvenile court.
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Affiliation(s)
- Steven N Zane
- College of Criminology and Criminal Justice, Florida State University, Tallahassee, FL, USA.
| | - Jhon A Pupo
- College of Criminology and Criminal Justice, Florida State University, Tallahassee, FL, USA
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4
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Park RF, Boshoff WHP, Cabral AL, Chong J, Martinelli JA, McMullen MS, Fetch JWM, Paczos-Grzęda E, Prats E, Roake J, Sowa S, Ziems L, Singh D. Breeding oat for resistance to the crown rust pathogen Puccinia coronata f. sp. avenae: achievements and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3709-3734. [PMID: 35665827 PMCID: PMC9729147 DOI: 10.1007/s00122-022-04121-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 05/01/2022] [Indexed: 05/05/2023]
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae (Pca), is a significant impediment to global oat production. Some 98 alleles at 92 loci conferring resistance to Pca in Avena have been designated; however, allelic relationships and chromosomal locations of many of these are unknown. Long-term monitoring of Pca in Australia, North America and elsewhere has shown that it is highly variable even in the absence of sexual recombination, likely due to large pathogen populations that cycle between wild oat communities and oat crops. Efforts to develop cultivars with genetic resistance to Pca began in the 1950s. Based almost solely on all all-stage resistance, this has had temporary benefits but very limited success. The inability to eradicate wild oats, and their common occurrence in many oat growing regions, means that future strategies to control Pca must be based on the assumption of a large and variable prevailing pathogen population with high evolutionary potential, even if cultivars with durable resistance are deployed and grown widely. The presence of minor gene, additive APR to Pca in hexaploid oat germplasm opens the possibility of pyramiding several such genes to give high levels of resistance. The recent availability of reference genomes for diploid and hexaploid oat will undoubtedly accelerate efforts to discover, characterise and develop high throughput diagnostic markers to introgress and pyramid resistance to Pca in high yielding adapted oat germplasm.
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Affiliation(s)
- R F Park
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia.
| | - W H P Boshoff
- Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - A L Cabral
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Canada
| | - J Chong
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Canada
| | - J A Martinelli
- Department of Crop Science, Agronomy School, Federal University of Rio Grande Do Sul (UFRGS), Av. Bento Gonçalves, 7712, Porto Alegre, RS, 91501-970, Brazil
| | - M S McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58105-5051, USA
| | - J W Mitchell Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, Canada
| | - E Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - E Prats
- CSIC-Institute for Sustainable Agriculture, Avda. Menéndez Pidal s/n. , 14004, Córdoba, Spain
| | - J Roake
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - S Sowa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, 20-950, Lublin, Poland
| | - L Ziems
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | - D Singh
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
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Admassu-Yimer B, Klos KE, Griffiths I, Cowan A, Howarth C. Mapping of Crown Rust ( Puccinia coronata f. sp. avenae) Resistance Gene Pc54 and a Novel Quantitative Trait Locus Effective Against Powdery Mildew ( Blumeria graminis f. sp. avenae) in the Oat ( Avena sativa) Line Pc54. PHYTOPATHOLOGY 2022; 112:1316-1322. [PMID: 34982574 DOI: 10.1094/phyto-10-21-0445-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The Pc54 oat line carries the crown rust resistance gene Pc54 and an unknown gene effective against powdery mildew. In this study, two recombinant inbred line (RIL) populations were developed to identify the genomic locations of the two genes and produce lists of molecular markers with a potential for marker-assisted selection. The RILs and parents were phenotyped for crown rust and powdery mildew in a controlled environment. They were also genotyped using the 6K Illumina Infinium iSelect oat single nucleotide polymorphism (SNP) chip. Multiple interval mapping placed Pc54 on the linkage group Mrg02 (chromosome 7D) and the novel powdery mildew quantitative trait locus (QTL) QPm.18 on Mrg18 (chromosome 1A) both in mapping and in the validating populations. A total of 9 and 31 significant molecular markers were identified linked with the Pc54 gene and QPm.18, respectively. Reactions to crown rust inoculations have justified separate identities of Pc54 from other genes and QTLs that have previously been reported on Mrg02 except for qPCRFd. Pm3 is the only powdery mildew resistance gene previously mapped on Mrg18. However, the pm3 differential line, Mostyn, was susceptible to the powdery mildew race used in this study, suggesting that Pm3 and QPm.18 are different genes. Determining the chromosomal locations of Pc54 and QPm.18 is helpful for better understanding of the molecular mechanism of resistance to crown rust and powdery mildew in oats. Furthermore, SNPs and single sequence repeats that are closely linked with the genes could be valuable for developing PCR-based molecular markers and facilitating the utilization of these genes in oat breeding programs.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Belayneh Admassu-Yimer
- Oak Ridge Institute for Science and Education Research Participant, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
| | - Kathy Esvelt Klos
- United States Department of Agriculture, Agricultural Research Service, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, U.S.A
| | - Irene Griffiths
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, United Kingdom
| | - Alexander Cowan
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, United Kingdom
| | - Catherine Howarth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth SY23 3EE, United Kingdom
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Yan H, Yu K, Xu Y, Zhou P, Zhao J, Li Y, Liu X, Ren C, Peng Y. Position Validation of the Dwarfing Gene Dw6 in Oat ( Avena sativa L.) and Its Correlated Effects on Agronomic Traits. FRONTIERS IN PLANT SCIENCE 2021; 12:668847. [PMID: 34093626 PMCID: PMC8172587 DOI: 10.3389/fpls.2021.668847] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/26/2021] [Indexed: 06/12/2023]
Abstract
An F6 : 8 recombinant inbred line (RIL) population derived from the cross between WAOAT2132 (Dw6) and Caracas along with the two parents were used to evaluate the genetic effects of Dw6 dwarfing gene on plant height and other agronomic traits in oat (Avena sativa L.) across three environments, and develop closely linked markers for marker-assisted selection (MAS) for Dw6. The two parents differed in all investigated agronomic traits except for the number of whorls. The RIL lines showed a bimodal distribution for plant height in all three tested environments, supporting the height of this population was controlled by a single gene. Dw6 significantly reduced plant height (37.66∼44.29%) and panicle length (13.99∼22.10%) but without compromising the coleoptile length which was often positively associated with the reduced stature caused by dwarfing genes. Dw6 has also strong negative effects on hundred kernel weight (14.00∼29.55%), and kernel length (4.21∼9.47%), whereas the effects of Dw6 on the kernel width were not uniform across three environments. By contrast, lines with Dw6 produced more productive tillers (10.11∼10.53%) than lines without Dw6. All these together suggested the potential yield penalty associated with Dw6 might be partially due to the decrease of kernel weight which is attributed largely to the reduction of kernel length. Eighty-one simple sequence repeat (SSR) primer pairs from chromosome 6D were tested, five of them were polymorphic in two parents and in two contrasting bulks, confirming the 6D location of Dw6. By using the five polymorphic markers, Dw6 was mapped to an interval of 1.0 cM flanked by markers SSR83 and SSR120. Caution should be applied in using this information since maker order conflicts were observed. The close linkages of these two markers to Dw6 were further validated in a range of oat lines. The newly developed markers will provide a solid basis for future efforts both in the identification of Dw6 in oat germplasm and in the determination of the nature of the gene through positional cloning.
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Affiliation(s)
- Honghai Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Kaiquan Yu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yinghong Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pingping Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jun Zhao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ying Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaomeng Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Changzhong Ren
- Baicheng Academy of Agricultural Sciences, Baicheng, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
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Yan H, Ren Z, Deng D, Yang K, Yang C, Zhou P, Wight CP, Ren C, Peng Y. New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum. PLoS One 2021; 16:e0240703. [PMID: 33417607 PMCID: PMC7793304 DOI: 10.1371/journal.pone.0240703] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/21/2020] [Indexed: 11/28/2022] Open
Abstract
The tetraploid Avena species in the section Pachycarpa Baum, including A. insularis, A. maroccana, and A. murphyi, are thought to be involved in the evolution of hexaploid oats; however, their genome designations are still being debated. Repetitive DNA sequences play an important role in genome structuring and evolution, so understanding the chromosomal organization and distribution of these sequences in Avena species could provide valuable information concerning genome evolution in this genus. In this study, the chromosomal organizations and distributions of six repetitive DNA sequences (including three SSR motifs (TTC, AAC, CAG), one 5S rRNA gene fragment, and two oat A and C genome specific repeats) were investigated using non-denaturing fluorescence in situ hybridization (ND-FISH) in the three tetraploid species mentioned above and in two hexaploid oat species. Preferential distribution of the SSRs in centromeric regions was seen in the A and D genomes, whereas few signals were detected in the C genomes. Some intergenomic translocations were observed in the tetraploids; such translocations were also detected between the C and D genomes in the hexaploids. These results provide robust evidence for the presence of the D genome in all three tetraploids, strongly suggesting that the genomic constitution of these species is DC and not AC, as had been thought previously.
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Affiliation(s)
- Honghai Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zichao Ren
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Di Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kehan Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chuang Yang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pingping Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Charlene P. Wight
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Changzhong Ren
- Baicheng Academy of Agricultural Sciences, Baicheng, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- * E-mail:
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Yan H, Zhou P, Peng Y, Bekele WA, Ren C, Tinker NA, Peng Y. Genetic diversity and genome-wide association analysis in Chinese hulless oat germplasm. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3365-3380. [PMID: 32888041 DOI: 10.1007/s00122-020-03674-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/21/2020] [Indexed: 05/12/2023]
Abstract
Genotyping-by-sequencing (GBS)-derived molecular markers reveal the distinct genetic population structure and relatively narrow genetic diversity of Chinese hulless oat landraces. Four markers linked to the naked grain gene (N1) are identified by genome-wide association study (GWAS). Interest in hulless oat (Avena sativa ssp. nuda), a variant of common oat (A. sativa) domesticated in Western Asia, has increased in recent years due to its free-threshing attribute and its domestication history. However, the genetic diversity and population structure of hulless oat, as well as the genetic mechanism of hullessness, are poorly understood. In this study, the genetic diversity and population structure of a worldwide sample of 805 oat lines including 186 hulless oats were investigated using genotyping-by-sequencing. Population structure analyses showed a strong genetic differentiation between hulless landraces vs other oat lines, including the modern hulless cultivars. The distinct subpopulation stratification of hulless landraces and their low genetic diversity suggests that a domestication bottleneck existed in hulless landraces. Additionally, low genetic diversity within European oats and strong differentiation between the spring oats and southern origin oat lines revealed by previous studies were also observed in this study. Genomic regions contributing to these genetic differentiations suggest that genetic loci related to growth habit and stress resistance may have been under intense selection, rather than the hulless-related genomic regions. Genome-wide association analysis detected four markers that were highly associated with hullessness. Three of these were mapped on linkage group Mrg21 at a genetic position between 195.7 and 212.1 cM, providing robust evidence that the dominant N1 locus located on Mrg21 is the single major factor controlling this trait.
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Affiliation(s)
- Honghai Yan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pingping Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yun Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wubishet A Bekele
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave, Ottawa, ON, K1A0C6, Canada
| | - Changzhong Ren
- Baicheng Academy of Agricultural Sciences, Baicheng, 137000, China
| | - Nicholas A Tinker
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, 960 Carling Ave, Ottawa, ON, K1A0C6, Canada.
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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9
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Isidro-Sánchez J, D'Arcy Cusack K, Verheecke-Vaessen C, Kahla A, Bekele W, Doohan F, Magan N, Medina A. Genome-wide association mapping of Fusarium langsethiae infection and mycotoxin accumulation in oat (Avena sativa L.). THE PLANT GENOME 2020; 13:e20023. [PMID: 33016604 DOI: 10.1002/tpg2.20023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/04/2020] [Indexed: 06/11/2023]
Abstract
Fusarium langsethiae is a symptomless pathogen of oat panicles that produces T-2 and HT-2 mycotoxins, two of the most potent trichothecenes produced by Fusarium fungi in cereals. In the last few years, the levels of these mycotoxin in oat grain has increased and the European commission have already recommended a maximum level for of 1000 μg kg-1 for unprocessed oat for human consumption. The optimal and most sustainable way of combating infection and mycotoxin contamination is by releasing resistant oat varieties. Here the objective was to determine if we could identify any genomic loci associated with either the accumulation of F. langsethiae DNA or mycotoxins in the grain. In each of two years, field trials were conducted wherein 190 spring oat varieties were inoculated with a mixture of three isolate of the pathogen. Mycotoxins were quantified using liquid chromatography-tandem mass spectrometry. Varieties were genotyped using 16,863 genotyping by sequencing markers. Genome-wide association studies associated 5 SNPs in the linkage group Mr06 with T-2 + HT-2 mycotoxin accumulation. Markers were highly correlated, and a single QTL was identified. The marker avgbs_6K_95238.1 mapped within genes showing similarity to lipase, lipase-like or lipase precursor mRNA sequences and zinc-finger proteins. These regions have previously been shown to confer a significant increase in resistance to Fusarium species.
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Affiliation(s)
- Julio Isidro-Sánchez
- UCD Agriculture & Food Science, College of Health and Agriculture Science, University College Dublin, Belfield, Dublin, 4, Ireland
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo-UPM, 28223-Pozuelo de Alarcón (Madrid), Spain
| | - Kane D'Arcy Cusack
- UCD Agriculture & Food Science, College of Health and Agriculture Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Carol Verheecke-Vaessen
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Amal Kahla
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Wubishet Bekele
- Ottawa Research and Development Center, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, Ontario, K1A 0C6, Canada
| | - Fiona Doohan
- UCD School of Biology and Environmental Science and Earth Institute, College of Science, University College Dublin, Belfield, Dublin, 4, Ireland
| | - Naresh Magan
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Angel Medina
- Applied Mycology Group, Environment and AgriFood Theme, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
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10
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Zhao J, Kebede AZ, Bekele WA, Menzies JG, Chong J, Mitchell Fetch JW, Tinker NA, Beattie AD, Peng YY, McCartney CA. Mapping of the Oat Crown Rust Resistance Gene Pc39 Relative to Single Nucleotide Polymorphism Markers. PLANT DISEASE 2020; 104:1507-1513. [PMID: 32150502 DOI: 10.1094/pdis-09-19-2002-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Crown rust, caused by Puccinia coronata f. sp. avenae Eriks. (Pca), is among the most important oat diseases resulting in significant yield losses in many growing regions. A gene-for-gene interaction is well established in this pathosystem and has been exploited by oat breeders to control crown rust. Pc39 is a seedling crown rust resistance gene that has been widely deployed in North American oat breeding. DNA markers are desired to accurately predict the specific Pc genes present in breeding germplasm. The objectives of the study were as follows: (i) to map Pc39 in two recombinant inbred line (RIL) populations (AC Assiniboia/MN841801 and AC Medallion/MN841801) and (ii) to identify single nucleotide polymorphism (SNP) markers for postulation of Pc39 in oat germplasm. Pc39 was mapped to a linkage group consisting of 16 SNP markers, which placed the gene on linkage group Mrg11 (chromosome 1C) of the oat consensus map. Pc39 cosegregated with SNP marker GMI_ES01_c12570_390 in the AC Assiniboia/MN841801 RIL population and was flanked by the SNP markers avgbs_126086.1.41 and GMI_ES15_c276_702, with genetic distances of 1.7 and 0.3 cM, respectively. In the AC Medallion/MN841801 RIL population, similar results were obtained but the genetic distances of the flanking markers were 0.4 and 0.4 cM, respectively. Kompetitive Allele-Specific PCR assays were successfully designed for Pc39-linked SNP loci. Two SNP loci defined a haplotype that accurately predicted Pc39 status in a diverse panel of oat germplasm and will be useful for marker-assisted selection in oat breeding.
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Affiliation(s)
- Jun Zhao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Aida Z Kebede
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - James Chong
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
| | - Jennifer W Mitchell Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, Manitoba, Canada
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Aaron D Beattie
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuan-Ying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, Manitoba, Canada
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11
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Blake VC, Woodhouse MR, Lazo GR, Odell SG, Wight CP, Tinker NA, Wang Y, Gu YQ, Birkett CL, Jannink JL, Matthews DE, Hane DL, Michel SL, Yao E, Sen TZ. GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5513438. [PMID: 31210272 DOI: 10.1093/database/baz065] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/18/2019] [Accepted: 04/22/2019] [Indexed: 11/13/2022]
Abstract
GrainGenes (https://wheat.pw.usda.gov or https://graingenes.org) is an international centralized repository for curated, peer-reviewed datasets useful to researchers working on wheat, barley, rye and oat. GrainGenes manages genomic, genetic, germplasm and phenotypic datasets through a dynamically generated web interface for facilitated data discovery. Since 1992, GrainGenes has served geneticists and breeders in both the public and private sectors on six continents. Recently, several new datasets were curated into the database along with new tools for analysis. The GrainGenes homepage was enhanced by making it more visually intuitive and by adding links to commonly used pages. Several genome assemblies and genomic tracks are displayed through the genome browsers at GrainGenes, including the Triticum aestivum (bread wheat) cv. 'Chinese Spring' IWGSC RefSeq v1.0 genome assembly, the Aegilops tauschii (D genome progenitor) Aet v4.0 genome assembly, the Triticum turgidum ssp. dicoccoides (wild emmer wheat) cv. 'Zavitan' WEWSeq v.1.0 genome assembly, a T. aestivum (bread wheat) pangenome, the Hordeum vulgare (barley) cv. 'Morex' IBSC genome assembly, the Secale cereale (rye) select 'Lo7' assembly, a partial hexaploid Avena sativa (oat) assembly and the Triticum durum cv. 'Svevo' (durum wheat) RefSeq Release 1.0 assembly. New genetic maps and markers were added and can be displayed through CMAP. Quantitative trait loci, genetic maps and genes from the Wheat Gene Catalogue are indexed and linked through the Wheat Information System (WheatIS) portal. Training videos were created to help users query and reach the data they need. GSP (Genome Specific Primers) and PIECE2 (Plant Intron Exon Comparison and Evolution) tools were implemented and are available to use. As more small grains reference sequences become available, GrainGenes will play an increasingly vital role in helping researchers improve crops.
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Affiliation(s)
- Victoria C Blake
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Margaret R Woodhouse
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Gerard R Lazo
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Sarah G Odell
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA.,Department of Plant Sciences, University of California, Davis, CA, USA
| | - Charlene P Wight
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Yi Wang
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Yong Q Gu
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Clay L Birkett
- Robert Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - Jean-Luc Jannink
- Robert Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA.,Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Dave E Matthews
- Robert Holley Center, United States Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - David L Hane
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Steve L Michel
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA
| | - Eric Yao
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Taner Z Sen
- Western Regional Research Center, Crop Improvement and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Albany, CA, USA.,Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
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12
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Kebede AZ, Admassu-Yimer B, Bekele WA, Gordon T, Bonman JM, Babiker E, Jin Y, Gale S, Wight CP, Tinker NA, Menzies JG, Beattie AD, Mitchell Fetch J, Fetch TG, Esvelt Klos K, McCartney CA. Mapping of the stem rust resistance gene Pg13 in cultivated oat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:259-270. [PMID: 31637459 DOI: 10.1007/s00122-019-03455-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/09/2019] [Indexed: 05/19/2023]
Abstract
The widely deployed, oat stem rust resistance gene Pg13 was mapped by linkage analysis and association mapping, and KASP markers were developed for marker-assisted selection in breeding programs. Pg13 is one of the most extensively deployed stem rust resistance genes in North American oat cultivars. Identification of markers tightly linked to this gene will be useful for routine marker-assisted selection, identification of gene pyramids, and retention of the gene in backcrosses and three-way crosses. To this end, high-density linkage maps were constructed in four bi-parental mapping populations using SNP markers identified from 6K oat Infinium iSelect and genotyping-by-sequencing platforms. Additionally, genome-wide associations were identified using two sets of association panels consisting of diverse elite oat lines in one set and landrace accessions in the other. The results showed that Pg13 was located at approximately 67.7 cM on linkage group Mrg18 of the consensus genetic map. The gene co-segregated with the 7C-17A translocation breakpoint and with crown rust resistance gene Pc91. Co-segregating markers with the best prediction accuracy were identified at 67.7-68.5 cM on Mrg18. KASP assays were developed for linked SNP loci for use in oat breeding.
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Affiliation(s)
- Aida Z Kebede
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Belayneh Admassu-Yimer
- Small Grains and Potato Germplasm Research Unit, Oak Ridge Institute for Science and Education (ORISE) Research Participant, 1691 South 2700 West, Aberdeen, ID, 83210, USA
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Tyler Gordon
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, 1691 South 2700 West, Aberdeen, ID, 83210, USA
| | - J Michael Bonman
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, 1691 South 2700 West, Aberdeen, ID, 83210, USA
| | - Ebrahiem Babiker
- Southern Horticultural Research Laboratory, USDA-ARS, 810 Hwy 26, West Polarville, MS, 39470-0287, USA
| | - Yue Jin
- Cereal Disease Laboratory, USDA-ARS, 1551 Lindig Street, St. Paul, MN, 55108, USA
| | - Sam Gale
- Cereal Disease Laboratory, USDA-ARS, 1551 Lindig Street, St. Paul, MN, 55108, USA
| | - Charlene P Wight
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada
| | - Jim G Menzies
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| | - Aaron D Beattie
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Jennifer Mitchell Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB, R7C 1A1, Canada
| | - Thomas G Fetch
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, 2701 Grand Valley Road, Brandon, MB, R7C 1A1, Canada
| | - Kathy Esvelt Klos
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, 1691 South 2700 West, Aberdeen, ID, 83210, USA
| | - Curt A McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada.
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13
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Ociepa T, Okoń S, Nucia A, Leśniowska-Nowak J, Paczos-Grzęda E, Bisaga M. Molecular identification and chromosomal localization of new powdery mildew resistance gene Pm11 in oat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:179-185. [PMID: 31570968 PMCID: PMC6952345 DOI: 10.1007/s00122-019-03449-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
The appropriate selection of various traits in valuable plants is very important for modern plant breeding. Effective resistance to fungal diseases, such as powdery mildew, is an example of such a trait in oats. Marker-assisted selection is an important tool that reduces the time and cost of selection. The aims of the present study were the identification of dominant DArTseq markers associated with a new resistance gene, annotated as Pm11 and derived from Avena sterilis genotype CN113536, and the subsequent conversion of these markers into a PCR-based assay. Among the obtained 30,620 silicoDArT markers, 202 markers were highly associated with resistance in the analysed population. Of these, 71 were selected for potential conversion: 42 specific to resistant and 29 to susceptible individuals. Finally, 40 silicoDArT markers were suitable for primer design. From this pool, five markers, 3 for resistant and 2 for susceptible plants, were selected for product amplification in the expected groups. The developed method, based on 2 selection markers, provides certain identification of resistant and susceptible homozygotes. Also, the use of these markers allowed the determination of heterozygotes in the analysed population. Selected silicoDArT markers were also used for chromosomal localization of new resistance genes. Five out of 71 segregating silicoDArT markers for the Pm11 gene were found on the available consensus genetic map of oat. Five markers were placed on linkage groups corresponding to Mrg12 on the Avena sativa consensus map.
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Affiliation(s)
- Tomasz Ociepa
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Sylwia Okoń
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland.
| | - Aleksandra Nucia
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Justyna Leśniowska-Nowak
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Edyta Paczos-Grzęda
- Institute of Plant Genetics, Breeding and Biotechnology, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
| | - Maciej Bisaga
- Department of Cell Biology, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
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14
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Maughan PJ, Lee R, Walstead R, Vickerstaff RJ, Fogarty MC, Brouwer CR, Reid RR, Jay JJ, Bekele WA, Jackson EW, Tinker NA, Langdon T, Schlueter JA, Jellen EN. Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species. BMC Biol 2019; 17:92. [PMID: 31757219 PMCID: PMC6874827 DOI: 10.1186/s12915-019-0712-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/21/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat's adaptive and food quality characteristics. RESULTS The A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species-including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species. CONCLUSIONS The genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.
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Affiliation(s)
- Peter J Maughan
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA.
| | - Rebekah Lee
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
| | - Rachel Walstead
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | | | - Melissa C Fogarty
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
| | - Cory R Brouwer
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Robert R Reid
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Jeremy J Jay
- University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | | | | | | | - Tim Langdon
- IBERS, Aberystwyth University, Aberystwyth, Wales, UK
| | | | - Eric N Jellen
- Department of Plant & Wildlife Sciences, Brigham Young University, 4105 LSB, Provo, UT, 84602, USA
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15
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You Q, Yang X, Peng Z, Islam MS, Sood S, Luo Z, Comstock J, Xu L, Wang J. Development of an Axiom Sugarcane100K SNP array for genetic map construction and QTL identification. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2829-2845. [PMID: 31321474 DOI: 10.1007/s00122-019-03391-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/05/2019] [Indexed: 05/13/2023]
Abstract
An Axiom Sugarcane100K SNP array has been designed and successfully utilized to construct the sugarcane genetic map and to identify the QTLs associated with SCYLV resistance. To accelerate genetic studies in sugarcane, an Axiom Sugarcane100K single-nucleotide polymorphism (SNP) array was designed and customized in this study. Target enrichment sequencing 300 sugarcane accessions selected from the world collection of sugarcane and related grass species yielded more than four million SNPs, from which a total of 31,449 single-dose (SD) SNPs and 68,648 low-dosage (33,277 SD and 35,371 double dose) SNPs from two datasets, respectively, were selected and tiled on Affymetrix Axiom SNP array. Most of selected SNPs (91.77%) were located within genic regions (12,935 genes), with an average of 7.1 SNPs/gene according to sorghum gene models. This array was used to genotype 469 sugarcane clones, including one F1 population derived from the cross between Green German and IND81-146, one selfing population derived from CP80-1827, and 11 diverse sugarcane accessions as controls. Results of genotyping revealed a high polymorphic SNP rate (77.04%) among the 469 samples. Three linkage maps were constructed by using SD SNP markers, including a genetic map for Green German with 3482 SD SNP markers spanning 3336 cM, a map for IND81-146 with 1513 SD SNP markers spanning 2615 cM, and a map for CP80-1827 with 536 SD SNP markers spanning 3651 cM. Quantitative trait loci (QTL) analysis identified 18 QTLs controlling Sugarcane yellow leaf virus resistance segregating in the two mapping populations, harboring 27 disease-resistant genes. This study demonstrated the successful development and utilization of a SNP array as an efficient genetic tool for high-throughput genotyping in highly polyploid sugarcane.
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Affiliation(s)
- Qian You
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | | | - Sushma Sood
- USDA-ARS, Sugarcane Field Station, Canal Point, FL, 33438, USA
| | - Ziliang Luo
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Jack Comstock
- USDA-ARS, Sugarcane Field Station, Canal Point, FL, 33438, USA
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
- Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA.
- Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350001, Fujian, China.
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16
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Liu Q, Li X, Zhou X, Li M, Zhang F, Schwarzacher T, Heslop-Harrison JS. The repetitive DNA landscape in Avena (Poaceae): chromosome and genome evolution defined by major repeat classes in whole-genome sequence reads. BMC PLANT BIOLOGY 2019; 19:226. [PMID: 31146681 PMCID: PMC6543597 DOI: 10.1186/s12870-019-1769-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/09/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Repetitive DNA motifs - not coding genetic information and repeated millions to hundreds of times - make up the majority of many genomes. Here, we identify the nature, abundance and organization of all the repetitive DNA families in oats (Avena sativa, 2n = 6x = 42, AACCDD), a recognized health-food, and its wild relatives. RESULTS Whole-genome sequencing followed by k-mer and RepeatExplorer graph-based clustering analyses enabled assessment of repetitive DNA composition in common oat and its wild relatives' genomes. Fluorescence in situ hybridization (FISH)-based karyotypes are developed to understand chromosome and repetitive sequence evolution of common oat. We show that some 200 repeated DNA motifs make up 70% of the Avena genome, with less than 20 families making up 20% of the total. Retroelements represent the major component, with Ty3/Gypsy elements representing more than 40% of all the DNA, nearly three times more abundant than Ty1/Copia elements. DNA transposons are about 5% of the total, while tandemly repeated, satellite DNA sequences fit into 55 families and represent about 2% of the genome. The Avena species are monophyletic, but both bioinformatic comparisons of repeats in the different genomes, and in situ hybridization to metaphase chromosomes from the hexaploid species, shows that some repeat families are specific to individual genomes, or the A and D genomes together. Notably, there are terminal regions of many chromosomes showing different repeat families from the rest of the chromosome, suggesting presence of translocations between the genomes. CONCLUSIONS The relatively small number of repeat families shows there are evolutionary constraints on their nature and amplification, with mechanisms leading to homogenization, while repeat characterization is useful in providing genome markers and to assist with future assemblies of this large genome (c. 4100 Mb in the diploid). The frequency of inter-genomic translocations suggests optimum strategies to exploit genetic variation from diploid oats for improvement of the hexaploid may differ from those used widely in bread wheat.
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Affiliation(s)
- Qing Liu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
| | - Xiaoyu Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangying Zhou
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingzhi Li
- Genepioneer Biotechnologies Co. Ltd., Nanjing, China
| | - Fengjiao Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Trude Schwarzacher
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - John Seymour Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization / Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
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17
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Mapping Oat Crown Rust Resistance Gene Pc45 Confirms Association with PcKM. G3-GENES GENOMES GENETICS 2019; 9:505-511. [PMID: 30554147 PMCID: PMC6385968 DOI: 10.1534/g3.118.200757] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Molecular mapping of crown rust resistance genes is important to effectively utilize these genes and improve breeding efficiency through marker-assisted selection. Pc45 is a major race-specific crown rust resistance gene initially identified in the wild hexaploid oat Avena sterilis in the early 1970s. This gene was transferred to cultivated oat (Avena sativa) and has been used as a differential for identification of crown rust races since 1974. Previous research identified an association between virulence to Pc45 and PcKM, a crown rust resistance gene in the varieties ‘Kame’ and ‘Morton’. This study was undertaken to reveal the relationship between Pc45 and PcKM. Pc45 was studied in the crosses ‘AC Morgan’/Pc45 and ‘Kasztan’/Pc45, where Pc45 is the differential line carrying Pc45. F2 progenies and F2:3 families of both populations were inoculated with the crown rust isolate CR258 (race NTGG) and single gene segregation ratios were observed. SNP markers for PcKM were tested on these populations and linkage maps were generated. In addition, 17 newly developed SNP markers identified from genotyping-by-sequencing (GBS) data were mapped in these two populations, plus another three populations segregating for Pc45 or PcKM. Pc45 and PcKM mapped to the same location of Mrg08 (chromosome 12D) of the oat chromosome-anchored consensus map. These results strongly suggest that Pc45 and PcKM are the same resistance gene, but allelism (i.e., functionally different alleles of the same gene) or tight linkage (i.e., two tightly linked genes) cannot be ruled out based on the present data.
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18
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Admassu-Yimer B, Bonman JM, Esvelt Klos K. Mapping of crown rust resistance gene Pc53 in oat (Avena sativa). PLoS One 2018; 13:e0209105. [PMID: 30586454 PMCID: PMC6306165 DOI: 10.1371/journal.pone.0209105] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/29/2018] [Indexed: 01/08/2023] Open
Abstract
Crown rust disease caused by the fungus Puccinia coronata f. sp. avenae (Pca) is a major production constraint of oat in North America, Europe, and Australia. There are over 100 genes effective against one or more Pca races, but only a handful of seedling resistance (Pc) genes have been mapped to a known chromosomal location. The goal of the present study was to use linkage mapping to identify the genomic location of the Pc53 gene, and to produce a list of linked SNPs with potential as molecular markers for marker assisted breeding. The Pc53 gene was placed on the linkage group Mrg08 at 82.4 cM using F5-derived recombinant inbred lines (RILs) from a cross between the Pc53 carrier 6-112-1-15 (PI 311624) and the susceptible cultivar Otana. The map location was validated using RILs from a cross between 6-112-1-15 and the Pc50 differential line. Single nucleotide polymorphism marker GMI_ES02_c14533_567 was the closest to Pc53. A major seedling resistance gene 'PcKM' and QTL QcC.Core.08.1, QCr.Core.08.2, QCr.Core.08.3 and QCr.cdl9-12D were previously reported on Mrg08. QPc.Core.08.1 and PcKM were mapped to within 1 cM of Pc53; but previous virulence studies have indicated separate identities. The chromosomal location of Pc53 and SNPs linked with it will facilitate the utilization of Pc53 in oat breeding programs.
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Affiliation(s)
- Belayneh Admassu-Yimer
- Oak Ridge Institute for Science and Education (ORISE) Research Participant, Small Grains and Potato Germplasm Research Unit, Agricultural Research Service, United States Department of Agriculture, Aberdeen, Idaho, United States of America
| | - J. Michael Bonman
- Small Grains and Potato Germplasm Research Unit, Agricultural Research Service, United States Department of Agriculture, Aberdeen, Idaho, United States of America
| | - Kathy Esvelt Klos
- Small Grains and Potato Germplasm Research Unit, Agricultural Research Service, United States Department of Agriculture, Aberdeen, Idaho, United States of America
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19
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Bekele WA, Wight CP, Chao S, Howarth CJ, Tinker NA. Haplotype-based genotyping-by-sequencing in oat genome research. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1452-1463. [PMID: 29345800 PMCID: PMC6041447 DOI: 10.1111/pbi.12888] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/05/2018] [Accepted: 01/10/2018] [Indexed: 05/05/2023]
Abstract
In a de novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel. We then explored potential benefits of SNP vs. TL vs. CL GBS variants for mapping, high-resolution genome analysis and genomic selection in oats. A combined genome-wide association study (GWAS) of heading date from multiple locations using both TL haplotypes and individual SNP markers identified 184 significant associations. A comparative GWAS using TL haplotypes, CL haplotype blocks and their combinations demonstrated the superiority of using TL haplotype markers. Using a principal component-based genome-wide scan, genomic regions containing signatures of selection were identified. These regions may contain genes that are responsible for the local adaptation of oats to Northern American conditions. Genomic selection for heading date using TL haplotypes or SNP markers gave comparable and promising prediction accuracies of up to r = 0.74. Genomic selection carried out in an independent calibration and test population for heading date gave promising prediction accuracies that ranged between r = 0.42 and 0.67. In conclusion, TL haplotype GBS-derived markers facilitate genome analysis and genomic selection in oat.
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Affiliation(s)
- Wubishet A. Bekele
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
| | - Charlene P. Wight
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
| | - Shiaoman Chao
- USDA‐ARS Cereal Crops Research UnitRed River Valley Agricultural Research CenterFargoNDUSA
| | - Catherine J. Howarth
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Nicholas A. Tinker
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
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20
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Zhao J, Tang X, Wight CP, Tinker NA, Jiang Y, Yan H, Ma J, Lan X, Wei Y, Ren C, Chen G, Peng Y. Genetic mapping and a new PCR-based marker linked to a dwarfing gene in oat (Avena sativa L.). Genome 2018; 61:497-503. [PMID: 29733232 DOI: 10.1139/gen-2017-0006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Short straw is a desired trait in cultivated hexaploid oat (Avena sativa L.) for some production environments. Marker-assisted selection, a key tool for achieving this objective, is limited by a lack of mapping data and available markers. Here, bulked-segregant analysis was used to identify PCR-based markers associated with a dwarfing gene. Genetic analysis identified a monogenic dominant inheritance of one dwarfing gene from WAOAT2132, temporarily designated DwWA. A simple sequence repeat (SSR) marker (AME117) that was already available and a new codominant PCR-based marker (bi17) developed by homologous cloning in the present study were both associated with the dwarfing gene. The two markers were located 21 and 1.2 cM from DwWA, respectively. The bi17 marker was mapped to neighboring SNP markers on chromosome 18D of the oat consensus map. Since Dw6 was previously mapped on chromosome 18, and since our new marker bi17 is also diagnostic for NILs generated for Dw6, there is strong evidence that the dwarfing gene identified in WAOAT2132 is Dw6. The newly developed markers could find applications in the identification of this gene in oat germplasm and in the fine mapping or positional cloning of the gene.
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Affiliation(s)
- Jun Zhao
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Xueqin Tang
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China.,b Agricultural Bureau of Xingwen County, Yibin 644400, Sichuan, China
| | - Charlene P Wight
- c Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Nicholas A Tinker
- c Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Yunfeng Jiang
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Honghai Yan
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China.,c Ottawa Research and Development Centre, Agriculture & Agri-Food Canada, Ottawa, ON K1A 0C6, Canada
| | - Jian Ma
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Xiujin Lan
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Yuming Wei
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Changzhong Ren
- d Baicheng Academy of Agricultural Sciences, Baicheng 137000, Jilin, China
| | - Guoyue Chen
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
| | - Yuanying Peng
- a Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, 211 Huimin Road, Chengdu 611130, Sichuan, China
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21
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You Q, Yang X, Peng Z, Xu L, Wang J. Development and Applications of a High Throughput Genotyping Tool for Polyploid Crops: Single Nucleotide Polymorphism (SNP) Array. FRONTIERS IN PLANT SCIENCE 2018; 9:104. [PMID: 29467780 PMCID: PMC5808122 DOI: 10.3389/fpls.2018.00104] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/19/2018] [Indexed: 05/18/2023]
Abstract
Polypoid species play significant roles in agriculture and food production. Many crop species are polyploid, such as potato, wheat, strawberry, and sugarcane. Genotyping has been a daunting task for genetic studies of polyploid crops, which lags far behind the diploid crop species. Single nucleotide polymorphism (SNP) array is considered to be one of, high-throughput, relatively cost-efficient and automated genotyping approaches. However, there are significant challenges for SNP identification in complex, polyploid genomes, which has seriously slowed SNP discovery and array development in polyploid species. Ploidy is a significant factor impacting SNP qualities and validation rates of SNP markers in SNP arrays, which has been proven to be a very important tool for genetic studies and molecular breeding. In this review, we (1) discussed the pros and cons of SNP array in general for high throughput genotyping, (2) presented the challenges of and solutions to SNP calling in polyploid species, (3) summarized the SNP selection criteria and considerations of SNP array design for polyploid species, (4) illustrated SNP array applications in several different polyploid crop species, then (5) discussed challenges, available software, and their accuracy comparisons for genotype calling based on SNP array data in polyploids, and finally (6) provided a series of SNP array design and genotype calling recommendations. This review presents a complete overview of SNP array development and applications in polypoid crops, which will benefit the research in molecular breeding and genetics of crops with complex genomes.
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Affiliation(s)
- Qian You
- Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Liping Xu
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, United States
- Plant Molecular and Cellular Biology Program, Genetics Institute, University of Florida, Gainesville, FL, United States
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Jianping Wang
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22
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Scheben A, Batley J, Edwards D. Revolution in Genotyping Platforms for Crop Improvement. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 164:37-52. [PMID: 29356847 DOI: 10.1007/10_2017_47] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the past decade, the application of high-throughput sequencing to crop genotyping has given rise to novel platforms capable of genotyping tens of thousands of genome-wide DNA markers. Coupled with the decreasing costs of sequencing, this rapid increase in markers allows accelerated and highly accurate genotyping of entire crop populations and diversity sets using single nucleotide polymorphisms (SNPs). These revolutionary advances accelerate crop improvement by facilitating a more precise connection of phenotype to genotype through association studies, linkage mapping and diversity analysis. The platforms driving the advances in genotyping are array technologies and genotyping by sequencing (GBS) methods, which include both low-coverage whole genome resequencing (skim sequencing) and reduced representation sequencing (RRS) approaches. Here, we outline and compare these genotyping platforms and provide a perspective on the promising future of crop genotyping. While SNP arrays provide high quality, simple handling, and unchallenging analysis, the lower cost of RRS and the greater data volume produced by skim sequencing suggest that use of GBS will become more prevalent in crop genomics as sequencing costs decrease and data analysis becomes more streamlined. Graphical Abstract.
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Affiliation(s)
- Armin Scheben
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,Institute of Agriculture, University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia. .,Institute of Agriculture, University of Western Australia, Crawley, WA, Australia.
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23
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Abstract
Genotyping-by-sequencing (GBS) has emerged as a useful genomic approach for sampling genome-wide genetic variation, performing genome-wide association mapping, and conducting genomic selection. It is a combined one-step process of SNP marker discovery and genotyping through genome reduction with restriction enzymes and SNP calling with or without a sequenced genome. This approach has the advantage of being rapid, high throughput, cost effective, and applicable to organisms without sequenced genomes. It has been increasingly applied to generate SNP genotype data for plant genetic and genomic studies. To facilitate a wider GBS application, particularly in oat genetic and genomic research, we describe the GBS approach, review the current applications of GBS in plant species, and highlight some applications of GBS to oat research. We also discuss issues in various applications of GBS and provide some perspectives in GBS research. Recent developments of bioinformatics pipelines in high-quality SNP discovery for polyploid crops will enhance the application of GBS to oat genetic and genomic research.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2.
| | - Mo-Hua Yang
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, Canada, S7N 0X2
- College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
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24
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Fominaya A, Loarce Y, Montes A, Ferrer E. Chromosomal distribution patterns of the (AC) 10 microsatellite and other repetitive sequences, and their use in chromosome rearrangement analysis of species of the genus Avena. Genome 2016; 60:216-227. [PMID: 28156137 DOI: 10.1139/gen-2016-0146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fluorescence in situ hybridization (FISH) was used to determine the physical location of the (AC)10 microsatellite in metaphase chromosomes of six diploid species (AA or CC genomes), two tetraploid species (AACC genome), and five cultivars of two hexaploid species (AACCDD genome) of the genus Avena, a genus in which genomic relationships remain obscure. A preferential distribution of the (AC)10 microsatellite in the pericentromeric and interstitial regions was seen in both the A- and D-genome chromosomes, while in C-genome chromosomes the majority of signals were located in the pericentromeric heterochromatic regions. New large chromosome rearrangements were detected in two polyploid species: an intergenomic translocation involving chromosomes 17AL and 21DS in Avena sativa 'Araceli' and another involving chromosomes 4CL and 21DS in the analyzed cultivars of Avena byzantina. The latter 4CL-21DS intergenomic translocation differentiates clearly between A. sativa and A. byzantina. Searches for common hybridization patterns on the chromosomes of different species revealed chromosome 10A of Avena magna and 21D of hexaploid oats to be very similar in terms of the distribution of 45S and Am1 sequences. This suggests a common origin for these chromosomes and supports a CCDD rather than an AACC genomic designation for this species.
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Affiliation(s)
- Araceli Fominaya
- Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain.,Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain
| | - Yolanda Loarce
- Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain.,Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain
| | - Alexander Montes
- Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain.,Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain
| | - Esther Ferrer
- Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain.,Department of Biomedicine and Biotechnology, 28871 Alcalá de Henares, Madrid, Spain
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25
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Yan H, Bekele WA, Wight CP, Peng Y, Langdon T, Latta RG, Fu YB, Diederichsen A, Howarth CJ, Jellen EN, Boyle B, Wei Y, Tinker NA. High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2133-2149. [PMID: 27522358 PMCID: PMC5069325 DOI: 10.1007/s00122-016-2762-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/02/2016] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.
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Affiliation(s)
- Honghai Yan
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wubishet A Bekele
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Charlene P Wight
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Robert G Latta
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, B3H 4R2, Canada
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Axel Diederichsen
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Catherine J Howarth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, UK
| | - Eric N Jellen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Brian Boyle
- Plateforme d'analyses génomiques, Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, QC, G1V 0A6, Canada
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Nicholas A Tinker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada.
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26
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Gutierrez-Gonzalez JJ, Garvin DF. Subgenome-specific assembly of vitamin E biosynthesis genes and expression patterns during seed development provide insight into the evolution of oat genome. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:2147-2157. [PMID: 27135276 PMCID: PMC5096403 DOI: 10.1111/pbi.12571] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 04/13/2016] [Accepted: 04/23/2016] [Indexed: 05/05/2023]
Abstract
Vitamin E is essential for humans and thus must be a component of a healthy diet. Among the cereal grains, hexaploid oats (Avena sativa L.) have high vitamin E content. To date, no gene sequences in the vitamin E biosynthesis pathway have been reported for oats. Using deep sequencing and orthology-guided assembly, coding sequences of genes for each step in vitamin E synthesis in oats were reconstructed, including resolution of the sequences of homeologs. Three homeologs, presumably representing each of the three oat subgenomes, were identified for the main steps of the pathway. Partial sequences, likely representing pseudogenes, were recovered in some instances as well. Pairwise comparisons among homeologs revealed that two of the three putative subgenome-specific homeologs are almost identical for each gene. Synonymous substitution rates indicate the time of divergence of the two more similar subgenomes from the distinct one at 7.9-8.7 MYA, and a divergence between the similar subgenomes from a common ancestor 1.1 MYA. A new proposed evolutionary model for hexaploid oat formation is discussed. Homeolog-specific gene expression was quantified during oat seed development and compared with vitamin E accumulation. Homeolog expression largely appears to be similar for most of genes; however, for some genes, homoeolog-specific transcriptional bias was observed. The expression of HPPD, as well as certain homoeologs of VTE2 and VTE4, is highly correlated with seed vitamin E accumulation. Our findings expand our understanding of oat genome evolution and will assist efforts to modify vitamin E content and composition in oats.
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Affiliation(s)
| | - David F Garvin
- USDA-ARS Plant Science Research Unit, St. Paul, MN, USA.
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27
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Tumino G, Voorrips RE, Rizza F, Badeck FW, Morcia C, Ghizzoni R, Germeier CU, Paulo MJ, Terzi V, Smulders MJM. Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1711-24. [PMID: 27318699 PMCID: PMC4983288 DOI: 10.1007/s00122-016-2734-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Accepted: 05/21/2016] [Indexed: 05/19/2023]
Abstract
Infinium SNP data analysed as continuous intensity ratios enabled associating genotypic and phenotypic data from heterogeneous oat samples, showing that association mapping for frost tolerance is a feasible option. Oat is sensitive to freezing temperatures, which restricts the cultivation of fall-sown or winter oats to regions with milder winters. Fall-sown oats have a longer growth cycle, mature earlier, and have a higher productivity than spring-sown oats, therefore improving frost tolerance is an important goal in oat breeding. Our aim was to test the effectiveness of a Genome-Wide Association Study (GWAS) for mapping QTLs related to frost tolerance, using an approach that tolerates continuously distributed signals from SNPs in bulked samples from heterogeneous accessions. A collection of 138 European oat accessions, including landraces, old and modern varieties from 27 countries was genotyped using the Infinium 6K SNP array. The SNP data were analyzed as continuous intensity ratios, rather than converting them into discrete values by genotype calling. PCA and Ward's clustering of genetic similarities revealed the presence of two main groups of accessions, which roughly corresponded to Continental Europe and Mediterranean/Atlantic Europe, although a total of eight subgroups can be distinguished. The accessions were phenotyped for frost tolerance under controlled conditions by measuring fluorescence quantum yield of photosystem II after a freezing stress. GWAS were performed by a linear mixed model approach, comparing different corrections for population structure. All models detected three robust QTLs, two of which co-mapped with QTLs identified earlier in bi-parental mapping populations. The approach used in the present work shows that SNP array data of heterogeneous hexaploid oat samples can be successfully used to determine genetic similarities and to map associations to quantitative phenotypic traits.
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Affiliation(s)
- Giorgio Tumino
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands.
| | - Roeland E Voorrips
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Fulvia Rizza
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Franz W Badeck
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Caterina Morcia
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Roberta Ghizzoni
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Christoph U Germeier
- Julius Kühn Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, 06484, Quedlinburg, Germany
| | - Maria-João Paulo
- Biometris, Wageningen UR, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
| | - Valeria Terzi
- Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy
| | - Marinus J M Smulders
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands
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28
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Esvelt Klos K, Huang YF, Bekele WA, Obert DE, Babiker E, Beattie AD, Bjørnstad Å, Bonman JM, Carson ML, Chao S, Gnanesh BN, Griffiths I, Harrison SA, Howarth CJ, Hu G, Ibrahim A, Islamovic E, Jackson EW, Jannink JL, Kolb FL, McMullen MS, Mitchell Fetch J, Murphy JP, Ohm HW, Rines HW, Rossnagel BG, Schlueter JA, Sorrells ME, Wight CP, Yan W, Tinker NA. Population Genomics Related to Adaptation in Elite Oat Germplasm. THE PLANT GENOME 2016; 9. [PMID: 27898836 DOI: 10.3835/plantgenome2015.10.0103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Six hundred thirty five oat ( L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype-phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation ( < 0.0001). Single-locus -statistic () in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24.
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Chaffin AS, Huang YF, Smith S, Bekele WA, Babiker E, Gnanesh BN, Foresman BJ, Blanchard SG, Jay JJ, Reid RW, Wight CP, Chao S, Oliver R, Islamovic E, Kolb FL, McCartney C, Mitchell Fetch JW, Beattie AD, Bjørnstad Å, Bonman JM, Langdon T, Howarth CJ, Brouwer CR, Jellen EN, Klos KE, Poland JA, Hsieh TF, Brown R, Jackson E, Schlueter JA, Tinker NA. A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement. THE PLANT GENOME 2016; 9. [PMID: 27898818 DOI: 10.3835/plantgenome2015.10.0102] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Hexaploid oat ( L., 2 = 6 = 42) is a member of the Poaceae family and has a large genome (∼12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional 9678 markers were placed on this map with a lower degree of certainty. Assignment to physical chromosomes with high confidence was made for nine chromosomes. Comparison of homeologous regions among oat chromosomes and matches to orthologous regions of rice ( L.) reveal that the hexaploid oat genome has been highly rearranged relative to its ancestral diploid genomes as a result of frequent translocations among chromosomes. Heterogeneous chromosome rearrangements among populations were also evident, probably accounting for the failure of some linkage groups to match the consensus. This work contributes to a further understanding of the organization and evolution of hexaploid grass genomes.
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Singh AK, Singh R, Subramani R, Kumar R, Wankhede DP. Molecular Approaches to Understand Nutritional Potential of Coarse Cereals. Curr Genomics 2016; 17:177-92. [PMID: 27252585 PMCID: PMC4869005 DOI: 10.2174/1389202917666160202215308] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 01/01/2023] Open
Abstract
Coarse grains are important group of crops that constitutes staple food for large population residing primarily in the arid and semi-arid regions of the world. Coarse grains are designated as nutri-cereals as they are rich in essential amino acids, minerals and vitamins. In spite of having several nutritional virtues in coarse grain as mentioned above, there is still scope for improvement in quality parameters such as cooking qualities, modulation of nutritional constituents and reduction or elimination of anti-nutritional factors. Besides its use in traditional cooking, coarse grains have been used mainly in the weaning food preparation and other malted food production. Improvement in quality parameters will certainly increase consumer's preference for coarse grains and increase their demand. The overall genetic gain in quality traits of economic importance in the cultivated varieties will enhance their industrial value and simultaneously increase income of farmers growing these varieties. The urgent step for improvement of quality traits in coarse grains requires a detailed understanding of molecular mechanisms responsible for varied level of different nutritional contents in different genotypes of these crops. In this review we have discussed the progresses made in understanding of coarse grain biology with various omics tool coupled with modern breeding approaches and the current status with regard to our effort towards dissecting traits related to improvement of quality and nutritional constituents of grains.
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Affiliation(s)
- Amit Kumar Singh
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajkumar Subramani
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rajesh Kumar
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
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Loarce Y, Navas E, Paniagua C, Fominaya A, Manjón JL, Ferrer E. Identification of Genes in a Partially Resistant Genotype of Avena sativa Expressed in Response to Puccinia coronata Infection. FRONTIERS IN PLANT SCIENCE 2016; 7:731. [PMID: 27303424 PMCID: PMC4885874 DOI: 10.3389/fpls.2016.00731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/12/2016] [Indexed: 05/18/2023]
Abstract
Cultivated oat (Avena sativa), an important crop in many countries, can suffer significant losses through infection by the fungus Puccinia coronata, the causal agent of crown rust disease. Understanding the molecular basis of existing partial resistance to this disease might provide targets of interest for crop improvement programs. A suppressive subtractive hybridization (SSH) library was constructed using cDNA from the partially resistant oat genotype MN841801-1 after inoculation with the pathogen. A total of 929 genes returned a BLASTx hit and were annotated under different GO terms, including 139 genes previously described as participants in mechanisms related to the defense response and signal transduction. Among these were genes involved in pathogen recognition, cell-wall modification, oxidative burst/ROS scavenging, and abscisic acid biosynthesis, as well genes related to inducible defense responses mediated by salicylic and jasmonic acid (although none of which had been previously reported involved in strong responses). These findings support the hypothesis that basal defense mechanisms are the main systems operating in oat partial resistance to P. coronata. When the expression profiles of 20 selected genes were examined at different times following inoculation with the pathogen, the partially resistant genotype was much quicker in mounting a response than a susceptible genotype. Additionally, a number of genes not previously described in oat transcriptomes were identified in this work, increasing our molecular knowledge of this crop.
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Affiliation(s)
- Yolanda Loarce
- Department of Biomedicine and Biotechnology, University of Alcalá Alcalá de Henares, Spain
| | - Elisa Navas
- Department of Biomedicine and Biotechnology, University of Alcalá Alcalá de Henares, Spain
| | - Carlos Paniagua
- Department of Biomedicine and Biotechnology, University of Alcalá Alcalá de Henares, Spain
| | - Araceli Fominaya
- Department of Biomedicine and Biotechnology, University of Alcalá Alcalá de Henares, Spain
| | - José L Manjón
- Department of Life Sciences, University of Alcalá Alcalá de Henares, Spain
| | - Esther Ferrer
- Department of Biomedicine and Biotechnology, University of Alcalá Alcalá de Henares, Spain
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Foresman BJ, Oliver RE, Jackson EW, Chao S, Arruda MP, Kolb FL. Genome-Wide Association Mapping of Barley Yellow Dwarf Virus Tolerance in Spring Oat (Avena sativa L.). PLoS One 2016; 11:e0155376. [PMID: 27175781 PMCID: PMC4866777 DOI: 10.1371/journal.pone.0155376] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/27/2016] [Indexed: 11/18/2022] Open
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.
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Affiliation(s)
- Bradley J. Foresman
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Rebekah E. Oliver
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Eric W. Jackson
- General Mills Crop Bioscience, Manhattan, Kansas, United States of America
| | - Shiaoman Chao
- USDA-ARS Cereal Crops Research Unit, Fargo, North Dakota, United States of America
| | - Marcio P. Arruda
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Frederic L. Kolb
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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Drury C, Dale KE, Panlilio JM, Miller SV, Lirman D, Larson EA, Bartels E, Crawford DL, Oleksiak MF. Genomic variation among populations of threatened coral: Acropora cervicornis. BMC Genomics 2016; 17:286. [PMID: 27076191 PMCID: PMC4831158 DOI: 10.1186/s12864-016-2583-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Background Acropora cervicornis, a threatened, keystone reef-building coral has undergone severe declines (>90 %) throughout the Caribbean. These declines could reduce genetic variation and thus hamper the species’ ability to adapt. Active restoration strategies are a common conservation approach to mitigate species' declines and require genetic data on surviving populations to efficiently respond to declines while maintaining the genetic diversity needed to adapt to changing conditions. To evaluate active restoration strategies for the staghorn coral, the genetic diversity of A. cervicornis within and among populations was assessed in 77 individuals collected from 68 locations along the Florida Reef Tract (FRT) and in the Dominican Republic. Results Genotyping by Sequencing (GBS) identified 4,764 single nucleotide polymorphisms (SNPs). Pairwise nucleotide differences (π) within a population are large (~37 %) and similar to π across all individuals. This high level of genetic diversity along the FRT is similar to the diversity within a small, isolated reef. Much of the genetic diversity (>90 %) exists within a population, yet GBS analysis shows significant variation along the FRT, including 300 SNPs with significant FST values and significant divergence relative to distance. There are also significant differences in SNP allele frequencies over small spatial scales, exemplified by the large FST values among corals collected within Miami-Dade county. Conclusions Large standing diversity was found within each population even after recent declines in abundance, including significant, potentially adaptive divergence over short distances. The data here inform conservation and management actions by uncovering population structure and high levels of diversity maintained within coral collections among sites previously shown to have little genetic divergence. More broadly, this approach demonstrates the power of GBS to resolve differences among individuals and identify subtle genetic structure, informing conservation goals with evolutionary implications.
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Affiliation(s)
- C Drury
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - K E Dale
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - J M Panlilio
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - S V Miller
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - D Lirman
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - E A Larson
- Nova Southeastern University Oceanographic Center, 8000 N Ocean Drive, Dania Beach, FL, 33004, USA
| | - E Bartels
- Center for Coral Reef Research, Mote Marine Laboratory, 24244 Overseas Highway, Summerland Key, FL, 33042, USA
| | - D L Crawford
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - M F Oleksiak
- Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA.
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Menon R, Gonzalez T, Ferruzzi M, Jackson E, Winderl D, Watson J. Oats-From Farm to Fork. ADVANCES IN FOOD AND NUTRITION RESEARCH 2016; 77:1-55. [PMID: 26944101 DOI: 10.1016/bs.afnr.2015.12.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Oats have a long history of use as human food and animal feed. From its origins in the Fertile Crescent, the oat has adapted to a wide range of climatic conditions and geographic regions. Its unique macro-, micro-, and phytonutrient composition, high nutritional value, and relatively low agricultural input requirements makes oats unique among cereal crops. The health benefits of the oats are becoming well established. While the connection between oat β-glucan fiber in reducing the risk of cardiovascular disease and controlling glycemia have been unequivocally established, other potential benefits including modulation of intestinal microbiota and inflammation continue to be explored. Advances in food technology are continuing to expand the diversity of oat-based foods, creating opportunities to deliver the health benefits of oats to a larger segment of the population.
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Affiliation(s)
- Ravi Menon
- The Bell Institute of Health & Nutrition, Minneapolis, MN, United States; General Mills Inc., Minneapolis, MN, United States.
| | - Tanhia Gonzalez
- The Bell Institute of Health & Nutrition, Minneapolis, MN, United States; General Mills Inc., Minneapolis, MN, United States
| | | | - Eric Jackson
- General Mills Inc., Minneapolis, MN, United States
| | - Dan Winderl
- General Mills Inc., Minneapolis, MN, United States
| | - Jay Watson
- General Mills Inc., Minneapolis, MN, United States
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Gnanesh BN, McCartney CA, Eckstein PE, Mitchell Fetch JW, Menzies JG, Beattie AD. Genetic analysis and molecular mapping of a seedling crown rust resistance gene in oat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:247-58. [PMID: 25433497 DOI: 10.1007/s00122-014-2425-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/02/2014] [Indexed: 05/22/2023]
Abstract
Genetic analysis and genome mapping of a major seedling oat crown rust resistance gene, designated PcKM, are described. The chromosomal location of the PcKM gene was identified and linked markers were validated. Crown rust (Puccinia coronata Corda f. sp. avenae Eriks) is the most important foliar disease of oats and can cause considerable yield loss in the absence of appropriate management practices. Utilization of novel resistant genes is the most effective, economic and environmentally sound approach to control the disease. Crown rust resistance present in the cultivar 'Morton' was evaluated in a population developed from the cross OT3019 × 'Morton' to elucidate the genetic basis of resistance. Crown rust reaction evaluated in field nurseries and greenhouse tests demonstrated that resistance provided by 'Morton' was controlled by a single gene, temporarily designated as PcKM. The gene was initially linked to a random amplified polymorphic DNA band and subsequently converted into a sequence characterized amplified region (SCAR) marker. Genotyping with the PcKM SCAR on the 'Kanota' × 'Ogle' population, used to create the first oat chromosome-anchored linkage map, placed the PcKM gene on chromosome 12D. Consensus map markers present in the same region as the PcKM SCAR were tested on the OT3019 × 'Morton' population and two additional phenotyped populations segregating for PcKM to identify other markers useful for marker-assisted selection. Three markers were perfectly linked to the PcKM phenotype from which TaqMan and KBioscience competitive allele-specific PCR assays were developed and validated on a set of 25 oat lines. The assays correctly identified PcKM carriers. The markers developed in this study will facilitate fine mapping of the PcKM gene and simplify selection for this crown rust resistance.
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Affiliation(s)
- Belaghihalli N Gnanesh
- Agriculture and Agri-Food Canada, Cereal Research Centre, 101 Route 100, Morden, MB, R6M 1Y5, Canada
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Babiker EM, Gordon TC, Jackson EW, Chao S, Harrison SA, Carson ML, Obert DE, Bonman JM. Quantitative Trait Loci from Two Genotypes of Oat (Avena sativa) Conditioning Resistance to Puccinia coronata. PHYTOPATHOLOGY 2015; 105:239-45. [PMID: 25121640 DOI: 10.1094/phyto-04-14-0114-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Developing oat cultivars with partial resistance to crown rust would be beneficial and cost-effective for disease management. Two recombinant inbred-line populations were generated by crossing the susceptible cultivar Provena with two partially resistant sources, CDC Boyer and breeding line 94197A1-9-2-2-2-5. A third mapping population was generated by crossing the partially resistant sources to validate the quantitative trait locus (QTL) results. The three populations were evaluated for crown rust severity in the field at Louisiana State University (LSU) in 2009 and 2010 and at the Cereal Disease Laboratory (CDL) in St. Paul, MN, in 2009, 2010, and 2011. An iSelect platform assay containing 5,744 oat single nucleotide polymorphisms was used to genotype the populations. From the 2009 CDL test, linkage analyses revealed two QTLs for partial resistance in the Provena/CDC Boyer population on chromosome 19A. One of the 19A QTLs was also detected in the 2009 LSU test. Another QTL was detected on chromosome 12D in the CDL 2009 test. In the Provena/94197A1-9-2-2-2-5 population, only one QTL was detected, on chromosome 13A, in the CDL 2011 test. The 13A QTL from the Provena/94197A1-9-2-2-2-5 population was validated in the CDC Boyer/94197A1-9-2-2-2-5 population in the CDL 2010 and 2011 tests. Comparative analysis of the significant marker sequences with the rice genome database revealed 15 candidate genes for disease resistance on chromosomes 4 and 6 of rice. These genes could be potential targets for cloning from the two resistant parents.
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Montilla-Bascón G, Rispail N, Sánchez-Martín J, Rubiales D, Mur LAJ, Langdon T, Howarth CJ, Prats E. Genome-wide association study for crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) resistance in an oat (Avena sativa) collection of commercial varieties and landraces. FRONTIERS IN PLANT SCIENCE 2015; 6:103. [PMID: 25798140 PMCID: PMC4350391 DOI: 10.3389/fpls.2015.00103] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/08/2015] [Indexed: 05/19/2023]
Abstract
Diseases caused by crown rust (Puccinia coronata f. sp. avenae) and powdery mildew (Blumeria graminis f. sp. avenae) are among the most important constraints for the oat crop. Breeding for resistance is one of the most effective, economical, and environmentally friendly means to control these diseases. The purpose of this work was to identify elite alleles for rust and powdery mildew resistance in oat by association mapping to aid selection of resistant plants. To this aim, 177 oat accessions including white and red oat cultivars and landraces were evaluated for disease resistance and further genotyped with 31 simple sequence repeat and 15,000 Diversity Arrays Technology (DArT) markers to reveal association with disease resistance traits. After data curation, 1712 polymorphic markers were considered for association analysis. Principal component analysis and a Bayesian clustering approach were applied to infer population structure. Five different general and mixed linear models accounting for population structure and/or kinship corrections and two different statistical tests were carried out to reduce false positive. Five markers, two of them highly significant in all models tested were associated with rust resistance. No strong association between any marker and powdery mildew resistance at the seedling stage was identified. However, one DArT sequence, oPt-5014, was strongly associated with powdery mildew resistance in adult plants. Overall, the markers showing the strongest association in this study provide ideal candidates for further studies and future inclusion in strategies of marker-assisted selection.
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Affiliation(s)
- Gracia Montilla-Bascón
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Nicolas Rispail
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Javier Sánchez-Martín
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Diego Rubiales
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, University of AberystwythAberystwyth, UK
| | - Tim Langdon
- Institute of Biological, Environmental and Rural Sciences, University of AberystwythAberystwyth, UK
| | - Catherine J. Howarth
- Institute of Biological, Environmental and Rural Sciences, University of AberystwythAberystwyth, UK
| | - Elena Prats
- Institute for Sustainable Agriculture – Consejo Superior de Investigaciones CientíficasCórdoba, Spain
- *Correspondence: Elena Prats, Institute for Sustainable Agriculture – Consejo Superior de Investigaciones Científicas, Apartado 4084, E-14080 Córdoba, Spain e-mail:
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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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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, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:787-796. [PMID: 24646323 DOI: 10.1111/pbi.12183/pdf] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/29/2014] [Accepted: 02/05/2014] [Indexed: 05/29/2023]
Abstract
High-density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker-trait associations in mapping experiments. We developed a genotyping array including about 90,000 gene-associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome-wide distributed SNPs that are represented in populations of diverse geographical origin. We used density-based spatial clustering algorithms to enable high-throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model-free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low-intensity clusters can provide insight into the distribution of presence-absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.
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Affiliation(s)
- Shichen Wang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
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40
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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, 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, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E. Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:787-96. [PMID: 24646323 PMCID: PMC4265271 DOI: 10.1111/pbi.12183] [Citation(s) in RCA: 1073] [Impact Index Per Article: 107.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 01/29/2014] [Accepted: 02/05/2014] [Indexed: 05/18/2023]
Affiliation(s)
- Shichen Wang
- Department of Plant Pathology Kansas State University Manhattan KS USA
| | - Debbie Wong
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Kerrie Forrest
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Alexandra Allen
- School of Biological Sciences University of Bristol Bristol UK
| | - Shiaoman Chao
- US Department of Agriculture–Agricultural Research Service Biosciences Research Laboratory Fargo ND USA
| | - Bevan E. Huang
- Commonwealth Scientific and Industrial Research Organization Computational Informatics and Food Futures National Research Flagship Dutton Park Qld Australia
| | - Marco Maccaferri
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Silvio Salvi
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Sara G. Milner
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | - Luigi Cattivelli
- Consiglio per la Ricerca e la sperimentazione in Agricoltura Genomics Research Centre Fiorenzuola d'arda Italy
| | - Anna M. Mastrangelo
- Consiglio per la Ricerca e la sperimentazione in Agricoltura Cereal Research Centre Foggia Italy
| | - Alex Whan
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Stuart Stephen
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Gary Barker
- School of Biological Sciences University of Bristol Bristol UK
| | | | | | - Morten Lillemo
- Department of Plant Sciences Norwegian University of Life Sciences Ås Norway
| | - Diane Mather
- Waite Research Institute School of Agriculture, Food and Wine University of Adelaide Urrbrae SA Australia
| | | | - Rudy Dolferus
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Gina Brown‐Guedira
- US Department of Agriculture–Agricultural Research Service Eastern Regional Small Grains Genotyping Laboratory Raleigh NC USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology and Institute of Evolution University of Haifa Mount Carmel Haifa Israel
| | - Alina R. Akhunova
- K‐State Integrated Genomics Facility Kansas State University Manhattan KS USA
| | - Catherine Feuillet
- INRA – Université Blaise Pascal, UMR 1095 Genetics Diversity and Ecophysiology of Cereals Clermont‐Ferrand France
| | - Jerome Salse
- INRA – Université Blaise Pascal, UMR 1095 Genetics Diversity and Ecophysiology of Cereals Clermont‐Ferrand France
| | - Michele Morgante
- Department of Crop and Environmental Sciences University of Udine Via delle Scienze Udine Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences University of Saskatchewan Saskatoon SK Canada
| | - Ming‐Cheng Luo
- Department of Plant Sciences University of California Davis CA USA
| | - Jan Dvorak
- Department of Plant Sciences University of California Davis CA USA
| | - Matthew Morell
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | - Jorge Dubcovsky
- Department of Plant Sciences University of California Davis CA USA
- Howard Hughes Medical Institute Chevy Chase MD USA
| | | | - Roberto Tuberosa
- Department of Agricultural Sciences University of Bologna Bologna Italy
| | | | | | - Colin Cavanagh
- Commonwealth Scientific and Industrial Research Organization Plant Industry and Food Futures National Research Flagship Canberra ACT Australia
| | | | - Matthew Hayden
- Department of Environment and Primary Industry AgriBioSciences La Trobe R&D Park Bundoora Vic. Australia
| | - Eduard Akhunov
- Department of Plant Pathology Kansas State University Manhattan KS USA
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41
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Huang YF, Poland JA, Wight CP, Jackson EW, Tinker NA. Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PLoS One 2014; 9:e102448. [PMID: 25047601 PMCID: PMC4105502 DOI: 10.1371/journal.pone.0102448] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 06/19/2014] [Indexed: 01/23/2023] Open
Abstract
Advances in next-generation sequencing offer high-throughput and cost-effective genotyping alternatives, including genotyping-by-sequencing (GBS). Results have shown that this methodology is efficient for genotyping a variety of species, including those with complex genomes. To assess the utility of GBS in cultivated hexaploid oat (Avena sativa L.), seven bi-parental mapping populations and diverse inbred lines from breeding programs around the world were studied. We examined technical factors that influence GBS SNP calls, established a workflow that combines two bioinformatics pipelines for GBS SNP calling, and provided a nomenclature for oat GBS loci. The high-throughput GBS system enabled us to place 45,117 loci on an oat consensus map, thus establishing a positional reference for further genomic studies. Using the diversity lines, we estimated that a minimum density of one marker per 2 to 2.8 cM would be required for genome-wide association studies (GWAS), and GBS markers met this density requirement in most chromosome regions. We also demonstrated the utility of GBS in additional diagnostic applications related to oat breeding. We conclude that GBS is a powerful and useful approach, which will have many additional applications in oat breeding and genomic studies.
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Affiliation(s)
- Yung-Fen Huang
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jesse A. Poland
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Charlene P. Wight
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Eric W. Jackson
- General Mills Crop Biosciences, Manhattan, Kansas, United States of America
| | - Nicholas A. Tinker
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- * E-mail:
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42
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Hsam SLK, Mohler V, Zeller FJ. The genetics of resistance to powdery mildew in cultivated oats (Avena sativa L.): current status of major genes. J Appl Genet 2014; 55:155-62. [PMID: 24526453 DOI: 10.1007/s13353-014-0196-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 11/28/2022]
Abstract
The genetics of resistance to powdery mildew caused by Blumeria graminis f. sp. avenae of four cultivated oats was studied using monosomic analysis. Cultivar 'Bruno' carries a gene (Pm6) that shows a recessive mode of inheritance and is located on chromosome 10D. Cultivar 'Jumbo' possesses a dominant resistance gene (Pm1) on chromosome 1C. In cultivar 'Rollo', in addition to the gene Pm3 on chromosome 17A, a second dominant resistance gene (Pm8) was identified and assigned to chromosome 4C. In breeding line APR 122, resistance was conditioned by a dominant resistance gene (Pm7) that was allocated to chromosome 13A. Genetic maps established for resistance genes Pm1, Pm6 and Pm7 employing amplified fragment length polymorphism (AFLP) markers indicated that these genes are independent of each other, supporting the results from monosomic analysis.
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Affiliation(s)
- Sai L K Hsam
- Division of Plant Breeding and Applied Genetics, Technische Universität München, 85354, Freising-Weihenstephan, Germany
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43
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Oat Fungal Diseases and the Application of Molecular Marker Technology for Their Control. Fungal Biol 2014. [DOI: 10.1007/978-1-4939-1188-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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44
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Huang YF, Poland JA, Wight CP, Jackson EW, Tinker NA. Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PLoS One 2014. [PMID: 25047601 DOI: 10.1371/journalpone0102448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023] Open
Abstract
Advances in next-generation sequencing offer high-throughput and cost-effective genotyping alternatives, including genotyping-by-sequencing (GBS). Results have shown that this methodology is efficient for genotyping a variety of species, including those with complex genomes. To assess the utility of GBS in cultivated hexaploid oat (Avena sativa L.), seven bi-parental mapping populations and diverse inbred lines from breeding programs around the world were studied. We examined technical factors that influence GBS SNP calls, established a workflow that combines two bioinformatics pipelines for GBS SNP calling, and provided a nomenclature for oat GBS loci. The high-throughput GBS system enabled us to place 45,117 loci on an oat consensus map, thus establishing a positional reference for further genomic studies. Using the diversity lines, we estimated that a minimum density of one marker per 2 to 2.8 cM would be required for genome-wide association studies (GWAS), and GBS markers met this density requirement in most chromosome regions. We also demonstrated the utility of GBS in additional diagnostic applications related to oat breeding. We conclude that GBS is a powerful and useful approach, which will have many additional applications in oat breeding and genomic studies.
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Affiliation(s)
- Yung-Fen Huang
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jesse A Poland
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Charlene P Wight
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Eric W Jackson
- General Mills Crop Biosciences, Manhattan, Kansas, United States of America
| | - Nicholas A Tinker
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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He X, Skinnes H, Oliver RE, Jackson EW, Bjørnstad A. Linkage mapping and identification of QTL affecting deoxynivalenol (DON) content (Fusarium resistance) in oats (Avena sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2655-70. [PMID: 23959525 DOI: 10.1007/s00122-013-2163-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 07/12/2013] [Indexed: 05/22/2023]
Abstract
Mycotoxins caused by Fusarium spp. is a major concern on food and feed safety in oats, although Fusarium head blight (FHB) is often less apparent than in other small grain cereals. Breeding resistant cultivars is an economic and environment-friendly way to reduce toxin content, either by the identification of resistance QTL or phenotypic evaluation. Both are little explored in oats. A recombinant-inbred line population, Hurdal × Z595-7 (HZ595, with 184 lines), was used for QTL mapping and was phenotyped for 3 years. Spawn inoculation was applied and deoxynivalenol (DON) content, FHB severity, days to heading and maturity (DH and DM), and plant height (PH) were measured. The population was genotyped with DArTs, AFLPs, SSRs and selected SNPs, and a linkage map of 1,132 cM was constructed, covering all 21 oat chromosomes. A QTL for DON on chromosome 17A/7C, tentatively designated as Qdon.umb-17A/7C, was detected in all experiments using composite interval mapping, with phenotypic effects of 12.2–26.6 %. In addition, QTL for DON were also found on chromosomes 5C, 9D, 13A, 14D and unknown_3, while a QTL for FHB was found on 11A. Several of the DON/FHB QTL coincided with those for DH, DM and/or PH. A half-sib population of HZ595, Hurdal × Z615-4 (HZ615, with 91 lines), was phenotyped in 2011 for validation of QTL found in HZ595, and Qdon.umb-17A/7C was again localized with a phenotypic effect of 12.4 %. Three SNPs closely linked to Qdon.umb-17A/7C were identified in both populations, and one each for QTL on 5C, 11A and 13A were identified in HZ595. These SNPs, together with those yet to be identified, could be useful in marker-assisted selection to pyramiding resistance QTL.
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46
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Gutierrez-Gonzalez JJ, Tu ZJ, Garvin DF. Analysis and annotation of the hexaploid oat seed transcriptome. BMC Genomics 2013; 14:471. [PMID: 23845136 PMCID: PMC3720263 DOI: 10.1186/1471-2164-14-471] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 07/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next generation sequencing provides new opportunities to explore transcriptomes. However, challenges remain for accurate differentiation of homoeoalleles and paralogs, particularly in polyploid organisms with no supporting genome sequence. In this study, RNA-Seq was employed to generate and characterize the first gene expression atlas for hexaploid oat. RESULTS The software packages Trinity and Oases were used to produce a transcript assembly from nearly 134 million 100-bp paired-end reads from developing oat seeds. Based on the quality-parameters employed, Oases assemblies were superior. The Oases 67-kmer assembly, denoted dnOST (de novo Oat Seed Transcriptome), is over 55 million nucleotides in length and the average transcript length is 1,043 nucleotides. The 74.8× sequencing depth was adequate to differentiate a large proportion of putative homoeoalleles and paralogs. To assess the robustness of dnOST, we successfully identified gene transcripts associated with the biosynthetic pathways of three compounds with health-promoting properties (avenanthramides, tocols, β-glucans), and quantified their expression. CONCLUSIONS To our knowledge, this study provides the first direct performance comparison between two major assemblers in a polyploid organism. The workflow we developed provides a useful guide for comparable analyses in other organisms. The transcript assembly developed here is a major advance. It expands the number of oat ESTs 3-fold, and constitutes the first comprehensive transcriptome study in oat. This resource will be a useful new tool both for analysis of genes relevant to nutritional enhancement of oat, and for improvement of this crop in general.
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Affiliation(s)
- Juan J Gutierrez-Gonzalez
- USDA-ARS Plant Science Research Unit and Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, MN 55108, USA
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