Browsing by Author "Marlowe, Karol"

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Genotyping by Multiplexed Sequencing (GMS) protocol in Barley
(Springer Science and Business Media LLC, 2021-04) Eagle, Jonathan; Ruff, Travis; Hooker, Marcus; Sthapit, Sajal; Marston, Elliott; Marlowe, Karol; Covarrubias, Dolores; Skinner, Daniel; Hayes, Patrick; Sherman, Jamie; See, Deven
Genotyping by sequencing (GBS) and single nucleotide polymorphism (SNP) chip technologies are the primary SNP genotyping technologies used today. However, these genotyping technologies have some drawbacks that limit their usefulness in analysis. We have developed a robust protocol called genotyping by multiplexed sequencing (GMS) using SNP markers, providing informative genotypic data with greater flexibility. The genotypes derived from direct sequence reads reduce ambiguity in genetic analysis. The advantages of this protocol include: (1) This PCR-based direct sequencing protocol generates information from markers of interest and provides a more streamlined and accurate analysis process, by multiplexing hundreds of informative markers into a single sequencing run. (2) The marker sets are easily customized to the species of interest and can readily be changed. In this study we have taken the GMS protocol developed in wheat and adapted it to barley. We have identified 577 SNP markers that work well using this protocol providing adequate genome coverage for genomic selection and tag 267 QTL’s for genes of interest. Good markers have an adequate read depth of at least 5 amplicons and are reliably present across the population.
TAMFT‐3A and TAMFT‐3B2 homeologs are associated with wheat preharvest sprouting
(Wiley, 2022-08) Vetch, Justin Michael; Tillett, Brandon J.; Bruckner, Phil L.; Martin, John M.; Marlowe, Karol; Hooker, Marcus Alan; See, Deven Robert; Giroux, Michael J.
The phenomenon of preharvest sprouting (PHS), caused by rain after physiological maturity and prior to harvest, negatively affects wheat (Triticum aestivum L.) production and end use. Investigating the genetics that control PHS resistance may result in increased control of seed dormancy. Multiple genes involved in the development of seed dormancy are associated with PHS. In this study, the TaMFT (3A, 3B1, 3B2, 3D), TaMKK3-4A, and TaVP1-3B genes were assessed for association with PHS in a double-haploid line (DHL) hard red winter wheat population derived from a BC1 cross between the cultivars Loma and Warhorse, where Loma was the recurrent and PHS susceptible parent. The 162 BC1 DHL lines were grown over two field seasons and PHS susceptibility was assessed by measuring PHS resistance in physiologically mature heads. The PHS variation was associated with the TaMFT-A and the B2 homeolog with Loma carrying mutant forms of each gene. No sequence variation between Loma and Warhorse was detected in the exons of the TaMFT-B1 and D homeologs. No association between PHS resistance and TaMKK3-4A or TaVp1-3B variation was observed, though Loma and Warhorse vary for TaMKK3-4A and TaVp1-3B mutations reported to be PHS associated. Previous research has shown TaMFT-3A as having a large impact on PHS resistance. In the current study, the TaMFT-3A and TaMFT-3B2 alleles each explained 14% of observed PHS variation. Markers for both TaMFT-3A and TaMFT-3B2 should be used in selecting for increased wheat dormancy and PHS resistance.