Abstract
BackgroundCultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; although its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. We report the development of fully annotated, chromosome-scale assemblies for the extant progenitor species of the As- and Cp-subgenomes, Avena atlantica and Avena eriantha respectively. The diploid Avena species serve as important genetic resources for improving common oat’s adaptive and food quality characteristics.ResultsThe A. atlantica and A. eriantha genome assemblies span 3.69 and 3.78 Gb with an N50 of 513 and 535 Mb, respectively. Annotation of the genomes, using sequenced transcriptomes, identified ~ 50,000 gene models in each species—including 2965 resistance gene analogs across both species. Analysis of these assemblies classified much of each genome as repetitive sequence (~ 83%), including species-specific, centromeric-specific, and telomeric-specific repeats. LTR retrotransposons make up most of the classified elements. Genome-wide syntenic comparisons with other members of the Pooideae revealed orthologous relationships, while comparisons with genetic maps from common oat clarified subgenome origins for each of the 21 hexaploid linkage groups. The utility of the diploid genomes was demonstrated by identifying putative candidate genes for flowering time (HD3A) and crown rust resistance (Pc91). We also investigate the phylogenetic relationships among other A- and C-genome Avena species.ConclusionsThe genomes we report here are the first chromosome-scale assemblies for the tribe Poeae, subtribe Aveninae. Our analyses provide important insight into the evolution and complexity of common hexaploid oat, including subgenome origin, homoeologous relationships, and major intra- and intergenomic rearrangements. They also provide the annotation framework needed to accelerate gene discovery and plant breeding.
Highlights
Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption
From the node estimates reported by Schubert et al, we calculated an average substitution rate for the Pooideae lineage of 3.39E-09, suggesting that speciation between A. atlantica and A. eriantha occurred between 5.4–12.9 million years ago (Ma), depending on whether a core eukaryotic-based synonymous mutation rate or the calculated lineage specific rate for Pooideae was used in the calculation [81, 82]
The utility of these whole-genome references was demonstrated first by analyzing sequences homologous to heading-date quantitative trail loci (QTL)-containing regions that were previously identified via genomewide association studies (GWAS) in common hexaploid oat (A. sativa) to find linked candidate genes in A. atlantica and A. eriantha
Summary
Cultivated hexaploid oat (Common oat; Avena sativa) has held a significant place within the global crop community for centuries; its cultivation has decreased over the past century, its nutritional benefits have garnered increased interest for human consumption. Oat (Avena sativa L.) is a nutritionally important crop throughout the world. It is ranked 6th in world cereal production [1], and while its primary use continues to be as a livestock feed, its uses as a human food and for cosmetics continue to increase [2]. Oat contains two classes of saponins: avenacosides (sugars bound to steroids) and avenacins (sugars bound to triterpenoid), both of which have been shown to lower cholesterol, stimulate the immune system, and have anti-carcinogenic properties [7]. Oat has many topical uses, as it has a soothing effect on skin and has been used to treat dry, itchy skin [10]; oat has been shown to have sun-blocking properties [11], and it is often found in products to treat eczema, psoriasis, and other skin conditions [12, 13]
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