ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2021
High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 33 citations in OpenAlex.
- Genome and transcriptome analyses reveal parallel altitude adaptation in Chenopodium.Genome biology · 2026Article
- Harnessing genomics and transcriptomics to explore the genetic and molecular basis of abiotic stress tolerance in minor millets - a comprehensive review.Functional & integrative genomics · 2026Review
- Transcriptomics and resequencing reveal dual evolutionary strategies for salt tolerance in foxtail millet (Frontiers in plant science · 2026Article
- Genetic linkage map construction and QTL mapping for panicle-related traits in foxtail millet (Molecular breeding : new strategies in plant improvement · 2025Article
- Physiological and molecular mechanisms of drought adaptation in foxtail millet: insights and future perspectives.Frontiers in plant science · 2025Review
- Genomic resources, opportunities, and prospects for accelerated improvement of millets.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Review
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- Milletomics: a metabolomics centered integrated omics approach toward genetic progression.Functional & integrative genomics · 2024Review
- Multi-omics identification of a key glycosyl hydrolase gene FtGH1 involved in rutin hydrolysis in Tartary buckwheat (Fagopyrum tataricum).Plant biotechnology journal · 2024Article
- Crop Evolution of Foxtail Millet.Plants (Basel, Switzerland) · 2024Review
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- A graph-based genome and pan-genome variation of the model plant Setaria.Nature genetics · 2023Article
- The potentialities of omics resources for millet improvement.Functional & integrative genomics · 2023Review
- An E2-E3 pair contributes to seed size control in grain crops.Nature communications · 2023Article
- How ambient temperature affects the heading date of foxtail millet (Frontiers in plant science · 2023Article
- Genome-wide identification of quantitative trait loci for morpho-agronomic and yield-related traits in foxtail millet (Setaria italica) across multi-environments.Molecular genetics and genomics : MGG · 2022Article
- Exploring theFrontiers in plant science · 2022Article
- Multi-omics intervention inFrontiers in plant science · 2022Review
- Identification of QTL related to anther color and hull color by RAD sequencing in a RIL population of Setaria italica.BMC genomics · 2021Article
- Integrated Lipidomic and Transcriptomic Analysis Reveals Lipid Metabolism in Foxtail Millet (Frontiers in genetics · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
15 authors at 2 institutions in 1 country.
Funding
Abstract
key messageBased on the high-density variation map, we identified genome-level evidence for local adaptation and demonstrated that Siprr37 with transposon insertion contributes to the fitness of foxtail millet in the northeastern ecoregion. Adaptation is a robust way through which plants are able to overcome environmental constraints. The mechanisms of adaptation in heterogeneous natural environments are largely unknown. Deciphering the genomic basis of local adaptation will contribute to further improvement in domesticated plants. To this end, we describe a high-depth (19.4 ×) haplotype map of 3.02 million single nucleotide polymorphisms in foxtail millet (Setaria italica) from whole-genome resequencing of 312 accessions. In the genome-wide scan, we identified a set of improvement signals (including the homologous gene of OsIPA1, a key gene controlling ideal plant architecture) related to the geographical adaptation to four ecoregions in China. In particular, based on the genome-wide association analysis results, we identified the contribution of a pseudo-response regulator gene, SiPRR37, to heading date adaptation in foxtail millet. We observed the expression changes of SiPRR37 resulted from a key Tc1-Mariner transposon insertion in the first intron. Positive selection analyses revealed that SiPRR37 mainly contributed to the adaptation of northeastern ecoregions. Taken together, foxtail millet adapted to the northeastern region by regulating the function of SiPRR37, which sheds lights on genome-level evidence for adaptive geographical divergence. Besides, our data provide a nearly complete catalog of genomic variation aiding the identification of functionally important variants.
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