ArticleBMC plant biology2022
De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae).
Article in BMC plant biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- SSR and IRAP-based genetic diversity analysis for core collection of Idesia polycarpa.BMC plant biology · 2026Article
- First EST-SSRs ofPlants (Basel, Switzerland) · 2025Article
- Omics landscapes in molecular mechanisms withFood chemistry. Molecular sciences · 2025Review
- Transcriptomic and metabolomic study of the biosynthetic pathways of bioactive components in Amomum tsaoko fruits.BMC plant biology · 2025Article
- Geographic authentication ofFrontiers in plant science · 2025Article
- Population genetic differentiation and structure of rare plant Anemone shikokiana based on genotyping-by-sequencing (GBS).BMC plant biology · 2024Article
- Widely targeted volatilomics and transcriptome analyses reveal the differences in volatile organic components in differently shaped Amomum tsao-ko fruits.BMC plant biology · 2024Article
- Article
- Genetic Diversity and Association Mapping of Grain-Size Traits in Rice Landraces from the Honghe Hani Rice Terraces System in Yunnan Province.Plants (Basel, Switzerland) · 2023Article
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6 authors.
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Abstract
backgroundAmomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers.
resultsA total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species.
conclusionsOur study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.
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