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Kumar A, Dige M, Niranjan SK, Ahlawat S, Arora R, Kour A, Vijh RK. Whole genome resequencing revealed genomic variants and functional pathways related to adaptation in Indian yak populations. Anim Biotechnol 2024; 35:2282723. [PMID: 38006247 DOI: 10.1080/10495398.2023.2282723] [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] [Indexed: 11/26/2023]
Abstract
The present study aims to identify genomic variants through a whole genome sequencing (WGS) approach and uncover biological pathways associated with adaptation and fitness in Indian yak populations. A total of 30 samples (10 from each population) were included from Arunachali, Himachali and Ladakhi yak populations. WGS analysis revealed a total of 32171644, 27260825, and 32632460 SNPs and 4865254, 4429941, and 4847513 Indels in the Arunachali, Himachali, and Ladakhi yaks, respectively. Genes such as RYR2, SYNE2, BOLA, HF1, and the novel transcript ENSBGRG00000011079 were found to have the maximum number of high impact variants in all three yak populations, and might play a major role in local adaptation. Functional enrichment analysis of genes harboring high impact SNPs revealed overrepresented pathways related to response to stress, immune system regulation, and high-altitude adaptation. This study provides comprehensive information about genomic variants and their annotation in Indian yak populations, thus would serve as a data resource for researchers working on the yaks. Furthermore, it could be well exploited for better yak conservation strategies by estimating population genetics parameters viz., effective population size, inbreeding, and observed and expected heterozygosity.
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Affiliation(s)
- Amod Kumar
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, India
| | - Mahesh Dige
- Animal Genetic Resources Division, ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, India
| | - Saket Kumar Niranjan
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, India
| | - Sonika Ahlawat
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, India
| | - Reena Arora
- Animal Biotechnology Division, ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, India
| | - Aneet Kour
- ICAR-National Research Centre on Yak, Dirang, India
| | - Ramesh Kumar Vijh
- Animal Genetics Division, ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, India
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Peñafiel Loaiza N, Chafe AH, Moraes R M, Oleas NH, Roncal J. Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products. Evol Appl 2024; 17:e13765. [PMID: 39091352 PMCID: PMC11291087 DOI: 10.1111/eva.13765] [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: 04/06/2023] [Revised: 06/30/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus Parajubaea (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, P. torallyi and P. sunkha, are non-timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, P. cocoides, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of Parajubaea species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3753 bp) challenged the hypothesis that P. cocoides is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single-nucleotide polymorphism markers by genotyping-by-sequencing of 194 wild Parajubaea individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.
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Affiliation(s)
- Nicolás Peñafiel Loaiza
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
- Present address:
Chone y BabahoyoLojaEcuador
| | - Abigail H. Chafe
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Mónica Moraes R
- Herbario Nacional de Bolivia, Instituto de EcologíaUniversidad Mayor de San AndrésLa PazBolivia
| | - Nora H. Oleas
- Centro de Investigación de la Biodiversidad y Cambio Climático – BioCamb e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio AmbienteUniversidad IndoaméricaQuitoEcuador
| | - Julissa Roncal
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
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Liu H, Li L, Lu R. ZIP transporters-regulated Zn 2+ homeostasis: A novel determinant of human diseases. J Cell Physiol 2024; 239:e31223. [PMID: 38530191 DOI: 10.1002/jcp.31223] [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: 10/06/2023] [Revised: 01/16/2024] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
As an essential trace element for organisms, zinc participates in various physiological processes, such as RNA transcription, DNA replication, cell proliferation, and cell differentiation. The destruction of zinc homeostasis is associated with various diseases. Zinc homeostasis is controlled by the cooperative action of zinc transporter proteins that are responsible for the influx and efflux of zinc. Zinc transporter proteins are mainly categorized into two families: Zrt/Irt-like protein (SLC39A/ZIP) family and zinc transporter (SLC30A/ZNT) family. ZIP transporters contain 14 members, namely ZIP1-14, which can be further divided into four subfamilies. Currently, ZIP transporters-regulated zinc homeostasis is one of the research hotspots. Cumulative evidence suggests that ZIP transporters-regulated zinc homeostasis may cause physiological dysfunction and contribute to the onset and progression of diverse diseases, such as cancers, neurological diseases, and cardiovascular diseases. In this review, we initially discuss the structure and distribution of ZIP transporters. Furthermore, we comprehensively review the latest research progress of ZIP transporters-regulated zinc homeostasis in diseases, providing a new perspective into new therapeutic targets for treating related diseases.
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Affiliation(s)
- Huimei Liu
- Department of Pharmacology, Hengyang Medical School, University of South China, Hengyang, China
| | - Lanfang Li
- Department of Pharmacology, Hengyang Medical School, University of South China, Hengyang, China
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, China
| | - Ruirui Lu
- Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, School of Pharmaceutical Science, Hengyang Medical School, University of South China, Hengyang, China
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Zhang L, Zhang HL, Chen Y, Nizamani MM, Wu T, Liu T, Zhou Q. Assessing genetic diversity in critically endangered Chieniodendron hainanense populations within fragmented habitats in Hainan. Sci Rep 2024; 14:6988. [PMID: 38523175 PMCID: PMC10961303 DOI: 10.1038/s41598-024-56630-0] [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: 09/14/2023] [Accepted: 03/08/2024] [Indexed: 03/26/2024] Open
Abstract
Habitat fragmentation has led to a reduction in the geographic distribution of species, making small populations vulnerable to extinction due to environmental, demographic, and genetic factors. The wild plant Chieniodendron hainanense, a species with extremely small populations, is currently facing endangerment and thus requires urgent conservation efforts. Understanding its genetic diversity is essential for uncovering the underlying mechanisms of its vulnerability and for developing effective conservation strategies. In our study, we analyzed 35 specimens from six different populations of C. hainanense using genotyping-by-sequencing (GBS) and single nucleotide polymorphism (SNP) methodologies. Our findings indicate that C. hainanense has limited genetic diversity. The observed heterozygosity across the populations ranged from 10.79 to 14.55%, with an average of 13.15%. We categorized the six populations of C. hainanense into two distinct groups: (1) Diaoluoshan and Baishaling, and (2) Wuzhishan, Huishan, Bawangling, and Jianfengling. The genetic differentiation among these populations was found to be relatively weak. The observed loss of diversity is likely a result of the effects of natural selection.
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Affiliation(s)
- Li Zhang
- Guizhou Normal University Museum, Guizhou Normal University, Guiyang, 550001, China
| | - Hai-Li Zhang
- Sanya Nanfan Research Institute, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Yukai Chen
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China.
| | - Mir Muhammad Nizamani
- Department of Plant Pathology, Agricultural College, Guizhou University, Guiyang, 550001, China.
| | - Tingtian Wu
- Hainan Academy of Forestry, Hainan Academy of Mangrove, Haikou, 570228, China
| | - Tingting Liu
- Guizhou Normal University Museum, Guizhou Normal University, Guiyang, 550001, China
| | - Qin Zhou
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, 571158, China
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Barbosa CFC, Asunto JC, Koh RBL, Santos DMC, Zhang D, Cao EP, Galvez LC. Genome-Wide SNP and Indel Discovery in Abaca ( Musa textilis Née) and among Other Musa spp. for Abaca Genetic Resources Management. Curr Issues Mol Biol 2023; 45:5776-5797. [PMID: 37504281 PMCID: PMC10377871 DOI: 10.3390/cimb45070365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/29/2023] Open
Abstract
Abaca (Musa textilis Née) is an economically important fiber crop in the Philippines. Its economic potential, however, is hampered by biotic and abiotic stresses, which are exacerbated by insufficient genomic resources for varietal identification vital for crop improvement. To address these gaps, this study aimed to discover genome-wide polymorphisms among abaca cultivars and other Musa species and analyze their potential as genetic marker resources. This was achieved through whole-genome Illumina resequencing of abaca cultivars and variant calling using BCFtools, followed by genetic diversity and phylogenetic analyses. A total of 20,590,381 high-quality single-nucleotide polymorphisms (SNP) and DNA insertions/deletions (InDels) were mined across 16 abaca cultivars. Filtering based on linkage disequilibrium (LD) yielded 130,768 SNPs and 13,620 InDels, accounting for 0.396 ± 0.106 and 0.431 ± 0.111 of gene diversity across these cultivars. LD-pruned polymorphisms across abaca, M. troglodytarum, M. acuminata and M. balbisiana enabled genetic differentiation within abaca and across the four Musa spp. Phylogenetic analysis revealed the registered varieties Abuab and Inosa to accumulate a significant number of mutations, eliciting further studies linking mutations to their advantageous phenotypes. Overall, this study pioneered in producing marker resources in abaca based on genome-wide polymorphisms vital for varietal authentication and comparative genotyping with the more studied Musa spp.
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Affiliation(s)
- Cris Francis C Barbosa
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Building, Department of Agriculture (DA) Compound, Quezon City 1101, Philippines
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Jayson C Asunto
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Building, Department of Agriculture (DA) Compound, Quezon City 1101, Philippines
| | - Rhosener Bhea L Koh
- National Institute of Molecular Biology and Biotechnology, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Daisy May C Santos
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705, USA
| | - Ernelea P Cao
- Institute of Biology, College of Science, University of the Philippines Diliman, Quezon City 1101, Philippines
| | - Leny C Galvez
- Philippine Fiber Industry Development Authority (PhilFIDA), PCAF Building, Department of Agriculture (DA) Compound, Quezon City 1101, Philippines
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Singh A, Mahato AK, Maurya A, Rajkumar S, Singh AK, Bhardwaj R, Kaushik SK, Kumar S, Gupta V, Singh K, Singh R. Amaranth Genomic Resource Database: an integrated database resource of Amaranth genes and genomics. FRONTIERS IN PLANT SCIENCE 2023; 14:1203855. [PMID: 37448872 PMCID: PMC10337998 DOI: 10.3389/fpls.2023.1203855] [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: 04/11/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023]
Abstract
Amaranth (Amaranthus L.) is native to Mexico and North America, where it was cultivated thousands of years ago, but now amaranth is grown worldwide. Amaranth is one of the most promising food crops with high nutritional value and belongs to the family Amaranthaceae. The high-quality genome assembly of cultivated amaranth species (A. hypochondriacus, A. cruentus) and wild/weedy species (A. tuberculatus, A. hybridus, and A. palmeri) has already been reported; therefore, we developed an Amaranth Genomic Resource Database (AGRDB) to provide access to all the genomic information such as genes, SSRs, SNPs, TFs, miRNAs, and transporters in one place. The AGRDB database contains functionally annotated gene information with their sequence details, genic as well as genomic SSRs with their three sets of primers, transcription factors classified into different families with their sequence information and annotation details, putative miRNAs with their family, sequences, and targeted gene details, transporter genes with their superfamily, trans-membrane domain details, and details of genic as well as nongenic SNPs with 3' and 5' flanking sequence information of five amaranth species. A database search can be performed using the gene ID, sequence ID, sequence motif, motif repeat, family name, annotation keyword, scaffold or chromosome numbers, etc. This resource also includes some useful tools, including JBrowse for the visualization of genes, SSRs, SNPs, and TFs on the respective amaranth genomes and BLAST search to perform a BLAST search of the user's query sequence against the amaranth genome as well as protein sequences. The AGRDB database will serve as a potential platform for genetic improvement and characterization of this futuristic crop. The AGRDB database will be accessible via the link: http://www.nbpgr.ernet.in:8080/AmaranthGRD/.
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Affiliation(s)
- Akshay Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Avantika Maurya
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - S. Rajkumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - A. K. Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Bhardwaj
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - S. K. Kaushik
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sandeep Kumar
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Veena Gupta
- Division of Germplasm Conservation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kuldeep Singh
- International Crop Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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Jing Y, Bian L, Zhang X, Zhao B, Zheng R, Su S, Ye D, Zheng X, El-Kassaby YA, Shi J. Genetic diversity and structure of the 4 th cycle breeding population of Chinese fir ( Cunninghamia lanceolata (lamb.) hook). FRONTIERS IN PLANT SCIENCE 2023; 14:1106615. [PMID: 36778690 PMCID: PMC9911867 DOI: 10.3389/fpls.2023.1106615] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Studying population genetic structure and diversity is crucial for the marker-assisted selection and breeding of coniferous tree species. In this study, using RAD-seq technology, we developed 343,644 high-quality single nucleotide polymorphism (SNP) markers to resolve the genetic diversity and population genetic structure of 233 Chinese fir selected individuals from the 4th cycle breeding program, representing different breeding generations and provenances. The genetic diversity of the 4th cycle breeding population was high with nucleotide diversity (Pi ) of 0.003, and Ho and He of 0.215 and 0.233, respectively, indicating that the breeding population has a broad genetic base. The genetic differentiation level between the different breeding generations and different provenances was low (Fst < 0.05), with population structure analysis results dividing the 233 individuals into four subgroups. Each subgroup has a mixed branch with interpenetration and weak population structure, which might be related to breeding rather than provenance, with aggregation from the same source only being in the local branches. Our results provide a reference for further research on the marker-assisted selective breeding of Chinese fir and other coniferous trees.
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Affiliation(s)
- Yonglian Jing
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Liming Bian
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Xuefeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Benwen Zhao
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Renhua Zheng
- Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China, Fujian Academy of Forestry Science, Fuzhou, China
| | - Shunde Su
- Key Laboratory of Timber Forest Breeding and Cultivation for Mountainous Areas in Southern China, Fujian Academy of Forestry Science, Fuzhou, China
| | - Daiquan Ye
- Department of Tree Improvement, Yangkou State-owned Forest Farm, Nanping, China
| | - Xueyan Zheng
- Department of Tree Improvement, Yangkou State-owned Forest Farm, Nanping, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, The University of British Columbia, Vancouver, BC, Canada
| | - Jisen Shi
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
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Kerry RG, Montalbo FJP, Das R, Patra S, Mahapatra GP, Maurya GK, Nayak V, Jena AB, Ukhurebor KE, Jena RC, Gouda S, Majhi S, Rout JR. An overview of remote monitoring methods in biodiversity conservation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:80179-80221. [PMID: 36197618 PMCID: PMC9534007 DOI: 10.1007/s11356-022-23242-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Conservation of biodiversity is critical for the coexistence of humans and the sustenance of other living organisms within the ecosystem. Identification and prioritization of specific regions to be conserved are impossible without proper information about the sites. Advanced monitoring agencies like the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) had accredited that the sum total of species that are now threatened with extinction is higher than ever before in the past and are progressing toward extinct at an alarming rate. Besides this, the conceptualized global responses to these crises are still inadequate and entail drastic changes. Therefore, more sophisticated monitoring and conservation techniques are required which can simultaneously cover a larger surface area within a stipulated time frame and gather a large pool of data. Hence, this study is an overview of remote monitoring methods in biodiversity conservation via a survey of evidence-based reviews and related studies, wherein the description of the application of some technology for biodiversity conservation and monitoring is highlighted. Finally, the paper also describes various transformative smart technologies like artificial intelligence (AI) and/or machine learning algorithms for enhanced working efficiency of currently available techniques that will aid remote monitoring methods in biodiversity conservation.
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Affiliation(s)
- Rout George Kerry
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | | | - Rajeswari Das
- Department of Soil Science and Agricultural Chemistry, School of Agriculture, GIET University, Gunupur, Rayagada, Odisha 765022 India
| | - Sushmita Patra
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | | | - Ganesh Kumar Maurya
- Zoology Section, Mahila MahaVidyalya, Banaras Hindu University, Varanasi, 221005 India
| | - Vinayak Nayak
- Indian Council of Agricultural Research-Directorate of Foot and Mouth Disease-International Centre for Foot and Mouth Disease, Arugul, Bhubaneswar, Odisha 752050 India
| | - Atala Bihari Jena
- Department of Neurosurgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Ram Chandra Jena
- Department of Pharmaceutical Sciences, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Sushanto Gouda
- Department of Zoology, Mizoram University, Aizawl, 796009 India
| | - Sanatan Majhi
- Department of Biotechnology, Utkal University, Vani Vihar, Bhubaneswar, Odisha 751004 India
| | - Jyoti Ranjan Rout
- School of Biological Sciences, AIPH University, Bhubaneswar, Odisha 752101 India
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Yang W, Bai Z, Wang F, Zou M, Wang X, Xie J, Zhang F. Analysis of the genetic diversity and population structure of Monochasma savatieri Franch. ex Maxim using novel EST-SSR markers. BMC Genomics 2022; 23:597. [PMID: 35974306 PMCID: PMC9382759 DOI: 10.1186/s12864-022-08832-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background Monochasma savatieri Franch. ex Maxim is a medicinally valuable herb. However, the collection and protection of the wild germplasm resources of M. savatieri are still insufficient, and their genetic diversity and population structure have been poorly studied. Results We collected and examined 46 M. savatieri individuals from Fujian, Hunan, Jiangxi, and Zhejiang provinces for genetic diversity and population structure, using 33 newly developed expressed sequence tag-simple sequence repeat (EST-SSR) markers. Applying these markers, we detected a total of 208 alleles, with an average of 6.303 alleles per locus. The polymorphic information content varied from 0.138 to 0.884 (average: 0.668), indicating a high level of polymorphism. At the population level, there was a low degree of genetic diversity among populations (I = 0.535, He = 0.342), with Zhejiang individuals showing the highest genetic diversity among the four populations (Fst = 0.497), which indicated little gene flow within the M. savatieri populations (Nm = 0.253). Mantel test analysis revealed a significant positive correlation between geographical and genetic distance among populations (R2 = 0.3304, p < 0.05), and structure and principal coordinate analyses supported classification of populations into three clusters, which was consistent with the findings of cluster analysis. Conclusions As a rare medicinal plants, the protection of M. savatieri does not look optimistic, and accordingly, protective efforts should be beefed up on the natural wild populations. This study provided novel tools and insights for designing effective collection and conservation strategies for M. savatieri. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08832-x.
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Affiliation(s)
- Wanling Yang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Zhiyi Bai
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Fuqiang Wang
- Yichun Academy of Sciences, Yichun, 336000, China
| | - Mingzhu Zou
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Xinru Wang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Jiankun Xie
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China
| | - Fantao Zhang
- College of Life Sciences, Jiangxi Normal University, Nanchang, 330022, China.
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Winfield M, Wilkinson P, Burridge A, Allen A, Coghill J, Waterfall C, Edwards K, Barker G. CerealsDB: A Whistle-Stop Tour of an Open Access SNP Resource. Methods Mol Biol 2022; 2443:133-146. [PMID: 35037203 DOI: 10.1007/978-1-0716-2067-0_6] [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] [Indexed: 06/14/2023]
Abstract
The CerealsDB website, created by members of the Functional Genomics Group at the University of Bristol, provides access to a database containing SNP and genotyping data for hexaploid wheat and, to a lesser extent, its progenitors and several of its relatives. The site is principally aimed at plant breeders and research scientists who wish to obtain information regarding SNP markers; for example, obtain primers used for their identification or the sequences upon which they are based. The database underpinning the website contains circa one million putative varietal SNPs of which several hundreds of thousands have been experimentally validated on a range of common genotyping platforms. For each SNP marker, the site also hosts the allelic scores for thousands of elite wheat varieties, landrace cultivars, and wheat relatives. Tools are available to help negotiate and visualize the datasets. The website has been designed to be simple and straightforward to use and is completely open access.
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Affiliation(s)
- Mark Winfield
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | - Paul Wilkinson
- Department of Functional and Comparative Genomics, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Amanda Burridge
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Alexandra Allen
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Jane Coghill
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - Keith Edwards
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Gary Barker
- School of Biological Sciences, University of Bristol, Bristol, UK
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Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS). Genes (Basel) 2021; 12:genes12122007. [PMID: 34946959 PMCID: PMC8701156 DOI: 10.3390/genes12122007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022] Open
Abstract
Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.
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Portella RO, Cordeiro EMG, Marques APS, Ming LC, Zucchi MI, Lima MP, Martins ER, Hantao LW, Sawaya ACHF, Semir J, Pinheiro JB, Marques MOM. Evidence of altitudinal gradient modifying genomic and chemical diversity in populations of Lychnophora pinaster Mart. PHYTOCHEMISTRY 2021; 192:112898. [PMID: 34492545 DOI: 10.1016/j.phytochem.2021.112898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/27/2021] [Accepted: 08/03/2021] [Indexed: 05/28/2023]
Abstract
Lychnophora pinaster Mart. (Asteraceae) is endemic to the Brazilian Cerrado. It is distributed along the altitudinal gradient of the mountainous ranges of the state of Minas Gerais. This study aimed to evaluate the influence of altitude on the genetic diversity of L. pinaster populations and the effects of altitude and climatic factors on essential oil chemical composition. Essential oils from L. pinaster populations from the north (North 01, North 02, and North 03, 700-859 m) and the Metropolitan region of Belo Horizonte (MhBH 01 and MrBH 02, 1366-1498 m) were analyzed. SNP markers from L. pinaster in these regions and Campos das Vertentes (CV 01, CV 02, and CV 03, 1055-1292 m) were also analyzed. The main compounds in essential oils were 14-hydroxy-α-humulene (North 01 and North 03), cedr-8(15)-en-9-α-ol (North 02), 14-acetoxy-α-humulene (MrBH 01), and 4-oxo-15-nor-eudesman-11-ene (MrBH 02). Hierarchical cluster and heatmap analyses showed that the North and MrBH populations included five different groups, indicating the chemical composition of essential oils is distinct in each population. Furthermore, principal component analysis showed that higher altitudes (1366 m and 1498 m) in the MrBH influence the chemical composition of essential oils, and climatic factors determine the chemical composition in North region. The genetic diversity showed that most alleles are in Hardy-Weinberg equilibrium and imply high genetic variation and genetic polymorphisms between populations. Furthermore, the results of Mantel tests (R = 0.3861517; p = 0.04709529; R = 0.9423121; p = 0.02739726) also showed that higher altitude (>1360 m) shapes the genetic diversity at the MrBH. The genetic structure showed that higher altitudes (>1360 m) contribute to the structure of the MrBH populations, but not to North and CV populations. Therefore, the altitudinal ranges of Minas Gerais mountainous ranges determine the higher genetic and chemical diversity of L. pinaster populations.
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Affiliation(s)
- Roberto O Portella
- Universidade de Taubaté, Av. Tiradentes, 500, Bom Conselho, CEP: 12030-180, Taubaté, SP, Brazil; Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua Prof. Dr. Antônio Celso Wagner Zanin, 250 - Distrito de Rubião Junior, CEP: 18618-689, Botucatu, SP, Brazil
| | - Erick M G Cordeiro
- Agência Paulista de Tecnologia dos Agronegócios, Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Caixa Postal 28, CEP: 13400-970, Piracicaba, SP, Brazil
| | - Ana Paula S Marques
- Departamento de Botânica, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua Prof. Dr. Antônio Celso Wagner Zanin, 250 - Distrito de Rubião Junior, CEP: 18618-689, Botucatu, SP, Brazil
| | - Lin C Ming
- Departamento de Horticultura, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista "Júlio de Mesquita Filho," Rua José Barbosa de Barros, 1780, CEP: 18610-307, Botucatu, SP, Brazil
| | - Maria I Zucchi
- Agência Paulista de Tecnologia dos Agronegócios, Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Caixa Postal 28, CEP: 13400-970, Piracicaba, SP, Brazil
| | - Maria P Lima
- Coordenação de Inovação Tecnológica, Instituto Nacional de Pesquisas da Amazônia, Avenida André Araújo, 2936, Aleixo, CEP: 69011-970, Manaus, AM, Brazil
| | - Ernane R Martins
- Instituto de Ciências Agrárias, Universidade Federal de Minas Gerais, Av. Universitária, 1000, Universitário, CEP: 39404-547, Montes Claros, MG, Brazil
| | - Leandro W Hantao
- Instituto de Química, Universidade Estadual de Campinas, Rua Monteiro Lobato, 270, CEP: 13083-862, Campinas, SP, Brazil
| | - Alexandra C H F Sawaya
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Rua Cândido Portinari, 200, Cidade Universitária, CEP: 13083-871, Campinas, SP, Brazil
| | - João Semir
- Departamento de Botânica, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato, 255, Barão Geraldo, CEP: 13083-862, Campinas, SP, Brazil
| | - José B Pinheiro
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, CEP: 13418-900, Piracicaba, SP, Brazil
| | - Marcia O M Marques
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico, Avenida Barão de Itapura, 1481, Botafogo, CEP: 13020-902, Campinas, SP, Brazil.
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Rajesh MK, Gangurde SS, Pandey MK, Niral V, Sudha R, Jerard BA, Kadke GN, Sabana AA, Muralikrishna KS, Samsudeen K, Karun A, Prasad TSK. Insights on Genetic Diversity, Population Structure, and Linkage Disequilibrium in Globally Diverse Coconut Accessions Using Genotyping-by-Sequencing. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:796-809. [PMID: 34757849 DOI: 10.1089/omi.2021.0159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Genotyping-by-sequencing (GBS) has emerged as a cost-effective approach for genome-wide discovery of single-nucleotide polymorphism (SNP) markers and high-throughput genotyping. In this study, 96 coconut palms, representing 16 accessions from globally diverse origins, were genotyped using the GBS strategy. A total of 10,835 high-quality SNPs, which were identified after stringent filtering, were utilized to assess genetic diversity, population structure, and linkage disequilibrium (LD) analyses. The polymorphism information content (PIC) values of SNPs ranged from 0.1 to 0.4, with a large proportion of SNPs (8633 nos.; 79.7%) having a higher PIC in the range of 0.3-0.4. The genetic diversity analysis revealed the existence of a high level of variation in coconut accessions, with an average expected heterozygosity (He) value of 0.43. Unweighted neighbor-joining phylogenetic tree and Bayesian-based model population structure grouped coconut genotypes into four main clusters. The accessions are generally clustered based on their height (tall or dwarf), with a few accession clusterings based on geographical origins. Investigation of LD pattern in coconut indicated a relatively rapid LD decay with a short range (9 kb). The results obtained in this study will contribute to enhancing the capacity of coconut researchers to utilize genetic diversity for further genetic improvement. In addition, it would open up possibilities for performing genomic studies such as genome-wide association studies and genomic selection to accelerate the efficiency and speed of coconut genetic improvement.
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Affiliation(s)
- Muliyar Krishna Rajesh
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
| | - Sunil Shivaji Gangurde
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Manish Kumar Pandey
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Vittal Niral
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
| | - Raju Sudha
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
| | - Bosco Augustine Jerard
- ICAR-Central Island Agricultural Research Institute (ICAR-CIARI), Port Blair, Andaman and Nicobar Islands, India
| | | | - Abdulla Abdulla Sabana
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
| | | | - Kukkamgai Samsudeen
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
| | - Anitha Karun
- Division of Crop Improvement, ICAR-Central Plantation Crops Research Institute (ICAR-CPCRI), Kasaragod, Kerala, India
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Population Genetic Diversity and Structure of an Endangered Salicaceae Species in Northeast China: Chosenia arbutifolia (Pall.) A. Skv. FORESTS 2021. [DOI: 10.3390/f12091282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chosenia arbutifolia (Pall.) A. Skv. is a unique and endangered species belonging to the Salicaceae family. It has great potential for ornamental and industrial use. However, human interference has led to a decrease in and fragmentation of its natural populations in the past two decades. To effectively evaluate, utilize, and conserve available resources, the genetic diversity and population structure of C. arbutifolia were analyzed in this study. A total of 142 individuals from ten provenances were sampled and sequenced. Moderate diversity was detected among these, with a mean expected heterozygosity and Shannon’s Wiener index of 0.3505 and 0.5258, respectively. The inbreeding coefficient was negative, indicating a significant excess of heterozygotes. The fixation index varied from 0.0068 to 0.3063, showing a varied genetic differentiation between populations. Analysis of molecular variance demonstrated that differentiation accounted for 82.23% of the total variation among individuals, while the remaining 17.77% variation was between populations. Furthermore, the results of population structure analysis indicated that the 142 individuals originated from three primitive groups. To provide genetic information and help design conservation and management strategies, landscape genomics analysis was performed by investigating loci associated with environmental variables. Eighteen SNP markers were associated with altitude and annual average temperature, of which five were ascribed with specific functions. In conclusion, the current study furthers the understanding of C. arbutifolia genetic architecture and provides insights for germplasm protection.
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Gan ST, Teo CJ, Manirasa S, Wong WC, Wong CK. Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation. PLoS One 2021; 16:e0255418. [PMID: 34324602 PMCID: PMC8320974 DOI: 10.1371/journal.pone.0255418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/15/2021] [Indexed: 11/19/2022] Open
Abstract
Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright's fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei's genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.
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Affiliation(s)
- Siou Ting Gan
- Biotechnology Section, Advanced Agriecological Research Sdn. Bhd. (AAR), AAR-UNMC Biotechnology Research Centre, Semenyih, Selangor, Malaysia
| | - Chin Jit Teo
- Plant Breeding Section, Advanced Agriecological Research Sdn. Bhd. (AAR), Paloh, Johor, Malaysia
| | - Shobana Manirasa
- Biotechnology Section, Advanced Agriecological Research Sdn. Bhd. (AAR), AAR-UNMC Biotechnology Research Centre, Semenyih, Selangor, Malaysia
| | - Wei Chee Wong
- Biotechnology Section, Advanced Agriecological Research Sdn. Bhd. (AAR), AAR-UNMC Biotechnology Research Centre, Semenyih, Selangor, Malaysia
| | - Choo Kien Wong
- Plant Breeding Section, Advanced Agriecological Research Sdn. Bhd. (AAR), Paloh, Johor, Malaysia
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Gao J, Ning XL. SNP detection and population structure evaluation of Salix gordejevii Y. L. Chang et Skv. in Hunshandake Sandland, Inner Mongolia, China. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:997-1005. [PMID: 34108824 PMCID: PMC8140056 DOI: 10.1007/s12298-021-00994-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/20/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism and, hence, are highly favorable markers for genetic map construction and genome-wide association studies. Based on the DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection, the genetic diversity and population structure of Salix gordejevii Y. L. Chang et Skv., a valuable sand-fixing shrub, was assessed in 199 accessions from 20 populations in Hunshandake Sandland of northern China. A total of 623.15 M reads resulted in 30.49 × sequencing depth on average and a mean Q30 of 95.70%, and 2,287,715 SNPs in 178,509 polymorphic SLAF tags were obtained. By discarding minor allele frequency > 0.05 and integrity > 0.8, a total of 93,600 SNPs were retained for population genetic analyses, which revealed that 199 individuals could be divided into six groups based on cross-validation errors. However, this grouping pattern did not match the geographical distribution, indicating that there is no apparent geographic barrier in the blank areas where S. gordejevii was not distributed in Hunshandake Sandland. In addition, the physical distance of linkage disequilibrium decay in the analyzed S. gordejevii individuals was 18.5 kb when r 2 = 0.1. The linkage disequilibrium decay distances for different chromosomes varied from 4.6 kb (chromosome 16) to 37.8 kb (chromosome 3). The obtained SNPs offer suitable marker resources for further genetic and genomic studies and will benefit S. gordejevii breeding programs.
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Affiliation(s)
- Jian Gao
- Faculty of Resources and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Baotou, 014030 China
| | - Xiao-Li Ning
- Faculty of Resources and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Baotou, 014030 China
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17
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Sarimana U, Herrero J, Erika P, Indarto N, Wendra F, Santika B, Ritter E, Sembiring Z, Asmono D. Analysis of genetic diversity and discrimination of Oil Palm DxP populations based on the origins of pisifera elite parents. BREEDING SCIENCE 2021; 71:134-143. [PMID: 34377061 PMCID: PMC8329876 DOI: 10.1270/jsbbs.20043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/29/2020] [Indexed: 06/13/2023]
Abstract
A total of 251 Dura cross Pisifera (DxP) hybrid palms from six populations descending from six parental African Pisifera origins and involving 12 progenies were analyzed with 19 selected Simple Sequence Repeats (SSR) markers. A total of 110 alleles were produced, ranging from three to eight per SSR, with a mean of 5.8 alleles per SSR locus. Of these, 68.5% were considered shared alleles by more than one population and the remaining 31.5% were population specific alleles. They generated between six and 21 haplotypes in all populations, and depending on the SSR marker, between one and 10 haplotypes within populations. Various parameters for analyzing genetic variability, differentiation and genetic structure were computed using GenAlEx, Structure and Darwin software. The obtained results confirmed microsatellites as a robust, feasible and trustful method for obtaining DNA fingerprints, tracing the source of oil palm samples. With respect to the authenticity of materials or for solving legitimacy issues, accession belonging to each population by SSR markers could be distinguished, but additional SSR should be screened for improving this process.
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Affiliation(s)
- Upit Sarimana
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Javier Herrero
- NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Pratiwi Erika
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Nurcahyono Indarto
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Fahmi Wendra
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Baitha Santika
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Enrique Ritter
- NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Zulhermana Sembiring
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Dwi Asmono
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
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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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Jung J, Do HDK, Hyun J, Kim C, Kim JH. Comparative analysis and implications of the chloroplast genomes of three thistles ( Carduus L., Asteraceae). PeerJ 2021; 9:e10687. [PMID: 33520461 PMCID: PMC7811785 DOI: 10.7717/peerj.10687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 12/11/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Carduus, commonly known as plumeless thistles, is a genus in the Asteraceae family that exhibits both medicinal value and invasive tendencies. However, the genomic data of Carduus (i.e., complete chloroplast genomes) have not been sequenced. METHODS We sequenced and assembled the chloroplast genome (cpDNA) sequences of three Carduus species using the Illumina Miseq sequencing system and Geneious Prime. Phylogenetic relationships between Carduus and related taxa were reconstructed using Maximum Likelihood and Bayesian Inference analyses. In addition, we used a single nucleotide polymorphism (SNP) in the protein coding region of the matK gene to develop molecular markers to distinguish C. crispus from C. acanthoides and C. tenuiflorus. RESULTS The cpDNA sequences of C. crispus, C. acanthoides, and C. tenuiflorus ranged from 152,342 bp to 152,617 bp in length. Comparative genomic analysis revealed high conservation in terms of gene content (including 80 protein-coding, 30 tRNA, and four rRNA genes) and gene order within the three focal species and members of subfamily Carduoideae. Despite their high similarity, the three species differed with respect to the number and content of repeats in the chloroplast genome. Additionally, eight hotspot regions, including psbI-trnS_GCU, trnE_UUC-rpoB, trnR_UCU-trnG_UCC, psbC-trnS_UGA, trnT_UGU-trnL_UAA, psbT-psbN, petD-rpoA, and rpl16-rps3, were identified in the study species. Phylogenetic analyses inferred from 78 protein-coding and non-coding regions indicated that Carduus is polyphyletic, suggesting the need for additional studies to reconstruct relationships between thistles and related taxa. Based on a SNP in matK, we successfully developed a molecular marker and protocol for distinguishing C. crispus from the other two focal species. Our study provides preliminary chloroplast genome data for further studies on plastid genome evolution, phylogeny, and development of species-level markers in Carduus.
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Affiliation(s)
- Joonhyung Jung
- Department of Life Science, Gachon University, Seongnam, Gyeonggi, Korea
| | - Hoang Dang Khoa Do
- Department of Life Science, Gachon University, Seongnam, Gyeonggi, Korea
- Nguyen Tat Thanh Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - JongYoung Hyun
- Department of Life Science, Gachon University, Seongnam, Gyeonggi, Korea
| | - Changkyun Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi, Korea
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi, Korea
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Xia W, Dou Y, Liu R, Gong S, Huang D, Fan H, Xiao Y. Genome-wide discovery and characterization of long noncoding RNAs in African oil palm ( Elaeis guineensis Jacq.). PeerJ 2020; 8:e9585. [PMID: 33194332 PMCID: PMC7643553 DOI: 10.7717/peerj.9585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 06/30/2020] [Indexed: 01/04/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are an important class of genes and play important roles in a range of biological processes. However, few reports have described the identification of lncRNAs in oil palm. In this study, we applied strand specific RNA-seq with rRNA removal to identify 1,363 lncRNAs from the equally mixed tissues of oil palm spear leaf and six different developmental stages of mesocarp (8–24 weeks). Based on strand specific RNA-seq data and 18 released oil palm transcriptomes, we systematically characterized the expression patterns of lncRNA loci and their target genes. A total of 875 uniq target genes for natural antisense lncRNAs (NAT-lncRNA, 712), long intergenic noncoding RNAs (lincRNAs, 92), intronic-lncRNAs (33), and sense-lncRNAs (52) were predicted. A majority of lncRNA loci (77.8%–89.6%) had low expression in 18 transcriptomes, while only 89 lncRNA loci had medium to high expression in at least one transcriptome. Coexpression analysis between lncRNAs and their target genes indicated that 6% of lncRNAs had expression patterns positively correlated with those of target genes. Based on single nucleotide polymorphism (SNP) markers derived from our previous research, 6,882 SNPs were detected for lncRNAs and 28 SNPs belonging to 21 lncRNAs were associated with the variation of fatty acid contents. Moreover, seven lncRNAs showed expression patterns positively correlated expression pattern with those of genes in de novo fatty acid synthesis pathways. Our study identified a collection of lncRNAs for oil palm and provided clues for further research into lncRNAs that may regulate mesocarp development and lipid metabolism.
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Affiliation(s)
- Wei Xia
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yajing Dou
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rui Liu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Shufang Gong
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Dongyi Huang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Haikuo Fan
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yong Xiao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
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Reconstruction of the Largest Pedigree Network for Pear Cultivars and Evaluation of the Genetic Diversity of the USDA-ARS National Pyrus Collection. G3-GENES GENOMES GENETICS 2020; 10:3285-3297. [PMID: 32675069 PMCID: PMC7466967 DOI: 10.1534/g3.120.401327] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The USDA-ARS National Clonal Germplasm Repository (NCGR) in Corvallis, Oregon, maintains one of the world's largest and most diverse living Pyrus collection. A thorough genetic characterization of this germplasm will provide relevant information to optimize the conservation strategy of pear biodiversity, support the use of this germplasm in breeding, and increase our knowledge of Pyrus taxonomy, evolution, and domestication. In the last two decades simple sequence repeat (SSR) markers have been used at the NCGR for cultivar identification and small population structure analysis. However, the recent development of the Applied Biosystems Axiom Pear 70K Genotyping Array has allowed high-density single nucleotide polymorphism (SNP)-based genotyping of almost the entire collection. In this study, we have analyzed this rich dataset to discover new synonyms and mutants, identify putative labeling errors in the collection, reconstruct the largest pear cultivar pedigree and further elucidate the genetic diversity of Pyrus.
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Xiong S, Zhao Y, Chen Y, Gao M, Wu L, Wang Y. Genetic diversity and population structure of Quercus fabri Hance in China revealed by genotyping-by-sequencing. Ecol Evol 2020; 10:8949-8958. [PMID: 32884670 PMCID: PMC7452768 DOI: 10.1002/ece3.6598] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/17/2020] [Accepted: 06/29/2020] [Indexed: 11/11/2022] Open
Abstract
Analysis of genetic diversity and population structure among Quercus fabri populations is essential for the conservation and utilization of Q. fabri resources. Here, the genetic diversity and structure of 158 individuals from 13 natural populations of Quercus fabri in China were analyzed using genotyping-by-sequencing (GBS). A total of 459,564 high-quality single nucleotide polymorphisms (SNPs) were obtained after filtration for subsequent analysis. Genetic structure analysis revealed that these individuals can be clustered into two groups and the structure can be explained mainly by the geographic barrier, showed gene introgression from coastal to inland areas and high mountains could significantly hinder the mutual introgression of genes. Genetic diversity analysis indicated that the individual differences within groups are greater than the differences between the two groups. These results will help us better understand the genetic backgrounds of Q. fabri.
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Affiliation(s)
- Shifa Xiong
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
| | - Yunxiao Zhao
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
| | - Ming Gao
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
| | - Liwen Wu
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and BreedingChinese Academy of ForestryBeijingChina
- Research Institute of Subtropical ForestryChinese Academy of ForestryHangzhouChina
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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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Construction of a high density linkage map in Oil Palm using SPET markers. Sci Rep 2020; 10:9998. [PMID: 32561804 PMCID: PMC7305113 DOI: 10.1038/s41598-020-67118-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/01/2020] [Indexed: 11/08/2022] Open
Abstract
A high-density genetic linkage map from a controlled cross of two oil palm (Elaeis guineensis) genotypes was constructed based on Single Primer Enrichment Technology (SPET) markers. A 5K panel of hybridization probes were used for this purpose which was derived from previously developed SNP primers in oil palm. Initially, 13,384 SNPs were detected which were reduced to 13,073 SNPs after filtering for only bi-allelic SNP. Around 75% of the markers were found to be monomorphic in the progeny, reducing the markers left for linkage mapping to 3,501. Using Lep-MAP3 software, a linkage map was constructed which contained initially 2,388 markers and had a total length of 1,370 cM. In many cases several adjacent SNP were located on the same locus, due to missing recombination events between them, leading to a total of 1,054 loci on the 16 LG. Nevertheless, the marker density of 1.74 markers per cM (0.57 cM/marker) should allow the detection of QTLs in the future. This study shows that cost efficient SPET markers are suitable for linkage map construction in oil palm and probably, also in other species.
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Luo T, Xia W, Gong S, Mason AS, Li Z, Liu R, Dou Y, Tang W, Fan H, Zhang C, Xiao Y. Identifying Vitamin E Biosynthesis Genes in Elaeis guineensis by Genome-Wide Association Study. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:678-685. [PMID: 31858793 DOI: 10.1021/acs.jafc.9b03832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Elaeis guineensis is a tropical oil crop and has the highest oil yield per unit area. Palm oil has high palmitic acid content and is also rich in vitamins, including vitamin E. We conducted genome-wide association studies in a diversity panel of 161 E. guineensis accessions to identify single-nucleotide polymorphisms (SNPs) linked with vitamin E and validated candidate genes in these marker-associated intervals. Based on the SNPs reported in our previous research, 47 SNP markers were detected to be significantly associated with the variation of tocopherol and tocotrienol content at a cutoff P value of 6.3 × 10-7. A total of 656 candidate genes in the flanking regions of the 47 SNPs were identified, followed by pathway enrichment analysis. Of these candidate genes, EgHGGT (homogentisate geranylgeranyl transferase) involved in the biosynthesis of tocotrienols had a higher expression level in the mesocarp compared to other tissues. Expression of the EgHGGT gene was positively correlated with the variation in α-tocotrienol content. Induced overexpression of the gene in Arabidopsis caused a significant increase in vitamin E content and production of α-tocotrienols compared to wild Arabidopsis.
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Affiliation(s)
- Tingting Luo
- National Research Center of Rapeseed Engineering and Technology, College of Plant Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Wei Xia
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops , Hainan University , Haikou 570228 , P.R China
| | - Shufang Gong
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition , Justus Liebig University Giessen , Heinrich-Buff-Ring 26-32 , Giessen 35392i , Germany
| | - Zhiying Li
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
- Hainan Key Laboratory for Biosafe Monitoring and Molecular Breeding in Off-Season Reproduction Region , Institute of Tropical Bioscience and Biotechnology Chinese Academy of Tropical Agricultural Sciences , Haikou 571101 , China
| | - Rui Liu
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Yajing Dou
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Wenqi Tang
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Haikuo Fan
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
| | - Chunyu Zhang
- National Research Center of Rapeseed Engineering and Technology, College of Plant Science and Technology , Huazhong Agricultural University , Wuhan 430070 , China
| | - Yong Xiao
- Coconut Research Institute , Chinese Academy of Tropical Agricultural Sciences , Wenchang 571339 , P.R. China
- Hainan Key Laboratory for Biosafe Monitoring and Molecular Breeding in Off-Season Reproduction Region , Institute of Tropical Bioscience and Biotechnology Chinese Academy of Tropical Agricultural Sciences , Haikou 571101 , China
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Xia W, Luo T, Dou Y, Zhang W, Mason AS, Huang D, Huang X, Tang W, Wang J, Zhang C, Xiao Y. Identification and Validation of Candidate Genes Involved in Fatty Acid Content in Oil Palm by Genome-Wide Association Analysis. FRONTIERS IN PLANT SCIENCE 2019; 10:1263. [PMID: 31681369 PMCID: PMC6804545 DOI: 10.3389/fpls.2019.01263] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 09/11/2019] [Indexed: 05/15/2023]
Abstract
Oil palm (Elaeis guineensis) is the highest yielding oil crop per unit area worldwide, but its oil is considered unhealthy for human consumption due to its high palmitic acid content (C16:0). In order to facilitate breeding for fatty acid content in oil palm, genome-wide association analysis (GWAS) was used to identify and validate single-nucleotide polymorphism (SNP) markers and underlying candidate genes associated with fatty acid content in a diversity panel of 200 oil palm individuals. A total of 1,261,501 SNP markers previously developed using SLAF-seq (specific locus amplified fragment sequencing) were used for GWAS. Based on this analysis, 62 SNP markers were significantly associated with fatty acid composition, and 223 candidate genes were identified in the flanking regions of these SNPs. We found one gene (acyl-ACP thioesterase B genes) that was involved in fatty acid biosynthesis and that was associated with high palmitic acid content in the mesocarp. Over-expression of this gene caused a significant increase in palmitic acid content. Our study provides key loci that can be used for breeding oil palm cultivars with low palmitic acid content.
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Affiliation(s)
- Wei Xia
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Tingting Luo
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yajing Dou
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Wei Zhang
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Annaliese S. Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Dongyi Huang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Xiaolong Huang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Wenqi Tang
- Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Jihua Wang
- Guangdong Key Laboratory for Crops Genetic Genetic Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong, China
| | - Chunyu Zhang
- National Research Center of Rapeseed Engineering and Technology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yong Xiao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural sciences, Wenchang, China
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