Molecular and comparative mapping for heading date and plant height in oat

Zimmer, Cristiano Mathias; Ubert, I. P.; Pacheco, Marcelo Teixeira; Federizzi, Luiz Carlos

doi:10.1007/s10681-018-2182-7

Cited by 15 publications

(22 citation statements)

References 28 publications

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“…The marker GMI_ES_CC4504_192 located at 30.1 cM on Mrg02, associated with DTF and PH in the present study, was strongly associated with heading date at 10 locations across 2 years using a diversity panel comprising of 635 oat lines (Bekele et al, ; Esvelt Klos et al, ). The same region was also linked with QTL influencing flowering time in two bi‐parental mapping populations, each having parents of southern oat origin (Sunstrum et al, ; Zimmer, Ubert, Pacheco, & Federizzi, ). Several loci contributing to variation in flowering were identified on Mrg02 using bi‐parental populations, at locations ranging from 29.1 to 34.1 cM and 71.6 to 85.2 cM (De Koeyer et al, ; Esvelt Klos et al, ; Holland, Portyanko, Hoffman, & Lee, ; Locatelli et al, ; Siripoonwiwat et al, ) and a candidate gene, VRN3 , the orthologue of HD1 in rice ( Oryza sativa L.) or FT in Arabidopsis thaliana (L.) Heynh.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of agronomic performance and exploratory genome‐wide association study of a diverse oat panel for forage use in Taiwan

et al. 2020

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Oats (Avena sativa L.) ranks seventh among cereals in the world in terms of overall production (Food and Agriculture Organization Statistics, FAOSTAT, 2017) and is known for grain that is high in protein, soluble fiber and antioxidants (Welch, 2011). Oat can also be grown as a forage which can be grazed, cut-and-carried and made into silage or hay (Reynolds, 2004). Oat forage is high in protein, water-soluble carbohydrate and digestible neutral dietary fiber

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Section: Discussionmentioning

confidence: 99%

Evaluation of agronomic performance and exploratory genome‐wide association study of a diverse oat panel for forage use in Taiwan

et al. 2020

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“…The cultivated hexaploid oat, Avena sativa L. (2n = 6x = 42, genomes AACCDD), is the sixth most important cereal crop cultivated worldwide [ 1 ]. The superior nutraceutical properties of the oat grain have attracted considerable attention from both breeders and consumers [ 2 ]. The genus Avena L. comprises a number of closely related species with a basic chromosome number of seven, and includes diploids, tetraploids, and hexaploids [ 3 ].…”

Section: Introductionmentioning

confidence: 99%

New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum

et al. 2021

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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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“…c :* indicated markers having P-value below Bonferroni threshold. d : 1, ( Holland et al 1997 ); 2, ( Huang et al 2020 ); 3, ( Siripoonwiwat et al 1996 ); 4, ( Sunstrum et al 2019 ); 5, ( Wooten et al 2009 ); 6, ( Beer et al 1997 ); 7, ( Herrmann et al 2014 ); 8, ( Zimmer et al 2018 ). †: associated SNPs identified on Aberdeen replicate.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Association Study Reveals the Genetic Architecture of Seed Vigor in Oats

Huang

Klos

Huang

2020

G3 Genes|Genomes|Genetics

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Seed vigor is crucial for crop early establishment in the field and is particularly important for forage crop production. Oat (Avena sativa L.) is a nutritious food crop and also a valuable forage crop. However, little is known about the genetics of seed vigor in oats. In order to investigate seed vigor-related traits and their genetic architecture in oats, we developed an easy-to-implement image-based phenotyping pipeline and applied it to 650 elite oat lines from the Collaborative Oat Research Enterprise (CORE). Root number, root surface area, and shoot length were measured in two replicates. Variables such as growth rate were derived. Using a genome-wide association (GWA) approach, we identified 34 and 16 unique loci associated with root traits and shoot traits, respectively, which corresponded to 41 and 16 unique SNPs at a false discovery rate < 0.1. Nine root-associated loci were organized into four sets of homoeologous regions, while nine shoot-associated loci were organized into three sets of homoeologous regions. The context sequences of five trait-associated markers matched to the sequences of rice, Brachypodium and maize (E-value < 10-10), including three markers matched to known gene models with potential involvement in seed vigor. These were a glucuronosyltransferase, a mitochondrial carrier protein domain containing protein, and an iron-sulfur cluster protein. This study presents the first GWA study on oat seed vigor and data of this study can provide guidelines and foundation for further investigations.

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Molecular and comparative mapping for heading date and plant height in oat

Cited by 15 publications

References 28 publications

Evaluation of agronomic performance and exploratory genome‐wide association study of a diverse oat panel for forage use in Taiwan

Evaluation of agronomic performance and exploratory genome‐wide association study of a diverse oat panel for forage use in Taiwan

New evidence confirming the CD genomic constitutions of the tetraploid Avena species in the section Pachycarpa Baum

Genome-Wide Association Study Reveals the Genetic Architecture of Seed Vigor in Oats

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