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Zeng Y, Nong B, Xia X, Zhang Z, Wang Y, Xu Y, Feng R, Guo H, Liang Y, Chen C, Liang S, Jiang X, Yang X, Li D. Metabolome and Transcriptome Unveil the Correlated Metabolites and Transcripts with 2-acetyl-1-pyrroline in Fragrant Rice. Int J Mol Sci 2024; 25:8207. [PMID: 39125774 PMCID: PMC11311731 DOI: 10.3390/ijms25158207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/17/2024] [Accepted: 07/21/2024] [Indexed: 08/12/2024] Open
Abstract
Fragrance is a valuable trait in rice varieties, with its aroma significantly influencing consumer preference. In this study, we conducted comprehensive metabolome and transcriptome analyses to elucidate the genetic and biochemical basis of fragrance in the Shangsixiangnuo (SSXN) variety, a fragrant indica rice cultivated in Guangxi, China. Through sensory evaluation and genetic analysis, we confirmed SSXN as strongly fragrant, with an 806 bp deletion in the BADH2 gene associated with fragrance production. In the metabolome analysis, a total of 238, 233, 105 and 60 metabolic compounds exhibited significant changes at the seedling (S), reproductive (R), filling (F), and maturation (M) stages, respectively. We identified four compounds that exhibited significant changes in SSXN across all four development stages. Our analyses revealed a significant upregulation of 2-acetyl-1-pyrroline (2AP), the well-studied aromatic compound, in SSXN compared to the non-fragrant variety. Additionally, correlation analysis identified several metabolites strongly associated with 2AP, including ethanone, 1-(1H-pyrrol-2-yl)-, 1H-pyrrole, and pyrrole. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) analysis highlighted the magenta and yellow modules as particularly enriched in aroma-related metabolites, providing insights into the complex aromatic compounds underlying the fragrance of rice. In the transcriptome analysis, a total of 5582, 5506, 4965, and 4599 differential expressed genes (DEGs) were identified across the four developmental stages, with a notable enrichment of the common pathway amino sugar and nucleotide sugar metabolism in all stages. In our correlation analysis between metabolome and transcriptome data, the top three connected metabolites, phenol-, 3-amino-, and 2AP, along with ethanone, 1-(1H-pyrrol-2-yl)-, exhibited strong associations with transcripts, highlighting their potential roles in fragrance biosynthesis. Additionally, the downregulated expression of the P4H4 gene, encoding a procollagen-proline dioxygenase that specifically targets proline, in SSXN suggests its involvement in proline metabolism and potentially in aroma formation pathways. Overall, our study provides comprehensive insights into the genetic and biochemical mechanisms underlying fragrance production in rice, laying the foundation for further research aimed at enhancing fragrance quality in rice breeding programs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Xinghai Yang
- Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China; (Y.Z.); (B.N.); (X.X.); (Z.Z.); (Y.W.); (Y.X.); (R.F.); (H.G.); (Y.L.); (C.C.); (S.L.); (X.J.)
| | - Danting Li
- Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China; (Y.Z.); (B.N.); (X.X.); (Z.Z.); (Y.W.); (Y.X.); (R.F.); (H.G.); (Y.L.); (C.C.); (S.L.); (X.J.)
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Wang Y, Niu S, Deng X, Bai D, Chen Z, Deng X, Huang D. Genome-wide association study, population structure, and genetic diversity of the tea plant in Guizhou Plateau. BMC PLANT BIOLOGY 2024; 24:79. [PMID: 38287242 PMCID: PMC10826100 DOI: 10.1186/s12870-024-04761-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 01/23/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND Guizhou Plateau, as one of the original centers of tea plant, has a profound multi-ethnic cultural heritage and abundant tea germplasm resources. However, the impact of indigenous community factors on the genetic diversity, population structure and geographical distribution of tea plant is still unclear. RESULTS Using the genotyping-by-sequencing (GBS) approach, we collected 415 tea plant accessions from the study sites, estimated genetic diversity, developed a core collection, and conducted a genome-wide association study (GWAS) based on 99,363 high-quality single-nucleotide polymorphisms (SNPs). A total of 415 tea accessions were clustered into six populations (GP01, GP02, GP03, GP04, GP05 and GP06), and the results showed that GP04 and GP05 had the highest and lowest genetic diversity (Pi = 0.214 and Pi = 0.145, respectively). Moreover, 136 tea accessions (33%) were selected to construct the core set that can represent the genetic diversity of the whole collection. By analyzing seven significant SNP markers associated with the traits such as the germination period of one bud and two leaves (OTL) and the germination period of one bud and three leaves (OtL), four candidate genes possibly related to OTL and OtL were identified. CONCLUSIONS This study revealed the impact of indigenous communities on the population structure of 415 tea accessions, indicating the importance of cultural practices for protection and utilization of tea plant genetic resources. Four potential candidate genes associated with the OTL and OtL of tea plant were also identified, which will facilitate genetic research, germplasm conservation, and breeding.
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Affiliation(s)
- Yihan Wang
- College of Tea Science, Guizhou University, Guiyang, Guizhou Province, 550025, China
| | - Suzhen Niu
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, China.
| | - Xinyue Deng
- School of Architecture, Guizhou university, Guiyang, Guizhou Province, 550025, China
| | - Dingchen Bai
- College of Tea Science, Guizhou University, Guiyang, Guizhou Province, 550025, China
| | - Zhengwu Chen
- lnstitute of Tea, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou Province, 550006, China.
| | - Xiuling Deng
- College of Tea Science, Guizhou University, Guiyang, Guizhou Province, 550025, China
| | - Dejun Huang
- College of Tea Science, Guizhou University, Guiyang, Guizhou Province, 550025, China
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Li R, Huang Y, Yang X, Su M, Xiong H, Dai Y, Wu W, Pei X, Yuan Q. Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:2876. [PMID: 37571029 PMCID: PMC10421310 DOI: 10.3390/plants12152876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/15/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023]
Abstract
Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources.
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Affiliation(s)
- Rongju Li
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Yinling Huang
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Xinsen Yang
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Meng Su
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Huaiyang Xiong
- Hainan Guangling High-Tech Industrial Co., Ltd., Lingshui 572400, China; (H.X.); (Y.D.)
| | - Yang Dai
- Hainan Guangling High-Tech Industrial Co., Ltd., Lingshui 572400, China; (H.X.); (Y.D.)
| | - Wei Wu
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
| | - Xinwu Pei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qianhua Yuan
- College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China; (R.L.); (Y.H.); (X.Y.); (M.S.); (W.W.)
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Liu C, Wang T, Chen H, Ma X, Jiao C, Cui D, Han B, Li X, Jiao A, Ruan R, Xue D, Wang Y, Han L. Genomic footprints of Kam Sweet Rice domestication indicate possible migration routes of the Dong people in China and provide resources for future rice breeding. MOLECULAR PLANT 2023; 16:415-431. [PMID: 36578210 DOI: 10.1016/j.molp.2022.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
The Dong people are one of China's 55 recognized ethnic minorities, but there has been a long-standing debate about their origins. In this study, we performed whole-genome resequencing of Kam Sweet Rice (KSR), a valuable, rare, and ancient rice landrace unique to the Dong people. Through comparative genomic analyses of KSR and other rice landraces from south of the Yangtze River Basin in China, we provide evidence that the ancestors of the Dong people likely originated from the southeast coast of China at least 1000 years ago. Alien introgression and admixture in KSR demonstrated multiple migration events in the history of the Dong people. Genomic footprints of domestication demonstrated characteristics of KSR that arose from artificial selection and geographical adaptation by the Dong people. The key genes GS3, Hd1, and DPS1 (related to agronomic traits) and LTG1 and MYBS3 (related to cold tolerance) were identified as domestication targets, reflecting crop improvement and changes in the geographical environment of the Dong people during migration. A genome-wide association study revealed a candidate yield-associated gene, Os01g0923300, a specific haplotype in KSR that is important for regulating grain number per panicle. RNA-sequencing and quantitative reverse transcription-PCR results showed that this gene was more highly expressed in KSR than in ancestral populations, indicating that it may have great value in increasing yield potential in other rice accessions. In summary, our work develops a novel approach for studying human civilization and migration patterns and provides valuable genomic datasets and resources for future breeding of high-yield and climate-resilient rice varieties.
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Affiliation(s)
- Chunhui Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Tianyi Wang
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Huicha Chen
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengzhi Jiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaobing Li
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China
| | - Aixia Jiao
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China
| | - Renchao Ruan
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China
| | - Dayuan Xue
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yanjie Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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