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Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2.

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العنوان: Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2.
المؤلفون: Phitaktansakul R; Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea., Kim KW; Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea., Aung KM; Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea., Maung TZ; Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea., Min MH; Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea., Somsri A; Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea., Lee W; Seedpia, 85 Maesil-ro, Kwonsun-ku, Suwon 16395, Republic of Korea., Lee SB; Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea., Nam J; Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea., Kim SH; Department of Applied Bioscience, Konkuk University, Seoul 05029, Republic of Korea., Lee J; Department of Applied Bioscience, Konkuk University, Seoul 05029, Republic of Korea., Kwon SW; Department of Plant Bioscience, Pusan National University, Pusan 46241, Republic of Korea., Nawade B; Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea., Chu SH; Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea., Park SW; Chemical Safety Division, National Institute of Agriculture Science (NIAS), Wanju 55365, Republic of Korea., Kang KK; Department of Horticultural Life Science, Hankyong National University, Anseong 17579, Republic of Korea., Cho YH; Seedpia, 85 Maesil-ro, Kwonsun-ku, Suwon 16395, Republic of Korea., Lee YS; Department of Medical Biotechnology, Soonchunhyang University, Asan 31538, Republic of Korea., Chung IM; Department of Applied Bioscience, Konkuk University, Seoul 05029, Republic of Korea. Electronic address: imcim@konkuk.ac.kr., Park YJ; Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea; Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea. Electronic address: yjpark@kongju.ac.kr.
المصدر: Journal of advanced research [J Adv Res] 2022 Dec; Vol. 42, pp. 303-314. Date of Electronic Publication: 2021 Dec 18.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Cairo University, production and hosting by Elsevier B. V Country of Publication: Egypt NLM ID: 101546952 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2090-1224 (Electronic) Linking ISSN: 20901224 NLM ISO Abbreviation: J Adv Res Subsets: MEDLINE
أسماء مطبوعة: Original Publication: [Giza, Egypt] : Cairo University, production and hosting by Elsevier B. V.
مواضيع طبية MeSH: Oryza*/genetics , Oryza*/metabolism , Perfume*/metabolism, Betaine-Aldehyde Dehydrogenase/genetics ; Betaine-Aldehyde Dehydrogenase/metabolism ; Odorants ; Multiomics ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Plant Breeding
مستخلص: Introduction: Fragrance is an important economic and quality trait in rice. The trait is controlled by the recessive gene betaine aldehyde dehydrogenase 2 (BADH2) via the production of 2-acetyl-1-pyrroline (2AP).
Objectives: Variation in BADH2 was evaluated at the population, genetic, transcriptional, and metabolic levels to obtain insights into fragrance regulation in rice.
Methods: Whole-genome resequencing of the Korean World Rice Collection of 475 rice accessions, including 421 breeding lines and 54 wild accessions, was performed. Transcriptome analyses of a subset of 279 accessions, proteome analyses of 64 accessions, and volatile profiling of 421 breeding lines were also performed.
Results: We identified over 3.1 million high-quality single nucleotide polymorphisms (SNPs) in Korean rice collection. Most SNPs were present in intergenic regions (79%), and 190,148 SNPs (6%) were located in the coding sequence, of which 53% were nonsynonymous. In total, 38 haplotypes were identified in the BADH2 coding region, including four novel haplotypes (one in cultivated and three in wild accessions). Tajima's D values suggested that BADH2 was under balancing selection in japonica rice. Furthermore, we identified 316 expression quantitative trait loci (eQTL), including 185 cis-eQTLs and 131 trans-eQTLs, involved in BADH2 regulation. A protein quantitative trait loci (pQTL) analysis revealed the presence of trans-pQTLs; 13 pQTLs were mapped 1 Mbp from the BADH2 region. Based on variable importance in projection (VIP) scores, 15 volatile compounds, including 2AP, discriminated haplotypes and were potential biomarkers for rice fragrance.
Conclusion: We generated a catalog of haplotypes based on a resequencing analysis of a large number of rice accessions. eQTLs and pQTLs associated with BADH2 gene expression and protein accumulation are likely involved in the regulation of 2AP variation in fragrant rice. These data improve our understanding of fragrance and provide valuable information for rice breeding.
Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
(Copyright © 2021. Production and hosting by Elsevier B.V.)
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فهرسة مساهمة: Keywords: Betaine aldehyde dehydrogenase 2; Expression quantitative trait loci; Fragrant rice; Haplotype; Protein quantitative trait loci; Volatiles
المشرفين على المادة: EC 1.2.1.8 (Betaine-Aldehyde Dehydrogenase)
0 (Plant Proteins)
0 (Perfume)
تواريخ الأحداث: Date Created: 20221213 Date Completed: 20221215 Latest Revision: 20221227
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC9788947
DOI: 10.1016/j.jare.2021.12.004
PMID: 36513420
قاعدة البيانات: MEDLINE
الوصف
تدمد:2090-1224
DOI:10.1016/j.jare.2021.12.004