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Qi H, Yu F, Lü S, Damaris RN, Dong G, Yang P. Exploring domestication pattern in lotus: insights from dispensable genome assembly. Front Plant Sci 2023; 14:1294033. [PMID: 38034573 PMCID: PMC10687544 DOI: 10.3389/fpls.2023.1294033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023]
Abstract
Lotus (Nelumbo nucifera Gaertn.), an important aquatic plant in horticulture and ecosystems, has been cultivated for more than 7000 years and domesticated into three different subgroups: flower lotus, rhizome lotus, and seed lotus. To explore the domesticated regions of each subgroup, re-sequencing data of 371 lotus accessions collected from the public database were aligned to the genome of 'China-Antique (CA)'. Unmapped reads were used to build the dispensable genome of each subgroup using a metagenome-like assembly strategy. More than 27 Mb of the dispensable genome in these three subgroups and the wild group was assembled, of which 11,761 genes were annotated. Some of the contigs in the dispensable genome were similar to the genomic segments of other lotus accessions other than 'CA'. The annotated genes in each subgroup played essential roles in specific developmental processes. Dissection of selective signals in three cultivated subgroups also demonstrated that subgroup-specific metabolic pathways, such as the brassinosteroids metabolism enrichment in FL, associated with these selected genes in each subgroup and the contigs in dispensable genome nearly located in the domesticated regions of each subgroup, respectively. Our data presented a valuable resource for facilitating lotus genomic studies, complemented the helpful information to the reference genome, and shed light on the selective signals of domesticated subgroups.
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Affiliation(s)
- Huanhuan Qi
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Feng Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Shiyou Lü
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | | | - Guoqing Dong
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, China
| | - Pingfang Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
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Zhao M, Zhang J, Yang C, Cui Z, Chen L. Identification of QTLs and Putative Candidate Genes for Plant Architecture of Lotus Revealed by Regional Association Mapping. Plants (Basel) 2023; 12:1221. [PMID: 36986910 PMCID: PMC10051333 DOI: 10.3390/plants12061221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/26/2023] [Accepted: 03/02/2023] [Indexed: 06/18/2023]
Abstract
The lotus (Nelumbo Adans.) is one of the most economically relevant ornamental aquatic plants. Plant architecture (PA) is an important trait for lotus classification, cultivation, breeding, and applications. However, the underlying genetic and molecular basis controlling PA remains poorly understood. In this study, an association study for PA-related traits was performed with 93 genome-wide microsatellite markers (simple sequence repeat, SSR) and 51 insertion-deletion (InDel) markers derived from the candidate regions using a panel of 293 lotus accessions. Phenotypic data analysis of the five PA-related traits revealed a wide normal distribution and high heritability from 2013 to 2016, which indicated that lotus PA-related traits are highly polygenic traits. The population structure (Q-matrix) and the relative kinships (K-matrix) of the association panels were analyzed using 93 SSR markers. The mixed linear model (MLM) taking Q-matrix and K-matrix into account was used to estimate the association between markers and the traits. A total of 26 markers and 65 marker-trait associations were identified by considering associations with p < 0.001 and Q < 0.05. Based on the significant markers, two QTLs on Chromosome 1 were identified, and two candidate genes were preliminarily determined. The results of our study provided useful information for the lotus breeding aiming at different PA phenotypes using a molecular-assisted selection (MAS) method and also laid the foundation for the illustration of the molecular mechanism underlying the major QTL and key markers associated with lotus PA.
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Affiliation(s)
- Mei Zhao
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Jibin Zhang
- College of Landscape and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Chuxuan Yang
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Zhenhua Cui
- College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Longqing Chen
- Southwest Landscape Architecture Engineering Research Center (National Forestry and Grassland Administration), Southwest Forestry University, Kunming 650224, China
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Liu D, Pi J, Zhang B, Zeng H, Li C, Xiao Z, Fang F, Liu M, Deng N, Wang J. Phytosterol of lotus seed core powder alleviates hypercholesterolemia by regulating gut microbiota in high-cholesterol diet-induced C57BL/6J mice. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.102279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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Luo M, Jia H, Li Q, Meng X, Ferguson DK, Liu P, Han Z, Wang J, Quan C. Middle Miocene lotus (Nelumbonaceae, Nelumbo) from the Qaidam Basin, Northern Tibet Plateau. Biology (Basel) 2022; 11. [PMID: 36138740 DOI: 10.3390/biology11091261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
The Neogene environment and paleovegetation of today’s semi-arid and arid Central Asia remain elusive. Little is known about the effect of paleoclimatic change on the distribution and ecological response mechanisms of aquatic plants, especially on the Tibetan Plateau. Here, we report a new species of Nelumbo Adanson, including leaves, receptacles, and fruits, namely Nelumbo delinghaensis sp. nov., from the Upper Youshashan Formation of the upper Middle Miocene in the northern Qaidam Basin on the Tibetan Plateau. The new species comprises centrally peltate leaves with 12−15 actinodromous primary veins and a receptacle embedded with ca. 15−30 fruits, with an unlobed central disc. Megafossils of lotus from northwest China broaden the geographical and stratigraphic ranges of Nelumbo. Our findings suggest that a large freshwater lake body surrounded by temperate forests and grassland developed in the Qaidam Basin during the late Middle Miocene, in sharp contrast to the present desert vegetation. The climate used to be sufficiently warm and moist enough to support a forest-steppe ecosystem with abundant freshwater bodies.
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Cao X, Wan W, Mao H, Yin D, Deng X, Yan H, Ren L. Genome-Wide Identification and Expression Analysis of Dof Transcription Factors in Lotus (Nelumbo nucifera Gaertn.). Plants 2022; 11:2057. [PMID: 35956535 PMCID: PMC9370771 DOI: 10.3390/plants11152057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 12/03/2022]
Abstract
Lotus (Nelumbo nucifera Gaertn.) is a traditional Chinese aquatic flower with high ornamental and economic value, but water salinity seriously affects lotus cultivation and distribution. The Dof transcription factors (TFs) play a crucial function in the regulatory network of growth and defense in plants. However, no systematic investigations of the Dof TFs in lotus have been performed. In this study, comprehensive searches of the lotus genome yielded 29 potential NnDofs. We carried out a series of standardized analyses, which include physical properties, multiple sequence alignment, phylogenetic analysis, gene structure, motif composition, cis-acting element prediction, chromosome distribution, and synteny analysis. The results showed that segment duplication probably caused the NnDofs gene family expansion. The potential functions of NnDofs in lotus development and stress conditions are speculated by promoter analysis. Furthermore, a complete expression investigation of NnDofs utilizing an RNA-seq atlas and quantitative real-time polymerase chain reaction (qRT-PCR) was performed. The majority of the NnDofs exhibit tissue-specific expression patterns, and many genes have been identified as being extremely sensitive to salt stressors. Overall, this study is the first to report a genome-wide assessment of the Dof family in lotus, and the findings offer vital insights for prospective functional studies on lotus salinity stress.
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Qi H, Yu F, Deng J, Yang P. Studies on Lotus Genomics and the Contribution to Its Breeding. Int J Mol Sci 2022; 23:7270. [PMID: 35806274 PMCID: PMC9266308 DOI: 10.3390/ijms23137270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 02/01/2023] Open
Abstract
Lotus (Nelumbo nucifera), under the Nelumbonaceae family, is one of the relict plants possessing important scientific research and economic values. Because of this, much attention has been paid to this species on both its biology and breeding among the scientific community. In the last decade, the genome of lotus has been sequenced, and several high-quality genome assemblies are available, which have significantly facilitated functional genomics studies in lotus. Meanwhile, re-sequencing of the natural and genetic populations along with different levels of omics studies have not only helped to classify the germplasm resources but also to identify the domestication of selected regions and genes controlling different horticultural traits. This review summarizes the latest progress of all these studies on lotus and discusses their potential application in lotus breeding.
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Huang R, Liu Y, Chen J, Lu Z, Wang J, He W, Chao Z, Tian E. Limited genetic diversity and high differentiation in Angelica dahurica resulted from domestication: insights to breeding and conservation. BMC Plant Biol 2022; 22:141. [PMID: 35331143 PMCID: PMC8953045 DOI: 10.1186/s12870-022-03545-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/21/2022] [Indexed: 05/24/2023]
Abstract
BACKGROUND Angelica dahurica belongs to the Apiaceae family, whose dry root is a famous traditional Chinese medicine named as "Bai zhi". There are two cultivars (A. dahurica cv. 'Hangbaizhi' and A. dahurica cv. 'Qibaizhi'), which have been domesticated for thousands of years. Long term artificial selection has led to great changes in root phenotypes of the two cultivars, and also decreased their adaptability to environment. We proposed hypothesis that the cultivars may have lost some of the genetic diversity found in the wild species and may be highly differentiated from the latter during the domestication process. However, few studies have been carried out on how domestication affected the genetic variation of this species. Here, we accessed the levels of genetic variation and differentiation within and between wild A. dahurica populations and two cultivars using 12 microsatellite markers. RESULTS The results revealed that the genetic diversity of the cultivars was much lower than that of wild A. dahurica, and A. dahurica cv. 'Qibaizhi' had lower genetic diversity compared to A. dahurica cv. 'Hangbaizhi'. AMOVA analysis showed significant genetic differentiation between the wild and cultivated A. dahurica populations, and between A. dahurica cv. 'Hangbaizhi' and A. dahurica cv. 'Qibaizhi'. Results from Bayesian, UPGMA, NJ and PcoA clustering analysis indicated that all 15 populations were assigned to two genetic clusters corresponding to the wild and cultivated populations. Bayesian clustering analysis further divided the cultivated populations into two sub-clusters corresponding to the two cultivars. CONCLUSIONS Our study suggests that the domestication process is likely the major factor resulting in the loss of genetic diversity in cultivated A. dahurica populations and in significant genetic differentiation from the wild populations due to founder effect and/or artificially directional selections. This large-scale analysis of population genetics could provide valuable information for genetic resources conservation and breeding programs of Angelica dahurica.
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Affiliation(s)
- Rong Huang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yinrong Liu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jianling Chen
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Zuyu Lu
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jiajia Wang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Wei He
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Zhi Chao
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
| | - Enwei Tian
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China.
- Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
- Guangdong Provincial Engineering Laboratory of Chinese Medicine Preparation Technology, Guangzhou, 510515, China.
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Arooj M, Imran S, Inam‐ur‐Raheem M, Rajoka MSR, Sameen A, Siddique R, Sahar A, Tariq S, Riaz A, Hussain A, Siddeeg A, Aadil RM. Lotus seeds ( Nelumbinis semen) as an emerging therapeutic seed: A comprehensive review. Food Sci Nutr 2021; 9:3971-3987. [PMID: 34262752 PMCID: PMC8269573 DOI: 10.1002/fsn3.2313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/15/2021] [Accepted: 04/15/2021] [Indexed: 12/22/2022] Open
Abstract
Nelumbinis semen is commonly known as lotus seeds that have been used as a vegetable, functional food, and medicine for 7,000 years. These are low caloric, a rich source of multiple nutrients and bioactive constituents, which make it a unique therapeutic food. N. semen plays an important part in the physiological functions of the body. Nowadays, people are more conscious about their health and desire to treat disease naturally with minimal side effects. So, functional foods are getting popularity due to a wide range of essential constituents, which are associated to decrease the risk of chronic diseases. These bioactive compounds from seeds are involved in anti-adipogenic, antioxidant, antitumor, cardiovascular, hepato-protective, anti-inflammatory, anti-fertility, anti-microbial, anti-viral, hypoglycemic, etc. Moreover, the relationship between functional compounds along with their mechanism of action in the body, their extraction from the seeds for further research would be of great interest.
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Affiliation(s)
- Muzalfa Arooj
- National Institute of Food Science and TechnologyUniversity of AgricultureFaisalabadPakistan
| | - Saira Imran
- National Institute of Food Science and TechnologyUniversity of AgricultureFaisalabadPakistan
| | - Muhammad Inam‐ur‐Raheem
- National Institute of Food Science and TechnologyUniversity of AgricultureFaisalabadPakistan
| | | | - Aysha Sameen
- National Institute of Food Science and TechnologyUniversity of AgricultureFaisalabadPakistan
| | - Rabia Siddique
- Department of ChemistryGovernment College UniversityFaisalabadPakistan
| | - Amna Sahar
- Department of Food EngineeringUniversity of AgricultureFaisalabadPakistan
| | - Shiza Tariq
- National Institute of Food Science and TechnologyUniversity of AgricultureFaisalabadPakistan
| | - Ayesha Riaz
- Institute of Home SciencesUniversity of AgricultureFaisalabadPakistan
| | - Abid Hussain
- School of Food Science and EngineeringSouth China University of TechnologyGuangzhouChina
| | - Azhari Siddeeg
- Department of Food Engineering and TechnologyFaculty of Engineering and TechnologyUniversity of GeziraWad MedaniSudan
| | - Rana Muhammad Aadil
- National Institute of Food Science and TechnologyUniversity of AgricultureFaisalabadPakistan
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Li Y, Zhang J, Wang S, Zhang Y, Yang M. The Distribution and Origins of Pyrus hopeiensis-"Wild Plant With Tiny Population" Using Whole Genome Resequencing. Front Plant Sci 2021; 12:668796. [PMID: 34220890 PMCID: PMC8250157 DOI: 10.3389/fpls.2021.668796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/28/2021] [Indexed: 06/13/2023]
Abstract
Pyrus hopeiensis is a valuable but endangered wild resource in the genus Pyrus. It has been listed as one of the 120 wild species with tiny population in China. The specie has been little studied. A preliminary study of propagation modes in P. hopeiensis was performed through seed propagation, hybridization, self-crossing trials, bud grafting, branch grafting, and investigations of natural growth. The results showed that the population size of P. hopeiensis was very small, the distribution range was limited, and the habitat was extremely degraded. In the wild population, natural hybridization and root tiller production were the major modes of propagation. Whole genome re-sequencing of the 23 wild and cultivated accessions from Pyrus species collected was performed using an Illumina HiSeq sequencing platform. The sequencing depth range was 26.56x-44.85x and the average sequencing depth was 32x. Phylogenetic tree and principal component analyses (PCA) based on SNPs showed that the wild Pyrus species, such as PWH06, PWH07, PWH09, PWH10, PWH13, and PWH17, were closely related to both P. hopeiensis HB-1 and P. hopeiensis HB-2. Using these results in combination with morphological characteristics, it speculated that P. hopeiensis populations may form a natural hybrid group with frequent gene exchanges between and within groups. A selective elimination analysis on the P. hopeiensis population were performed using Fst and π radio and a total of 381 overlapping genes including SAUR72, IAA20, HSFA2, and RKP genes were obtained. These genes were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) function enrichment. And four KEGG pathways, including lysine degradation, sphingolipid metabolism, other glycan degradation, and betaine biosynthesis were significantly enriched in the P. hopeiensis population. Our study provided information on genetic variation, evolutionary relationships, and gene enrichment in P. hopeiensis population. These data will help reveal the evolutionary history and origin of P. hopeiensis and provide guidelines for subsequent research on the locations of functional genes.
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Affiliation(s)
- Yongtan Li
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Jun Zhang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Shijie Wang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Yiwen Zhang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
| | - Minsheng Yang
- Forest Department, Forestry College, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, China
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Li H, Yang X, Zhang Y, Gao Z, Liang Y, Chen J, Shi T. Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera. Sci Data 2021; 8:38. [PMID: 33514746 PMCID: PMC7846841 DOI: 10.1038/s41597-021-00828-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/08/2021] [Indexed: 12/20/2022] Open
Abstract
Sacred lotus (Nelumbo nucifera, or lotus) is one of the most widely grown aquatic plant species with important uses, such as in water gardening and in vegetable and herbal medicine. A public genomic database of lotus would facilitate studies of lotus and other aquatic plant species. Here, we constructed an integrative database: the Nelumbo Genome Database (NGD, http://nelumbo.biocloud.net). This database is a collection of the most updated lotus genome assembly and contains information on both gene expression in different tissues and coexpression networks. In the NGD, we also integrated genetic variants and key traits from our 62 newly sequenced lotus cultivars and 26 previously reported cultivars, which are valuable for lotus germplasm studies. As applications including BLAST, BLAT, Primer, Annotation Search, Variant and Trait Search are deployed, users can perform sequence analyses and gene searches via the NGD. Overall, the valuable genomic resources provided in the NGD will facilitate future studies on population genetics and molecular breeding of lotus. Measurement(s) | reference genome data • whole genome sequencing • transcriptome | Technology Type(s) | Hi-C • PacBio Sequel System • Illumina sequencing • RNA sequencing • DNA sequencing | Sample Characteristic - Organism | Nelumbo nucifera |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13487271
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Affiliation(s)
- Hui Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingyu Yang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Yue Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiyan Gao
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuting Liang
- Wuhan Institute of Landscape Architecture, Wuhan, 430081, China
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Tao Shi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China.
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Liu Z, Zhu H, Zhou J, Jiang S, Wang Y, Kuang J, Ji Q, Peng J, Wang J, Gao L, Bai M, Jian J, Ke W. Resequencing of 296 cultivated and wild lotus accessions unravels its evolution and breeding history. Plant J 2020; 104:1673-1684. [PMID: 33073434 DOI: 10.1111/tpj.15029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 08/02/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Lotus (family: Nelumbonaceae) are perennial aquatic plants that represent one of the most ancient basal dicots. In the present study, we resequenced 296 lotus accessions from various geographical locations and germplasms to explore their genomic diversity and population structure. This germplasm set consisted of four accessions of American wild lotus and 292 accessions of Asian lotus, which were divided into four subgroups: wild, rhizome, flower and seed. Total single nucleotide polymorphisms (SNPs) suggested that the wild lotus had the highest variant number (7 191 010). Population structure and genome diversity analysis indicated that the American wild lotus demonstrated a distant genetic relationship with the Asian lotus. Furthermore, the seed and rhizome lotus groups had not originated from a single source but rather had a more complex multisource origin. Besides that, the seed lotus showed higher genetic diversity, which might have been due to the gene flow from the flower lotus to seed lotus by artificial crossing, and the rhizome lotus showed a much lower genetic diversity than the other groups. The present study provides SNP markers for lotus genomic diversity analysis, which will be useful for guiding lotus breeding.
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Affiliation(s)
- Zhengwei Liu
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Honglian Zhu
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Juhong Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Sanjie Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Yun Wang
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Jing Kuang
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Qun Ji
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Jing Peng
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Jie Wang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, People's Republic of China
- BGI-Agro Seed Service (Wuhan) Co Ltd, Wuhan, 430090, People's Republic of China
| | - Li Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Mingzhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Weidong Ke
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
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