Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Peng, Yuanying; Yan, Huihuang; Guo, Laichun; Deng, Cao; Guo, Hongwei; Wang, Yübo; Kang, Lipeng; Zhou, Pingping; Yu, Kaiquan; Dong, Xinxin; Liu, Xiaomeng; Sun, Zongyi; Peng, Yun; Zhao, Jun; Deng, Di; Xu, Yinghong; Liu, Ying; Jiang, Qiantao; Li, Yan; Wei, Liming; Wang, Jirui; Ma, Jason; Hao, Ming; Li, Wei; Kang, Houyang; Peng, Zhengsong; Liu, Dengcai; Jia, Jizeng; Zheng, Youliang; Ma, Tao; Wei, Yuming; Lü, Fei; Ren, Changzhong

doi:10.1038/s41588-022-01127-7

Cited by 79 publications

(99 citation statements)

References 96 publications

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“…Whole genome multiplication and subsequent diploidization processes provide plants with increased allelic diversity, heterozygosity, and enhanced meiotic recombination, which may increase their adaptive plasticity and evolutionary success [ 89 ]. It is, therefore, not surprising that the domestication of some of the most economically important cultivated plants is associated with a polyploidization event, e.g., Avena sativa [ 90 ], Triticum sp. [ 91 ], Ipomoea batatas [ 92 ], Brassica rapa [ 93 ], and Musa sp.…”

Section: Resultsmentioning

confidence: 99%

Novel Insights into the Nature of Intraspecific Genome Size Diversity in Cannabis sativa L.

Balant

González

Garcia

et al. 2022

Plants

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Cannabis sativa has been used for millennia in traditional medicine for ritual purposes and for the production of food and fibres, thus, providing important and versatile services to humans. The species, which currently has a worldwide distribution, strikes out for displaying a huge morphological and chemical diversity. Differences in Cannabis genome size have also been found, suggesting it could be a useful character to differentiate between accessions. We used flow cytometry to investigate the extent of genome size diversity across 483 individuals belonging to 84 accessions, with a wide range of wild/feral, landrace, and cultivated accessions. We also carried out sex determination using the MADC2 marker and investigated the potential of flow cytometry as a method for early sex determination. All individuals were diploid, with genome sizes ranging from 1.810 up to 2.152 pg/2C (1.189-fold variation), apart from a triploid, with 2.884 pg/2C. Our results suggest that the geographical expansion of Cannabis and its domestication had little impact on its overall genome size. We found significant differences between the genome size of male and female individuals. Unfortunately, differences were, however, too small to be discriminated using flow cytometry through the direct processing of combined male and female individuals.

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Section: Resultsmentioning

confidence: 99%

Novel Insights into the Nature of Intraspecific Genome Size Diversity in Cannabis sativa L.

Balant

González

Garcia

et al. 2022

Plants

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“…Every duplication or doubling of the genome will leave indelible traces (such as loss, transfer, and recombination) on the chromosomes. For example, the tetraploid ancestors of oat were hexaploidized, with large segments of chromosome 6D splitting into different chromosomes and only a portion of the hexaploid chromosome remaining [ 57 ]. In this study, the distribution of the AsWRKY gene on each chromosome was lowest in chromosome 6D ( AsWRKY146 and AsWRKY147 ).…”

Section: Discussionmentioning

confidence: 99%

“…KaKs_Calculator 2.0 ( , accessed on 3 March 2022)was used to calculate non-synonymous (Ka) and synonymous (Ks) substitutions for each duplicated gene pair [ 56 ]. Based on 2.6 × 10 −9 substitution/synonymous site in oat [ 57 ], the approximate date of the repeat event (million years ago, Mya) was estimated using the formula T = Ks/2λ × 10 −6 .…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide Identification and Characterization of the Oat (Avena sativa L.) WRKY Transcription Factor Family

Liu

Jia

et al. 2022

Genes

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The WRKY family is widely involved in the regulation of plant growth and stress response and is one of the largest gene families related to plant environmental adaptation. However, no systematic studies on the WRKY family in oat (Avena sativa L.) have been conducted to date. The recently published complete genome sequence of oat enables the systematic analysis of the AsWRKYs. Based on a genome-wide study of oat, we identified 162 AsWRKYs that were unevenly distributed across 21 chromosomes; a phylogenetic tree of WRKY domains divided these genes into three groups (I, II, and III). We also analyzed the gene duplication events and identified a total of 111 gene pairs that showed strong purifying selection during the evolutionary process. Surprisingly, almost all genes evolved after the completion of subgenomic differentiation of hexaploid oat. Further studies on the functional analysis indicated that AsWRKYs were widely involved in various biological processes. Notably, expression patterns of 16 AsWRKY genes revealed that the response of AsWRKYs were affected by stress level and time. In conclusion, this study provides a reference for further analysis of the role of WRKY transcription factors in species evolution and functional differentiation.

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“…The assembly of hexaploid (AACCDD) oat reference genome sequences (Maughan et al, 2019;Kamal et al, 2022;Peng et al, 2022) now allows direct comparisons between the physical position of candidate phenology genes and the locations of genetic markers linked to variation in flowering behaviour. These comparisons support the idea that VRN1 and FT1 are likely to underlie variation in oat phenology, with VRN1 homeoalleles on chromosomes 4D, 7A and 7D, and FT1 homeoallele on 7A all linked to phenological variation (Tinker et al, 2022).…”

Section: Genes That Drive Variation In Oat Phenologymentioning

confidence: 99%

Advancing understanding of oat phenology for crop adaptation

et al. 2022

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Oat (Avena sativa) is an annual cereal grown for forage, fodder and grain. Seasonal flowering behaviour, or phenology, is a key contributor to the success of oat as a crop. As a species, oat is a vernalization-responsive long-day plant that flowers after winter as days lengthen in spring. Variation in both vernalization and daylength requirements broadens adaptation of oat and has been used to breed modern cultivars with seasonal flowering behaviours suited to different regions, sowing dates and farming practices. This review examines the importance of variation in oat phenology for crop adaptation. Strategies to advance understanding of the genetic basis of oat phenology are then outlined. These include the potential to transfer knowledge from related temperate cereals, particularly wheat (Triticum aestivum) and barley (Hordeum vulgare), to provide insights into the potential molecular basis of variation in oat phenology. Approaches that use emerging genomic resources to directly investigate the molecular basis of oat phenology are also described, including application of high-resolution genome-wide diversity surveys to map genes linked to variation in flowering behaviour. The need to resolve the contribution of individual phenology genes to crop performance by developing oat genetic resources, such as near-isogenic lines, is emphasised. Finally, ways that deeper knowledge of oat phenology can be applied to breed improved varieties and to inform on-farm decision-making are outlined.

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Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Cited by 79 publications

References 96 publications

Novel Insights into the Nature of Intraspecific Genome Size Diversity in Cannabis sativa L.

Novel Insights into the Nature of Intraspecific Genome Size Diversity in Cannabis sativa L.

Genome-Wide Identification and Characterization of the Oat (Avena sativa L.) WRKY Transcription Factor Family

Advancing understanding of oat phenology for crop adaptation

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