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Agro-morphological and genetic variability analysis in oat germplasms with special emphasis on food and feed. PLoS One 2023; 18:e0280450. [PMID: 36753474 PMCID: PMC9907803 DOI: 10.1371/journal.pone.0280450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/02/2023] [Indexed: 02/09/2023] Open
Abstract
The gaining attention of underutilized oat crops for both food and feed, mining of quality and yield related genes/QTLs from available germplasms of oat is need of the hour. The large family of grasses has a vast number of germplasms that could be harnessed for bio-prospecting. The selection of cross-compatible oat germplasms by molecular markers could be used for the introgression of the novel traits into the elite background of oats. The process needs a thorough study of genetic diversity to see the evolutionary relatedness among germplasms. Considering this, in the present study, the genetic diversity of 38 oat germplasms with 12 agro-morphological traits was carried out using 22 Inter Simple Sequence Repeat (ISSR) markers. We found a high level of polymorphism and 158 distinctive alleles; on average 7.18 alleles per primer, further, high-yielding genotypes were identified with the help of phenotypic data and genetic diversity was analyzed by using DNA fingerprint-based principal component analysis, UPGMA dendrogram. Among these 38 germplasms; eight were identified as superior under high grain yield (OS-424, OS-403, NDO-1101, OL-10, UPO-212, OS-405, OS-6, and OS-346) and another eight germplasms were identified as superior for the high fresh weight (for fodder purpose, NDO-711, RO-19, OL-14, OL-1760/OL-11, NDO-10, UPO-212, UPO-06-1, and RO-11-1). These results suggest that germplasms that are closely related (Cross-compatible) and have good potential for desirable traits could be used for varietal development by using marker-assisted selection.
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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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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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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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Sharma P, Tiwari S, Tripathi N, Mehta AK. Polymorphism analysis in advanced mutant population of oat (Avena sativa L.) using ISSR markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:115-120. [PMID: 27186025 PMCID: PMC4840139 DOI: 10.1007/s12298-015-0333-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/16/2015] [Accepted: 12/06/2015] [Indexed: 06/05/2023]
Abstract
Present investigation was carried out to evaluate genetic diversity among 38 M6 population of oat cv. JO-1. To validate the observed morpho-physiological variations, these lines were analyzed with 21 ISSR primers. A total of 132 loci were amplified by these 21 ISSR markers and 116 loci were found to be polymorphic (87.87 %). The genetic similarity coefficient values among 39 oat genotypes based on ISSR analysis ranged from 0.305 to 0.957. The cluster analysis divided the oat genotypes into two groups. Mutants JMO 81 and JMO 82 were found to be most divergent, hence can be used as parents in breeding program for the development of superior cultivars.
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Affiliation(s)
- Pawan Sharma
- />Biotechnology Centre, Jawaharlal Nehru Agricultural University, Jabalpur, 482004 India
| | - Sharad Tiwari
- />Biotechnology Centre, Jawaharlal Nehru Agricultural University, Jabalpur, 482004 India
| | - Niraj Tripathi
- />Biotechnology Centre, Jawaharlal Nehru Agricultural University, Jabalpur, 482004 India
| | - Anoop K. Mehta
- />Department of Agronomy, Jawaharlal Nehru Agricultural University, Jabalpur, 482004 India
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Yan H, Baum BR, Zhou P, Zhao J, Wei Y, Ren C, Xiong F, Liu G, Zhong L, Zhao G, Peng Y. Genetic diversity of seed storage proteins in diploid, tetraploid and hexaploid Avena species. Isr J Ecol Evol 2014. [DOI: 10.1080/15659801.2014.949114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Genetic diversities of 106 Avena accessions, including diploid, tetraploid and hexaploid species, derived from different countries were characterized based on seed storage proteins polymorphism using SDS-PAGE. A total of 24 protein bands and 72 protein patterns were detected in all 106 accessions. The genetic similarity value varied from 0.50 to 1.00. The seed storage protein patterns were largely independent of environmental fluctuation. Accessions of the same species or with identical genome constitutions had the same or similar protein patterns. Relatively lower within-species variations were observed compared with among-species variations. The AACCDD genome hexaploid species and the AA genome diploid species were more divergent than other species, with percentages of polymorphic bands of 85.7% and 61.1% respectively. In the AA genome diploid species, the AsAs genome diploids displayed higher variations than the modified AA genome diploid species. Clustering results showed a close relationship between the hexaploid species and the AACC genome tetraploid species. The AABB genome tetraploid species were similar to the AsAs genome diploid species, with the exception of the species A. agadiriana with AABB genome constitution, which showed a close relationship with the AcAc genome diploid species A. canariensis and the polyploid species carrying the A and C genomes.
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Affiliation(s)
- Honghai Yan
- Triticeae Research Institute, Sichuan Agricultural University
| | - B. R. Baum
- Agricultural & Agri-Food Canada,Eastern Cereal and Oilseed Research Centre
| | - Pingping Zhou
- Triticeae Research Institute, Sichuan Agricultural University
| | - Jun Zhao
- Triticeae Research Institute, Sichuan Agricultural University
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University
| | | | | | - Gang Liu
- Liangshan Academy of Agricultural Sciences
| | - Lin Zhong
- Liangshan Academy of Agricultural Sciences
| | - Gang Zhao
- College of Biological Industry, Chengdu University
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University
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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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Oliver RE, Tinker NA, Lazo GR, Chao S, Jellen EN, Carson ML, Rines HW, Obert DE, Lutz JD, Shackelford I, Korol AB, Wight CP, Gardner KM, Hattori J, Beattie AD, Bjørnstad Å, Bonman JM, Jannink JL, Sorrells ME, Brown-Guedira GL, Mitchell Fetch JW, Harrison SA, Howarth CJ, Ibrahim A, Kolb FL, McMullen MS, Murphy JP, Ohm HW, Rossnagel BG, Yan W, Miclaus KJ, Hiller J, Maughan PJ, Redman Hulse RR, Anderson JM, Islamovic E, Jackson EW. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS One 2013; 8:e58068. [PMID: 23533580 PMCID: PMC3606164 DOI: 10.1371/journal.pone.0058068] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 01/30/2013] [Indexed: 11/19/2022] Open
Abstract
A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.
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Affiliation(s)
- Rebekah E. Oliver
- General Mills Crop Biosciences, Kannapolis, North Carolina, United States of America
| | - Nicholas A. Tinker
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- * E-mail:
| | - Gerard R. Lazo
- Western Regional Research Center, Genomics and Gene Discovery, United States Department of Agriculture - Agricultural Research Service, Albany, California, United States of America
| | - Shiaoman Chao
- Biosciences Research Lab, United States Department of Agriculture - Agricultural Research Service, Fargo, North Dakota, United States of America
| | - Eric N. Jellen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Martin L. Carson
- Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service, Saint Paul, Minnesota, United States of America
| | - Howard W. Rines
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Donald E. Obert
- Limagrain Cereal Seeds, Lafayette, Indiana, United States of America
| | - Joseph D. Lutz
- General Mills Crop Biosciences, Kannapolis, North Carolina, United States of America
| | - Irene Shackelford
- Small Grains and Potato Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service, Aberdeen, Idaho, United States of America
| | - Abraham B. Korol
- Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Haifa, Israel
| | - Charlene P. Wight
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Kyle M. Gardner
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jiro Hattori
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Aaron D. Beattie
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Åsmund Bjørnstad
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - J. Michael Bonman
- Small Grains and Potato Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service, Aberdeen, Idaho, United States of America
| | - Jean-Luc Jannink
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture - Agricultural Research Service, Ithaca, New York, United States of America
| | - Mark E. Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Gina L. Brown-Guedira
- Eastern Regional Small Grains Genotyping Laboratory, North Carolina State University, United States Department of Agriculture - Agricultural Research Service, Raleigh, North Carolina, United States of America
| | | | - Stephen A. Harrison
- School of Plant, Environmental and Soil Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Catherine J. Howarth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - Amir Ibrahim
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Frederic L. Kolb
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Michael S. McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - J. Paul Murphy
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Herbert W. Ohm
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Brian G. Rossnagel
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Weikai Yan
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Kelci J. Miclaus
- JMP, SAS Institute Incorporated, Cary, North Carolina, United States of America
| | - Jordan Hiller
- JMP, SAS Institute Incorporated, Cary, North Carolina, United States of America
| | - Peter J. Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Rachel R. Redman Hulse
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Joseph M. Anderson
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Emir Islamovic
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Eric W. Jackson
- General Mills Crop Biosciences, Kannapolis, North Carolina, United States of America
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Wu B, Zhang Z, Chen L, He M. Isolation and characterization of novel microsatellite markers for Avena sativa (Poaceae) (oat). AMERICAN JOURNAL OF BOTANY 2012; 99:e69-e71. [PMID: 22275767 DOI: 10.3732/ajb.1100404] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
PREMISE OF THE STUDY A new set of microsatellite primers was developed for Avena sativa and characterized to assess the level of genetic diversity among cultivars and wild genotypes. METHODS AND RESULTS Using an enrichment genomic library, 14 simple sequence repeat markers were identified. The loci of these markers were characterized and found to be polymorphic in size among 48 genotypes of oat from diverse geographical locations. The number of alleles per locus ranged from two to eight, while the observed heterozygosity ranged from 0.031 to 0.75. CONCLUSIONS These newly identified microsatellite markers will facilitate genetic diversity studies, fingerprinting, and genetic mapping of oat. Moreover, these new primers for A. sativa will aid future studies of polyploidy and hybridization in other species in this genus.
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Affiliation(s)
- Bin Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No.12 Zhongguancun South Street, Beijing 100081, China
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Oliver RE, Jellen EN, Ladizinsky G, Korol AB, Kilian A, Beard JL, Dumlupinar Z, Wisniewski-Morehead NH, Svedin E, Coon M, Redman RR, Maughan PJ, Obert DE, Jackson EW. New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1159-71. [PMID: 21805339 DOI: 10.1007/s00122-011-1656-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 07/09/2011] [Indexed: 05/22/2023]
Abstract
Nutritional benefits of cultivated oat (Avena sativa L., 2n = 6x = 42, AACCDD) are well recognized; however, seed protein levels are modest and resources for genetic improvement are scarce. The wild tetraploid, A. magna Murphy et Terrell (syn A. maroccana Gdgr., 2n = 4x = 28, CCDD), which contains approximately 31% seed protein, was hybridized with cultivated oat to produce a domesticated A. magna. Wild and cultivated accessions were crossed to generate a recombinant inbred line (RIL) population. Although these materials could be used to develop domesticated, high-protein oat, mapping and quantitative trait loci introgression is hindered by a near absence of genetic markers. Objectives of this study were to develop high-throughput, A. magna-specific markers; generate a genetic linkage map based on the A. magna RIL population; and map genes controlling oat domestication. A Diversity Arrays Technology (DArT) array derived from 10 A. magna genotypes was used to generate 2,688 genome-specific probes. These, with 12,672 additional oat clones, produced 2,349 polymorphic markers, including 498 (21.2%) from A. magna arrays and 1,851 (78.8%) from other Avena libraries. Linkage analysis included 974 DArT markers, 26 microsatellites, 13 SNPs, and 4 phenotypic markers, and resulted in a 14-linkage-group map. Marker-to-marker correlation coefficient analysis allowed classification of shared markers as unique or redundant, and putative linkage-group-to-genome anchoring. Results of this study provide for the first time a collection of high-throughput tetraploid oat markers and a comprehensive map of the genome, providing insights to the genome ancestry of oat and affording a resource for study of oat domestication, gene transfer, and comparative genomics.
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Affiliation(s)
- R E Oliver
- USDA-ARS Small Grains and Potato Germplasm Research Unit, Aberdeen, ID, USA
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11
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Oliver RE, Lazo GR, Lutz JD, Rubenfield MJ, Tinker NA, Anderson JM, Wisniewski Morehead NH, Adhikary D, Jellen EN, Maughan PJ, Brown Guedira GL, Chao S, Beattie AD, Carson ML, Rines HW, Obert DE, Bonman JM, Jackson EW. Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology. BMC Genomics 2011; 12:77. [PMID: 21272354 PMCID: PMC3041746 DOI: 10.1186/1471-2164-12-77] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 01/27/2011] [Indexed: 11/16/2022] Open
Abstract
Background Genetic markers are pivotal to modern genomics research; however, discovery and genotyping of molecular markers in oat has been hindered by the size and complexity of the genome, and by a scarcity of sequence data. The purpose of this study was to generate oat expressed sequence tag (EST) information, develop a bioinformatics pipeline for SNP discovery, and establish a method for rapid, cost-effective, and straightforward genotyping of SNP markers in complex polyploid genomes such as oat. Results Based on cDNA libraries of four cultivated oat genotypes, approximately 127,000 contigs were assembled from approximately one million Roche 454 sequence reads. Contigs were filtered through a novel bioinformatics pipeline to eliminate ambiguous polymorphism caused by subgenome homology, and 96 in silico SNPs were selected from 9,448 candidate loci for validation using high-resolution melting (HRM) analysis. Of these, 52 (54%) were polymorphic between parents of the Ogle1040 × TAM O-301 (OT) mapping population, with 48 segregating as single Mendelian loci, and 44 being placed on the existing OT linkage map. Ogle and TAM amplicons from 12 primers were sequenced for SNP validation, revealing complex polymorphism in seven amplicons but general sequence conservation within SNP loci. Whole-amplicon interrogation with HRM revealed insertions, deletions, and heterozygotes in secondary oat germplasm pools, generating multiple alleles at some primer targets. To validate marker utility, 36 SNP assays were used to evaluate the genetic diversity of 34 diverse oat genotypes. Dendrogram clusters corresponded generally to known genome composition and genetic ancestry. Conclusions The high-throughput SNP discovery pipeline presented here is a rapid and effective method for identification of polymorphic SNP alleles in the oat genome. The current-generation HRM system is a simple and highly-informative platform for SNP genotyping. These techniques provide a model for SNP discovery and genotyping in other species with complex and poorly-characterized genomes.
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Affiliation(s)
- Rebekah E Oliver
- USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, ID, USA
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