A molecular marker map in 'Kanota' × 'Ogle' hexaploid oat (<i>Avena</i>spp.) enhanced by additional markers and a robust framework

Wight, Charlene P.; Tinker, Nicholas A.; Kianian, Shahryar F.; Sorrells, Mark E.; O’Donoughue, Louise S.; Hoffman, Donald L.; Groh, S.; Scoles, G. J.; Li, Cheng Dao; Webster, F. H.; Phillips, Ronald L.; Rines, H. W.; Livingston, Suzanne M.; Armstrong, K. C.; Fedak, George; Molnar, Stephen J.

doi:10.1139/g02-099

Cited by 102 publications

(156 citation statements)

References 53 publications

(66 reference statements)

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“…K Pellizzaro et al population encompassed a total genetic distance of 1,397.5 cM (Figure 1). These results are in agreement with the results of molecular mapping previously performed in hexaploid oats (O'Donoughue et al 1995, Wight et al 2003, Zhu and Kaeppler 2003, Tinker et al 2009). The expected number of linkage groups is 21, corresponding to the number of chromosomes in each haploid cell (n) of hexaploid oat.…”

Section: Resultssupporting

confidence: 92%

Genetics and identification of markers linked to multiflorous spikelet in hexaploid oat

Pellizzaro

Nava

Chao

et al. 2016

Crop Breed. Appl. Biotechnol.

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Section: Resultssupporting

confidence: 92%

Genetics and identification of markers linked to multiflorous spikelet in hexaploid oat

Pellizzaro

Nava

Chao

et al. 2016

Crop Breed. Appl. Biotechnol.

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“…This yielded 19 linkage blocks spanning 640 cM. Since A. barbata has 14 chromosome pairs and likely 1600 cM ( Jin et al 2000;Wight et al 2003), our map is clearly a partial map. However, additional AFLP and RAPD loci have so far failed to extend the map coverage (M. Morine, unpublished data).…”

Section: Methodsmentioning

confidence: 91%

Quantitative Trait Locus Mapping of Genes Under Selection Across Multiple Years and Sites inAvena barbata: Epistasis, Pleiotropy, and Genotype-by-Environment Interactions

Latta

Gardner²,

Staples³

2010

Genetics

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The genetic architecture of variation in evolutionary fitness determines the trajectory of adaptive change. We identified quantitative trait loci (QTL) affecting fitness in a mapping population of recombinant inbred lines (RILs) derived from a cross between moist-and dry-associated ecotypes of Avena barbata. We estimated fitness in 179 RILs in each of two natural environments in each of 4 years. Two loci account for over half of the variation in geometric mean fitness across environments. These loci are associated in repulsion phase in the wild ecotypes, suggesting the potential for strong transgressive segregation, but also show significant epistasis giving hybrid breakdown. This epistasis is the result of sharply lower fitness in only one of the recombinant genotypes, suggesting that the loci may contain synergistically acting mutations. Within each trial (year/site combination), we can explain less of the variation than for geometric mean fitness, but the two major loci are associated with variation in fitness in most environments. Tests for pleiotropic effects of QTL on fitness in different environments reveal that the same loci are under selection in all trials. Genotype-by-environment interactions are significant for some loci, but this reflects variation in the strength, not the direction of selection.

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“…Newell et al (2011) explored genome-wide LD in oat and showed that to attain values of r 2 = 0.2 between markers, one marker per centi-Morgan (cM) was needed. The most comprehensive oat map available, 'Kanota' 9 'Ogle,' is 1,890 cM (Wight et al 2003); thus, approximately 2,000 markers would be required to reach an average LD between markers and causal alleles of 0.2. Recent advances in Diversity Array Technology (DArT) markers in oat and current single nucleotide polymorphism (SNP) development can provide such density requirements for oat.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin

et al. 2012

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Detection of quantitative trait loci (QTL) controlling complex traits followed by selection has become a common approach for selection in crop plants. The QTL are most often identified by linkage mapping using experimental F2, backcross, advanced inbred, or doubled haploid families. An alternative approach for QTL detection are genome-wide association studies (GWAS) that use pre-existing lines such as those found in breeding programs. We explored the implementation of GWAS in oat (Avena sativa L.) to identify QTL affecting β-glucan concentration, a soluble dietary fiber with several human health benefits when consumed as a whole grain. A total of 431 lines of worldwide origin were tested over 2 years and genotyped using Diversity Array Technology (DArT) markers. A mixed model approach was used where both population structure fixed effects and pair-wise kinship random effects were included. Various mixed models that differed with respect to population structure and kinship were tested for their ability to control for false positives. As expected, given the level of population structure previously described in oat, population structure did not play a large role in controlling for false positives. Three independent markers were significantly associated with β-glucan concentration. Significant marker sequences were compared with rice and one of the three showed sequence homology to genes localized on rice chromosome seven adjacent to the CslFgene family, known to have β-glucan synthase function. Results indicate that GWAS in oat can be a successful option for QTL detection, more so with future development of higher-density markers. Abstract Detection of quantitative trait loci (QTL) controlling complex traits followed by selection has become a common approach for selection in crop plants. The QTL are most often identified by linkage mapping using experimental F 2 , backcross, advanced inbred, or doubled haploid families. An alternative approach for QTL detection are genome-wide association studies (GWAS) that use pre-existing lines such as those found in breeding programs. We explored the implementation of GWAS in oat (Avena sativa L.) to identify QTL affecting b-glucan concentration, a soluble dietary fiber with several human health benefits when consumed as a whole grain. A total of 431 lines of worldwide origin were tested over 2 years and genotyped using Diversity Array Technology (DArT) markers. A mixed model approach was used where both population structure fixed effects and pair-wise kinship random effects were included. Various mixed models that differed with respect to population structure and kinship were tested for their ability to control for false positives. As expected, given the level of population structure previously described in oat, population structure did not play a large role in controlling for false positives. Three independent markers were significantly associated with b-glucan concentration. Significant marker sequences were compared with rice and one of the three showed sequence hom...

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A molecular marker map in 'Kanota' × 'Ogle' hexaploid oat (Avenaspp.) enhanced by additional markers and a robust framework

Cited by 102 publications

References 53 publications

Genetics and identification of markers linked to multiflorous spikelet in hexaploid oat

Genetics and identification of markers linked to multiflorous spikelet in hexaploid oat

Quantitative Trait Locus Mapping of Genes Under Selection Across Multiple Years and Sites inAvena barbata: Epistasis, Pleiotropy, and Genotype-by-Environment Interactions

Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin

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