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

Abstract

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.

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

“…This both strengthens our confidence in these associations and suggests that conserved regions from different subgenomes might influence these similar traits. Ten loci identified in our study overlapped with, or were close to (< 5 cM), previously reported plant height QTL (Holland et al 1997;Huang et al 2020;Siripoonwiwat et al 1996;Sunstrum et al 2019;Wooten et al 2009;Beer et al 1997;Herrmann et al 2014)., providing further support for these QTL. We have focused on plant height QTL in the literature because the information on oat seedling QTL is lacking and the positive correlation between root size and plant height has been revealed in field studies for oats (Li et al 2008;Zhang et al 2009).…”

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

“…Unlike other temperate cereals where the denomination “winter” refers to a pattern of sowing in autumn, remaining dormant for the winter and continuing development the next spring, the denomination of “winter oats” encompasses not only the aforementioned standard winter type, but also oats which are sown and grown during winter and harvested in late spring, as in the southern United States and countries where winter is mild. Germplasm developed for this later system are also called “southern oats” (Esvelt Klos et al, ; Sunstrum et al, ). The oat panel used in this study did not exhibit heavy population structure.…”

Genomics-assisted breeding in minor and pseudo-cereals

“…Studies involving the QTL mapping of other minor and pseudo-cereals, however, are relatively limited and mostly include studies in rye (Erath et al 2016, Miedaner et al 2018, Myśków et al 2018, Wang et al 2015, oat (Admassu-Yimer et al 2019, Babiker et al 2015, Pellizzaro et al 2016, Schneider et al 2015, Sunstrum et al 2018, Zimmer et al 2018, and millet. Of the various types of millet, pearl millet (Ambawat et al 2016, Aparna et al 2015, Kumar et al 2016b, 2018, Pucher et al 2018, Punnuri et al 2016, Taunk et al 2018 and foxtail millet (Fang et al 2016, Mauro-Herrera and Doust 2016, Ni et al 2017, Odonkor et al 2018, Wang et al 2017a, 2017b have received the majority of research attention, although one study also focused on proso millet (Rajput et al 2016).…”

“…Among the strategies used for QTL mapping, the use of single nucleotide polymorphism (SNP) markers is the most common. Such markers can be investigated using either DNA array technologies (e.g., Babiker et al 2015, Dhariwal et al 2018, Erath et al 2017, Schneider et al 2015 or next-generation sequencing (NGS) technologies, such as genotyping-by-sequencing (GBS; Elshire et al 2011) and restriction site-associated DNA sequencing (RAD-Seq; Baird et al 2008, Miller et al 2007, (e.g., Punnuri et al 2016, Rajput et al 2016, Sunstrum et al 2018, Wang et al 2017a, Wen et al 2018. Not a few studies have used simple sequence repeats (SSRs) as markers (e.g., Aparna et al 2015, Fang et al 2016, Taunk et al 2018.…”

“…Studies frequently focused on biotic and abiotic stress resistance, including disease resistance, drought tolerance, frost tolerance, aluminum tolerance, etc. (e.g., Aparna et al 2015, Erath et al 2017, Schneider et al 2015, Sunstrum et al 2018, as well as a variety of general agronomical and morphological traits. QTL mapping has also been performed in minor cereals to identify loci associated with nutrient content (e.g., Kumar et al 2018).…”