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Gutiérrez-Larruscain D, Donat S, Pausas JG, Segarra-Moragues JG. Development and characterization of microsatellite loci in Ulex parviflorus Pourr. And its cross-transferability to other Genisteae. Mol Biol Rep 2023; 50:9721-9729. [PMID: 37814034 DOI: 10.1007/s11033-023-08813-7] [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: 04/13/2023] [Accepted: 09/11/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND The genus Ulex is composed by 15 species distributed in Europe and Africa, but the majority of them are restricted to the Iberian Peninsula and Northwest Africa. Some of these species are common elements at the landscape level, and others contribute to global biodiversity as narrow endemics. Assayed nuclear and plastid Sanger-sequenced regions do not provide enough resolution to perform evolutionary studies on the genus, neither at the intraspecific population level nor at the interspecific phylogenetic level. Thus, we have developed and characterized a set of nuclear microsatellite loci in U. parviflorus to provide new highly polymorphic molecular markers for the genus Ulex. METHODS AND RESULTS Genomic DNA enriched in microsatellite motifs using streptavidin-coated M-280 magnetic beads attached to 5'-biotinylated oligonucleotides was sequenced in a 454GS Junior System. After primer design, fluorescent-dyed amplicons were analyzed through capillary sequencing (ABI3730XL). Here we present twelve new high polimorphic SSRs markers developed in U. parviflorus specimens and tested in 120 individuals. The 12 SSR loci amplified a total of 152 alleles, and detected expected heterozygosities that ranged from 0.674 to 0.725 in the genotyped populations. Successful cross-species transferability of the 12 SSR loci to the rest of species included in the genus Ulex and three other representative Genisteae was achieved. CONCLUSIONS The 12 novel proposed SSRs loci will contribute to perform evolutionary studies and genetic research on the genus Ulex and in other Genisteae.
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Affiliation(s)
- David Gutiérrez-Larruscain
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC), Ctra. Náquera Km. 4.5, Moncada, E-46113, Valencia, Spain.
| | - Santiago Donat
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC), Ctra. Náquera Km. 4.5, Moncada, E-46113, Valencia, Spain
| | - Juli G Pausas
- Centro de Investigaciones sobre Desertificación (CIDE-CSIC), Ctra. Náquera Km. 4.5, Moncada, E-46113, Valencia, Spain
| | - José Gabriel Segarra-Moragues
- Departamento de Botánica y Geología, Facultad de Ciencias Biológicas, Universitat de València, Avda. Dr. Moliner 50, Burjassot, E-46100, Valencia, Spain
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2
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High genetic diversity in American chestnut (Castanea dentata) despite a century of decline. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01473-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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3
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Xiong Y, Yang J, Xiong Y, Zhao J, Liu L, Liu W, Sha L, Zhou J, You M, Li D, Lei X, Bai S, Ma X. Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers in Kengyilia melanthera. FRONTIERS IN PLANT SCIENCE 2022; 13:959042. [PMID: 35958193 PMCID: PMC9358441 DOI: 10.3389/fpls.2022.959042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 11/03/2023]
Abstract
As a typical psammophyte of the Triticeae, Kengyilia melanthera possesses high feeding potential and great utilization values in desertification control in the Qinghai-Tibet Plateau. However, few gene function and genetic studies have been performed in K. melanthera. In this study, single-molecule real-time sequencing technology was used to obtain the full-length transcriptome sequence of K. melanthera, following the functional annotation of transcripts and prediction of coding sequences (CDSs), transcription factors (TFs), and long noncoding RNA (lncRNA) sequences. Meanwhile, a total of 42,433 SSR loci were detected, with 5'-UTRs having the most SSR loci and trinucleotide being the most abundant type. In total, 108,399 SSR markers were designed, and 300 SSR markers were randomly selected for diversity verification of K. melanthera. A total of 49 polymorphic SSR markers were used to construct the genetic relationships of 56 K. melanthera accessions, among which 21 SSR markers showed good cross-species transferability among the related species. In conclusion, the full-length transcriptome sequence of the K. melanthera will assist gene prediction and promote molecular biology and genomics research, and the polymorphic SSR markers will promote molecular-assisted breeding and related research of K. melanthera and its relatives.
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Affiliation(s)
- Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jian Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lin Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wei Liu
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lina Sha
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jiqiong Zhou
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Minghong You
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
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4
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Antunes AM, Nunes Stival JG, Targueta CP, de Campos Telles MP, Soares TN. A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data. Curr Genomics 2022; 23:175-181. [PMID: 36777003 PMCID: PMC9878831 DOI: 10.2174/1389202923666220428101350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Also known as Simple Sequence Repetitions (SSRs), microsatellites are profoundly informative molecular markers and powerful tools in genetics and ecology studies on plants. Objective: This research presents a workflow for developing microsatellite markers using genome skimming. Methods: The pipeline was proposed in several stages that must be performed sequentially: obtaining DNA sequences, identifying microsatellite regions, designing primers, and selecting candidate microsatellite regions to develop the markers. Our pipeline efficiency was analyzed using Illumina sequencing data from the non-model tree species Pterodon emarginatus Vog. Results: The pipeline revealed 4,382 microsatellite regions and drew 7,411 pairs of primers for P. emarginatus. However, a much larger number of microsatellite regions with the potential to develop markers were discovered from our pipeline. We selected 50 microsatellite regions with high potential for developing markers and organized 29 microsatellite regions in sets for multiplex PCR. Conclusion: The proposed pipeline is a powerful tool for fast and efficient development of microsatellite markers on a large scale in several species, especially nonmodel plant species.
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Affiliation(s)
- Adriana Maria Antunes
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil;,Address correspondence to this author at the Department of Genetics, Institute of Biological Sciences, Goias Federal University, Goiânia, Brazil; Tel/Fax: +55 62 981660987; E-mail:
| | - Júlio Gabriel Nunes Stival
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Mariana Pires de Campos Telles
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brasil
| | - Thannya Nascimentos Soares
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil
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5
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Fukui Y, Saito M, Nakamura N, Mizuno T, Sato S, Tsukuda M, Nakaoka S, Tsuboi K, Sasaki A, Kuramochi K, Boonyaritthongchai P, Kaewmanee N, Thirapanmethee K, Chomnawang MT, Bongcheewin B, Nguyen TL, Nguyen HLT, Le HT, Okamoto S, Nakamura T, Nakamura Y, Kubo N. Classification of Southeast Asian mints ( Mentha spp.) based on simple sequence repeat markers. BREEDING SCIENCE 2022; 72:181-187. [PMID: 36275937 PMCID: PMC9522532 DOI: 10.1270/jsbbs.21058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/21/2022] [Indexed: 06/16/2023]
Abstract
Mentha is a complex genus encompassing many species as a consequence of their interspecific hybridization and polyploidy. Southeast Asian mints have been poorly distinguished though they are widely used for culinary and medical purposes. In this study, we have analyzed Southeast Asian mints and known varieties as well as a related Lamiaceae species (Nepeta sp.) using simple sequence repeat (SSR) markers and leaf morphology. Two types of mints were clearly distinguished based on their venation pattern and leaf shape index. We developed 12 SSR markers that allowed good amplification in the Mentha and another Lamiaceae species. In the SSR-based phylogram, the Mentha lines could be delimited into groups I-VI. The Southeast Asian mints divided into groups I and II, and the phylogram separated most of the available species, with groups I and II containing the known species M. × cordifolia and M. arvensis, respectively. The separation of the two groups was supported by a population structure analysis. The SSR markers developed in this study enabled the simultaneous classification of mints and will help improve our understanding of the genetic composition of known mint varieties and as yet unclassified Southeast Asian mints.
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Affiliation(s)
- Yuri Fukui
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Moeko Saito
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Natsuno Nakamura
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Taichi Mizuno
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Shuichi Sato
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Mayu Tsukuda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Saori Nakaoka
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Keita Tsuboi
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Azusa Sasaki
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Kouji Kuramochi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Panida Boonyaritthongchai
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Nichapat Kaewmanee
- School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Bangkhuntien, Bangkok 10150, Thailand
| | - Krit Thirapanmethee
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayuthaya, Rajathevi, Bangkok 10400, Thailand
| | - Mullika Traidej Chomnawang
- Department of Microbiology, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayuthaya, Rajathevi, Bangkok 10400, Thailand
| | - Bhanubong Bongcheewin
- Department of Pharmaceutical Botany, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayuthaya, Rajathevi, Bangkok 10400, Thailand
| | - Thuy Linh Nguyen
- Institute for Preventive Medicine and Public Health and Hanoi Medical University Hospital, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi 116001, Vietnam
| | - Huong Lan Thi Nguyen
- Institute for Preventive Medicine and Public Health and Hanoi Medical University Hospital, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi 116001, Vietnam
| | - Huong Thi Le
- Institute for Preventive Medicine and Public Health and Hanoi Medical University Hospital, Hanoi Medical University, 1 Ton That Tung, Dong Da, Hanoi 116001, Vietnam
| | - Shigehisa Okamoto
- Department of Food Science and Biotechnology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Takako Nakamura
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Yasushi Nakamura
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
- Planning Office, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, 9 Wakunari, Amarube-cho, Kameoka, Kyoto 621-0806, Japan
| | - Nakao Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, 74 Oji, Kitainayazuma, Seika-cho, Soraku-gun, Kyoto 619-0244, Japan
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6
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Kubo N, Matsuda T, Yanagida C, Hotta Y, Mimura Y, Kanda M. Parentage analysis of tea cultivars in Japan based on simple sequence repeat markers. BREEDING SCIENCE 2021; 71:594-600. [PMID: 35087323 PMCID: PMC8784347 DOI: 10.1270/jsbbs.20156] [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: 12/04/2020] [Accepted: 07/09/2021] [Indexed: 06/14/2023]
Abstract
Tea cultivars have been bred by individual selection of landraces and by crossbreeding, but the validation of the parentage is limited. In this study, we performed parentage analysis of 79 tea cultivars in Japan based on SSR markers to confirm or identify the parent-offspring relationships among them. The effectiveness of nine SSR markers for parentage analysis was validated by comparing them to the existing cleaved amplified polymorphic sequence markers. The former markers were detectable more alleles than the latter. Simulation of parentage analysis of the tea cultivars predicted biparental origins for 12 cultivars ('Houshun', 'Mie ryokuhou no. 1', 'Surugawase', 'Tenmyo', 'Yamanoibuki', 'Harumidori', 'Koushun', 'Minekaori', 'Okumusashi', 'Saemidori', 'Sofu', and 'Toyoka'), in the first five of which candidate parents of yet-to-be-defined pedigree were newly identified. Comparisons of a total of 41 SSR genotypes confirmed the newly-identified parentages of 'Asahi' for 'Tenmyo', 'Rokurou' for 'Houshun', 'Surugawase', and 'Yamanoibuki', and 'Yamatomidori' for 'Mie ryokuhou no. 1'. The maternity of seven cultivars out of the 12 was also confirmed with chloroplast DNA sequences. Uniparental origins were confirmed for 25 cultivars. This parentage analysis has improved our knowledge of tea pedigrees and will aid in the development of new cultivars.
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Affiliation(s)
- Nakao Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, 74 Oji, Kitainayazuma, Seika-cho, Soraku-gun, Kyoto 619-0244, Japan
| | - Tomohiro Matsuda
- Tea Industry Research Division, Agriculture and Forestry Technology Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, 1 Nakanosono, Shirakawa, Uji, Kyoto 611-0022, Japan
| | - Chisaki Yanagida
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Yuna Hotta
- Tea Industry Research Division, Agriculture and Forestry Technology Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, 1 Nakanosono, Shirakawa, Uji, Kyoto 611-0022, Japan
| | - Yutaka Mimura
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, 74 Oji, Kitainayazuma, Seika-cho, Soraku-gun, Kyoto 619-0244, Japan
| | - Maho Kanda
- Tea Industry Research Division, Agriculture and Forestry Technology Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, 1 Nakanosono, Shirakawa, Uji, Kyoto 611-0022, Japan
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7
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An empirical analysis of mtSSRs: could microsatellite distribution patterns explain the evolution of mitogenomes in plants? Funct Integr Genomics 2021; 22:35-53. [PMID: 34751851 DOI: 10.1007/s10142-021-00815-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 10/19/2022]
Abstract
Microsatellites (SSRs) are tandem repeat sequences in eukaryote genomes, including plant cytoplasmic genomes. The mitochondrial genome (mtDNA) has been shown to vary in size, number, and distribution of SSRs among different plant groups. Thus, SSRs contribute with genomic diversity in mtDNAs. However, the abundance, distribution, and evolutionary significance of SSRs in mtDNA from a wide range of algae and plants have not been explored. In this study, the mtDNAs of 204 plant and algal species were investigated related to the presence of SSRs. The number of SSRs was positively correlated with genome size. Its distribution is dependent on plant and algal groups analyzed, although the cluster analysis indicates the conservation of some common motifs in algal and terrestrial plants that reflect common ancestry of groups. Many SSRs in coding and non-coding regions can be useful for molecular markers. Moreover, mitochondrial SSRs are highly abundant, representing an important source for natural or induced genetic variation, i.e., for biotechnological approaches that can modulate mtDNA gene regulation. Thus, this comparative study increases the understanding of the plant and algal SSR evolution and brings perspectives for further studies.
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8
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Cao HP, He YT, Zhong L, Wang XJ, Barrett SCH, Wang H, Li DZ, Zhou W. Characterization of 30 microsatellite markers for distylous Primula denticulata (Primulaceae) using HiSeq sequencing. Genes Genet Syst 2020; 95:275-279. [PMID: 33328391 DOI: 10.1266/ggs.20-00003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Primula denticulata exhibits considerable variation in floral morphology and flowering phenology along elevational gradients in SW China. We isolated 30 microsatellite markers from P. denticulata to facilitate further investigation of population genetics and floral evolution in this species. We used the HiSeq X-Ten sequencing system to develop a set of markers, and measured polymorphism and genetic diversity in a sample of 72 individuals from three natural populations of P. denticulata subsp. denticulata. The markers displayed relatively high polymorphism, with the number of alleles ranging from two to seven (mean = 3.567). The observed and expected heterozygosity ranged from 0 to 1.000 and 0.041 to 0.702, respectively. Twenty-eight of the loci were also successfully amplified in P. denticulata subsp. sinodenticulata. The microsatellite markers we have identified will provide valuable tools for investigations of the population genetic structure, mating systems and phylogeography of the P. denticulata complex, and will help to address questions concerning the ecological and genetic mechanisms responsible for the evolution of reproductive traits in the species.
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Affiliation(s)
- Hao-Pu Cao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences.,School of Life Science, Yunnan University
| | - Yu-Ting He
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences.,University of Chinese Academy of Sciences
| | - Li Zhong
- University of Chinese Academy of Sciences.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
| | - Xin-Jia Wang
- University of Chinese Academy of Sciences.,Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
| | | | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences
| | - Wei Zhou
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences
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9
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Quantitative Trait Locus Analysis in Squash (Cucurbita moschata) Based on Simple Sequence Repeat Markers and Restriction Site-Associated DNA Sequencing Analysis. HORTICULTURAE 2020. [DOI: 10.3390/horticulturae6040071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Squash (Cucurbita moschata) displays wide morphological and genetic variations; however, limited information is available regarding the genetic loci of squash that control its agronomic traits. To obtain basic genetic information for C. moschata, an F2 population was prepared derived from a cross between the Vietnamese cultivar ‘Bí Hồ Lô TN 6 (TN 6)’ and the Japanese cultivar ‘Shishigatani’, and flowering and fruit traits were examined. Overall, the traits showed a continuous distribution in the F2 population, suggesting that they were quantitative traits. A linkage map was constructed based on simple sequence repeat and restriction site-associated DNA (RAD) markers to detect quantitative trait loci (QTLs). Twelve QTLs for flowering and fruit traits, as well as one phenotypic trait locus, were successfully localized on the map. The present QTLs explained the phenotypic variations at a moderate to relatively high level (16.0%–47.3%). RAD markers linked to the QTLs were converted to codominant cleaved amplified polymorphic sequence (CAPS) and derived CAPS markers for the easy detection of alleles. The information reported here provides useful information for understanding the genetics of Cucurbita and other cucurbit species, and for the selection of individuals with ideal traits during the breeding of Cucurbita vegetables.
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10
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Daemi-Saeidabad M, Shojaeiyan A, Vivian-Smith A, Stenøien HK, Falahati-Anbaran M. The taxonomic significance of ddRADseq based microsatellite markers in the closely related species of Heracleum (Apiaceae). PLoS One 2020; 15:e0232471. [PMID: 32379780 PMCID: PMC7205262 DOI: 10.1371/journal.pone.0232471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 04/15/2020] [Indexed: 11/28/2022] Open
Abstract
Many studies on Heracleum have shown poor correspondence between observed molecular clusters and established taxonomic classification amongst closely related species. This might reflect both unresolved taxonomy but perhaps also a lack of good genetic markers. This lack of appropriate and cost effective species-specific genetic markers hinders a resolved relationship for the species complex, and this in turn causes profound management challenges for a genus that contains both endemic species, with important ecological roles, and species with an invasive potential. Microsatellites are traditionally considered markers of choice for comprehensive, yet inexpensive, analyses of genetic variation, including examination of population structure, species identity, linkage map construction and cryptic speciation. In this study, we have used double digest restriction site associated DNA sequencing (ddRADseq) to develop microsatellite markers in Heracleum rechingeri. Genomic DNA from three individuals were digested with Sbf1 and Nde1 and size selected for library construction. The size-selected fragments were sequenced on an Ion Torrent sequencer and a total of 54 microsatellite sequences were bioinformatically confirmed. Twenty five loci were then tested for amplification, resulting in 19 of these being successfully amplified across eight species, comprising both the so-called thick-stemmed species (H. persicum, H. rechingeri, H. gorganicum and H. lasiopetalum), and thin-stemmed species (H. anisactis, H. pastinasifolium and H. transcaucasicum). Both Bayesian and distance-based clustering, and principal coordinate analyses clearly separated these into two groups. Surprisingly, three H. pastinacifolium populations were not separated from populations of the morphologically similar endemic species, H. anisactis, suggesting lack of genetic differentiation. Likewise, high genetic similarity was found between H. persicum and H. rechingeri populations, questioning taxonomic separation at the species level between these taxa. Further analyses are needed to re-evaluate the taxonomic significance of observed morphological variability currently applied to distinguish these sister taxa. Nevertheless, our results represent progress in the effort to develop cost-efficient molecular tools for species discrimination in this genus.
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Affiliation(s)
- Mehdi Daemi-Saeidabad
- Department of Plant Sciences, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Abdolali Shojaeiyan
- Department of Horticultural Science, Faculty of Agriculture, Tarbiat Modares University (TMU), Tehran, Iran
| | - Adam Vivian-Smith
- Department of Forest Genetics and Biodiversity, Norwegian Institute for Bioeconomy Research, Ås, Norway
| | - Hans K. Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Mohsen Falahati-Anbaran
- Department of Plant Sciences, School of Biology, College of Science, University of Tehran, Tehran, Iran
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11
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Pern YC, Lee SY, Ng WL, Mohamed R. Cross-amplification of microsatellite markers across agarwood-producing species of the Aquilarieae tribe (Thymelaeaceae). 3 Biotech 2020; 10:103. [PMID: 32099744 DOI: 10.1007/s13205-020-2072-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 01/18/2020] [Indexed: 01/09/2023] Open
Abstract
Tree species in the Aquilarieae tribe of the Thymelaeaceae family produce agarwood, a natural product highly valued for its fragrance, but the species are under threat due to indiscriminate harvesting. For conservation of these species, molecular techniques such as DNA profiling have been used. In this study, we assessed cross-amplification of microsatellite markers, initially developed for three Aquilaria species (A. crassna, A. malaccensis, and A. sinensis), on ten other agarwood-producing species, including members of Aquilaria (A. beccariana, A. hirta, A. microcarpa, A. rostrata, A. rugosa, A. subintegra, and A. yunnanensis) and Gyrinops (G. caudata, G. versteegii, and G. walla), both from the Aquilarieae tribe. Primers for 18 out of the 30 microsatellite markers successfully amplified bands of expected sizes in 1 sample each of at least 10 species. These were further used to genotype 74 individuals representing all the 13 studied species, yielding 13 cross-amplifiable markers, of which only 1 being polymorphic across all species. At each locus, the number of alleles ranged from 7 to 23, indicating a rather high variability. Four markers had relatively high species discrimination power. Our results demonstrated that genetic fingerprinting can be an effective tool in helping to manage agarwood genetic resources by potentially supporting the chain-of-custody of agarwood and its products in the market.
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Affiliation(s)
- Yu Cong Pern
- 1Forest Biotech Laboratory, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Malaysia
| | - Shiou Yih Lee
- 1Forest Biotech Laboratory, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Malaysia.,2Present Address: State Key Laboratory of Biocontrol & Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 Guangdong China
| | - Wei Lun Ng
- 3China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor Malaysia
| | - Rozi Mohamed
- 1Forest Biotech Laboratory, Department of Forest Management, Faculty of Forestry, Universiti Putra Malaysia, UPM, 43400 Serdang, Selangor Malaysia
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Kubo N, Onnazaka K, Mizuno S, Tsuji G. Classification of "nabana" ( Brassica rapa) cultivars and landraces based on simple sequence repeat markers. BREEDING SCIENCE 2019; 69:179-185. [PMID: 31086496 PMCID: PMC6507715 DOI: 10.1270/jsbbs.18126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/15/2018] [Indexed: 06/09/2023]
Abstract
Brassica rapa or B. napus vegetables for eating as young inflorescences and stalks are called "nabana". Japanese nabana includes "flower-bud type" and "stem-and-leaf type". Chinese and European types are also known (cai-xin, zicaitai, and broccoletto). We classified nabana belonging to B. rapa and other B. rapa vegetables. In a simple sequence repeat-based phylogram, 49 ingroup samples were classified into four groups (I-IV). Flower-bud and stem-and-leaf types were separated into groups I and III, respectively, with a slight overlap in group II. Cai-xin and non-heading Chinese cabbages were included in group IV. Broccoletto was placed in group III, close to turnips. Zicaitai cultivars were included in group II. We tested for clubroot resistance (CR) and its marker genotypes in nabana because of their agronomical importance. Ten cultivars were resistant to group 4 pathogen but not to group 2. Most of the CR cultivars had heterozygous resistance alleles in the CRb and Crr1 loci, consistent with inoculation tests. Our results suggest that Japanese nabana lines and foreign types were differentiated according to their consumption parts and cultivar origins, respectively. This study elucidates the relationships and CR properties of nabana and provides valuable information for the breeding of nabana cultivars.
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Affiliation(s)
- Nakao Kubo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University,
1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522,
Japan
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center,
74 Oji, Kitainayazuma, Seika-cho, Soraku-gun, Kyoto 619-0244,
Japan
| | - Kumiko Onnazaka
- Kyoto Prefectural Kyoto Otokuni Agriculture Improvement Extension Center,
15 Tokudaiji Dangoden-cho, Nishikyogoku, Ukyo-ku, Kyoto 615-0846,
Japan
- Present address: Kyoto Prefectural Nantan Agriculture Improvement Extension Center21 Fujinoki, Oyama Higashi-machi, Sonobecho, Nantan, Kyoto 622-0041,
Japan
| | - Shinji Mizuno
- Warm Region Horticulture Institute, Chiba Prefectural Agriculture and Forestry Research Center,
1762 Yamamoto, Tateyama, Chiba 294-0014,
Japan
- Present address: College of Bioresource Sciences, Nihon University1866 Kameino, Fujisawa, Kanagawa 252-0880,
Japan
| | - Gento Tsuji
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University,
1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522,
Japan
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Yurkevich OY, Samatadze TE, Levinskikh MA, Zoshchuk SA, Signalova OB, Surzhikov SA, Sychev VN, Amosova AV, Muravenko OV. Molecular Cytogenetics of Pisum sativum L. Grown under Spaceflight-Related Stress. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4549294. [PMID: 30627557 PMCID: PMC6304655 DOI: 10.1155/2018/4549294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/26/2018] [Accepted: 11/22/2018] [Indexed: 11/17/2022]
Abstract
The ontogenesis and reproduction of plants cultivated aboard a spacecraft occur inside the unique closed ecological system wherein plants are subjected to serious abiotic stresses. For the first time, a comparative molecular cytogenetic analysis of Pisum sativum L. (Fabaceae) grown on board the RS ISS during the Expedition-14 and Expedition-16 and also plants of their succeeding (F1 and F2) generations cultivated on Earth was performed in order to reveal possible structural chromosome changes in the pea genome. The karyotypes of these plants were studied by multicolour fluorescence in situ hybridization (FISH) with five different repeated DNA sequences (45S rDNA, 5S rDNA, PisTR-B/1, microsatellite motifs (AG)12, and (GAA)9) as probes. A chromosome aberration was revealed in one F1 plant. Significant changes in distribution of the examined repeated DNAs in karyotypes of the "space grown" pea plants as well as in F1 and F2 plants cultivated on Earth were not observed if compared with control plants. Additional oligo-(GAA)9 sites were detected on chromosomes 6 and 7 in karyotypes of F1 and F2 plants. The detected changes might be related to intraspecific genomic polymorphism or plant cell adaptive responses to spaceflight-related stress factors. Our findings suggest that, despite gradual total trace contamination of the atmosphere on board the ISS associated with the extension of the space station operating life, exposure to the space environment did not induce serious chromosome reorganizations in genomes of the "space grown" pea plants and generations of these plants cultivated on Earth.
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Affiliation(s)
- Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | - Svyatoslav A. Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga B. Signalova
- Institute of Biomedical Problems, Russian Academy of Sciences, 123007 Moscow, Russia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir N. Sychev
- Institute of Biomedical Problems, Russian Academy of Sciences, 123007 Moscow, Russia
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Viruel J, Haguenauer A, Juin M, Mirleau F, Bouteiller D, Boudagher‐Kharrat M, Ouahmane L, La Malfa S, Médail F, Sanguin H, Nieto Feliner G, Baumel A. Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae). APPLICATIONS IN PLANT SCIENCES 2018; 6:e01201. [PMID: 30598859 PMCID: PMC6303155 DOI: 10.1002/aps3.1201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/28/2018] [Indexed: 05/25/2023]
Abstract
PREMISE OF THE STUDY Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected. METHODS In this study, we implemented a next-generation sequencing-based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results. RESULTS The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates. DISCUSSION Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.
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Affiliation(s)
- Juan Viruel
- Royal Botanic GardensKew, RichmondSurreyTW9 3DSUnited Kingdom
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Anne Haguenauer
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Marianick Juin
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Fatma Mirleau
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Delphine Bouteiller
- Institut du Cerveau et de la Moelle épinière (ICM)Hôpital Pitié Salpêtrière47 Boulevard de l'Hôpital75013ParisFrance
| | - Magda Boudagher‐Kharrat
- Laboratoire Caractérisation Génétique des PlantesFaculté des sciencesUniversité Saint‐JosephB.P. 11‐514 Riad El SolhBeirut1107 2050Lebanon
| | - Lahcen Ouahmane
- Laboratoire d'Ecologie et EnvironnementFaculté des Sciences SemlaliaUniversité Cadi AyyadMarrakeshMorocco
| | - Stefano La Malfa
- Dipartimento di Agricoltura, Alimentazione e Ambiente (Di3A)Università degli Studi di CataniaVia Valdisavoia 595123CataniaItaly
| | - Frédéric Médail
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
| | - Hervé Sanguin
- Centre de coopération internationale en recherche agronomique pour le développement (CIRAD)Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM)MontpellierFrance
- LSTM [LSTM is sponsored by University of Montpellier, CIRAD, IRD, INRA, Montpellier SupAgro]TA A‐82/J Campus International de BaillarguetFR‐34398Montpellier CEDEX 5France
| | | | - Alex Baumel
- Institut Méditerranéen de Biodiversité et d’Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)]Station marine d'Endoume, Chemin de la Batterie des LionsFR‐13007MarseilleFrance
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Choudhary S, Thakur S, Najar RA, Majeed A, Singh A, Bhardwaj P. Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum). Genome 2018; 61:417-428. [DOI: 10.1139/gen-2017-0143] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Rhododendron arboreum is an ecologically prominent species, which also lends commercial and medicinal benefits in the form of palatable juices and useful herbal drugs. Local abundance and survival of the species under a highly fluctuating climate make it an ideal model for genetic structure and functional analysis. However, a lack of genomic data has hampered additional research. In the present study, cDNA libraries from floral and foliar tissues of the species were sequenced to provide a foundation for understanding the functional aspects of the genome and to construct an enriched repository that will promote genomics studies in the genera. Illumina’s platform facilitated the generation of ∼100 million high-quality paired-end reads. De novo assembly, clustering, and filtering out of shorter transcripts predicted 113 167 non-redundant transcripts with an average length of 1164.6 bases. Of these, 71 961 transcripts were categorized based on functional annotations in the Gene Ontology database, whereby 5710 were grouped into 141 pathways and 23 746 encoded for different transcription factors. Transcriptome screening further identified 35 419 microsatellite regions, of which, 43 polymorphic loci were characterized on 30 genotypes. Seven hundred and nineteen transcripts had 811 high-quality single-nucleotide polymorphic variants with a minimum coverage of 10, a total score of 20, and SNP% of 50.
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Affiliation(s)
- Shruti Choudhary
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
| | - Sapna Thakur
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
| | - Raoof Ahmad Najar
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
| | - Aasim Majeed
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
| | - Amandeep Singh
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
| | - Pankaj Bhardwaj
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
- Molecular Genetics Laboratory, Centre for Plant Sciences, Central University of Punjab, City Campus, Mansa Road, Bathinda 151001, India
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Camacho L MD, De Freitas Schatzer CA, Alves-Pereira A, Zucchi MI, De Carvalho M AM, Gaspar M. Development, characterization and cross-amplification of microsatellite markers for Chrysolaena obovata, an important Asteraceae from Brazilian Cerrado. J Genet 2017; 96:e47-e53. [PMID: 28947700 DOI: 10.1007/s12041-017-0812-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Milena Diaz Camacho L
- Núcleo de Pesquisa em Fisiologia e Bioquímica, Instituto de Botânica, São Paulo, SP CEP 04301-902, Brazil.
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17
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Gutiérrez-Ozuna R, Hamilton MB. Identification and characterization of microsatellite loci in the tuliptree, Liriodendron tulipifera (Magnoliaceae). APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1700032. [PMID: 28924513 PMCID: PMC5584817 DOI: 10.3732/apps.1700032] [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: 04/06/2017] [Accepted: 05/23/2017] [Indexed: 06/07/2023]
Abstract
PREMISE OF THE STUDY Twenty-three polymorphic microsatellite loci (simple sequence repeats) were identified and characterized for Liriodendron tulipifera (Magnoliaceae), a species native to eastern North America, to investigate its genetic diversity, population structure, and mating system. METHODS AND RESULTS Using Illumina HiSeq paired-end reads from genomic DNA, searches for repeat motifs identified approximately 280,000 potentially amplifiable loci. Of 77 loci tested, 51 amplified consistently. When genotyped using 30 to 52 total adult trees from three old-growth populations in Maryland, Virginia, and New Jersey, USA, 23 loci were polymorphic. These loci exhibited four to 13 alleles, and observed and expected heterozygosities ranged from 0.233 to 0.865 and 0.272 to 0.876, respectively. CONCLUSIONS The microsatellite marker loci presented here will be valuable in population genetic studies of L. tulipifera because they do not suffer from ascertainment bias and show high polymorphism.
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Affiliation(s)
- Ricardo Gutiérrez-Ozuna
- Department of Biology, Georgetown University, 37th and O Streets NW, Washington, D.C. 20057 USA
| | - Matthew B. Hamilton
- Department of Biology, Georgetown University, 37th and O Streets NW, Washington, D.C. 20057 USA
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18
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Závada T, Malik RJ, Kesseli RV. Population structure in chicory ( Cichorium intybus): A successful U.S. weed since the American revolutionary war. Ecol Evol 2017. [PMID: 28649334 PMCID: PMC5478081 DOI: 10.1002/ece3.2994] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Plant invasions are recognized as major drivers of ecosystem change, yet the precise cause of these invasions remains unknown for many species. Frequency and modes of introductions during the first, transport and colonization, stages of the invasion process as well as phenotypic changes due to plasticity or changing genetic diversity and adaptation during later establishment and expansion stages can all influence the "success" of invasion. Here, we examine some of these factors in, and the origin of, a very successful weed, Cichorium intybus (chicory) which was introduced to North America in the 18th century and which now can be found in all 48 continental U.S. states and much of Canada. We genotyped a Eurasian collection of 11 chicory cultivars, nine native populations and a North American collection of 20 introduced wild populations which span the species range (592 individuals in total). To detect the geographic sources of North American chicory populations and to assess the genetic diversity among cultivars, native, and introduced populations, we used both a sequenced cpDNA region and 12 nuclear simple sequence repeat (SSR), microsatellite loci. Four cpDNA haplotypes were identified and revealed clear geographic subdivisions in the chicory native range and an interspecific hybrid origin of Radicchio group. Nuclear data suggested that domesticated lines deliberately introduced to North America were major contributors to extant weedy populations, although unintended sources such as seed contaminants likely also played important roles. The high private allelic richness and novel genetic groups were detected in some introduced populations, suggesting the potential for local adaptation in natural sites such as deserts and nature reserves. Our findings suggest that the current populations of weedy U.S. chicory have evolved primarily from several sources of domesticated and weedy ancestors and subsequent admixture among escaped lineages.
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Affiliation(s)
- Tomáš Závada
- Biology Department University of Massachusetts Boston Boston MA USA.,Present address: Sterling College Craftsbury Common VT USA and
| | - Rondy J Malik
- Biology Department University of Massachusetts Boston Boston MA USA.,Present address: Department of Ecosystem Science and Management Pennsylvania State University University Park PA USA
| | - Rick V Kesseli
- Biology Department University of Massachusetts Boston Boston MA USA
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Oder A, Lannes R, Viruel MA. A Set of 20 New SSR Markers Developed and Evaluated in Mandevilla Lindl. Molecules 2016; 21:E1316. [PMID: 27706055 PMCID: PMC6274059 DOI: 10.3390/molecules21101316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/15/2016] [Accepted: 09/22/2016] [Indexed: 11/16/2022] Open
Abstract
Mandevilla is an ornamental crop with a bright future worldwide because of its high commercial acceptance and added value. However, as with most ornamental species, there are few molecular tools to support cultivar breeding and innovation. In this work, we report the development and analysis of 20 new Simple Sequence Repeat (SSR) markers in Mandevilla. Microsatellites were isolated from two enriched small-insert genomic libraries of Mandevilla × amabilis. The diversity parameters estimated after their amplification in a group of 11 commercial genotypes illustrate the effect of two opposite drifts: the high relatedness of cultivars belonging to the same commercial group and the high divergence of other cultivars, especially M. × amabilis. Based on their different band patterns, six genotypes were uniquely distinguished, and two groups of sport mutations remained undistinguishable. The amplification of the SSRs in three wild species suggested the existence of unexploited diversity available to be introgressed into the commercial pool. This is the first report of available microsatellites in Mandevilla. The development process has provided some clues concerning the genome structure of the species, and the SSRs obtained will help to create new products and to protect existing and upcoming plant innovations.
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Affiliation(s)
- Alev Oder
- S.A.S. DHMINNOVATION 18, Avenue du Quercy-BP5, 82200 Malause, France.
| | - Robert Lannes
- S.A.S. DHMINNOVATION 18, Avenue du Quercy-BP5, 82200 Malause, France.
| | - Maria Angeles Viruel
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM-UMA-CSIC), 29750 Algarrobo-Costa (Málaga), Spain.
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20
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Bastías A, Correa F, Rojas P, Almada R, Muñoz C, Sagredo B. Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS). PLoS One 2016; 11:e0159825. [PMID: 27459734 PMCID: PMC4961369 DOI: 10.1371/journal.pone.0159825] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 07/09/2016] [Indexed: 12/18/2022] Open
Abstract
Maqui (Aristotelia chilensis [Molina] Stunz) is a small dioecious tree native to South America with edible fruit characterized by very high antioxidant capacity and anthocyanin content. To preserve maqui as a genetic resource it is essential to study its genetic diversity. However, the complete genome is unknown and only a few gene sequences are available in databases. Simple sequence repeats (SSR) markers, which are neutral, co-dominant, reproducible and highly variable, are desirable to support genetic studies in maqui populations. By means of identification and characterization of microsatellite loci from a maqui genotype, using 454 sequencing technology, we develop a set of SSR for this species. Obtaining a total of 165,043 shotgun genome sequences, with an average read length of 387 bases, we covered 64 Mb of the maqui genome. Reads were assembled into 4,832 contigs, while 98,546 reads remained as singletons, generating a total of 103,378 consensus genomic sequences. A total of 24,494 SSR maqui markers were identified. Of them, 15,950 SSR maqui markers were classified as perfects. The most common SSR motifs were dinucleotide (31%), followed by tetranucleotide (26%) and trinucleotide motifs (24%). The motif AG/CT (28.4%) was the most abundant, while the motif AC (89 bp) was the largest. Eleven polymorphic SSRs were selected and used to analyze a population of 40 maqui genotypes. Polymorphism information content (PIC) ranged from 0.117 to 0.82, with an average of 0.58. Non-significant groups were observed in the maqui population, showing a panmictic genetic structure. In addition, we also predicted 11150 putative genes and 3 microRNAs (miRNAs) in maqui sequences. This results, including partial sequences of genes, some miRNAs and SSR markers from high throughput next generation sequencing (NGS) of maqui genomic DNA, constitute the first platform to undertake genetic and molecular studies of this important species.
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Affiliation(s)
- Adriana Bastías
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Av. Salamanca s/n, Sector Los Choapinos, Rengo, Chile
| | - Francisco Correa
- Facultad de Ingeniería, Universidad de Talca, Avenida Lircay s/n, Talca
| | - Pamela Rojas
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Av. Salamanca s/n, Sector Los Choapinos, Rengo, Chile
| | - Rubén Almada
- Centro de Estudios Avanzados en Fruticultura (CEAF), Av. Salamanca s/n, Sector Los Choapinos, Rengo, Chile
| | - Carlos Muñoz
- Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa N° 11315, La Pintana, Santiago de Chile, Chile
| | - Boris Sagredo
- Instituto de Investigaciones Agropecuarias (INIA) CRI Rayentué, Av. Salamanca s/n, Sector Los Choapinos, Rengo, Chile
- * E-mail:
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Gimode D, Odeny DA, de Villiers EP, Wanyonyi S, Dida MM, Mneney EE, Muchugi A, Machuka J, de Villiers SM. Identification of SNP and SSR Markers in Finger Millet Using Next Generation Sequencing Technologies. PLoS One 2016; 11:e0159437. [PMID: 27454301 PMCID: PMC4959724 DOI: 10.1371/journal.pone.0159437] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/01/2016] [Indexed: 01/18/2023] Open
Abstract
Finger millet is an important cereal crop in eastern Africa and southern India with excellent grain storage quality and unique ability to thrive in extreme environmental conditions. Since negligible attention has been paid to improving this crop to date, the current study used Next Generation Sequencing (NGS) technologies to develop both Simple Sequence Repeat (SSR) and Single Nucleotide Polymorphism (SNP) markers. Genomic DNA from cultivated finger millet genotypes KNE755 and KNE796 was sequenced using both Roche 454 and Illumina technologies. Non-organelle sequencing reads were assembled into 207 Mbp representing approximately 13% of the finger millet genome. We identified 10,327 SSRs and 23,285 non-homeologous SNPs and tested 101 of each for polymorphism across a diverse set of wild and cultivated finger millet germplasm. For the 49 polymorphic SSRs, the mean polymorphism information content (PIC) was 0.42, ranging from 0.16 to 0.77. We also validated 92 SNP markers, 80 of which were polymorphic with a mean PIC of 0.29 across 30 wild and 59 cultivated accessions. Seventy-six of the 80 SNPs were polymorphic across 30 wild germplasm with a mean PIC of 0.30 while only 22 of the SNP markers showed polymorphism among the 59 cultivated accessions with an average PIC value of 0.15. Genetic diversity analysis using the polymorphic SNP markers revealed two major clusters; one of wild and another of cultivated accessions. Detailed STRUCTURE analysis confirmed this grouping pattern and further revealed 2 sub-populations within wild E. coracana subsp. africana. Both STRUCTURE and genetic diversity analysis assisted with the correct identification of the new germplasm collections. These polymorphic SSR and SNP markers are a significant addition to the existing 82 published SSRs, especially with regard to the previously reported low polymorphism levels in finger millet. Our results also reveal an unexploited finger millet genetic resource that can be included in the regional breeding programs in order to efficiently optimize productivity.
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Affiliation(s)
- Davis Gimode
- Kenyatta University, P.O. Box 43844–00100, Nairobi, Kenya
| | | | | | | | | | - Emmarold E. Mneney
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar-Es-Salaam, Tanzania
| | - Alice Muchugi
- Kenyatta University, P.O. Box 43844–00100, Nairobi, Kenya
- ICRAF-Nairobi, P.O Box 30677, Nairobi, Kenya
| | - Jesse Machuka
- Kenyatta University, P.O. Box 43844–00100, Nairobi, Kenya
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Saeed AF, Wang R, Wang S. Microsatellites in Pursuit of Microbial Genome Evolution. Front Microbiol 2016; 6:1462. [PMID: 26779133 PMCID: PMC4700210 DOI: 10.3389/fmicb.2015.01462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 12/07/2015] [Indexed: 12/27/2022] Open
Abstract
Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.
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Affiliation(s)
- Abdullah F. Saeed
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
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Yan YB, Duke NC, Sun M. Comparative Analysis of the Pattern of Population Genetic Diversity in Three Indo-West Pacific Rhizophora Mangrove Species. FRONTIERS IN PLANT SCIENCE 2016; 7:1434. [PMID: 27746790 PMCID: PMC5043064 DOI: 10.3389/fpls.2016.01434] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/08/2016] [Indexed: 05/08/2023]
Abstract
Rhizophora species are the most widely distributed mangrove trees in the Indo-West Pacific (IWP) region. Comparative studies of these species with shared life history traits can help identify evolutionary factors that have played most important roles in determining genetic diversity within and between populations in ocean-current dispersed mangrove tree species. We sampled 935 individuals from 54 natural populations for genotyping with 13 microsatellite markers to investigate the level of genetic variation, population structure, and gene flow on a broad geographic scale in Rhizophora apiculata, Rhizophora mucronata, and Rhizophora stylosa across the IWP region. In contrast to the pattern expected of long-lived woody plants with predominant wind-pollination, water-dispersed seeds and wide geographic range, genetic variation within populations was generally low in all the three species, especially in those peripheral populations from geographic range limits. Although the large water-buoyant propagules of Rhizophora have capacity for long distance dispersal, such events might be rare in reality, as reflected by the low level of gene flow and high genetic differentiation between most of population pairs within each species. Phylogeographic separation of Australian and Pacific island populations from SE Asian lineages previously revealed with DNA sequence data was still detectable in R. apiculata based on genetic distances, but this pattern of disjunction was not always evident in R. mucronata and R. stylosa, suggesting that fast-evolving molecular markers could be more suitable for detecting contemporary genetic structure but not deep evolutionary divergence caused by historical vicariance. Given that mangrove species generally have small effective population sizes, we conclude that genetic drift coupled with limited gene flow have played a dominant role in producing the current pattern of population genetic diversity in the IWP Rhizophora species, overshadowing the effects of their life history traits. Recent population fragmentation and disturbances arising from human activities could further endanger genetic diversity in mangrove trees.
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Affiliation(s)
- Yu-Bin Yan
- School of Biological Sciences, The University of Hong KongHong Kong, China
| | - Norm C. Duke
- The Centre for Tropical Water and Aquatic Ecosystem Research, James Cook UniversityTownsville, QLD, Australia
| | - Mei Sun
- School of Biological Sciences, The University of Hong KongHong Kong, China
- *Correspondence: Mei Sun
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