Tagging and mapping candidate loci for vernalization and flower initiation in hexaploid oat

Nava, Itamar Cristiano; Wight, Charlene P.; Pacheco, Marcelo Teixeira; Federizzi, Luiz Carlos; Tinker, Nicholas A.

doi:10.1007/s11032-012-9715-x

Cited by 23 publications

(46 citation statements)

References 43 publications

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“…This suggests that Hidalgo may contain an allele conferring a small quantitative response to vernalization, and reinforces the suggestion by Nava et al. () that vernalization response in oat is a complex trait, with multiple alleles at multiple loci having variable quantitative effects.…”

Section: Discussionsupporting

confidence: 88%

“…Mrg02 and Mrg12 are probably homeologous chromosomes (Chaffin et al., ) that originate from the D and A genomes, respectively (Yan et al., ). Both QTL positions have been implicated with candidate locus HD1 or Vrn3 (Esvelt Klos et al., ; Locatelli et al., ; Nava, Wight, Pacheco, Federizzi, & Tinker, ), suggesting that these loci may be related to vernalization and photoperiod. Although the highest LOD scores and strongest additive effects were found in the two trials that were either early‐planted (HD15E) or vernalized (HD14V), it is also notable that both QTLs were detected with strong and significant effects in all trials and also that they were detected by Esvelt Klos et al.…”

Section: Discussionmentioning

confidence: 99%

“…Both QTLs correspond to numerous other QTLs reported in the literature (Esvelt Klos et al., , and Supporting Information Data ) including several QTLs reported by Holland, Portyanko, Hoffman, and Lee () under vernalized or non‐vernalized conditions. The QTL positions on both homeologous chromosomes have been associated with candidate locus Vrn1 (Esvelt Klos et al., ; Nava et al., ). However, contrary to what we would expect for a vernalization‐dependent locus, the effects of these QTLs are either consistent (on Mrg21) or are detected uniquely under early or vernalized conditions (Mrg20) with an early allele originating from the spring parent.…”

Section: Discussionmentioning

confidence: 99%

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A genetic linkage map in southern‐by‐spring oat identifies multiple quantitative trait loci for adaptation and rust resistance

et al. 2018

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We developed 178 recombinant inbred lines from a southern‐by‐spring oat population designated as “TxH.” These lines were genotyped to generate a high‐quality linkage map that resolved 6,902 markers into 21 linkage groups that matched closely with the latest hexaploid oat consensus map. Three major quantitative trait loci (QTLs) affecting heading date were found in locations that are consistent with known QTLs and candidate genes, and two other QTLs affecting heading date were found in novel locations. Five QTLs affecting plant height were found. Both sets of QTLs are responsible for transgressive segregation observed for these two traits. Four QTLs affecting resistance to crown rust, caused by the pathogen Puccinia coronata f. sp. avenae, were identified. Two of these QTLs are consistent with known clusters of rust resistance genes, while two may represent new locations of novel rust resistance genes. A complete set of SNP sequences suitable for generating markers for molecular selection is provided.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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A genetic linkage map in southern‐by‐spring oat identifies multiple quantitative trait loci for adaptation and rust resistance

et al. 2018

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“…In the southern set, Mrg21 harbours the biggest haplotype block (20.5 cM), and this is close to the oat vernalization locus Vrn2 (Nava et al ., ). The regions homeologous to Vrn2 on Mrg20 and Mrg12 (Nava et al ., ) also contain several haplotype blocks, including the third‐longest block on Mrg12 (48.7–51.7 cM). These genomic regions on Mrg20 and 21 were detected by a recent GWAS that investigated frost tolerance in European oat lines (Tumino et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Haplotype‐based genotyping‐by‐sequencing in oat genome research

Bekele

Wight

Chao

et al. 2018

Plant Biotechnology Journal

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125

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SummaryIn a de novo genotyping‐by‐sequencing (GBS) analysis of short, 64‐base tag‐level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag‐level (TL) genetic variants containing 241224 SNPs. From this, the marker density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635‐line diversity panel were used to infer chromosome‐level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel. We then explored potential benefits of SNP vs. TL vs. CL GBS variants for mapping, high‐resolution genome analysis and genomic selection in oats. A combined genome‐wide association study (GWAS) of heading date from multiple locations using both TL haplotypes and individual SNP markers identified 184 significant associations. A comparative GWAS using TL haplotypes, CL haplotype blocks and their combinations demonstrated the superiority of using TL haplotype markers. Using a principal component‐based genome‐wide scan, genomic regions containing signatures of selection were identified. These regions may contain genes that are responsible for the local adaptation of oats to Northern American conditions. Genomic selection for heading date using TL haplotypes or SNP markers gave comparable and promising prediction accuracies of up to r = 0.74. Genomic selection carried out in an independent calibration and test population for heading date gave promising prediction accuracies that ranged between r = 0.42 and 0.67. In conclusion, TL haplotype GBS‐derived markers facilitate genome analysis and genomic selection in oat.

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“…The relative locations (in 10‐cM bins) of positive evidence for quantitative trait loci (QTL) influencing adaptation in oat. Reported QTL were for days to heading or days to maturity in the field under standard management or after early or late sowing, days from emergence to heading under controlled conditions with or without prior vernalization, and vernalization response (Holland et al, 1997, 2002; Nava et al, 2012; Tanhuanpää et al, 2012). Extreme F ST observed for single‐nucleotide polymorphisms mapped to the same genomic position are summarized by a single point.…”

Section: Discussionmentioning

confidence: 99%

Population Genomics Related to Adaptation in Elite Oat Germplasm

et al. 2016

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Six hundred thirty five oat (Avena sativa L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotypephenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from K = 1 to 20 model-based analyses suggested a structured population. However, the PC and K = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation (p < 0.0001). Single-locus F-statistic (F ST ) in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of r 2 = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24. Core Ideas• An oat association-mapping panel contributed by active breeding programs worldwide.• Characterized population structure and found subdivisions related to adaptation• Characterized genome-wide and chromosomespecific linkage disequilibrium• Performed association-mapping and post hoc modeling of heading date• Found several consistently associated QTL

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Tagging and mapping candidate loci for vernalization and flower initiation in hexaploid oat

Cited by 23 publications

References 43 publications

A genetic linkage map in southern‐by‐spring oat identifies multiple quantitative trait loci for adaptation and rust resistance

A genetic linkage map in southern‐by‐spring oat identifies multiple quantitative trait loci for adaptation and rust resistance

Haplotype‐based genotyping‐by‐sequencing in oat genome research

Population Genomics Related to Adaptation in Elite Oat Germplasm

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