The art of attrition: development of robust oat microsatellites

Dumlupınar, Ziya; Brown, Raymond S.; Campbell, R D; Jellen, Eric N.; Anderson, Joe; Bonman, J. Michael; Carson, M. L.; Chao, Shiaoman; Obert, D. E.; Jackson, Eric W.

doi:10.1111/pbr.12362

Cited by 9 publications

(8 citation statements)

References 49 publications

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“…In the study, 13 genotypes obtained from reciprocal crosses of B28 and Kunduru-1149 and the parents were used as plant material. Seeds of the genotypes were planted and two leaves seedling were harvested to extract DNAs (Dumlupinar, 2016). The DNA content and purity were determined by spectrophotometer (Thermo-Scientific Nanodrop 2000 spectrophotometer).…”

Section: Methodsmentioning

confidence: 99%

B28×Kunduru-1149 Resiproklu Melez Popülasyonundan Elde Edilen F5 Bireylerinin Fonksiyonel Markörlerle Değerlendirilmesi

Aydemir

Dumlupınar

Yüce

et al. 2020

Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi

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In the study, B28 and Kunduru-1149 durum wheat genotypes were crossed as reciprocal in 2012-2013 cropping season. 13 (B28/Kunduru-1149 and Kunduru-1149/B28) reciprocal crosses were obtained and were used as materials at F5 stage. The cross combinations and the parents were screened with 10 DNA markers to determine alleles of gluten strength (Bx7 OE ), Yellow rust (Sun104, Xgwm18, Xwgp115 and Xgwm47), stem rust (Sun209 and Sun479), high protein ratio (UHW89), powdery mildew (Xgwm66) and leaf rust (Xgwm130). In the study, the average polymorphism information content (PIC) was calculated as 0.98 and the lowest PIC value was obtained from Xwgp115 marker with 0.96, while the rest of the markers had 0.99 PIC values. Stem rust resistance allele Sr49 was detected in B28/Kunduru-1149_F5_4 (Sun479) and B28/Kunduru-1149_F5_1 (Sun209) genotypes. One of the yellow rust resistance alleles Yr15 (Xgwm18) was detected in B28/Kunduru-1149_F5_2 and B28/Kunduru-1149_F5_3 genotypes, while Yr51 (Sun104) was identified in B28/Kunduru-1149_F5_3, B28/Kunduru-1149_F5_6, B28/Kunduru-1149_F5_7, Kunduru-1149/B28_F5_2 and Kunduru-1149/B28_F5_6 genotypes. A dendrogram was created to determine kinship of the individuals with the parents. The highest genetic similarity was observed between B28 / Kunduru-1149_F5_6 and Kunduru-1149 / B28_F5_2 genotypes with 0.714, while the most diverse ones were Kunduru-1149 and B28/Kunduru_F5_7 with 0.10.

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Section: Methodsmentioning

confidence: 99%

B28×Kunduru-1149 Resiproklu Melez Popülasyonundan Elde Edilen F5 Bireylerinin Fonksiyonel Markörlerle Değerlendirilmesi

Aydemir

Dumlupınar

Yüce

et al. 2020

Kahramanmaraş Sütçü İmam Üniversitesi Tarım Ve Doğa Dergisi

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“…Short microsatellite tandems are commonly used as genetic markers for the study of many species. In Avena they have been used to infer genetic relationships within species, among closely related species [44] and in the construction of linkage maps [45][46][47]. Since microsatellites can also organize themselves into large arrays containing thousands of units, they can also be used as physical markers.…”

Section: Introductionmentioning

confidence: 99%

Cytogenetic evidence supports Avena insularis being closely related to hexaploid oats

et al. 2021

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Cytogenetic observations, phylogenetic studies and genome analysis using high-density genetic markers have suggested a tetraploid Avena species carrying the C and D genomes (formerly C and A) to be the donor of all hexaploid oats (AACCDD). However, controversy surrounds which of the three extant CCDD tetraploid species—A. insularis, A. magna and A. murphyi—is most closely related to hexaploid oats. The present work describes a comparative karyotype analysis of these three CCDD tetraploid species and two hexaploid species, A. sativa and A. byzantina. This involved the use of FISH with six simple sequence repeats (SSRs) with the motifs CT, AAC, AAG, ACG, ATC and ACT, two repeated ribosomal sequences, and C genome-specific repetitive DNA. The hybridization pattern of A. insularis with oligonucleotide (AC)10 was also determined and compared with those previously published for A. sativa and A. byzantina. Significant differences in the 5S sites and SSR hybridization patterns of A. murphyi compared to the other CCDD species rule out its being directly involved in the origin of the hexaploids. In contrast, the repetitive and SSR hybridization patterns shown by the D genome chromosomes, and by most of the C genome chromosomes of A. magna and A. insularis, can be equated with the corresponding chromosomes of the hexaploids. Several chromosome hybridization signals seen for A. insularis, but not for A. magna, were shared with the hexaploid oats species, especially with A. byzantina. These diagnostic signals add weight to the idea that the extant A. insularis, or a direct ancestor of it, is the most closely related progenitor of hexaploid oats. The similarity of the chromosome hybridization patterns of the hexaploids and CCDD tetraploids was taken as being indicative of homology. A common chromosome nomenclature for CCDD species based on that of the hexaploid species is proposed.

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“…A genetic diversity analysis in oats themselves was performed using various molecular markers [10][11][12][13][14][15]. Relatively high polymorphism and ease of use favor SSRs located in non-coding (SSRs) as well as in coding (EST-SSRs) DNA sequences [16][17][18]. Oat breeders are also interested in the effect of heterosis obtained by the crossing of thoroughly selected parent components.…”

Section: Introductionmentioning

confidence: 99%

Formation of Potential Heterotic Groups of Oat Using Variation at Microsatellite Loci

Havrlentová

Ondreičková

Hozlár

et al. 2021

Plants

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An evaluation of polymorphism at the microsatellite loci was applied in distinguishing 85 oat (Avena sativa L.) genotypes selected from the collection of genetic resources. The set of genotypes included oats with white, yellow, and brown seeds as well as a subgroup of naked oat (Avena sativa var. nuda Koern). Variation at these loci was used to form potential heterotic groups potentially used in the oat breeding program. Seven from 20 analyzed microsatellite loci revealed polymorphism. Altogether, 35 microsatellite alleles were detected (2–10 per locus). Polymorphic patterns completely differentiated all genotypes within the subgroups of white, brown, and naked oats, respectively. Only within the greatest subgroup of yellow genotypes, four pairs of genotypes remained unseparated. Genetic differentiation between the oat subgroups allowed the formation of seven potential heterotic groups using the STRUCTURE analysis. The overall value of the fixation index (Fst) suggested a high genetic differentiation between the subgroups and validated a heterotic grouping. This approach can be implemented as a simple predictor of heterosis in parental crosses prior to extensive field testing or development and implementation of more accurate genomic selection.

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The art of attrition: development of robust oat microsatellites

Cited by 9 publications

References 49 publications

B28×Kunduru-1149 Resiproklu Melez Popülasyonundan Elde Edilen F5 Bireylerinin Fonksiyonel Markörlerle Değerlendirilmesi

B28×Kunduru-1149 Resiproklu Melez Popülasyonundan Elde Edilen F5 Bireylerinin Fonksiyonel Markörlerle Değerlendirilmesi

Cytogenetic evidence supports Avena insularis being closely related to hexaploid oats

Formation of Potential Heterotic Groups of Oat Using Variation at Microsatellite Loci

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