Population Structure and Genotype–Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars

Winkler, Louisa; Bonman, J. Michael; Chao, Shiaoman; Admassu-Yimer, Belayneh; Bockelman, Harold E.; Klos, Kathy Esvelt

doi:10.3389/fpls.2016.01077

Cited by 33 publications

(48 citation statements)

References 63 publications

(89 reference statements)

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“…In the tested accessions we did not found any links between genetic and morphological variation. A similar result was obtained in the study of Winkler et al [46]. …”

Section: Discussionsupporting

confidence: 91%

“…Those studies based on bulk samples, so the internal diversity of oat accessions was not evaluated. In the most recent study performed on 1 000 oat accession from NSGC, DNA from only one plantlet per accession was analysed by iSelect 6K beaded chip array [46]. The authors identified as much as 324 lines as duplicates with one or many other lines.…”

Section: Discussionmentioning

confidence: 99%

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Promoting the Use of Common Oat Genetic Resources through Diversity Analysis and Core Collection Construction

et al. 2016

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The assessment of diversity and population structure and construction of a core collection is beneficial for the efficient use and management of germplasm. A unique collection of common oat landraces, cultivated in the temperate climate of central Europe until the end of the twentieth century, is preserved in the Polish gene bank. It consists of 91 accessions that have never been used in breeding programs. In order to optimise the use of this genetic resource, we aimed to: (1) determine genetic and agro-morphological diversity, (2) identify internal genetic variation of the tested accessions, (3) form a core collection and (4) recognise the accessions useful for breeding programs or re-release for cultivation. The collection was screened using ISSR markers (1520 loci) and eight agro-morphological traits. Uniquely, we performed molecular studies based on 24 individuals of every accession instead of bulk samples. Therefore, assessment of the degree of diversity within each population and the identification of overlapping gene pools were possible. The observed internal diversity (Nei unbiased coefficient) was in the range of 0.17–0.31. Based on combined genetic and agro-morphological data, we established the core collection composed of 21 landraces. Due to valuable compositions of important traits, some accessions were also identified as useful for breeding programs. The population structure and principal coordinate analysis revealed two major clusters. Based on the previous results, the accessions classified within the smaller one were identified as obsolete varieties instead of landraces. Our results show that the oat landraces are, in general, resistant to local races of diseases, well adapted to local conditions and, in some cases, yielding at the level of modern varieties. Therefore, in situ conservation of the landraces in the near future may be satisfactory for both farmers and researchers in terms of the genetic resources preservation.

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“…In the tested accessions we did not found any links between genetic and morphological variation. A similar result was obtained in the study of Winkler et al [46]. …”

Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Promoting the Use of Common Oat Genetic Resources through Diversity Analysis and Core Collection Construction

et al. 2016

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“…QTL mapping for plant height is complicated by pleiotropic effects of genes controlling heading date (vernalization requirement and photoperiod sensitivity), as they affect duration of vegetative stage and therefore height of plant. In fact, many studies reported co-localization of QTLs for height with those for heading date or vernalization (Holland et al 1997;De Koeyer et al 2004;Wooten et al 2009;Winkler et al 2016). We also have found that the associations with plant height in Mrg01 and Mrg13 co-mapped with QTLs for heading date previously identified in this collection (Tumino et al 2016) and an association with plant height in Mrg11 co-mapped with a QTL for frost tolerance (Tumino et al 2016).…”

Section: Lodging Tolerance and Plant Heightmentioning

confidence: 52%

“…The recent development of new genomic tools, notably the 6K Infinium SNP array (Tinker et al 2014) and the dense hexaploid oat consensus map (12,000 markers) based on 12 bi-parental populations (Chaffin et al 2016;Yan et al 2016), have made it possible to map oat traits at a high resolution (Esvelt Klos et al 2016). Winkler et al (2016) used the array for a genome-wide association study (GWAS) in a diverse panel of oat accessions from the USDA National Small Grains Collection, assembled to represent a gene pool relatively unaffected by 20th century breeding activities, but failed to find significant associations for lodging tolerance.…”

Section: Introductionmentioning

confidence: 99%

“…Winkler et al (2016) used the array for a genome-wide association study (GWAS) in a diverse panel of oat accessions from the USDA National Small Grains Collection, assembled to represent a gene pool relatively unaffected by 20th century breeding activities, but failed to find significant associations for lodging tolerance. In the present work we used this map and SNP array for a GWAS for lodging tolerance in a new European oat collection, established by the AVEQ project (http://aveq.jki.…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide association analysis for lodging tolerance and plant height in a diverse European hexaploid oat collection

Tumino

Voorrips

Morcia³

et al. 2017

Euphytica

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Sensitivity to lodging of oat varieties has been reduced in the last decades through the introduction of dwarfing genes. However, lodging may still cause significant yield loss, underscoring the need for new oat varieties with higher levels of lodging tolerance. In the present study, we analysed lodging and plant height in a collection of European oat accessions including landraces, old and modern varieties, in order to perform a genome-wide association study (GWAS) for identifying markers associated to lodging tolerance. This collection has been recently genotyped by the Infinium 6K SNP array for oat and SNP data were analysed as continuous intensity ratios, rather than as discrete genotypes (Tumino et al. 2016, Theor Appl Genet 129, pp. 1711-1724). Phenotypes for lodging severity, plant height and growth habit were collected under natural conditions in eight European countries. Plant height correlated to lodging severity as previously observed in many studies, explaining about 30% of lodging variation. GWAS analyses detected six significant associations for lodging and two for plant height. These results indicate that GWAS can successfully be used for identifying markers associated to lodging in oat, even though lodging is a quantitative trait influenced by several plant characteristics.

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Mapping crown rust resistance at multiple time points in elite oat germplasm

et al. 2020

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Crown rust, caused by Puccinia coronata f. sp. avenae Erikss., is the most important disease impacting cultivated oat (Avena sativa L.). Genetic resistance is the most desirable management strategy. The genetic architecture of crown rust resistance is not fully understood, and previous mapping investigations have mostly ignored temporal variation. A collection of elite oat lines sourced from oat breeding programs in the American Upper Midwest and Canada was genotyped using a high-density genotyping-by-sequencing system and evaluated for crown rust disease severity at multiple time points throughout the growing season in three disease nursery environments. Genome-wide association mapping was conducted for disease severity on each observation date of each trial, area under the disease progress curve for each trial, heading date for each trial, and area under the disease progress curve in a multienvironment model. Crown rust resistance quantitative trait loci (QTL) were detected on linkage groups Mrg05, Mrg12, Mrg15, Mrg18, Mrg20, and Mrg33. None of these QTL were coincident with a days-to-heading QTL detected on Mrg02. Only the QTL detected on Mrg15 was detected in multiple mapping models. The QTL on Mrg05, Mrg12, Mrg18, Mrg20, and Mrg33 were detected on only a single observation date and were not detected on observations just days before and after. This result uncovers the importance of temporal variation in mapping experiments which is usually ignored. It is possible that high density temporal data could be used to more precisely characterize the nature of plant resistance in other systems.

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Population Structure and Genotype–Phenotype Associations in a Collection of Oat Landraces and Historic Cultivars

Cited by 33 publications

References 63 publications

Promoting the Use of Common Oat Genetic Resources through Diversity Analysis and Core Collection Construction

Promoting the Use of Common Oat Genetic Resources through Diversity Analysis and Core Collection Construction

Genome-wide association analysis for lodging tolerance and plant height in a diverse European hexaploid oat collection

Mapping crown rust resistance at multiple time points in elite oat germplasm

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