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Tong W, Wang Y, Li F, Zhai F, Su J, Wu D, Yi L, Gao Q, Wu Q, Xia E. Genomic variation of 363 diverse tea accessions unveils the genetic diversity, domestication, and structural variations associated with tea adaptation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38990113 DOI: 10.1111/jipb.13737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 06/14/2024] [Indexed: 07/12/2024]
Abstract
Domestication has shaped the population structure and agronomic traits of tea plants, yet the complexity of tea population structure and genetic variation that determines these traits remains unclear. We here investigated the resequencing data of 363 diverse tea accessions collected extensively from almost all tea distributions and found that the population structure of tea plants was divided into eight subgroups, which were basically consistent with their geographical distributions. The genetic diversity of tea plants in China decreased from southwest to east as latitude increased. Results also indicated that Camellia sinensis var. assamica (CSA) illustrated divergent selection signatures with Camellia sinensis var. sinensis (CSS). The domesticated genes of CSA were mainly involved in leaf development, flavonoid and alkaloid biosynthesis, while the domesticated genes in CSS mainly participated in amino acid metabolism, aroma compounds biosynthesis, and cold stress. Comparative population genomics further identified ~730 Mb novel sequences, generating 6,058 full-length protein-encoding genes, significantly expanding the gene pool of tea plants. We also discovered 217,376 large-scale structural variations and 56,583 presence and absence variations (PAVs) across diverse tea accessions, some of which were associated with tea quality and stress resistance. Functional experiments demonstrated that two PAV genes (CSS0049975 and CSS0006599) were likely to drive trait diversification in cold tolerance between CSA and CSS tea plants. The overall findings not only revealed the genetic diversity and domestication of tea plants, but also underscored the vital role of structural variations in the diversification of tea plant traits.
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Affiliation(s)
- Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, 230036, China
| | - Fei Zhai
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jingjing Su
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Didi Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Lianghui Yi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Qijuan Gao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- School of Computer and Artificial Intelligence, Hefei Normal University, Hefei, 230061, China
| | - Qiong Wu
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
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Han P, Chen J, Chen Z, Che X, Peng Z, Ding P. Exploring genetic diversity and population structure in Cinnamomum cassia (L.) J.Presl germplasm in China through phenotypic, chemical component, and molecular marker analyses. FRONTIERS IN PLANT SCIENCE 2024; 15:1374648. [PMID: 39055357 PMCID: PMC11270630 DOI: 10.3389/fpls.2024.1374648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
Cinnamomum cassia (L.) J.Presl, a tropical aromatic evergreen tree belonging to the Lauraceae family, is commonly used in traditional Chinese medicine. It is also a traditional spice used worldwide. However, little is currently known about the extent of the genetic variability and population structure of C. cassia. In this study, 71 individuals were collected from seven populations across two geographical provinces in China. Nine morphological features, three chemical components, and single nucleotide polymorphism (SNP) markers were used in an integrated study of C. cassia germplasm variations. Remarkable genetic variation exists in both phenotypic and chemical compositions, and certain traits, such as leaf length, leaf width, volatile oil content, and geographic distribution, are correlated with each other. One-year-old C. cassia seedling leaf length, leaf width, elevation, and volatile oil content were found to be the main contributors to diversity, according to principal component analysis (PCA). Three major groupings were identified by cluster analysis based on the phenotypic and volatile oil data. This was in line with the findings of related research using 1,387,213 SNP markers; crucially, they all demonstrated a substantial link with geographic origin. However, there was little similarity between the results of the two clusters. Analysis of molecular variance (AMOVA) revealed that the genetic diversity of C. Cassia populations was low, primarily among individuals within populations, accounting for 95.87% of the total. Shannon's information index (I) varied from 0.418 to 0.513, with a mean of 0.478 (Na=1.860, Ne =1.584, Ho =0.481, He =0.325, and PPB =86.04%). Genetic differentiation across populations was not significant because natural adaptation or extensive exchange of seeds among farmers between environments, thus maintaining the relationship. Following a population structure analysis using the ADMIXTURE software, 71 accessions were found to be clustered into three groups, with 38% of them being of the pure type, a finding that was further supported by PCA. Future breeding strategies and our understanding of the evolutionary relationships within the C. cassia population would benefit greatly from a thorough investigation of phenotypic, chemical, and molecular markers.
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Affiliation(s)
| | | | | | | | | | - Ping Ding
- College of Traditional Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
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Huang D, Niu S, Bai D, Zhao Z, Li C, Deng X, Wang Y. Analysis of population structure and genetic diversity of Camellia tachangensis in Guizhou based on SNP markers. Mol Biol Rep 2024; 51:715. [PMID: 38824248 PMCID: PMC11144125 DOI: 10.1007/s11033-024-09632-0] [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: 12/04/2023] [Accepted: 05/10/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Camellia tachangensis F. C. Zhang is a five-compartment species in the ovary of tea group plants, which represents the original germline of early differentiation of some tea group plants. METHODS AND RESULTS In this study, we analyzed single-nucleotide polymorphisms (SNPs) at the genome level, constructed a phylogenetic tree, analyzed the genetic diversity, and further investigated the population structure of 100 C. tachangensis accessions using the genotyping-by-sequencing (GBS) method. A total of 91,959 high-quality SNPs were obtained. Population structure analysis showed that the 100 C. tachangensis accessions clustered into three groups: YQ-1 (Village Group), YQ-2 (Forest Group) and YQ-3 (Transition Group), which was further consistent with the results of phylogenetic analysis and principal component analyses (PCA). In addition, a comparative analysis of the genetic diversity among the three populations (Forest, Village, and Transition Groups) detected the highest genetic diversity in the Transition Group and the highest differentiation between Forest and Village Groups. CONCLUSIONS C. tachangensis plants growing in the forest had different genetic backgrounds from those growing in villages. This study provides a basis for the effective protection and utilization of C. tachangensis populations and lays a foundation for future C. tachangensis breeding.
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Grants
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- Project of the National key R & D plan
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Affiliation(s)
- Dejun Huang
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
| | - Suzhen Niu
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China.
- Institute of Agro-Bioengineering, Guizhou university, Xueshi Road, Guiyang, Guizhou, China.
| | - Dingchen Bai
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
| | - Zhifei Zhao
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
| | - Caiyun Li
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
| | - Xiuling Deng
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
| | - Yihan Wang
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
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Yadav LK, Bellis D, Smith ZC, Ony M, Hale C, Richards C, Klingeman WE, Staton ME, Granger JJ, Hadziabdic D. Genetic diversity and population structure of a rare flowering tree endemic to Appalachia, Stewartia ovata. Ecol Evol 2024; 14:e11547. [PMID: 38932967 PMCID: PMC11199121 DOI: 10.1002/ece3.11547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/08/2024] [Accepted: 05/26/2024] [Indexed: 06/28/2024] Open
Abstract
Stewartia ovata (cav.) Weatherby, commonly known as mountain stewartia, is an understory tree native to the southeastern United States (U.S.). This relatively rare species occurs in isolated populations in Virginia, Kentucky, Tennessee, North Carolina, South Carolina, Georgia, Alabama, and Mississippi. As a species, S. ovata has largely been overlooked, and limited information is available regarding its ecology, which presents obstacles to conservation efforts. Stewartia ovata has vibrant, large white flowers that bloom in summer with a variety of filament colors, suggesting potential horticultural traits prized by ornamental industry. However, S. ovata is relatively slow growing and, due to long seed dormancy, propagation is challenging with limited success rates. This has created a need to assess the present genetic diversity in S. ovata populations to inform potential conservation and restoration of the species. Here, we employ a genotyping-by-sequencing (GBS) approach to characterize the spatial distribution and genetic diversity of S. ovata in the southern Appalachia region of the eastern United States. A total of 4475 single nucleotide polymorphisms (SNPs) were identified across 147 individuals from 11 collection sites. Our results indicate low genetic diversity (He = 0.216), the presence of population structure (K = 2), limited differentiation (F ST = 0.039), and high gene flow (Nm = 6.16) between our subpopulations. Principal component analysis corroborated the findings of STRUCTURE, confirming the presence of two distinct S. ovata subpopulations. One subpopulation mainly contains genotypes from the Cumberland Plateau, Tennessee, while the other consists of genotypes present in the Great Smoky Mountain ranges in Tennessee, North Carolina, and portions of Nantahala, Chattahoochee-Oconee national forests in Georgia, highlighting that elevation likely plays a major role in its distribution. Our results further suggested low inbreeding coefficient (F IS = 0.070), which is expected with an outcrossing tree species. This research further provides necessary insight into extant subpopulations and has generated valuable resources needed for conservation efforts of S. ovata.
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Affiliation(s)
- L. K. Yadav
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - D. Bellis
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - Z. C. Smith
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - M. Ony
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - C. Hale
- Department of Plant BiologyUniversity of GeorgiaAthensGeorgiaUSA
- Forest and Wildlife Research CenterMississippi State UniversityMississippi StateMississippiUSA
| | - C. Richards
- Department of Ecology and EvolutionUniversity of ChicagoChicagoIllinoisUSA
| | - W. E. Klingeman
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTennesseeUSA
| | - M. E. Staton
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
| | - J. J. Granger
- Forest and Wildlife Research CenterMississippi State UniversityMississippi StateMississippiUSA
| | - D. Hadziabdic
- Department of Entomology and Plant PathologyUniversity of TennesseeKnoxvilleTennesseeUSA
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Danakumara T, Kumar N, Patil BS, Kumar T, Bharadwaj C, Jain PK, Nimmy MS, Joshi N, Parida SK, Bindra S, Kole C, Varshney RK. Unraveling the genetics of heat tolerance in chickpea landraces ( Cicer arietinum L.) using genome-wide association studies. FRONTIERS IN PLANT SCIENCE 2024; 15:1376381. [PMID: 38590753 PMCID: PMC10999645 DOI: 10.3389/fpls.2024.1376381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
Chickpea, being an important grain legume crop, is often confronted with the adverse effects of high temperatures at the reproductive stage of crop growth, drastically affecting yield and overall productivity. The current study deals with an extensive evaluation of chickpea genotypes, focusing on the traits associated with yield and their response to heat stress. Notably, we observed significant variations for these traits under both normal and high-temperature conditions, forming a robust basis for genetic research and breeding initiatives. Furthermore, the study revealed that yield-related traits exhibited high heritability, suggesting their potential suitability for marker-assisted selection. We carried out single-nucleotide polymorphism (SNP) genotyping using the genotyping-by-sequencing (GBS) method for a genome-wide association study (GWAS). Overall, 27 marker-trait associations (MTAs) linked to yield-related traits, among which we identified five common MTAs displaying pleiotropic effects after applying a stringent Bonferroni-corrected p-value threshold of <0.05 [-log10(p) > 4.95] using the BLINK (Bayesian-information and linkage-disequilibrium iteratively nested keyway) model. Through an in-depth in silico analysis of these markers against the CDC Frontier v1 reference genome, we discovered that the majority of the SNPs were located at or in proximity to gene-coding regions. We further explored candidate genes situated near these MTAs, shedding light on the molecular mechanisms governing heat stress tolerance and yield enhancement in chickpeas such as indole-3-acetic acid-amido synthetase GH3.1 with GH3 auxin-responsive promoter and pentatricopeptide repeat-containing protein, etc. The harvest index (HI) trait was associated with marker Ca3:37444451 encoding aspartic proteinase ortholog sequence of Oryza sativa subsp. japonica and Medicago truncatula, which is known for contributing to heat stress tolerance. These identified MTAs and associated candidate genes may serve as valuable assets for breeding programs dedicated to tailoring chickpea varieties resilient to heat stress and climate change.
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Affiliation(s)
| | - Neeraj Kumar
- ICAR- Indian Agricultural Research Institute, New Delhi, India
| | | | - Tapan Kumar
- International Centre for Agricultural Research in the Dry Areas, Amlaha, Madhya Pradesh, India
| | | | | | | | - Nilesh Joshi
- ICAR- Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Chittaranjan Kole
- Prof. Chittaranjan Kole Foundation for Science & Society, Kolkatta, India
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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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7
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Li X, Zuo L, Zhao H, Hu J, Tang T, Wang K, Li Y, Zhao M. Efficacy of small back optic zone design on myopia control for corneal refractive therapy (CRT): a one-year prospective cohort study. EYE AND VISION (LONDON, ENGLAND) 2023; 10:47. [PMID: 37986014 PMCID: PMC10658859 DOI: 10.1186/s40662-023-00364-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/26/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND To investigate the control effect on the axial length elongation using corneal refractive therapy (CRT) with different optical zone diameters (BOZDs). We also sought to compare the difference in higher-order aberrations (HOAs), treatment zone (TZ) size and Zernike defocus coefficient with different BOZDs and seek the optimal parameter for predicting axial elongation. METHODS This prospective cohort study included 7- to 14-year-olds fitted with orthokeratology (ortho-K) lenses of 5-mm (5-mm group) or 6-mm BOZD (6-mm group). Axial length (AL), corneal topography, HOAs and Zernike defocus coefficient were obtained at baseline, and 1, 3, 6, 9 and 12 months follow-up visits. Multivariate regression analyses were used to explore the association between AL change and ocular biometric parameters. Receiver operating characteristic (ROC) curve analysis was used to determine the best diagnostic value for AL change in ocular biometric parameters. RESULTS In total, 301 participants completed the one-year follow-up. The mean AL change in the 5-mm group (0.13 ± 0.18 mm) was less than that in the 6-mm group (0.27 ± 0.15 mm) at the 12 months visit. The TZ size and decentration were smaller, while the Zernike defocus coefficient and HOAs were higher in the 5-mm group (all P < 0.05). Older age and smaller TZ size were protective factors against AL elongation in multiple regression. In predicting AL elongation, TZ diameter yielded an area under the ROC curve of 0.684 with a cut-off value of 3.82 mm. CONCLUSION The 5-mm group showed 0.14 mm (51.8%) less axial elongation than the 6-mm group. The 5-mm BOZD produced a smaller TZ size, higher Zernike defocus coefficient and higher HOA after reshaping of the cornea. TZ size was the best predictor of AL elongation. TZ diameter less than 3.82 mm may lead to AL elongation less than 0.2 mm in one year.
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Affiliation(s)
- Xuewei Li
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Ophthalmology and Clinical Centre of Optometry, Peking University People's Hospital, Beijing, 100044, China
- College of Optometry, Peking University Health Science Center, Beijing, China
- Eye Disease and Optometry Institute, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of the Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
| | - Lili Zuo
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Ophthalmology and Clinical Centre of Optometry, Peking University People's Hospital, Beijing, 100044, China
- College of Optometry, Peking University Health Science Center, Beijing, China
- Eye Disease and Optometry Institute, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of the Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
| | - Heng Zhao
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Ophthalmology and Clinical Centre of Optometry, Peking University People's Hospital, Beijing, 100044, China
- College of Optometry, Peking University Health Science Center, Beijing, China
- Eye Disease and Optometry Institute, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of the Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
| | - Jie Hu
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Ophthalmology and Clinical Centre of Optometry, Peking University People's Hospital, Beijing, 100044, China
- College of Optometry, Peking University Health Science Center, Beijing, China
- Eye Disease and Optometry Institute, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of the Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
| | - Tao Tang
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Ophthalmology and Clinical Centre of Optometry, Peking University People's Hospital, Beijing, 100044, China
- College of Optometry, Peking University Health Science Center, Beijing, China
- Eye Disease and Optometry Institute, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of the Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
| | - Kai Wang
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China.
- Department of Ophthalmology and Clinical Centre of Optometry, Peking University People's Hospital, Beijing, 100044, China.
- College of Optometry, Peking University Health Science Center, Beijing, China.
- Eye Disease and Optometry Institute, Peking University People's Hospital, Beijing, China.
- Beijing Key Laboratory of the Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China.
| | - Yan Li
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Ophthalmology and Clinical Centre of Optometry, Peking University People's Hospital, Beijing, 100044, China
- College of Optometry, Peking University Health Science Center, Beijing, China
- Eye Disease and Optometry Institute, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of the Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
| | - Mingwei Zhao
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Ophthalmology and Clinical Centre of Optometry, Peking University People's Hospital, Beijing, 100044, China
- College of Optometry, Peking University Health Science Center, Beijing, China
- Eye Disease and Optometry Institute, Peking University People's Hospital, Beijing, China
- Beijing Key Laboratory of the Diagnosis and Therapy of Retinal and Choroid Diseases, Beijing, China
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Lei X, Li H, Li P, Zhang H, Han Z, Yang B, Duan Y, Njeri NS, Yang D, Zheng J, Ma Y, Zhu X, Fang W. Genome-Wide Association Studies of Biluochun Tea Plant Populations in Dongting Mountain and Comprehensive Identification of Candidate Genes Associated with Core Agronomic Traits by Four Analysis Models. PLANTS (BASEL, SWITZERLAND) 2023; 12:3719. [PMID: 37960075 PMCID: PMC10650078 DOI: 10.3390/plants12213719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
The elite germplasm resources are key to the beautiful appearance and pleasant flavor of Biluochun tea. We collected and measured the agronomic traits of 95 tea plants to reveal the trait diversity and breeding value of Biluochun tea plant populations. The results revealed that the agronomic traits of Biluochun tea plant populations were diverse and had high breeding value. Additionally, we resequenced these tea plant populations to reveal genetic diversity, population structure, and selection pressure. The Biluochun tea plant populations contained two groups and were least affected by natural selection based on the results of population structure and selection pressure. More importantly, four non-synonymous single nucleotide polymorphisms (nsSNPs) and candidate genes associated with (-)-gallocatechin gallate (GCG), (-)-gallocatechin (GC), and caffeine (CAF) were detected using at least two GWAS models. The results will promote the development and application of molecular markers and the utilization of elite germplasm from Biluochun populations.
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Affiliation(s)
- Xiaogang Lei
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Haoyu Li
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Pingping Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Huan Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Zhaolan Han
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Bin Yang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Yu Duan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Ndombi Salome Njeri
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Daqiang Yang
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Junhua Zheng
- Dongshan Agriculture and Forestry Service Station, Suzhou 215100, China; (H.L.); (D.Y.); (J.Z.)
| | - Yuanchun Ma
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Xujun Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
| | - Wanping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China; (X.L.); (P.L.); (H.Z.); (Z.H.); (B.Y.); (Y.D.); (N.S.N.); (Y.M.); (X.Z.)
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9
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Gonçalves-Dias J, Singh A, Graf C, Stetter MG. Genetic Incompatibilities and Evolutionary Rescue by Wild Relatives Shaped Grain Amaranth Domestication. Mol Biol Evol 2023; 40:msad177. [PMID: 37552934 PMCID: PMC10439364 DOI: 10.1093/molbev/msad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Crop domestication and the subsequent expansion of crops have long been thought of as a linear process from a wild ancestor to a domesticate. However, evidence of gene flow from locally adapted wild relatives that provided adaptive alleles into crops has been identified in multiple species. Yet, little is known about the evolutionary consequences of gene flow during domestication and the interaction of gene flow and genetic load in crop populations. We study the pseudo-cereal grain amaranth that has been domesticated three times in different geographic regions of the Americas. We quantify the amount and distribution of gene flow and genetic load along the genome of the three grain amaranth species and their two wild relatives. Our results show ample gene flow between crop species and between crops and their wild relatives. Gene flow from wild relatives decreased genetic load in the three crop species. This suggests that wild relatives could provide evolutionary rescue by replacing deleterious alleles in crops. We assess experimental hybrids between the three crop species and found genetic incompatibilities between one Central American grain amaranth and the other two crop species. These incompatibilities might have created recent reproductive barriers and maintained species integrity today. Together, our results show that gene flow played an important role in the domestication and expansion of grain amaranth, despite genetic species barriers. The domestication of plants was likely not linear and created a genomic mosaic by multiple contributors with varying fitness effects for today's crops.
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Affiliation(s)
| | - Akanksha Singh
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Corbinian Graf
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Markus G Stetter
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne, Germany
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10
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Oliveira GF, Nascimento ACC, Azevedo CF, de Oliveira Celeri M, Barroso LMA, de Castro Sant'Anna I, Viana JMS, de Resende MDV, Nascimento M. Population size in QTL detection using quantile regression in genome-wide association studies. Sci Rep 2023; 13:9585. [PMID: 37311810 DOI: 10.1038/s41598-023-36730-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/08/2023] [Indexed: 06/15/2023] Open
Abstract
The aim of this study was to evaluate the performance of Quantile Regression (QR) in Genome-Wide Association Studies (GWAS) regarding the ability to detect QTLs (Quantitative Trait Locus) associated with phenotypic traits of interest, considering different population sizes. For this, simulated data was used, with traits of different levels of heritability (0.30 and 0.50), and controlled by 3 and 100 QTLs. Populations of 1,000 to 200 individuals were defined, with a random reduction of 100 individuals for each population. The power of detection of QTLs and the false positive rate were obtained by means of QR considering three different quantiles (0.10, 0.50 and 0.90) and also by means of the General Linear Model (GLM). In general, it was observed that the QR models showed greater power of detection of QTLs in all scenarios evaluated and a relatively low false positive rate in scenarios with a greater number of individuals. The models with the highest detection power of true QTLs at the extreme quantils (0.10 and 0.90) were the ones with the highest detection power of true QTLs. In contrast, the analysis based on the GLM detected few (scenarios with larger population size) or no QTLs in the evaluated scenarios. In the scenarios with low heritability, QR obtained a high detection power. Thus, it was verified that the use of QR in GWAS is effective, allowing the detection of QTLs associated with traits of interest even in scenarios with few genotyped and phenotyped individuals.
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Affiliation(s)
- Gabriela França Oliveira
- Department of Statistics, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, 36570.900, Viçosa, Minas Gerais, Brazil.
| | - Ana Carolina Campana Nascimento
- Department of Statistics, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, 36570.900, Viçosa, Minas Gerais, Brazil
| | - Camila Ferreira Azevedo
- Department of Statistics, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, 36570.900, Viçosa, Minas Gerais, Brazil
| | - Maurício de Oliveira Celeri
- Department of Statistics, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, 36570.900, Viçosa, Minas Gerais, Brazil
| | | | - Isabela de Castro Sant'Anna
- Rubber Tree and Agroforestry Systems Research Center, Campinas Agronomy Institute (IAC), Votuporanga, São Paulo, Brazil
| | | | | | - Moysés Nascimento
- Department of Statistics, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, 36570.900, Viçosa, Minas Gerais, Brazil
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11
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He L, Luo J, Niu S, Bai D, Chen Y. Population structure analysis to explore genetic diversity and geographical distribution characteristics of wild tea plant in Guizhou Plateau. BMC PLANT BIOLOGY 2023; 23:255. [PMID: 37189087 DOI: 10.1186/s12870-023-04239-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
BACKGROUND Tea, the second largest consumer beverage in the world after water, is widely cultivated in tropical and subtropical areas. However, the effect of environmental factors on the distribution of wild tea plants is unclear. RESULTS A total of 159 wild tea plants were collected from different altitudes and geological types of the Guizhou Plateau. Using the genotyping-by-sequencing method, 98,241 high-quality single nucleotide polymorphisms were identified. Genetic diversity, population structure analysis, principal component analysis, phylogenetic analysis, and linkage disequilibrium were performed. The genetic diversity of the wild tea plant population from the Silicate Rock Classes of Camellia gymnogyna was higher than that from the Carbonate Rock Classes of Camellia tachangensis. In addition, the genetic diversity of wild tea plants from the second altitude gradient was significantly higher than that of wild tea plants from the third and first altitude gradients. Two inferred pure groups (GP01 and GP02) and one inferred admixture group (GP03) were identified by population structure analysis and were verified by principal component and phylogenetic analyses. The highest differentiation coefficients were determined for GP01 vs. GP02, while the lowest differentiation coefficients were determined for GP01 vs. GP03. CONCLUSIONS This study revealed the genetic diversity and geographical distribution characteristics of wild tea plants in the Guizhou Plateau. There are significant differences in genetic diversity and evolutionary direction between Camellia tachangensis with Carbonate Rock Classes at the first altitude gradient and Camellia gymnogyna with Silicate Rock Classes at the third altitude gradient. Geological environment, soil mineral element content, soil pH, and altitude markedly contributed to the genetic differentiation between Camellia tachangensis and Camellia gymnogyna.
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Affiliation(s)
- Limin He
- College of Tea Science / Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Jing Luo
- College of Tea Science / Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Suzhen Niu
- College of Tea Science / Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, People's Republic of China.
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Guizhou University, Ministry of Education, Institute of Agro-Bioengineering, Guiyang, 550025, Guizhou Province, People's Republic of China.
| | - Dingchen Bai
- College of Tea Science / Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Yanjun Chen
- College of Tea Science / Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, 550025, People's Republic of China
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12
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Li JW, Li H, Liu ZW, Wang YX, Chen Y, Yang N, Hu ZH, Li T, Zhuang J. Molecular markers in tea plant (Camellia sinensis): Applications to evolution, genetic identification, and molecular breeding. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107704. [PMID: 37086694 DOI: 10.1016/j.plaphy.2023.107704] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Tea plants have a long cultivation history in the world, and the beverage (tea) made from its leaves is well known in the world. Due to the characteristics of self-incompatibility, long-term natural and artificial hybridization, tea plants have a very complex genetic background, which make the classification of tea plants unclear. Molecular marker, one type of genetic markers, has the advantages of stable inheritance, large amount of information, and high reliability. The development of molecular marker has facilitated the understanding of complex tea germplasm resources. So far, molecular markers had played important roles in the study of the origin and evolution, the preservation and identification of tea germplasms, and the excellent cultivars breeding of tea plants. However, the information is scattered, making it difficult to understand the advance of molecular markers in tea plants. In this paper, we summarized the development process and types of molecular markers in tea plants. In addition, the application advance of these molecular markers in tea plants was reviewed. Perspectives of molecular markers in tea plants were also systematically provided and discussed. The elaboration of molecular markers in this paper should help us to renew understanding of its application in tea plants.
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Affiliation(s)
- Jing-Wen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Wei Liu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yi Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Hang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tong Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
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13
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Chen Y, Niu S, Deng X, Song Q, He L, Bai D, He Y. Genome-wide association study of leaf-related traits in tea plant in Guizhou based on genotyping-by-sequencing. BMC PLANT BIOLOGY 2023; 23:196. [PMID: 37046207 PMCID: PMC10091845 DOI: 10.1186/s12870-023-04192-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Studying the genetic characteristics of tea plant (Camellia spp.) leaf traits is essential for improving yield and quality through breeding and selection. Guizhou Plateau, an important part of the original center of tea plants, has rich genetic resources. However, few studies have explored the associations between tea plant leaf traits and single nucleotide polymorphism (SNP) markers in Guizhou. RESULTS In this study, we used the genotyping-by-sequencing (GBS) method to identify 100,829 SNP markers from 338 accessions of tea germplasm in Guizhou Plateau, a region with rich genetic resources. We assessed population structure based on high-quality SNPs, constructed phylogenetic relationships, and performed genome-wide association studies (GWASs). Four inferred pure groups (G-I, G-II, G-III, and G-IV) and one inferred admixture group (G-V), were identified by a population structure analysis, and verified by principal component analyses and phylogenetic analyses. Through GWAS, we identified six candidate genes associated with four leaf traits, including mature leaf size, texture, color and shape. Specifically, two candidate genes, located on chromosomes 1 and 9, were significantly associated with mature leaf size, while two genes, located on chromosomes 8 and 11, were significantly associated with mature leaf texture. Additionally, two candidate genes, located on chromosomes 1 and 2 were identified as being associated with mature leaf color and mature leaf shape, respectively. We verified the expression level of two candidate genes was verified using reverse transcription quantitative polymerase chain reaction (RT-qPCR) and designed a derived cleaved amplified polymorphism (dCAPS) marker that co-segregated with mature leaf size, which could be used for marker-assisted selection (MAS) breeding in Camellia sinensis. CONCLUSIONS In the present study, by using GWAS approaches with the 338 tea accessions population in Guizhou, we revealed a list of SNPs markers and candidate genes that were significantly associated with four leaf traits. This work provides theoretical and practical basis for the genetic breeding of related traits in tea plant leaves.
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Affiliation(s)
- Yanjun Chen
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Suzhen Niu
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region, Ministry of Education, Institute of Agro-Bioengineering, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Xinyue Deng
- School of Architecture, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Qinfei Song
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Limin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Dingchen Bai
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
| | - Yingqin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province People’s Republic of China
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14
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Tong H, Deng H, Han Z. Genetic differentiation and genetic structure of mixed-ploidy Camellia hainanica populations. PeerJ 2023; 11:e14756. [PMID: 36852222 PMCID: PMC9961093 DOI: 10.7717/peerj.14756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/27/2022] [Indexed: 02/24/2023] Open
Abstract
Camellia hainanica, which is common in China's Hainan Province, is an important woody olive tree species. Due to many years of geographic isolation, C. hainanica has not received the attention it deserves, which limits the exploitation of germplasm resources. Therefore, it is necessary to study population genetic characteristics for further utilization and conservation of C. hainanica. In this study, 96 individuals in six wild Camellia hainanica populations were used for ploidy analysis of the chromosome number, and the genetic diversity and population structure were investigated using 12 pairs of SSR primers. The results show complex ploidy differentiation in C. hainanica species. The ploidy of wild C. hainanica includes tetraploid, pentaploid, hexaploid, heptaploid, octoploid and decaploid species. Genetic analysis shows that genetic diversity and genetic differentiation among populations are low. Populations can be divided into two clusters based on their genetic structure, which matches their geographic location. Finally, to further maintain the genetic diversity of C. hainanica, ex-situ cultivation and in-situ management measures should be considered to protect it in the future.
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Affiliation(s)
- Hailang Tong
- Central South University of Forestry and Technology, The College of Forestry, Changsha, China,Central South University of Forestry and Technology, The Laboratory of Forestry Genetics, Changsha, China
| | - Hongda Deng
- Central South University of Forestry and Technology, The College of Forestry, Changsha, China,Central South University of Forestry and Technology, The Laboratory of Forestry Genetics, Changsha, China
| | - Zhiqiang Han
- Central South University of Forestry and Technology, The College of Forestry, Changsha, China,Central South University of Forestry and Technology, The Laboratory of Forestry Genetics, Changsha, China
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15
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Sun M, Zhang Y, Bai H, Sun G, Zhang J, Shi L. Population diversity analyses provide insights into key horticultural traits of Chinese native thymes. HORTICULTURE RESEARCH 2023; 10:uhac262. [PMID: 36778183 PMCID: PMC9907056 DOI: 10.1093/hr/uhac262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Revised: 12/02/2022] [Accepted: 11/25/2022] [Indexed: 06/18/2023]
Abstract
Chinese native thymes (CNTs) in the genus Thymus (family Lamiaceae) are rich in bioactive terpenes, which exert antiviral, anti-inflammatory, antioxidation, immunological, and antimicrobial effects. Plants exhibit morphological variation, including erect-type and creeping-type growth forms; however, the molecular mechanisms underlying important horticultural traits have not been determined. Here, we collected 39 CNTs providing strategic plant resources for studies of lignin, terpenoids, and glandular trichomes of thymes. Using resequencing data as well as phenotypic, metabonomic, phylogenetic, population genetic, and transcriptomic analyses, we identified and characterized key genes involved in lignin biosynthesis, terpenoid biosynthesis, and glandular trichome formation. We found many regulatory genes or transcription factors related to these three important horticultural traits, including genes encoding caffeic acid O-methyltransferase (COMT), terpene synthase (TPS), v-myb avian myeloblastosis viral oncogene homolog (MYB), and homeodomain-leucine zipper (HD-ZIP). Population diversity analyses provided insights into growth form, terpenoid, and glandular trichome evolution in CNTs. Furthermore, our results revealed that T. mongolicus accessions might be wild ancestors, and T. quinquecostatus, T. quinquecostatus var. asiaticus, and T. quinquecostatus var. przewalskii might be transitional accessions that derived from T. mongolicus accessions. Finally, T. nervulosus, T. inaequalis, T. mandschuricus, T. curtus, T. amurensis, T. proximus, T. altaicus, T. roseus, and T. marschallianus showed high divergence. We found evidence for introgression between erect-type European cultivated thymes and CNTs. These findings improve our understanding of the determinants of variation in horticultural traits and provide candidate loci for research and breeding.
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Affiliation(s)
| | | | - Hongtong Bai
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Guofeng Sun
- China National Botanical Garden, Beijing 100093, China
| | | | - Lei Shi
- Corresponding author. E-mail: ,
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16
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Qiao D, Yang C, Guo Y. The complete chloroplast genome sequence of Camellia sinensis var. sinensis cultivar 'FuDingDaBaiCha'. Mitochondrial DNA B Resour 2023; 8:100-104. [PMID: 36643810 PMCID: PMC9833401 DOI: 10.1080/23802359.2022.2161327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The complete chloroplast (cp) genome sequence of Camellia sinensis var. sinensis cultivar 'FuDingDaBaiCha' (FD), one of the key contributors to the history of tea breeding in China, was determined in this study. The cp genome of FD is 157,025 bp in length, including a large single-copy (LSC, 86,586 bp), a small single-copy (SSC, 18,277 bp), and a pair of inverted repeats (IRa and IRb, 26,081 bp). The overall GC content is 37.3%. A total of 137 genes were predicted, including 92 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis showed that FD was closely related to C. sinensis cv. 'AnHua', C. sinensis cv. 'QianCha 1', and C. sinensis cv. 'BanTianYao'. The determination of the complete cp genome sequence of FD provides a way for the subsequent study of the genetic background and phylogenetic relationships of different tea plant cultivars.
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Affiliation(s)
- Dahe Qiao
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China,CONTACT Dahe Qiao Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Chun Yang
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Yan Guo
- Tea Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
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17
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ZHANG Y, LI X, LI H, HUANG L, HUANG J, TANG Q. Rapid and non-destructive determination of tea polyphenols content in Chongzhou new loquat tea lines based on near infrared spectroscopy. FOOD SCIENCE AND TECHNOLOGY 2023. [DOI: 10.1590/fst.004023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Affiliation(s)
- Ying ZHANG
- Sichuan Agricultural University, China; Chongqing Academy of Agricultural Sciences, China
| | | | - Hui LI
- Sichuan Agricultural University, China
| | | | | | - Qian TANG
- Sichuan Agricultural University, China
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18
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Valderrama E, Landis JB, Skinner D, Maas PJM, Maas-van de Kramer H, André T, Grunder N, Sass C, Pinilla-Vargas M, Guan CJ, Phillips HR, de Almeida AMR, Specht CD. The genetic mechanisms underlying the convergent evolution of pollination syndromes in the Neotropical radiation of Costus L. FRONTIERS IN PLANT SCIENCE 2022; 13:874322. [PMID: 36161003 PMCID: PMC9493542 DOI: 10.3389/fpls.2022.874322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 06/27/2022] [Indexed: 06/16/2023]
Abstract
Selection together with variation in floral traits can act to mold floral form, often driven by a plant's predominant or most effective pollinators. To investigate the evolution of traits associated with pollination, we developed a phylogenetic framework for evaluating tempo and mode of pollination shifts across the genus Costus L., known for its evolutionary toggle between traits related to bee and bird pollination. Using a target enrichment approach, we obtained 957 loci for 171 accessions to expand the phylogenetic sampling of Neotropical Costus. In addition, we performed whole genome resequencing for a subset of 20 closely related species with contrasting pollination syndromes. For each of these 20 genomes, a high-quality assembled transcriptome was used as reference for consensus calling of candidate loci hypothesized to be associated with pollination-related traits of interest. To test for the role these candidate genes may play in evolutionary shifts in pollinators, signatures of selection were estimated as dN/dS across the identified candidate loci. We obtained a well-resolved phylogeny for Neotropical Costus despite conflict among gene trees that provide evidence of incomplete lineage sorting and/or reticulation. The overall topology and the network of genome-wide single nucleotide polymorphisms (SNPs) indicate that multiple shifts in pollination strategy have occurred across Costus, while also suggesting the presence of previously undetected signatures of hybridization between distantly related taxa. Traits related to pollination syndromes are strongly correlated and have been gained and lost in concert several times throughout the evolution of the genus. The presence of bract appendages is correlated with two traits associated with defenses against herbivory. Although labellum shape is strongly correlated with overall pollination syndrome, we found no significant impact of labellum shape on diversification rates. Evidence suggests an interplay of pollination success with other selective pressures shaping the evolution of the Costus inflorescence. Although most of the loci used for phylogenetic inference appear to be under purifying selection, many candidate genes associated with functional traits show evidence of being under positive selection. Together these results indicate an interplay of phylogenetic history with adaptive evolution leading to the diversification of pollination-associated traits in Neotropical Costus.
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Affiliation(s)
- Eugenio Valderrama
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Jacob B. Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
- BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY, United States
| | - Dave Skinner
- Le Jardin Ombragé, Tallahassee, FL, United States
| | - Paul J. M. Maas
- Section Botany, Naturalis Biodiversity Center, Leiden, Netherlands
| | | | - Thiago André
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brazil
| | - Nikolaus Grunder
- Department of Biological Sciences, California State University, East Bay, Hayward, CA, United States
| | - Chodon Sass
- University and Jepson Herbaria, University of California, Berkeley, Berkeley, CA, United States
| | - Maria Pinilla-Vargas
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Clarice J. Guan
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Heather R. Phillips
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | | | - Chelsea D. Specht
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
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Luo Z, Chen Z, Liu M, Yang L, Zhao Z, Yang D, Ding P. Phenotypic, chemical component and molecular assessment of genetic diversity and population structure of Morinda officinalis germplasm. BMC Genomics 2022; 23:605. [PMID: 35986256 PMCID: PMC9392303 DOI: 10.1186/s12864-022-08817-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 08/02/2022] [Indexed: 11/30/2022] Open
Abstract
Background Morinda officinalis How (MO) is a perennial herb distributed in tropical and subtropical regions, which known as one of the “Four Southern Herbal Medicines”. The extent of genetic variability and the population structure of MO are presently little understood. Here, nine morphological traits, six chemical components and Single nucleotide polymorphism (SNP) markers were used in integrative research of MO germplasm variation among 88 individuals collected from ten populations across four geographical provinces of China. Results Both phenotype and chemical composition have significant genetic variation, and there is a certain correlation between them such as root diameter and the nystose content, as well as geographical distribution. The principal component analysis (PCA) showed the leaf length, leaf width, nystose, 1F-furanosaccharide nystose, and the section color were the major contributors to diversity. The cluster analysis based on phenotypic and oligosaccharide data distinguished three significant groups, which was consistent with the result of a corresponding analysis with 228,615 SNP markers, and importantly, they all showed a significant correlation with geographical origin. However, there was little similarity between two cluster results. The Shannon’s information index (I) varied from 0.17 to 0.53 with a mean of 0.37, suggesting a high level of genetic diversity in MO populations, which mainly existed among individuals within populations, accounting for 99.66% of the total according to the analysis of molecular variance (AMOVA) results. Each population also maintains the connection because of certain gene communication, so that the genetic differentiation between populations was not very significant. The STRUCTURE software was used to analyse the population structure and the result showed that 88 accessions were clustered into three groups, and 67% of them were pure type, which was also confirmed through PCA. Conclusions The comprehensive study of phenotypic, chemical and molecular markers will provide valuable information for future breeding plans and understanding the phylogenetic relationship of MO population. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08817-w.
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Srungarapu R, Mahendrakar MD, Mohammad LA, Chand U, Jagarlamudi VR, Kondamudi KP, Kudapa H, Samineni S. Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm. Cells 2022; 11:cells11152457. [PMID: 35954301 PMCID: PMC9367858 DOI: 10.3390/cells11152457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In the current study, a chickpea reference set of 280 accessions, including landraces, breeding lines, and advanced cultivars, was evaluated for grain protein, Fe, Zn content and agronomic traits over two seasons. Using a mid-density 5k SNP array, 4603 highly informative SNPs distributed across the chickpea genome were used for GWAS analysis. Population structure analysis revealed three subpopulations (K = 3). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 20 and 46 marker-trait associations (MTAs) were identified for grain nutrient and agronomic traits, respectively, using FarmCPU and BLINK models. Of which seven SNPs for grain protein, twelve for Fe, and one for Zn content were distributed on chromosomes 1, 4, 6, and 7. The marker S4_4477846 on chr4 was found to be co-associated with grain protein over seasons. The markers S1_11613376 and S1_2772537 co-associated with grain Fe content under NSII and pooled seasons and S7_9379786 marker under NSI and pooled seasons. The markers S4_31996956 co-associated with grain Fe and days to maturity. SNP annotation of associated markers were found to be related to gene functions of metal ion binding, transporters, protein kinases, transcription factors, and many more functions involved in plant metabolism along with Fe and protein homeostasis. The identified significant MTAs has potential use in marker-assisted selection for developing nutrient-rich chickpea cultivars after validation in the breeding populations.
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Affiliation(s)
- Rajasekhar Srungarapu
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
- Department of Molecular Biology and Biotechnology, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Mahesh Damodhar Mahendrakar
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Lal Ahamed Mohammad
- Department of Genetics and Plant Breeding, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Uttam Chand
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Venkata Ramana Jagarlamudi
- Department of Genetics and Plant Breeding, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Kiran Prakash Kondamudi
- Department of Statistics and Computer Applications, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Himabindu Kudapa
- Genomics, Pre-Breeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Srinivasan Samineni
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
- Correspondence:
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21
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Kinhoégbè G, Djèdatin G, Saxena RK, Chitikineni A, Bajaj P, Molla J, Agbangla C, Dansi A, Varshney RK. Genetic diversity and population structure of pigeonpea (Cajanus cajan [L.] Millspaugh) landraces grown in Benin revealed by Genotyping-By-Sequencing. PLoS One 2022; 17:e0271565. [PMID: 35857738 PMCID: PMC9299330 DOI: 10.1371/journal.pone.0271565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/04/2022] [Indexed: 11/18/2022] Open
Abstract
Genetic diversity studies provide important details on target trait availability and its variability, for the success of breeding programs. In this study, GBS approach was used to reveal a new structuration of genetic diversity and population structure of pigeonpea in Benin. We used a total of 688 high-quality Single Nucleotide Polymorphism markers for a total of 44 pigeonpea genotypes. The distribution of SNP markers on the 11 chromosomes ranged from 14 on chromosome 5 to 133 on chromosome 2. The Polymorphism Information Content and gene diversity values were 0.30 and 0.34 respectively. The analysis of population structure revealed four clear subpopulations. The Weighted Neighbor Joining tree agreed with structure analyses by grouping the 44 genotypes into four clusters. The PCoA revealed that genotypes from subpopulations 1, 2 and 3 intermixed among themselves. The Analysis of Molecular Variance showed 7% of the total variation among genotypes while the rest of variation (93%) was within genotypes from subpopulations indicating a high gene exchange (Nm = 7.13) and low genetic differentiation (PhiPT = 0.07) between subpopulations. Subpopulation 2 presented the highest mean values of number of different alleles (Na = 1.57), number of loci with private alleles (Pa = 0.11) and the percentage of polymorphic loci (P = 57.12%). We discuss our findings and demonstrate how the genetic diversity and the population structure of this specie can be used through the Genome Wide Association Studies and Marker-Assisted Selection to enhance genetic gain in pigeonpea breeding programs in Benin.
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Affiliation(s)
- Géofroy Kinhoégbè
- Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National University of Sciences, Technologies Engineering and Mathematics of Abomey, Dassa-Zoumé, Benin
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
- * E-mail:
| | - Gustave Djèdatin
- Laboratory of Molecular Biology and Bioinformatics Applied to Genomics, National University of Sciences, Technologies Engineering and Mathematics of Abomey, Dassa-Zoumé, Benin
| | - Rachit Kumar Saxena
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Anu Chitikineni
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Prasad Bajaj
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Johiruddin Molla
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Clément Agbangla
- Laboratory of Molecular Genetic and Genomes Analysis, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Alexandre Dansi
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding, National University of Sciences Technologies Engineering and Mathematics of Abomey, Dassa-Zoumé, Benin
| | - Rajeev Kumar Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
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Bai Q, He B, Cai Y, Lian H, Zhang Q, Liang D, Wang Y. Genetic Diversity and Population Structure of Schima superba From Southern China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.879512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The tree Schima superba is important for afforestation and fire prevention in southern China. The wood of this tree can also be used for furniture and buildings. However, the lack of genetic background and genomic information for this species has lowered wood yield speed and quality improvement. Here, we aimed to discover genome-wide single nucleotide polymorphisms (SNPs) in 302 S. superba germplasms collected from southern China and to use these SNPs to investigate the population structure. Using genotyping by sequencing, a total of 785 high-quality SNP markers (minor allele frequency [MAF] ≥ 0.05) were identified from 302 accessions collected from seven geographical locations. Population structure analyses and principal coordinate analyses (PCoAs) indicated that these germplasm resources can be clearly separated into different populations. The S. superba accessions originating from Yunnan (YN) and Guangxi (GX) fell into the same population, separate from the accessions originating from Guangdong (GD), which indicated that these two regions should be regarded as major provenances of this species. In addition, two independent core germplasm sets with abundant genetic polymorphisms were constructed to support the breeding work. The identification of SNP markers, analyses of population genetics, and construction of core germplasm sets will greatly promote the molecular breeding work of S. superba.
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23
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Tea (Camellia sinensis): A Review of Nutritional Composition, Potential Applications, and Omics Research. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12125874] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Tea (Camelliasinensis) is the world’s most widely consumed non-alcoholic beverage with essential economic and health benefits since it is an excellent source of polyphenols, catechins, amino acids, flavonoids, carotenoids, vitamins, and polysaccharides. The aim of this review is to summarize the main secondary metabolites in tea plants, and the content and distribution of these compounds in six different types of tea and different organs of tea plant were further investigated. The application of these secondary metabolites on food processing, cosmetics industry, and pharmaceutical industry was reviewed in this study. With the rapid advancements in biotechnology and sequencing technology, omics analyses, including genome, transcriptome, and metabolome, were widely used to detect the main secondary metabolites and their molecular regulatory mechanisms in tea plants. Numerous functional genes and regulatory factors have been discovered, studied, and applied to improve tea plants. Research advances, including secondary metabolites, applications, omics research, and functional gene mining, are comprehensively reviewed here. Further exploration and application trends are briefly described. This review provides a reference for basic and applied research on tea plants.
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Yang G, Zhou D, Wan R, Wang C, Xie J, Ma C, Li Y. HPLC and high-throughput sequencing revealed higher tea-leaves quality, soil fertility and microbial community diversity in ancient tea plantations: compared with modern tea plantations. BMC PLANT BIOLOGY 2022; 22:239. [PMID: 35550027 PMCID: PMC9097118 DOI: 10.1186/s12870-022-03633-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/18/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Ancient tea plantations with an age over 100 years still reserved at Mengku Town in Lincang Region of Yunan Province, China. However, the characteristic of soil chemicophysical properties and microbial ecosystem in the ancient tea plantations and their correlation with tea-leaves chemical components remained unclear. Tea-leaves chemical components including free amino acids, phenolic compounds and purine alkaloids collected from modern and ancient tea plantations in five geographic sites (i.e. Bingdao, Baqishan, Banuo, Dongguo and Jiulong) were determined by high performance liquid chromatography (HPLC), while their soil microbial community structure was analyzed by high-throughput sequencing, respectively. Additionally, soil microbial quantity and chemicophysical properties including pH, cation exchange capacity (CEC), soil organic matter (SOM), soil organic carbon (SOC), total nitrogen (TN), total phosphorus (TP), total potassium (TK), alkali-hydrolyzable nitrogen (AN), available phosphorous (AP) and available potassium (AK) were determined in modern and ancient tea plantations. RESULTS Tea-leaves chemical components, soil chemicophysical properties and microbial community structures including bacterial and fungal community abundance and diversity evaluated by Chao 1 and Shannon varied with geographic location and tea plantation type. Ancient tea plantations were observed to possess significantly (P < 0.05) higher free amino acids, gallic acid, caffeine and epigallocatechin (EGC) in tea-leaves, as well as soil fertility. The bacterial community structure kept stable, while fungal community abundance and diversity significantly (P < 0.05) increased in ancient tea plantation because of higher soil fertility and lower pH. The long-term plantation in natural cultivation way might significantly (P < 0.05) improve the abundances of Nitrospirota, Methylomirabilota, Ascomycota and Mortierellomycota phyla. CONCLUSIONS Due to the natural cultivation way, the ancient tea plantations still maintained relatively higher soil fertility and soil microbial ecosystem, which contributed to the sustainable development of tea-leaves with higher quality.
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Affiliation(s)
- Guangrong Yang
- College of Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Dapeng Zhou
- College of Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Renyuan Wan
- College of Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Conglian Wang
- College of Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Jin Xie
- College of Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | - Cunqiang Ma
- College of Tea, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
- College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Yongmei Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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25
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Jiang S, Chen F, Qin P, Xie H, Peng G, Li Y, Guo X. The specific DNA barcodes based on chloroplast genes for species identification of Theaceae plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:837-848. [PMID: 35592487 PMCID: PMC9110604 DOI: 10.1007/s12298-022-01175-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 03/14/2022] [Accepted: 04/06/2022] [Indexed: 05/07/2023]
Abstract
UNLABELLED More than 600 species in over 40 genera have been identified in family Theaceae worldwide. The accurate identification of Theaceae plants can ensure the market economic order, and it plays a vital role in achieving the sustainable utilization of germplasm resources. DNA barcoding, one of the most potential species identification technologies at present, has advanced in the rapid, accurate and repetitive discrimination of species. In this study, matK + ndhF + ycf1 was observed as the optimal combined candidate gene sequence of DNA barcodes by analyzing genetic information of four single chloroplast DNA sequences, including matK, rbcL, ndhF and ycf1, as well as six combined gene sequences. Subsequently, the experiments were performed on phylogenetic analysis based on genetic distance to study the phylogenetic relationship of Theaceae plants and evaluate the species identification accuracy of matK + ndhF + ycf1. Lastly, the species-specific DNA barcodes were designed by searching the variable sites (one type of single nucleotide polymorphism sites) for the accurate identification of Camellia amplexicaulis, Franklinia alatamaha, Gordonia brandegeei and Stewartia micrantha. The previous methods of screening and testing candidate gene sequences were optimized, and innovation was made in the above methods. The process of making visual DNA barcodes was standardized. Besides, DNA barcoding technology increased the accuracy of species identification and DNA barcoding was analyzed in accordance with the theories of population genetics (e.g., neutral theory of molecular evolution). The results of the study will lay a basis for the identification and protection of Theaceae species and germplasm resources. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01175-7.
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Affiliation(s)
- Shuai Jiang
- College of Biology, Hunan University, Changsha, 410082 China
| | - Fenglin Chen
- College of Biology, Hunan University, Changsha, 410082 China
| | - Pai Qin
- College of Biology, Hunan University, Changsha, 410082 China
| | - Hai Xie
- College of Biology, Hunan University, Changsha, 410082 China
| | - Guo Peng
- College of Biology, Hunan University, Changsha, 410082 China
| | - Yongliang Li
- College of Biology, Hunan University, Changsha, 410082 China
| | - Xinhong Guo
- College of Biology, Hunan University, Changsha, 410082 China
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Samarina LS, Matskiv AO, Shkhalakhova RM, Koninskaya NG, Hanke MV, Flachowsky H, Shumeev AN, Manakhova KA, Malyukova LS, Liu S, Zhu J, Gvasaliya MV, Malyarovskaya VI, Ryndin AV, Pchikhachev EK, Reim S. Genetic Diversity and Genome Size Variability in the Russian Genebank Collection of Tea Plant [ Camellia sinensis (L). O. Kuntze]. FRONTIERS IN PLANT SCIENCE 2022; 12:800141. [PMID: 35185954 PMCID: PMC8847156 DOI: 10.3389/fpls.2021.800141] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/20/2021] [Indexed: 06/01/2023]
Abstract
The tea collection of the FRC SSC RAS (Sochi, Maykop in Russia) represents one of the northernmost germplasm comprising a number of locally derived cultivars and ɣ-irradiation mutants. The latter are often characterized by larger genome size, which may lead to better adaptation to biotic and abiotic stress. Such genotypes may be a valuable genetic resource for better adaptability to extreme environmental conditions, which could enable tea cultivation outside global growing regions. Microsatellite markers are often the best choice for genetic diversity analysis in genebank collections. However, their use in polyploid species is questionable because simple sequence repeat (SSR) allele dosage cannot be readily determined. Therefore, the efficiency of SSR and start codon targeted (SCoT) markers was investigated using 43 selected cultivars from the Russian genebank collection derived from mutant breeding and clonal selection. Previously, the increase in genome size was confirmed in 18 mutants within this collection. Despite the presence of polyploid tea genotypes, our study revealed higher efficiency of SSR markers than SCoT markers. Subsequent SSR analysis of the 106 genotypes in the Russian genebank collection revealed three distinct genetic clusters after STRUCTURE analysis. Greater genetic variation was observed within genetic clusters than between clusters, indicating low genetic variation between collections. Nevertheless, the northernmost tea collection exhibited a greater genetic distance from the other two clusters than they did from each other. Close genetic relationships were found between many cultivars with particularly large leaves and mutant forms. Pearson's correlation analysis revealed a significant, moderate correlation between genome size and leaf area size. Our study shows that microsatellite fingerprinting is useful to estimate the genetic diversity and genetic background of tea germplasm in Russia despite polyploid tea accessions. Thus, the results of our study contribute to the development of future tea germplasm conservation strategies and modern tea breeding programs.
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Affiliation(s)
- Lidiia S. Samarina
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Alexandra O. Matskiv
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Ruset M. Shkhalakhova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Natalia G. Koninskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Magda-Viola Hanke
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Julius Kühn-Institute (JKI), Dresden, Germany
| | - Henryk Flachowsky
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Julius Kühn-Institute (JKI), Dresden, Germany
| | - Alexander N. Shumeev
- Center of Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
| | - Karina A. Manakhova
- Center of Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
| | - Lyudmila S. Malyukova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Anhui, China
| | - Juanyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Anhui, China
| | - Maya V. Gvasaliya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Valentina I. Malyarovskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Alexey V. Ryndin
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Eduard K. Pchikhachev
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi, Russia
| | - Stefanie Reim
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Fruit Crops, Julius Kühn-Institute (JKI), Dresden, Germany
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Tandayu E, Borpatragohain P, Mauleon R, Kretzschmar T. Genome-Wide Association Reveals Trait Loci for Seed Glucosinolate Accumulation in Indian Mustard ( Brassica juncea L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030364. [PMID: 35161346 PMCID: PMC8838242 DOI: 10.3390/plants11030364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/18/2022] [Accepted: 01/26/2022] [Indexed: 05/05/2023]
Abstract
Glucosinolates (GSLs) are sulphur- and nitrogen-containing secondary metabolites implicated in the fitness of Brassicaceae and appreciated for their pungency and health-conferring properties. In Indian mustard (Brassica juncea L.), GSL content and composition are seed-quality-determining traits affecting its economic value. Depending on the end use, i.e., condiment or oil, different GSL levels constitute breeding targets. The genetic control of GSL accumulation in Indian mustard, however, is poorly understood, and current knowledge of GSL biosynthesis and regulation is largely based on Arabidopsis thaliana. A genome-wide association study was carried out to dissect the genetic architecture of total GSL content and the content of two major GSLs, sinigrin and gluconapin, in a diverse panel of 158 Indian mustard lines, which broadly grouped into a South Asia cluster and outside-South-Asia cluster. Using 14,125 single-nucleotide polymorphisms (SNPs) as genotyping input, seven distinct significant associations were discovered for total GSL content, eight associations for sinigrin content and 19 for gluconapin. Close homologues of known GSL structural and regulatory genes were identified as candidate genes in proximity to peak SNPs. Our results provide a comprehensive map of the genetic control of GLS biosynthesis in Indian mustard, including priority targets for further investigation and molecular marker development.
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Zhao Z, Song Q, Bai D, Niu S, He Y, Qiao D, Chen Z, Li C, Luo J, Li F. Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau. BMC PLANT BIOLOGY 2022; 22:55. [PMID: 35086484 PMCID: PMC8793275 DOI: 10.1186/s12870-022-03438-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/12/2022] [Indexed: 05/17/2023]
Abstract
BACKGROUND Tea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau. RESULTS We used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies. CONCLUSIONS The present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.
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Affiliation(s)
- Zhifei Zhao
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Qinfei Song
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Dingchen Bai
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Suzhen Niu
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Yingqin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Dahe Qiao
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Zhengwu Chen
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Caiyun Li
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Jing Luo
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Fang Li
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
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Singh N, Rawal HC, Angadi UB, Sharma TR, Singh NK, Mondal TK. A first-generation haplotype map (HapMap-1) of tea (Camellia sinensis L. O. Kuntz). Bioinformatics 2022; 38:318-324. [PMID: 34601584 DOI: 10.1093/bioinformatics/btab690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/30/2021] [Accepted: 09/29/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Tea is a cross-pollinated woody perennial plant, which is why, application of conventional breeding is limited for its genetic improvement. However, lack of the genome-wide high-density SNP markers and genome-wide haplotype information has greatly hampered the utilization of tea genetic resources toward fast-track tea breeding programs. To address this challenge, we have generated a first-generation haplotype map of tea (Tea HapMap-1). Out-crossing and highly heterozygous nature of tea plants, make them more complicated for DNA-level variant discovery. RESULTS In this study, whole genome re-sequencing data of 369 tea genotypes were used to generate 2,334,564 biallelic SNPs and 1,447,985 InDels. Around 2928.04 million paired-end reads were used with an average mapping depth of ∼0.31× per accession. Identified polymorphic sites in this study will be useful in mapping the genomic regions responsible for important traits of tea. These resources lay the foundation for future research to understand the genetic diversity within tea germplasm and utilize genes that determine tea quality. This will further facilitate the understanding of tea genome evolution and tea metabolite pathways thus, offers an effective germplasm utilization for breeding the tea varieties. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nisha Singh
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa campus, New Delhi 110012, India
| | - Hukam C Rawal
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa campus, New Delhi 110012, India
| | - Ulavappa B Angadi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Tilak Raj Sharma
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa campus, New Delhi 110012, India
| | - Nagendra Kumar Singh
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa campus, New Delhi 110012, India
| | - Tapan Kumar Mondal
- ICAR-National Institute for Plant Biotechnology, LBS Building, Pusa campus, New Delhi 110012, India
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Genetic, morphological, and chemical discrepancies between Camellia sinensis (L.) O. Kuntze and its close relatives. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Guo R, Xia X, Chen J, An Y, Mi X, Li R, Zhang C, Chen M, Wei C, Liu S. Genetic relationship analysis and molecular fingerprint identification of the tea germplasms from Guangxi Province, China. BREEDING SCIENCE 2021; 71:584-593. [PMID: 35087322 PMCID: PMC8784351 DOI: 10.1270/jsbbs.21007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/08/2021] [Indexed: 05/07/2023]
Abstract
The tea plant (Camellia sinensis) is an evergreen woody plant with a high economic value. Guangxi Province is adjacent to the origin center of the tea plant in southern China. It has abundant germplasm resources and is a historically important tea-producing province. However, there is little information about the genetic diversity, genetic introgression, and fingerprints of the tea germplasms from Guangxi Province. Here, we constructed a phylogenetic tree of 126 tea accessions from Guangxi Province using 20 SSR markers. This tree classified these tea accessions into three subgroups containing 19, 47, and 60 members, respectively. High genetic similarity was observed among the three subgroups, and the genetic diversity of the populations was ranked as follows: subgroup 3 > subgroup 2 > subgroup 1. Furthermore, we analyzed the genetic relationships among 168 tea accessions from Guangxi Province and neighboring provinces. The results of the population structure analysis were highly consistent with the clustering results, and genetic introgression was observed. We identified six SSRs as the core marker set, because they could sufficiently distinguish between all 126 tea accessions. The results provide a crucial theoretical basis for utilization and protection of tea germplasms from Guangxi Province, and will help improve the breeding and popularization of elite tea cultivars.
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Affiliation(s)
- Rui Guo
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, People’s Republic of China, 230036
| | - Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, People’s Republic of China, 230036
| | - Jia Chen
- Guangxi Guilin Institute of Tea Science and Research, Guilin, People’s Republic of China, 541004
| | - Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, People’s Republic of China, 230036
| | - Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, People’s Republic of China, 230036
| | - Rui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, People’s Republic of China, 230036
| | - Cao Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, People’s Republic of China, 230036
| | - Minyi Chen
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, People’s Republic of China, 230036
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, People’s Republic of China, 230036
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, 130 Changjiang West Road, Hefei, People’s Republic of China, 230036
- Corresponding author (e-mail: )
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Liu W, Xie J, Zhou H, Kong H, Hao G, Fritsch PW, Gong W. Population dynamics linked to glacial cycles in Cercis chuniana F. P. Metcalf (Fabaceae) endemic to the montane regions of subtropical China. Evol Appl 2021; 14:2647-2663. [PMID: 34815745 PMCID: PMC8591333 DOI: 10.1111/eva.13301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 08/19/2021] [Accepted: 09/01/2021] [Indexed: 01/03/2023] Open
Abstract
The mountains of subtropical China are an excellent system for investigating the processes driving the geographical distribution of biodiversity and radiation of plant populations in response to Pleistocene climate fluctuations. How the major mountain ranges in subtropical China have affected the evolution of plant species in the subtropical evergreen broadleaved forest is an issue with long-term concern. Here, we focused on Cercis chuniana, a woody species endemic to the southern mountain ranges in subtropical China, to elucidate its population dynamics. We used genotyping by sequencing (GBS) to investigate the spatial pattern of genetic variation among 11 populations. Geographical isolation was detected between the populations located in adjacent mountain ranges, thought to function as geographical barriers due to their complex physiography. Bayesian time estimation revealed that population divergence occurred in the middle Pleistocene, when populations in the Nanling Mts. separated from those to the east. The orientation and physiography of the mountain ranges of subtropical China appear to have contributed to the geographical pattern of genetic variation between the eastern and western populations of C. chuniana. Complex physiography plus long-term stable ecological conditions across glacial cycles facilitated the demographic expansion in the Nanling Mts., from which contemporary migration began. The Nanling Mts. are thus considered as a suitable area for preserving population diversity and large population sizes of C. chuniana compared with other regions. As inferred by ecological niche modeling and coalescent simulations, secondary contact occurred during the warm Lushan-Tali Interglacial period, with intensified East Asia summer monsoon and continuous habitat available for occupation. Our data support the strong influence of both climatic history and topographic characteristics on the high regional phytodiversity of the subtropical evergreen broadleaved forest in subtropical China.
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Affiliation(s)
- Wanzhen Liu
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Jianguang Xie
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hui Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Hanghui Kong
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation BiologyCore Botanical GardensChinese Academy of SciencesGuangzhouChina
| | - Gang Hao
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | | | - Wei Gong
- Guangdong Laboratory for Lingnan Modern Agriculture, & College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
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Genetic Diversity of Ancient Camellia sinensis (L.) O.Kuntze in Sandu County of Guizhou Province in China. DIVERSITY 2021. [DOI: 10.3390/d13060276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The ancient tea plant germplasm is an important resource for breeding new tea plant varieties and has great economic value. However, due to man-made and natural disturbances, it has become endangered. In order to have a better management of the conserved tea plant germplasm, it is a requirement to understand the genetic and phenotypic diversity. The aim of this study was to evaluate the genetic and phenotypic diversity of 145 ancient tea plant germplasm resources from five populations in Sandu County of Guizhou province in China. To explore the population genetics of tea plant, we successfully identified 15 simple sequence repeat (SSR) markers, which were highly polymorphic. Additionally, we applied traditional phenotypic methods to evaluate the tea plant diversity. The results suggested that the genetic and phenotypic diversity were relatively high. A total of 96 alleles were identified, and the mean polymorphic information content (PIC) value was found to be 0.66. The analysis of molecular variance (AMOVA) showed that genetic variation within the populations was greater than among the populations. Overall, our results are the valuable baseline data in developing more efficient management and breeding plans for one of the most popular non-alcoholic beverage crops, the tea plant species.
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Ogbonna AC, Braatz de Andrade LR, Mueller LA, de Oliveira EJ, Bauchet GJ. Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1343-1362. [PMID: 33575821 PMCID: PMC8081687 DOI: 10.1007/s00122-021-03775-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/11/2021] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300-4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity [Formula: see text], effective population size estimate [Formula: see text]) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava's center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.
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Affiliation(s)
- Alex C Ogbonna
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | | | - Lukas A Mueller
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
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35
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Ogbonna AC, Braatz de Andrade LR, Mueller LA, de Oliveira EJ, Bauchet GJ. Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1343-1362. [PMID: 33575821 DOI: 10.1101/2020.07.13.200816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/11/2021] [Indexed: 05/25/2023]
Abstract
Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300-4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity [Formula: see text], effective population size estimate [Formula: see text]) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava's center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.
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Affiliation(s)
- Alex C Ogbonna
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
| | | | - Lukas A Mueller
- Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, USA
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Peng J, Zhao Y, Dong M, Liu S, Hu Z, Zhong X, Xu Z. Exploring the evolutionary characteristics between cultivated tea and its wild relatives using complete chloroplast genomes. BMC Ecol Evol 2021; 21:71. [PMID: 33931026 PMCID: PMC8086295 DOI: 10.1186/s12862-021-01800-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/22/2021] [Indexed: 01/18/2023] Open
Abstract
Background Cultivated tea is one of the most important economic and ecological trees distributed worldwide. Cultivated tea suffer from long-term targeted selection of traits and overexploitation of habitats by human beings, which may have changed its genetic structure. The chloroplast is an organelle with a conserved cyclic genomic structure, and it can help us better understand the evolutionary relationship of Camellia plants. Results We conducted comparative and evolutionary analyses on cultivated tea and wild tea, and we detected the evolutionary characteristics of cultivated tea. The chloroplast genome sizes of cultivated tea were slightly different, ranging from 157,025 to 157,100 bp. In addition, the cultivated species were more conserved than the wild species, in terms of the genome length, gene number, gene arrangement and GC content. However, comparing Camellia sinensis var. sinensis and Camellia sinensis var. assamica with their cultivars, the IR length variation was approximately 20 bp and 30 bp, respectively. The nucleotide diversity of 14 sequences in cultivated tea was higher than that in wild tea. Detailed analysis on the genomic variation and evolution of Camellia sinensis var. sinensis cultivars revealed 67 single nucleotide polymorphisms (SNPs), 46 insertions/deletions (indels), and 16 protein coding genes with nucleotide substitutions, while Camellia sinensis var. assamica cultivars revealed 4 indels. In cultivated tea, the most variable gene was ycf1. The largest number of nucleotide substitutions, five amino acids exhibited site-specific selection, and a 9 bp sequence insertion were found in the Camellia sinensis var. sinensis cultivars. In addition, phylogenetic relationship in the ycf1 tree suggested that the ycf1 gene has diverged in cultivated tea. Because C. sinensis var. sinensis and its cultivated species were not tightly clustered. Conclusions The cultivated species were more conserved than the wild species in terms of architecture and linear sequence order. The variation of the chloroplast genome in cultivated tea was mainly manifested in the nucleotide polymorphisms and sequence insertions. These results provided evidence regarding the influence of human activities on tea. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01800-1.
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Affiliation(s)
- Jiao Peng
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, 410004, Hunan, People's Republic of China.,Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Yunlin Zhao
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, 410004, Hunan, People's Republic of China.,Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Meng Dong
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Shiquan Liu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Zhiyuan Hu
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Xiaofen Zhong
- Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China
| | - Zhenggang Xu
- Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, Central South University of Forestry and Technology, Changsha, 410004, Hunan, People's Republic of China. .,Hunan Provincial Key Lab of Dark Tea and Jin-Hua, Hunan City University, Yiyang, 413000, Hunan, People's Republic of China. .,Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China.
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Ithnin M, Vu WT, Shin MG, Suryawanshi V, Sherbina K, Zolkafli SH, Serdari NM, Amiruddin MD, Abdullah N, Mustaffa S, Marjuni M, Nookiah R, Kushairi A, Marjoram P, Nuzhdin SV, Chang PL, Singh R. Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110731. [PMID: 33568284 DOI: 10.1016/j.plantsci.2020.110731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 05/15/2023]
Abstract
Existing Elaeis guineensis cultivars lack sufficient genetic diversity due to extensive breeding. Harnessing variation in wild crop relatives is necessary to expand the breadth of agronomically valuable traits. Using RAD sequencing, we examine the natural diversity of wild American oil palm populations (Elaeis oleifera), a sister species of the cultivated Elaeis guineensis oil palm. We genotyped 192 wild E. oleifera palms collected from seven Latin American countries along with four cultivated E. guineensis palms. Honduras, Costa Rica, Panama and Colombia palms are panmictic and genetically similar. Genomic patterns of diversity suggest that these populations likely originated from the Amazon Basin. Despite evidence of a genetic bottleneck and high inbreeding observed in these populations, there is considerable genetic and phenotypic variation for agronomically valuable traits. Genome-wide association revealed several candidate genes associated with fatty acid composition along with vegetative and yield-related traits. These observations provide valuable insight into the geographic distribution of diversity, phenotypic variation and its genetic architecture that will guide choices of wild genotypes for crop improvement.
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Affiliation(s)
- Maizura Ithnin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Wendy T Vu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Min-Gyoung Shin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Vasantika Suryawanshi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Katrina Sherbina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Siti Hazirah Zolkafli
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norhalida Mohamed Serdari
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Din Amiruddin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norziha Abdullah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Suzana Mustaffa
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Marhalil Marjuni
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Rajanaidu Nookiah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Ahmad Kushairi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Paul Marjoram
- Department of Preventative Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter L Chang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Rajinder Singh
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia.
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An Y, Chen L, Tao L, Liu S, Wei C. QTL Mapping for Leaf Area of Tea Plants ( Camellia sinensis) Based on a High-Quality Genetic Map Constructed by Whole Genome Resequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:705285. [PMID: 34394160 PMCID: PMC8358608 DOI: 10.3389/fpls.2021.705285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/07/2021] [Indexed: 05/08/2023]
Abstract
High-quality genetic maps play important roles in QTL mapping and molecular marker-assisted breeding. Tea leaves are not only important vegetative organs but are also the organ for harvest with important economic value. However, the key genes and genetic mechanism of regulating leaf area have not been clarified. In this study, we performed whole-genome resequencing on "Jinxuan," "Yuncha 1" and their 96 F1 hybrid offspring. From the 1.84 Tb of original sequencing data, abundant genetic variation loci were identified, including 28,144,625 SNPs and 2,780,380 indels. By integrating the markers of a previously reported genetic map, a high-density genetic map consisting of 15 linkage groups including 8,956 high-quality SNPs was constructed. The total length of the genetic map is 1,490.81 cM, which shows good collinearity with the genome. A total of 25 representative markers (potential QTLs) related to leaf area were identified, and there were genes differentially expressed in large and small leaf samples near these markers. GWAS analysis further verified the reliability of QTL mapping. Thirty-one pairs of newly developed indel markers located near these potential QTLs showed high polymorphism and had good discrimination between large and small leaf tea plant samples. Our research will provide necessary support and new insights for tea plant genetic breeding, quantitative trait mapping and yield improvement.
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Affiliation(s)
- Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Linbo Chen
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, China
| | - Lingling Tao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- *Correspondence: Chaoling Wei,
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Yamashita H, Uchida T, Tanaka Y, Katai H, Nagano AJ, Morita A, Ikka T. Genomic predictions and genome-wide association studies based on RAD-seq of quality-related metabolites for the genomics-assisted breeding of tea plants. Sci Rep 2020; 10:17480. [PMID: 33060786 PMCID: PMC7562905 DOI: 10.1038/s41598-020-74623-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/14/2020] [Indexed: 12/01/2022] Open
Abstract
Effectively using genomic information greatly accelerates conventional breeding and applying it to long-lived crops promotes the conversion to genomic breeding. Because tea plants are bred using conventional methods, we evaluated the potential of genomic predictions (GPs) and genome-wide association studies (GWASs) for the genetic breeding of tea quality-related metabolites using genome-wide single nucleotide polymorphisms (SNPs) detected from restriction site-associated DNA sequencing of 150 tea accessions. The present GP, based on genome-wide SNPs, and six models produced moderate prediction accuracy values (r) for the levels of most catechins, represented by ( -)-epigallocatechin gallate (r = 0.32-0.41) and caffeine (r = 0.44-0.51), but low r values for free amino acids and chlorophylls. Integrated analysis of GWAS and GP detected potential candidate genes for each metabolite using 80-160 top-ranked SNPs that resulted in the maximum cumulative prediction value. Applying GPs and GWASs to tea accession traits will contribute to genomics-assisted tea breeding.
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Affiliation(s)
- Hiroto Yamashita
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagito, Gifu, 501-1193, Japan
| | - Tomoki Uchida
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
| | - Yasuno Tanaka
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagito, Gifu, 501-1193, Japan
| | - Hideyuki Katai
- Shizuoka Prefectural Research Institute of Agriculture and Forestry, Tea Research Center, 1706-11 Kurasawa, Kikugawa, Shizuoka, 439-0002, Japan
- Shizuoka Prefecture Chubu Agriculture and Forestry Office, 2-20 Ariake-cho, Suruga-ku, Shizuoka, 422-8031, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
| | - Akio Morita
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan
- Institute for Tea Science, Shizuoka University, 836 Ohya, Shizuoka, 422-8529, Japan
| | - Takashi Ikka
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.
- Institute for Tea Science, Shizuoka University, 836 Ohya, Shizuoka, 422-8529, Japan.
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40
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Abd El-Wahab MMH, Aljabri M, Sarhan MS, Osman G, Wang S, Mabrouk M, El-Shabrawi HM, Gabr AMM, Abd El-Haliem AM, O’Sullivan DM, El-Soda M. High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover. Genes (Basel) 2020; 11:E893. [PMID: 32764325 PMCID: PMC7464718 DOI: 10.3390/genes11080893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 07/28/2020] [Accepted: 08/02/2020] [Indexed: 12/02/2022] Open
Abstract
Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs.
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Affiliation(s)
- Mustafa M. H. Abd El-Wahab
- Department of Agronomy, Faculty of Agriculture, Cairo University, Giza 12613, Egypt; (M.M.H.A.E.-W.); (M.M.)
| | - Maha Aljabri
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (M.A.); (G.O.)
- Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohamed S. Sarhan
- Environmental Studies and Research Unit, Cairo University, Giza 12613, Egypt;
| | - Gamal Osman
- Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, Makkah 21955, Saudi Arabia; (M.A.); (G.O.)
- Research Laboratories Centre, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
- Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza 12915, Egypt
| | - Shichen Wang
- Genomics and Bioinformatics Service Texas A&M AgriLife Research, Amarillo College Station, Amarillo, TX 77845, USA;
| | - Mahmoud Mabrouk
- Department of Agronomy, Faculty of Agriculture, Cairo University, Giza 12613, Egypt; (M.M.H.A.E.-W.); (M.M.)
| | - Hattem M. El-Shabrawi
- Plant Biotechnology Department, National Research Center, Giza 12622, Egypt; (H.M.E.-S.); (A.M.M.G.)
| | - Ahmed M. M. Gabr
- Plant Biotechnology Department, National Research Center, Giza 12622, Egypt; (H.M.E.-S.); (A.M.M.G.)
| | - Ahmed M. Abd El-Haliem
- Plant Physiology, University of Amsterdam, Swammerdam Institute for Life Sciences Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Donal M. O’Sullivan
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading RG6 6AR, UK;
| | - Mohamed El-Soda
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
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41
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Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties. Nat Commun 2020; 11:3719. [PMID: 32709943 PMCID: PMC7381669 DOI: 10.1038/s41467-020-17498-6] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 07/01/2020] [Indexed: 01/30/2023] Open
Abstract
Wild teas are valuable genetic resources for studying domestication and breeding. Here we report the assembly of a high-quality chromosome-scale reference genome for an ancient tea tree. The further RNA sequencing of 217 diverse tea accessions clarifies the pedigree of tea cultivars and reveals key contributors in the breeding of Chinese tea. Candidate genes associated with flavonoid biosynthesis are identified by genome-wide association study. Specifically, diverse allelic function of CsANR, CsF3'5'H and CsMYB5 is verified by transient overexpression and enzymatic assays, providing comprehensive insights into the biosynthesis of catechins, the most important bioactive compounds in tea plants. The inconspicuous differentiation between ancient trees and cultivars at both genetic and metabolic levels implies that tea may not have undergone long-term artificial directional selection in terms of flavor-related metabolites. These genomic resources provide evolutionary insight into tea plants and lay the foundation for better understanding the biosynthesis of beneficial natural compounds.
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42
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Haas FB, Fernandez-Pozo N, Meyberg R, Perroud PF, Göttig M, Stingl N, Saint-Marcoux D, Langdale JA, Rensing SA. Single Nucleotide Polymorphism Charting of P. patens Reveals Accumulation of Somatic Mutations During in vitro Culture on the Scale of Natural Variation by Selfing. FRONTIERS IN PLANT SCIENCE 2020; 11:813. [PMID: 32733496 PMCID: PMC7358436 DOI: 10.3389/fpls.2020.00813] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/20/2020] [Indexed: 06/01/2023]
Abstract
Introduction: Physcomitrium patens (Hedw.) Mitten (previously known as Physcomitrella patens) was collected by H.L.K. Whitehouse in Gransden Wood (Huntingdonshire, United Kingdom) in 1962 and distributed across the globe starting in 1974. Hence, the Gransden accession has been cultured in vitro in laboratories for half a century. Today, there are more than 13 different pedigrees derived from the original accession. Additionally, accessions from other sites worldwide were collected during the last decades. Methods and Results: In this study, 250 high throughput RNA sequencing (RNA-seq) samples and 25 gDNA samples were used to detect single nucleotide polymorphisms (SNPs). Analyses were performed using five different P. patens accessions and 13 different Gransden pedigrees. SNPs were overlaid with metadata and known phenotypic variations. Unique SNPs defining Gransden pedigrees and accessions were identified and experimentally confirmed. They can be successfully employed for PCR-based identification. Conclusion: We show independent mutations in different Gransden laboratory pedigrees, demonstrating that somatic mutations occur and accumulate during in vitro culture. The frequency of such mutations is similar to those observed in naturally occurring populations. We present evidence that vegetative propagation leads to accumulation of deleterious mutations, and that sexual reproduction purges those. Unique SNP sets for five different P. patens accessions were isolated and can be used to determine individual accessions as well as Gransden pedigrees. Based on that, laboratory methods to easily determine P. patens accessions and Gransden pedigrees are presented.
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Affiliation(s)
- Fabian B. Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Rabea Meyberg
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | | | - Marco Göttig
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Nora Stingl
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Denis Saint-Marcoux
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Université de Lyon, UJM-Saint-Etienne, CNRS, Laboratoire BVpam - FRE 3727, Saint-Étienne, France
| | - Jane A. Langdale
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Stefan A. Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Freiburg, Germany
- SYNMIKRO Center for Synthetic Microbiology, University of Marburg, Marburg, Germany
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43
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Xia E, Tong W, Hou Y, An Y, Chen L, Wu Q, Liu Y, Yu J, Li F, Li R, Li P, Zhao H, Ge R, Huang J, Mallano AI, Zhang Y, Liu S, Deng W, Song C, Zhang Z, Zhao J, Wei S, Zhang Z, Xia T, Wei C, Wan X. The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation. MOLECULAR PLANT 2020; 13:1013-1026. [PMID: 32353625 DOI: 10.1016/j.molp.2020.04.010] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/29/2020] [Accepted: 04/24/2020] [Indexed: 05/19/2023]
Abstract
Tea plant is an important economic crop, which is used to produce the world's oldest and most widely consumed tea beverages. Here, we present a high-quality reference genome assembly of the tea plant (Camellia sinensis var. sinensis) consisting of 15 pseudo-chromosomes. LTR retrotransposons (LTR-RTs) account for 70.38% of the genome, and we present evidence that LTR-RTs play critical roles in genome size expansion and the transcriptional diversification of tea plant genes through preferential insertion in promoter regions and introns. Genes, particularly those coding for terpene biosynthesis proteins, associated with tea aroma and stress resistance were significantly amplified through recent tandem duplications and exist as gene clusters in tea plant genome. Phylogenetic analysis of the sequences of 81 tea plant accessions with diverse origins revealed three well-differentiated tea plant populations, supporting the proposition for the southwest origin of the Chinese cultivated tea plant and its later spread to western Asia through introduction. Domestication and modern breeding left significant signatures on hundreds of genes in the tea plant genome, particularly those associated with tea quality and stress resistance. The genomic sequences of the reported reference and resequenced tea plant accessions provide valuable resources for future functional genomics study and molecular breeding of improved cultivars of tea plants.
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Affiliation(s)
- Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yan Hou
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Linbo Chen
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai 666201, China
| | - Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yunlong Liu
- Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China
| | - Jie Yu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Ruopei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Jin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Ali Inayat Mallano
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yanrui Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Zhaoliang Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Zhengzhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China.
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China.
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44
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Ji Y, Liu R, Hu J, Huang Y, Wang D, Li G, Rahman MM, Zhang H, Wang C, Li M, Yang T, Zong X. Genetic diversity analysis for narrow-leafed lupin (Lupinus angustifolius L.) by SSR markers. Mol Biol Rep 2020; 47:5215-5224. [PMID: 32577990 DOI: 10.1007/s11033-020-05596-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/17/2020] [Indexed: 11/28/2022]
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) is used as grain legumes, fodder for livestock and green manure in the world and has a great potential to be developed as a new crop in China. In this study, we assessed the genetic diversity among a set of 109 newly introduced accessions of narrow-leafed lupin using 76 genomic SSR markers. Data analysis suggested that the average gene diversity index and average polymorphism information content (PIC) were 0.4758 and 0.4328, respectively. The mean allele number per loci (Na) was 6.3816. The population structure analysis identified two subgroups based on delta K (ΔK) values. This result is in accordance with that of a PCA. The AMOVA analysis showed that most of molecular variance were within population. These results will be useful to guide the genetic improvement of the narrow-leafed lupin crop in China.
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Affiliation(s)
- Yishan Ji
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinguo Hu
- USDA-ARS Western Regional Plant Introduction Station (WRPIS), Pullman, WA, USA
| | - Yuning Huang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guan Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Md Mosiur Rahman
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,Pulses Research Center, Bangladesh Agricultural Research Institute (BARI), Gazipur, Bangladesh
| | - Hongyan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chenyu Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengwei Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Yang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Xuxiao Zong
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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45
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Zhao J, Li P, Xia T, Wan X. Exploring plant metabolic genomics: chemical diversity, metabolic complexity in the biosynthesis and transport of specialized metabolites with the tea plant as a model. Crit Rev Biotechnol 2020; 40:667-688. [PMID: 32321331 DOI: 10.1080/07388551.2020.1752617] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The diversity and complexity of secondary metabolites in tea plants contribute substantially to the popularity of tea, by determining tea flavors and their numerous health benefits. The most significant characteristics of tea plants are that they concentrate the complex plant secondary metabolites into one leaf: flavonoids, alkaloids, theanine, volatiles, and saponins. Many fundamental questions regarding tea plant secondary metabolism remain unanswered. This includes how tea plants accumulate high levels of monomeric galloylated catechins, unlike the polymerized flavan-3-ols in most other plants, as well as how they are evolved to selectively synthesize theanine and caffeine, and how tea plants properly transport and store these cytotoxic products and then reuse them in defense. Tea plants coordinate many metabolic pathways that simultaneously take place in young tea leaves in response to both developmental and environmental cues. With the available genome sequences of tea plants and high-throughput metabolomic tools as great platforms, it is of particular interest to launch metabolic genomics studies using tea plants as a model system. Plant metabolic genomics are to investigate all aspects of plant secondary metabolism at the genetic, genome, and molecular levels. This includes plant domestication and adaptation, divergence and convergence of secondary metaboloic pathways. The biosynthesis, transport, storage, and transcriptional regulation mechanisms of all metabolites are of core interest in the plant as a whole. This review highlights relevant contexts of metabolic genomics, outstanding questions, and strategies for answering them, with aim to guide future research for genetic improvement of nutrition quality for healthier plant foods.
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Affiliation(s)
- Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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46
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Niu S, Koiwa H, Song Q, Qiao D, Chen J, Zhao D, Chen Z, Wang Y, Zhang T. Development of core-collections for Guizhou tea genetic resources and GWAS of leaf size using SNP developed by genotyping-by-sequencing. PeerJ 2020; 8:e8572. [PMID: 32206447 PMCID: PMC7075365 DOI: 10.7717/peerj.8572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 01/15/2020] [Indexed: 11/20/2022] Open
Abstract
An accurate depiction of the genetic relationship, the development of core collection, and genome-wide association analysis (GWAS) are key for the effective exploitation and utilization of genetic resources. Here, genotyping-by-sequencing (GBS) was used to characterize 415 tea accessions mostly collected from the Guizhou region in China. A total of 30,282 high-quality SNPs was used to estimate the genetic relationships, develop core collections, and perform GWAS. We suggest 198 and 148 accessions to represent the core set and mini-core set, which consist of 47% and 37% of the whole collection, respectively, and contain 93–95% of the total SNPs. Furthermore, the frequencies of all alleles and genotypes in the whole set were very well retained in the core set and mini-core set. The 415 accessions were clustered into 14 groups and the core and the mini-core collections contain accessions from each group, species, cultivation status and growth habit. By analyzing the significant SNP markers associated with multiple traits, nine SNPs were found to be significantly associated with four leaf size traits, namely MLL, MLW, MLA and MLSI (P < 1.655E−06). This study characterized the genetic distance and relationship of tea collections, suggested the core collections, and established an efficient GWAS analysis of GBS result.
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Affiliation(s)
- Suzhen Niu
- Guiyang Station for DUS Testing Center of New Plant Varteties (MOA) / Institute of Tea, Guizhou Academy of Agricultural Sciences, Guiyang, China.,The Key Laboratory of Plant Resources Conservation and Germplasm Innovationin Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering / College of Tea Science, Guizhou University, Guiyang, China
| | - Hisashi Koiwa
- Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Molecular and Environmental Plant Sciences Program, Texas A&M University, College Station, Texas, USA
| | - Qinfei Song
- The Key Laboratory of Plant Resources Conservation and Germplasm Innovationin Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering / College of Tea Science, Guizhou University, Guiyang, China
| | - Dahe Qiao
- Guiyang Station for DUS Testing Center of New Plant Varteties (MOA) / Institute of Tea, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Juan Chen
- Guiyang Station for DUS Testing Center of New Plant Varteties (MOA) / Institute of Tea, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Degang Zhao
- Guiyang Station for DUS Testing Center of New Plant Varteties (MOA) / Institute of Tea, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Zhengwu Chen
- Guiyang Station for DUS Testing Center of New Plant Varteties (MOA) / Institute of Tea, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Ying Wang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
| | - Tianyuan Zhang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, China
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47
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Jiang CK, Ma JQ, Liu YF, Chen JD, Ni DJ, Chen L. Identification and distribution of a single nucleotide polymorphism responsible for the catechin content in tea plants. HORTICULTURE RESEARCH 2020; 7:24. [PMID: 32140233 PMCID: PMC7049304 DOI: 10.1038/s41438-020-0247-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/23/2019] [Accepted: 01/04/2020] [Indexed: 05/15/2023]
Abstract
Catechins are the predominant products in tea plants and have essential functions for both plants and humans. Several genes encoding the enzymes regulating catechin biosynthesis have been identified, and the identification of single nucleotide polymorphisms (SNPs) resulting in nonsynonymous mutations within these genes can be used to establish a functional link to catechin content. Therefore, the transcriptomes of two parents and four filial offspring were sequenced using next-generation sequencing technology and aligned to the reference genome to enable SNP mining. Subsequently, 176 tea plant accessions were genotyped based on candidate SNPs using kompetitive allele-specific polymerase chain reaction (KASP). The catechin contents of these samples were characterized by high-performance liquid chromatography (HPLC), and analysis of variance (ANOVA) was subsequently performed to determine the relationship between genotypes and catechin content. As a result of these efforts, a SNP within the chalcone synthase (CHS) gene was shown to be functionally associated with catechin content. Furthermore, the geographical and interspecific distribution of this SNP was investigated. Collectively, these results will contribute to the early evaluation of tea plants and serve as a rapid tool for accelerating targeted efforts in tea breeding.
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Affiliation(s)
- Chen-Kai Jiang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, 9 South Meiling Road, Hangzhou, Zhejiang 310008 China
- College of Horticulture and Forestry Science, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, Hubei 430070 China
| | - Jian-Qiang Ma
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, 9 South Meiling Road, Hangzhou, Zhejiang 310008 China
| | - Yu-Fei Liu
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, 9 South Meiling Road, Hangzhou, Zhejiang 310008 China
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, Yunnan 666201 China
| | - Jie-Dan Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, 9 South Meiling Road, Hangzhou, Zhejiang 310008 China
| | - De-Jiang Ni
- College of Horticulture and Forestry Science, Huazhong Agricultural University, 1 Shizishan Street, Hongshan District, Wuhan, Hubei 430070 China
| | - Liang Chen
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute of the Chinese Academy of Agricultural Sciences, 9 South Meiling Road, Hangzhou, Zhejiang 310008 China
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48
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Cao H, Li J, Ye Y, Lin H, Hao Z, Ye N, Yue C. Integrative Transcriptomic and Metabolic Analyses Provide Insights into the Role of Trichomes in Tea Plant ( Camellia Sinensis). Biomolecules 2020; 10:biom10020311. [PMID: 32079100 PMCID: PMC7072466 DOI: 10.3390/biom10020311] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 02/01/2020] [Accepted: 02/12/2020] [Indexed: 12/31/2022] Open
Abstract
Trichomes, which develop from epidermal cells, are regarded as one of the key features that are involved in the evaluation of tea quality and tea germplasm resources. The metabolites from trichomes have been well characterized in tea products. However, little is known regarding the metabolites in fresh tea trichomes and the molecular differences in trichomes and tea leaves per se. In this study, we developed a method to collect trichomes from tea plant tender shoots, and their main secondary metabolites, including catechins, caffeine, amino acids, and aroma compounds, were determined. We found that the majority of these compounds were significantly less abundant in trichomes than in tea leaves. RNA-Seq was used to investigate the differences in the molecular regulatory mechanism between trichomes and leaves to gain further insight into the differences in trichomes and tea leaves. In total, 52.96 Gb of clean data were generated, and 6560 differentially expressed genes (DEGs), including 4471 upregulated and 2089 downregulated genes, were identified in the trichomes vs. leaves comparison. Notably, the structural genes of the major metabolite biosynthesis pathways, transcription factors, and other key DEGs were identified and comparatively analyzed between trichomes and leaves, while trichome-specific genes were also identified. Our results provide new insights into the differences between tea trichomes and leaves at the metabolic and transcriptomic levels, and open up new doors to further recognize and re-evaluate the role of trichomes in tea quality formation and tea plant growth and development.
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Affiliation(s)
| | | | | | | | | | | | - Chuan Yue
- Correspondence: ; Tel.: +86-591-83789281
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An Y, Mi X, Zhao S, Guo R, Xia X, Liu S, Wei C. Revealing Distinctions in Genetic Diversity and Adaptive Evolution Between Two Varieties of Camellia sinensis by Whole-Genome Resequencing. FRONTIERS IN PLANT SCIENCE 2020; 11:603819. [PMID: 33329675 PMCID: PMC7732639 DOI: 10.3389/fpls.2020.603819] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/03/2020] [Indexed: 05/07/2023]
Abstract
Camellia sinensis var. sinensis (CSS) and C. sinensis var. assamica (CSA) are the two most economically important tea varieties. They have different characteristics and geographical distribution. Their genetic diversity and differentiation are unclear. Here, we identified 18,903,625 single nucleotide polymorphisms (SNPs) and 7,314,133 insertion-deletion mutations (indels) by whole-genome resequencing of 30 cultivated and three wild related species. Population structure and phylogenetic tree analyses divided the cultivated accessions into CSS and CSA containing 6,440,419 and 6,176,510 unique variations, respectively. The CSS subgroup possessed higher genetic diversity and was enriched for rare alleles. The CSA subgroup had more non-synonymous mutations and might have experienced a greater degree of balancing selection. The evolution rate (dN/dS) and KEGG enrichment indicated that genes involved in the synthesis and metabolism of flavor substances were positively selected in both CSS and CSA subpopulations. However, there are extensive genome differentiation regions (2959 bins and approximately 148 M in size) between the two subgroups. Compared with CSA (141 selected regions containing 124 genes), the CSS subgroup (830 selected regions containing 687 genes) displayed more selection regions potentially related to environmental adaptability. Fifty-three pairs of polymorphic indel markers were developed. Some markers were located in hormone-related genes with distinct alleles in the two cultivated subgroups. These identified variations and selected regions provide clues for the differentiation and adaptive evolution of tea varieties. The newly developed indel markers will be valuable in further genetic research on tea plants.
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