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Guo C, He Y, Zeng X, Xiong X, Qiu P, Huang X, Yang H. Chloroplast DNA reveals genetic population structure in Sinomenium acutum in subtropical China. CHINESE HERBAL MEDICINES 2023. [DOI: 10.1016/j.chmed.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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Laux M, Oliveira RRM, Vasconcelos S, Pires ES, Lima TGL, Pastore M, Nunes GL, Alves R, Oliveira G. New plastomes of eight Ipomoea species and four putative hybrids from Eastern Amazon. PLoS One 2022; 17:e0265449. [PMID: 35298523 PMCID: PMC8929602 DOI: 10.1371/journal.pone.0265449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
Ipomoea is a large pantropical genus globally distributed, which importance goes beyond the economic value as food resources or ornamental crops. This highly diverse genus has been the focus of a great number of studies, enriching the plant genomics knowledge, and challenging the plant evolution models. In the Carajás mountain range, located in Eastern Amazon, the savannah-like ferruginous ecosystem known as canga harbors highly specialized plant and animal populations, and Ipomoea is substantially representative in such restrictive habitat. Thus, to provide genetic data and insights into whole plastome phylogenetic relationships among key Ipomoea species from Eastern Amazon with little to none previously available data, we present the complete plastome sequences of twelve lineages of the genus, including the canga microendemic I. cavalcantei, the closely related I. marabaensis, and their putative hybrids. The twelve plastomes presented similar gene content as most publicly available Ipomoea plastomes, although the putative hybrids were correctly placed as closely related to the two parental species. The cavalcantei-marabaensis group was consistently grouped between phylogenetic methods. The closer relationship of the I. carnea plastome with the cavalcantei-marabaensis group, as well as the branch formed by I. quamoclit, I. asarifolia and I. maurandioides, were probably a consequence of insufficient taxonomic representativity, instead of true genetic closeness, reinforcing the importance of new plastome assemblies to resolve inconsistencies and boost statistical confidence, especially the case for South American clades of Ipomoea. The search for k-mers presenting high dispersion among the frequency distributions pointed to highly variable coding and intergenic regions, which may potentially contribute to the genetic diversity observed at species level. Our results contribute to the resolution of uncertain clades within Ipomoea and future phylogenomic studies, bringing unprecedented results to Ipomoea species with restricted distribution, such as I. cavalcantei.
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Affiliation(s)
| | - Renato R. M. Oliveira
- Instituto Tecnológico Vale, Belém, Pará, Brazil
- Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | | | | | - Mayara Pastore
- Programa de Pós-Graduação em Botânica Tropical, Museu Paraense Emílio Goeldi, Belém, Pará, Brazil
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Genomic Insight into Differentiation and Selection Sweeps in the Improvement of Upland Cotton. PLANTS 2020; 9:plants9060711. [PMID: 32503111 PMCID: PMC7356552 DOI: 10.3390/plants9060711] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/21/2020] [Accepted: 05/29/2020] [Indexed: 01/13/2023]
Abstract
Upland cotton is the most economically important fibre crop. The human-mediated selection has resulted in modern upland cultivars with higher yield and better fibre quality. However, changes in genome structure resulted from human-mediated selection are poorly understood. Comparative population genomics offers us tools to dissect the genetic history of domestication and helps to understand the genome-wide effects of human-mediated selection. Hereby, we report a comprehensive assessment of Gossypium hirsutum landraces, obsolete cultivars and modern cultivars based on high throughput genome-wide sequencing of the core set of genotypes. As a result of the genome-wide scan, we identified 93 differential regions and 311 selection sweeps associated with domestication and improvement. Furthermore, we performed genome-wide association studies to identify traits associated with the differential regions and selection sweeps. Our study provides a genetic basis to understand the domestication process in Chinese cotton cultivars. It also provides a comprehensive insight into changes in genome structure due to selection and improvement during the last century. We also identified multiple genome-wide associations (GWAS associations) for fibre yield, quality and other morphological characteristics.
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Ross PM, Knox MA, Smith S, Smith H, Williams J, Hogg ID. Historical translocations by Māori may explain the distribution and genetic structure of a threatened surf clam in Aotearoa (New Zealand). Sci Rep 2018; 8:17241. [PMID: 30467395 PMCID: PMC6250687 DOI: 10.1038/s41598-018-35564-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/06/2018] [Indexed: 11/08/2022] Open
Abstract
The population genetic structure of toheroa (Paphies ventricosa), an Aotearoa (New Zealand) endemic surf clam, was assessed to determine levels of inter-population connectivity and test hypotheses regarding life history, habitat distribution and connectivity in coastal vs. estuarine taxa. Ninety-eight toheroa from populations across the length of New Zealand were sequenced for the mitochondrial cytochrome c oxidase I gene with analyses suggesting a population genetic structure unique among New Zealand marine invertebrates. Toheroa genetic diversity was high in Te Ika-a Māui (the North Island of New Zealand) but completely lacking in the south of Te Waipounamu (the South Island), an indication of recent isolation. Changes in habitat availability, long distance dispersal events or translocation of toheroa to southern New Zealand by Māori could explain the observed geographic distribution of toheroa and their genetic diversity. Given that early-Māori and their ancestors, were adept at food cultivation and relocation, the toheroa translocation hypothesis is plausible and may explain the disjointed modern distribution of this species. Translocation would also explain the limited success in restoring what may in some cases be ecologically isolated populations located outside their natural distributions and preferred niches.
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Affiliation(s)
- Philip M Ross
- Environmental Research Institute, University of Waikato, Tauranga, New Zealand.
| | - Matthew A Knox
- School of Science, University of Waikato, Hamilton, New Zealand
- Hopkirk Research Institute, Massey University, Palmerston North, New Zealand
| | - Shade Smith
- Triplefin Environmental Consultants, Napier, New Zealand
| | - Huhana Smith
- Te Rangitāwhia Whakatupu Mātauranga Ltd, Kuku, New Zealand
| | - James Williams
- National Institute of Water and Atmospheric Research, Auckland, New Zealand
| | - Ian D Hogg
- School of Science, University of Waikato, Hamilton, New Zealand
- Canadian High Arctic Research Station, Polar Knowledge Canada, Cambridge Bay, Canada
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Shepherd LD, Bulgarella M, de Lange PJ. Genetic structuring of the coastal herb Arthropodium cirratum (Asparagaceae) is shaped by low gene flow, hybridization and prehistoric translocation. PLoS One 2018; 13:e0204943. [PMID: 30332433 PMCID: PMC6192600 DOI: 10.1371/journal.pone.0204943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 09/16/2018] [Indexed: 11/19/2022] Open
Abstract
We examined the genetic structuring of rengarenga (Arthropodium cirratum; Asparagaceae), an endemic New Zealand coastal herb, using nuclear microsatellite markers. This species was brought into cultivation by Māori within the last 700–800 years for its edible roots and was transplanted beyond its natural distribution as part of its cultivation. We found very high levels of genetic structuring in the natural populations (FST = 0.84), indicating low levels of gene flow. Reduced genetic diversity was found in the translocated populations, suggesting a large loss of genetic diversity early in the domestication process. The data indicates that rengarenga was brought into cultivation independently at least three times, with the sources of these introductions located within a narrow area encompassing about 250km of coastline. Hybridization was inferred between A. cirratum and the closely related A. bifurcatum, despite A. birfucatum not occurring in the vicinity.
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Affiliation(s)
- Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
- * E-mail:
| | | | - Peter J. de Lange
- Environment and Animal Sciences, Unitec Institute of Technology, Auckland, New Zealand
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Bulgarella M, Biggs PJ, de Lange PJ, Shepherd LD. Isolation and characterization of microsatellite loci from Arthropodium cirratum (Asparagaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1700041. [PMID: 28924514 PMCID: PMC5584818 DOI: 10.3732/apps.1700041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 05/22/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Microsatellite markers were developed for Arthropodium cirratum (Asparagaceae) to study population genetic structure and translocation of this species. These markers were tested for cross-amplification in two other Arthropodium species. METHODS AND RESULTS Sixteen microsatellite markers were developed from a genomic library and tested in three populations of A. cirratum. The loci exhibited one to five alleles per locus, with private alleles present in each of the populations. Cross-amplification tests in the two other New Zealand Arthropodium species revealed that many of the loci amplify and demonstrate polymorphism in A. bifurcatum. CONCLUSIONS These markers will be useful for determining genetic structure in A. cirratum and for determining the origins of translocated populations of this species.
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Affiliation(s)
- Mariana Bulgarella
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand
| | - Patrick J. Biggs
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Peter J. de Lange
- Science and Capability Group, Terrestrial Ecosystems, Department of Conservation, Newton, Auckland, New Zealand
| | - Lara D. Shepherd
- Museum of New Zealand Te Papa Tongarewa, P.O. Box 467, Wellington, New Zealand
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Santosa E, Lian CL, Sugiyama N, Misra RS, Boonkorkaew P, Thanomchit K. Population structure of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) in Asia. PLoS One 2017; 12:e0180000. [PMID: 28658282 PMCID: PMC5489206 DOI: 10.1371/journal.pone.0180000] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 06/07/2017] [Indexed: 12/16/2022] Open
Abstract
The corms and leaves of elephant foot yams (Amorphophallus paeoniifolius (Dennst.) Nicolson) are important foods in the local diet in many Asian regions. The crop has high productivity and wide agroecological adaptation and exhibits suitability for the agroforestry system. Although the plant is assumed to reproduce via panmixia, a comprehensive study on the genetic background across regions to enhance wider consumer palatability is still lacking. Here, ten informative microsatellites were analyzed in 29 populations across regions in India, Indonesia and Thailand to understand the genetic diversity, population structure and distribution to improve breeding and conservation programs. The genetic diversity was high among and within regions. Some populations exhibited excess heterozygosity and bottlenecking. Pairwise FST indicated very high genetic differentiation across regions (FST = 0.274), and the Asian population was unlikely to be panmictic. Phylogenetic tree construction grouped the populations according to country of origin with the exception of the Medan population from Indonesia. The current gene flow was apparent within the regions but was restricted among the regions. The present study revealed that Indonesia and Thailand populations could be alternative centers of the gene pool, together with India. Consequently, regional action should be incorporated in genetic conservation and breeding efforts to develop new varieties with global acceptance.
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Affiliation(s)
- Edi Santosa
- Department of Agronomy and Horticulture, Faculty of Agriculture, Bogor Agricultural University, Bogor, West Java, Indonesia
| | - Chun Lan Lian
- Asian Natural Environmental Science Center, The University of Tokyo, Nishitokyo-shi, Tokyo, Japan
| | - Nobuo Sugiyama
- Department of Horticulture, Faculty of Agriculture, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Raj Shekhar Misra
- Central Tuber Crops Research Institute, Sreekariyam, Thiruvananthapuram, Kerala, India
| | | | - Kanokwan Thanomchit
- Department of Horticulture, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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