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Sukhija N, Malik AA, Devadasan JM, Dash A, Bidyalaxmi K, Ravi Kumar D, Kousalaya Devi M, Choudhary A, Kanaka KK, Sharma R, Tripathi SB, Niranjan SK, Sivalingam J, Verma A. Genome-wide selection signatures address trait specific candidate genes in cattle indigenous to arid regions of India. Anim Biotechnol 2024; 35:2290521. [PMID: 38088885 DOI: 10.1080/10495398.2023.2290521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
The peculiarity of Indian cattle lies in milk quality, resistance to diseases and stressors as well as adaptability. The investigation addressed selection signatures in Gir and Tharparkar cattle, belonging to arid ecotypes of India. Double digest restriction-site associated DNA sequencing (ddRAD-seq) yielded nearly 26 million high-quality reads from unrelated seven Gir and seven Tharparkar cows. In all, 19,127 high-quality SNPs were processed for selection signature analysis. An approach involving within-population composite likelihood ratio (CLR) statistics and between-population FST statistics was used to capture selection signatures within and between the breeds, respectively. A total of 191 selection signatures were addressed using CLR and FST approaches. Selection signatures overlapping 86 and 73 genes were detected as Gir- and Tharparkar-specific, respectively. Notably, genes related to production (CACNA1D, GHRHR), reproduction (ESR1, RBMS3), immunity (NOSTRIN, IL12B) and adaptation (ADAM22, ASL) were annotated to selection signatures. Gene pathway analysis revealed genes in insulin/IGF pathway for milk production, gonadotropin releasing hormone pathway for reproduction, Wnt signalling pathway and chemokine and cytokine signalling pathway for adaptation. This is the first study where selection signatures are identified using ddRAD-seq in indicine cattle breeds. The study shall help in conservation and leveraging genetic improvements in Gir and Tharparkar cattle.
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Affiliation(s)
- Nidhi Sukhija
- ICAR-National Dairy Research Institute, Karnal, India
| | - Anoop Anand Malik
- TERI School of Advanced Studies, Delhi, India
- The Energy and Resources Institute, North Eastern Regional Centre, Guwahati, India
| | | | | | - Kangabam Bidyalaxmi
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - D Ravi Kumar
- ICAR-National Dairy Research Institute, Karnal, India
| | | | | | - K K Kanaka
- ICAR-National Dairy Research Institute, Karnal, India
- ICAR- Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | | | | | - Archana Verma
- ICAR-National Dairy Research Institute, Karnal, India
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Liu Y, Wang H, Yang J, Dao Z, Sun W. Conservation genetics and potential geographic distribution modeling of Corybas taliensis, a small 'sky Island' orchid species in China. BMC Plant Biol 2024; 24:11. [PMID: 38163918 PMCID: PMC10759615 DOI: 10.1186/s12870-023-04693-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 12/15/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Corybas taliensis is an endemic species of sky islands in China. Its habitat is fragile and unstable, and it is likely that the species is threatened. However, it is difficult to determine the conservation priority or unit without knowing the genetic background and the overall distribution of this species. In this study, we used double digest restriction-site associated DNA-sequencing (ddRAD-seq) to investigate the conservation genomics of C. taliensis. At the same time, we modeled the extent of suitable habitat for C. taliensis in present and future (2030 and 2090) habitat using the maximum-entropy (MaxEnt) model. RESULTS The results suggested that the related C. fanjingshanensis belongs to C. taliensis and should not be considered a separate species. All the sampling locations were divided into three genetic groups: the Sichuan & Guizhou population (SG population), the Hengduan Mountains population (HD population) and Himalayan population (HM population), and we found that there was complex gene flow between the sampling locations of HD population. MT was distinct genetically from the other sampling locations due to the unique environment in Motuo. The genetic diversity (π, He) of C. taliensis was relatively high, but its contemporary effective population size (Ne) was small. C. taliensis might be currently affected by inbreeding depression, although its large population density may be able to reduce the effect of this. The predicted areas of suitable habitat currently found in higher mountains will not change significantly in the future, and these suitable habitats are predicted to spread to other higher mountains under future climate change. However, suitable habitat in relatively low altitude areas may disappear in the future. This suggests that C. taliensis will be caught in a 'summit trap' in low altitude areas, however, in contrast, the high altitude of the Himalaya and the Hengduan Mountains are predicted to act as 'biological refuges' for C. taliensis in the future. CONCLUSIONS These results not only provide a new understanding of the genetic background and potential resource distribution of C. taliensis, but also lay the foundation for its conservation and management.
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Affiliation(s)
- Yuhang Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huichun Wang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
| | - Zhiling Dao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, Yunnan, 650201, China.
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Muharromah AF, Reyes JIL, Kagia N, Watanabe K. Genome-wide detection of Wolbachia in natural Aedes aegypti populations using ddRAD-Seq. Front Cell Infect Microbiol 2023; 13:1252656. [PMID: 38162582 PMCID: PMC10755911 DOI: 10.3389/fcimb.2023.1252656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Background Wolbachia, an endosymbiotic bacterium, is globally used to control arboviruses because of its ability to block arboviral replication and manipulate the reproduction of Wolbachia host, Aedes aegypti. Polymerase chain reaction (PCR)-based Wolbachia detection has been recently reported from natural Ae. aegypti populations. However, due to the technical limitations of PCR, such as primer incompatibility, PCR-based assays are not sufficiently reliable or accurate. In this study, we examined double digestion restriction site-associated DNA sequencing (ddRAD-Seq) efficiency and limitations in Wolbachia detection and quantification in field-collected Ae. aegypti natural populations in Metro Manila, the Philippines, compared with PCR-based assays. Methods A total of 217 individuals Ae. aegypti were collected from Metropolitan Manila, Philippines. We separated it into 14 populations consisting of 7 female and male populations. We constructed a library for pool ddRAD-Seq per population and also screened for Wolbachia by PCR assays using wsp and 16S rRNA. Wolbachia density per population were measured using RPS17 as the housekeeping gene. Results From 146,239,637 sequence reads obtained, 26,299 and 43,778 reads were mapped across the entire Wolbachia genome (with the wAlbA and wAlbB strains, respectively), suggesting that ddRAD-Seq complements PCR assays and supports more reliable Wolbachia detection from a genome-wide perspective. The number of reads mapped to the Wolbachia genome per population positively correlated with the number of Wolbachia-infected individuals per population based on PCR assays and the relative density of Wolbachia in the Ae. aegypti populations based on qPCR, suggesting ddRAD-Seq-based semi-quantification of Wolbachia by ddRAD-Seq. Male Ae. aegypti exhibited more reads mapped to the Wolbachia genome than females, suggesting higher Wolbachia prevalence rates in their case. We detected 150 single nucleotide polymorphism loci across the Wolbachia genome, allowing for more accurate the detection of four strains: wPip, wRi, TRS of Brugia malayi, and wMel. Conclusions Taken together, our results demonstrate the feasibility of ddRAD-Seq-based Wolbachia detection from field-collected Ae. aegypti mosquitoes.
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Affiliation(s)
- Atikah Fitria Muharromah
- Molecular Ecology and Health Laboratory, Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
- Entomology Laboratory, Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Jerica Isabel L. Reyes
- Molecular Ecology and Health Laboratory, Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
| | - Ngure Kagia
- Molecular Ecology and Health Laboratory, Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
| | - Kozo Watanabe
- Molecular Ecology and Health Laboratory, Center for Marine Environmental Studies (CMES), Ehime University, Matsuyama, Japan
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Samake JN, Lavretsky P, Gunarathna I, Follis M, Brown JI, Ali S, Yared S, Carter TE. Population genomic analyses reveal population structure and major hubs of invasive Anopheles stephensi in the Horn of Africa. Mol Ecol 2023; 32:5695-5708. [PMID: 37795951 DOI: 10.1111/mec.17136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 08/15/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023]
Abstract
Anopheles stephensi invasion in the Horn of Africa (HoA) poses a substantial risk of increased malaria disease burden in the region. An understanding of the history of introduction(s), establishment(s) and potential A. stephensi sources in the HoA is needed to predict future expansions and establish where they may be effectively controlled. To this end, we take a landscape genomic approach to assess A. stephensi origins and spread throughout the HoA, information essential for vector control. Specifically, we assayed 2070 genome-wide single nucleotide polymorphisms across 214 samples spanning 13 populations of A. stephensi from Ethiopia and Somaliland collected in 2018 and 2020, respectively. Principal component and genetic ancestry analyses revealed clustering that followed an isolation-by-distance pattern, with genetic divergence among the Ethiopian samples significantly correlating with geographical distance. Additionally, genetic relatedness was observed between the northeastern and east central Ethiopian A. stephensi populations and the Somaliland A. stephensi populations. These results reveal population differentiation and genetic connectivity within HoA A. stephensi populations. Furthermore, based on genetic network analysis, we uncovered that Dire Dawa, the site of a spring 2022 malaria outbreak, was one of the major hubs from which sequential founder events occurred in the rest of the eastern Ethiopian region. These findings can be useful for the selection of sites for heightened control to prevent future malaria outbreaks. Finally, we did not detect significant genotype-environmental associations, potentially due to the recency of their colonization and/or other anthropogenic factors leading to the initial spread and establishment of A. stephensi. Our study highlights how coupling genomic data at landscape levels can shed light into even ongoing invasions.
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Affiliation(s)
| | - Philip Lavretsky
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, USA
| | | | - Madison Follis
- Department of Biology, Baylor University, Waco, Texas, USA
| | - Joshua I Brown
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| | - Said Ali
- Ministry of Health Somaliland, Hargeisa, Somalia
| | - Solomon Yared
- Department of Biology, Jigjiga University, Jigjiga, Ethiopia
| | - Tamar E Carter
- Department of Biology, Baylor University, Waco, Texas, USA
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Dong X, Zhang H, Zhu X, Wang K, Xue H, Ye Z, Zheng C, Bu W. Mitochondrial introgression and mito-nuclear discordance obscured the closely related species boundaries in Cletus Stål from China (Heteroptera: Coreidae). Mol Phylogenet Evol 2023; 184:107802. [PMID: 37221926 DOI: 10.1016/j.ympev.2023.107802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 04/07/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Accurate taxonomy and delimitation are of great importance for pest control strategies and management programs. Here, we focus on Cletus (Insecta: Hemiptera: Coreidae), which includes many crop pests. The species boundaries still conflict and only cytochrome c oxidase subunit I (COI) barcoding has been previously used for molecular studies. We generated new mitochondrial genome and nuclear genome-wide SNPs to explore the species boundaries of 46 Cletus samples from China using multiple species delimitation approaches. All results recovered a monophyly with high support, except for two closely related species in clade I - C. punctiger and C. graminis. Mitochondrial data demonstrated admixture in clade I, while genome-wide SNPs unambiguously identified two separate species, which were confirmed by morphological classification. Inconsistent nuclear and mitochondrial data indicated mito-nuclear discordance. Mitochondrial introgression is the most likely explanation, and more extensive sampling and more comprehensive data are needed to ascertain a pattern. Accurate species delimitation will shed light on species status; thus, an accurate taxonomy is of particular concern, as there is a pressing need to implement precise control of agricultural pests and to perform further research on diversification.
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Affiliation(s)
- Xue Dong
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Haiguang Zhang
- College of Life Science, Linyi University, Linyi 276000, China
| | - Xiuxiu Zhu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Kaibin Wang
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Huaijun Xue
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Zhen Ye
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Chenguang Zheng
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
| | - Wenjun Bu
- Institute of Entomology, College of Life Sciences, Nankai University, Tianjin 300071, China.
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Guden B, Yol E, Erdurmus C, Lucas SJ, Uzun B. Construction of a high-density genetic linkage map and QTL mapping for bioenergy-related traits in sweet sorghum [ Sorghum bicolor (L.) Moench]. Front Plant Sci 2023; 14:1081931. [PMID: 37342135 PMCID: PMC10278949 DOI: 10.3389/fpls.2023.1081931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/15/2023] [Indexed: 06/22/2023]
Abstract
Sorghum is an important but arguably undervalued cereal crop, grown in large areas in Asia and Africa due to its natural resilience to drought and heat. There is growing demand for sweet sorghum as a source of bioethanol as well as food and feed. The improvement of bioenergy-related traits directly affects bioethanol production from sweet sorghum; therefore, understanding the genetic basis of these traits would enable new cultivars to be developed for bioenergy production. In order to reveal the genetic architecture behind bioenergy-related traits, we generated an F2 population from a cross between sweet sorghum cv. 'Erdurmus' and grain sorghum cv. 'Ogretmenoglu'. This was used to construct a genetic map from SNPs discovered by double-digest restriction-site associated DNA sequencing (ddRAD-seq). F3 lines derived from each F2 individual were phenotyped for bioenergy-related traits in two different locations and their genotypes were analyzed with the SNPs to identify QTL regions. On chromosomes 1, 7, and 9, three major plant height (PH) QTLs (qPH1.1, qPH7.1, and qPH9.1) were identified, with phenotypic variation explained (PVE) ranging from 10.8 to 34.8%. One major QTL (qPJ6.1) on chromosome 6 was associated with the plant juice trait (PJ) and explained 35.2% of its phenotypic variation. For fresh biomass weight (FBW), four major QTLs (qFBW1.1, qFBW6.1, qFBW7.1, and qFBW9.1) were determined on chromosomes 1, 6, 7, and 9, which explained 12.3, 14.5, 10.6, and 11.9% of the phenotypic variation, respectively. Moreover, two minor QTLs (qBX3.1 and qBX7.1) of Brix (BX) were mapped on chromosomes 3 and 7, explaining 8.6 and 9.7% of the phenotypic variation, respectively. The QTLs in two clusters (qPH7.1/qBX7.1 and qPH7.1/qFBW7.1) overlapped for PH, FBW and BX. The QTL, qFBW6.1, has not been previously reported. In addition, eight SNPs were converted into cleaved amplified polymorphic sequences (CAPS) markers, which can be easily detected by agarose gel electrophoresis. These QTLs and molecular markers can be used for pyramiding and marker-assisted selection studies in sorghum, to develop advanced lines that include desirable bioenergy-related traits.
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Affiliation(s)
- Birgul Guden
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Engin Yol
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
| | - Cengiz Erdurmus
- Department of Field Crops, West Mediterranean Agricultural Research Institute, Antalya, Türkiye
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Centre, Sabanci University, Istanbul, Türkiye
| | - Bulent Uzun
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, Antalya, Türkiye
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Arick MA, Grover CE, Hsu CY, Magbanua Z, Pechanova O, Miller ER, Thrash A, Youngblood RC, Ezzell L, Alam MS, Benzie JAH, Hamilton MG, Karsi A, Lawrence ML, Peterson DG. A high-quality chromosome-level genome assembly of rohu carp, Labeo rohita, and its utilization in SNP-based exploration of gene flow and sex determination. G3 (Bethesda) 2023; 13:6987299. [PMID: 36639248 PMCID: PMC9997561 DOI: 10.1093/g3journal/jkad009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023]
Abstract
Labeo rohita (rohu) is a carp important to aquaculture in South Asia, with a production volume close to Atlantic salmon. While genetic improvements to rohu are ongoing, the genomic methods commonly used in other aquaculture improvement programs have historically been precluded in rohu, partially due to the lack of a high-quality reference genome. Here we present a high-quality de novo genome produced using a combination of next-generation sequencing technologies, resulting in a 946 Mb genome consisting of 25 chromosomes and 2,844 unplaced scaffolds. Notably, while approximately half the size of the existing genome sequence, our genome represents 97.9% of the genome size newly estimated here using flow cytometry. Sequencing from 120 individuals was used in conjunction with this genome to predict the population structure, diversity, and divergence in three major rivers (Jamuna, Padma, and Halda), in addition to infer a likely sex determination mechism in rohu. These results demonstrate the utility of the new rohu genome in modernizing some aspects of rohu genetic improvement programs.
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Affiliation(s)
- Mark A Arick
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Corrinne E Grover
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Chuan-Yu Hsu
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Zenaida Magbanua
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Olga Pechanova
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Emma R Miller
- Ecology, Evolution, and Organismal Biology Department, Iowa State University, Ames, IA 50010, USA
| | - Adam Thrash
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Ramey C Youngblood
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Lauren Ezzell
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Md Samsul Alam
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - John A H Benzie
- WorldFish, Jalan Batu Maung, 11960 Bayan Lepas, Penang, Malaysia
| | | | - Attila Karsi
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS 39762, USA
| | - Mark L Lawrence
- Global Center for Aquatic Health and Food Security, Mississippi State University, Mississippi State, MS 39762, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
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Peres PA, Bracken-Grissom H, Timm LE, Mantelatto FL. Genomic Analyses Implicate the Amazon-Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab. Genes (Basel) 2022; 13:genes13122263. [PMID: 36553531 PMCID: PMC9777557 DOI: 10.3390/genes13122263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022] Open
Abstract
The Amazon-Orinoco plume (AOP) is the world's largest freshwater and sediment discharge into the ocean. Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, diversification time, and species delimitation are unresolved. Densely sampling markers across the genome (SNPs) could elucidate the evolutionary processes within this species. Here, we combined mtDNA data and ddRAD-seq to explore the diversification patterns and processes within the swimming crab C. ornatus. We show great genetic differentiation between groups on the north and south sides of the plume but also signs of hybridization. Demographic modeling indicates the divergence between groups starting around 8 Mya following the AOP's formation. After a period of isolation, we detect two incidences of secondary contact with stronger migration in concordance with the North Brazil Current flow. Our results suggest speciation with gene flow explained by the interplay among the AOP, oceanographic currents, and long larval dispersal. This work represents the first investigation employing ddRAD-seq in a marine invertebrate species with distribution encompassing the north and south Atlantic and sheds light on the role of the AOP in the diversification of a marine species.
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Affiliation(s)
- Pedro A. Peres
- Department of Biology, Institute of Environment, Florida International University (FIU), Miami, FL 33199, USA
- Laboratory of Bioecology and Systematics of Crustaceans (LBSC), Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto 14040-901, Brazil
- Correspondence:
| | - Heather Bracken-Grissom
- Department of Biology, Institute of Environment, Florida International University (FIU), Miami, FL 33199, USA
- Department of Invertebrate Zoology, National Museum of Natural History-Smithsonian, Washington, WA 20013-7012, USA
| | - Laura E. Timm
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
- Auke Bay Laboratories, Alaska Fisheries Science Center, NOAA National Marine Fisheries Service, Juneau, AK 99801, USA
| | - Fernando L. Mantelatto
- Laboratory of Bioecology and Systematics of Crustaceans (LBSC), Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto 14040-901, Brazil
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Chiba M, Hirano T, Yamazaki D, Ye B, Ito S, Kagawa O, Endo K, Nishida S, Hara S, Aratake K, Chiba S. The mutual history of Schlegel's Japanese gecko (Reptilia: Squamata: Gekkonidae) and humans inscribed in genes and ancient literature. PNAS Nexus 2022; 1:pgac245. [PMID: 36712337 PMCID: PMC9802249 DOI: 10.1093/pnasnexus/pgac245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/31/2022] [Indexed: 06/18/2023]
Abstract
Knowing how the present distribution of organisms was formed is an essential issue in evolutionary ecology. Recently, the distribution of organisms on Earth has been significantly changed by human-mediated dispersal due to globalization. Therefore, significant attention has been paid to such processes. However, although humankind has taken considerable time to achieve modernization, the impact of ancient human activity on ecosystems has not yet been thoroughly studied. We hypothesized that ancient urban development and transitions had a non-negligible effect on species distribution. Inferring the impact of past human activity on ecosystems from ancient literature and verifying that impact by genetic analysis and human history is an effective means of tackling this problem. As geckos, a popular neighbor of human dwellings, are good material for this model, we performed this combination approach using Schlegel's Japanese gecko, Gekko japonicus. We show that G. japonicus migrated from China to the western Japanese archipelago before Christ. The gecko species dispersed itself from western to eastern the archipelago on a time scale of thousands of years. There are many synchronizations between the dispersal history of G. japonicus and the historical development of human society. It is suggested by such synchronizations that humans have influenced the distribution of G. japonicus many times throughout its dispersal history.
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Affiliation(s)
| | - Takahiro Hirano
- Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
| | - Daishi Yamazaki
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Bin Ye
- Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
- Institute of Biomedical and Health Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shun Ito
- Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
| | - Osamu Kagawa
- Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Komei Endo
- Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Shu Nishida
- Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Seiji Hara
- Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
| | - Kenichiro Aratake
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
| | - Satoshi Chiba
- Graduate School of Life Sciences, Tohoku University, Miyagi, Japan
- Center for Northeast Asian Studies, Tohoku University, Miyagi, Japan
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10
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Seki K, Toda Y. QTL mapping for seed morphology using the instance segmentation neural network in Lactuca spp. Front Plant Sci 2022; 13:949470. [PMID: 36311127 PMCID: PMC9606697 DOI: 10.3389/fpls.2022.949470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Wild species of lettuce (Lactuca sp.) are thought to have first been domesticated for oilseed contents to provide seed oil for human consumption. Although seed morphology is an important trait contributing to oilseed in lettuce, the underlying genetic mechanisms remain elusive. Since lettuce seeds are small, a manual phenotypic determination required for a genetic dissection of such traits is challenging. In this study, we built and applied an instance segmentation-based seed morphology quantification pipeline to measure traits in seeds generated from a cross between the domesticated oilseed type cultivar 'Oilseed' and the wild species 'UenoyamaMaruba' in an automated manner. Quantitative trait locus (QTL) mapping following ddRAD-seq revealed 11 QTLs linked to 7 seed traits (area, width, length, length-to-width ratio, eccentricity, perimeter length, and circularity). Remarkably, the three QTLs with the highest LOD scores, qLWR-3.1, qECC-3.1, and qCIR-3.1, for length-to-width ratio, eccentricity, and circularity, respectively, mapped to linkage group 3 (LG3) around 161.5 to 214.6 Mb, a region previously reported to be associated with domestication traits from wild species. These results suggest that the oilseed cultivar harbors genes acquired during domestication to control seed shape in this genomic region. This study also provides genetic evidence that domestication arose, at least in part, by selection for the oilseed type from wild species and demonstrates the effectiveness of image-based phenotyping to accelerate discoveries of the genetic basis for small morphological features such as seed size and shape.
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Affiliation(s)
- Kousuke Seki
- Nagano Vegetable and Ornamental Crops Experiment Station, Shiojiri, Japan
| | - Yosuke Toda
- Phytometrics Co., Ltd., Shizuoka, Japan
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan
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11
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Kushwah A, Bhatia D, Barmukh R, Singh I, Singh G, Bindra S, Vij S, Chellapilla B, Pratap A, Roorkiwal M, Kumar S, Varshney RK, Singh S. Genetic mapping of QTLs for drought tolerance in chickpea ( Cicer arietinum L.). Front Genet 2022; 13:953898. [PMID: 36061197 PMCID: PMC9437436 DOI: 10.3389/fgene.2022.953898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/05/2022] [Indexed: 01/24/2023] Open
Abstract
Chickpea yield is severely affected by drought stress, which is a complex quantitative trait regulated by multiple small-effect genes. Identifying genomic regions associated with drought tolerance component traits may increase our understanding of drought tolerance mechanisms and assist in the development of drought-tolerant varieties. Here, a total of 187 F8 recombinant inbred lines (RILs) developed from an interspecific cross between drought-tolerant genotype GPF 2 (Cicer arietinum) and drought-sensitive accession ILWC 292 (C. reticulatum) were evaluated to identify quantitative trait loci (QTLs) associated with drought tolerance component traits. A total of 21 traits, including 12 morpho-physiological traits and nine root-related traits, were studied under rainfed and irrigated conditions. Composite interval mapping identified 31 QTLs at Ludhiana and 23 QTLs at Faridkot locations for morphological and physiological traits, and seven QTLs were identified for root-related traits. QTL analysis identified eight consensus QTLs for six traits and five QTL clusters containing QTLs for multiple traits on linkage groups CaLG04 and CaLG06. The identified major QTLs and genomic regions associated with drought tolerance component traits can be introgressed into elite cultivars using genomics-assisted breeding to enhance drought tolerance in chickpea.
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Affiliation(s)
- Ashutosh Kushwah
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Dharminder Bhatia
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gurpreet Singh
- Regional Research Station, Punjab Agricultural University, Faridkot, India
| | - Shayla Bindra
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Suruchi Vij
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | | | - Aditya Pratap
- Crop Improvement Division, ICAR- Indian Institute of Pulses Research, Kanpur, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Office, Rabat, Morocco
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Murdoch’s Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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12
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Sano I, Saito T, Ito S, Ye B, Uechi T, Seo T, Do VT, Kimura K, Hirano T, Yamazaki D, Shirai A, Kondo T, Miura O, Miyazaki JI, Chiba S. Resolving species-level diversity of Beringiana and Sinanodonta mussels (Bivalvia: Unionidae) in the Japanese archipelago using genome-wide data. Mol Phylogenet Evol 2022; 175:107563. [PMID: 35809852 DOI: 10.1016/j.ympev.2022.107563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 06/04/2022] [Accepted: 06/27/2022] [Indexed: 11/22/2022]
Abstract
Accurate species identification is of primary importance in ecology and evolutionary biology. For a long time, the unionid mussels Beringiana and Sinanodonta have puzzled researchers trying to unravel their diversity because of their poorly discernible morphologies. A recent study conducted species delineation of unionid mussels based on mitochondrial DNA variation, opening up a new avenue to grasp species diversity of the mussels. However, mtDNA-based classification may not align with species boundaries because mtDNA is prone to introgression and incomplete lineage sorting that cause discordance between species affiliation and gene phylogeny. In this study, we evaluated the validity of the mtDNA-based classification of unionid mussels Beringiana and Sinanodonta in Japan using mitochondrial sequence data, double digest restriction site-associated DNA library (ddRAD) sequencing, and morphological data. We found significant inconsistencies in the mitochondrial and nuclear DNA phylogenies, casting doubt on the reliability of the mtDNA-based classification in this group. In addition, nuclear DNA phylogeny revealed that there are at least two unionid lineages hidden in the mtDNA phylogeny. Although molecular dating technique indicates that Beringiana and Sinanodonta diverged >35 million years ago, their shell morphologies are often indistinguishable. Specifically, morphological analyses exhibited the parallel appearance of nearly identical ball-like shell forms in the two genera in Lake Biwa, which further complicates species identification and the morphological evolution of unionid mussels. Our study adds to a growing body of literature that accurate species identification of unionid mussels is difficult when using morphological characters alone. Although mtDNA-based classification is a simple and convenient way to classify unionid mussels, considerable caution is warranted for its application in ecological and evolutionary studies.
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13
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Edgeloe JM, Severn-Ellis AA, Bayer PE, Mehravi S, Breed MF, Krauss SL, Batley J, Kendrick GA, Sinclair EA. Extensive polyploid clonality was a successful strategy for seagrass to expand into a newly submerged environment. Proc Biol Sci 2022; 289:20220538. [PMID: 35642363 PMCID: PMC9156900 DOI: 10.1098/rspb.2022.0538] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Polyploidy has the potential to allow organisms to outcompete their diploid progenitor(s) and occupy new environments. Shark Bay, Western Australia, is a World Heritage Area dominated by temperate seagrass meadows including Poseidon's ribbon weed, Posidonia australis. This seagrass is at the northern extent of its natural geographic range and experiences extremes in temperature and salinity. Our genomic and cytogenetic assessments of 10 meadows identified geographically restricted, diploid clones (2n = 20) in a single location, and a single widespread, high-heterozygosity, polyploid clone (2n = 40) in all other locations. The polyploid clone spanned at least 180 km, making it the largest known example of a clone in any environment on earth. Whole-genome duplication through polyploidy, combined with clonality, may have provided the mechanism for P. australis to expand into new habitats and adapt to new environments that became increasingly stressful for its diploid progenitor(s). The new polyploid clone probably formed in shallow waters after the inundation of Shark Bay less than 8500 years ago and subsequently expanded via vegetative growth into newly submerged habitats.
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Affiliation(s)
- Jane M. Edgeloe
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia,Oceans Institute, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Anita A. Severn-Ellis
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Philipp E. Bayer
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Shaghayegh Mehravi
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Martin F. Breed
- College of Science and Engineering, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Siegfried L. Krauss
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia,Kings Park Science, Department of Biodiversity Conservation and Attractions, 1 Kattidj Close, West Perth, Western Australia 6005, Australia
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Gary A. Kendrick
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia,Oceans Institute, University of Western Australia, Crawley, Western Australia, 6009, Australia
| | - Elizabeth A. Sinclair
- School of Biological Sciences, University of Western Australia, Crawley, Western Australia, 6009, Australia,Oceans Institute, University of Western Australia, Crawley, Western Australia, 6009, Australia,Kings Park Science, Department of Biodiversity Conservation and Attractions, 1 Kattidj Close, West Perth, Western Australia 6005, Australia
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14
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Chimura K, Akita S, Iwasaki T, Nagano AJ, Shimada S. Phylogeography of a canopy-forming kelp, Eisenia bicyclis (Laminariales, Phaeophyceae), based on a genome-wide sequencing analysis. J Phycol 2022; 58:318-329. [PMID: 35000198 DOI: 10.1111/jpy.13233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 12/29/2021] [Indexed: 06/14/2023]
Abstract
Analyses of phylogeographic patterns and genetic diversity provide fundamental information for the management and conservation of species. However, little is published about these patterns in Japanese kelp species. In this study, we conducted phylogeographic analyses of a canopy-forming kelp, Eisenia bicyclis, based on genome-wide SNPs identified by ddRAD-seq. We obtained 1,299 SNPs for 76 samples from nine localities across the distribution. STRUCTURE, NeighborNet, and discriminant analysis of principal components consistently showed high genetic differentiation among the Eastern Pacific, Central Pacific, and Sea of Japan coastal regions. Relatively strong gene flow was detected only within populations in the Eastern Pacific and in the Sea of Japan. Genetic diversity and genetic uniqueness were high in the Central Pacific and low in the Sea of Japan. These results suggest that there were at least three independent refugia corresponding to the three regions during the Last Glacial Maximum (LGM). Furthermore, relatively larger populations in the Central Pacific and smaller populations in the Sea of Japan have been maintained in the demographic history from before the LGM to the present. These phylogeographic histories were supported by an Approximate Bayesian Computation analysis. From a conservation genetics perspective, the loss of southern populations in the Central Pacific would greatly reduce the total genetic diversity of the species. Southern populations in the Sea of Japan, which have relatively low genetic diversity, may be highly vulnerable to environmental change, such as heat waves and increased feeding. Therefore, careful monitoring and conservation are needed in the two regions.
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Affiliation(s)
- Kanako Chimura
- Humanities and Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyoku, Tokyo, 112-8610, Japan
| | - Shingo Akita
- Natural Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyoku, Tokyo, 112-8610, Japan
- Faculty of Fisheries Sciences, Hokkaido University, 3-1-1 Minato, Hakodate, Hokkaido, 041-8611, Japan
| | - Takaya Iwasaki
- Natural Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyoku, Tokyo, 112-8610, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| | - Satoshi Shimada
- Natural Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyoku, Tokyo, 112-8610, Japan
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15
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Tran Lu Y A, Ruault S, Daguin-Thiébaut C, Castel J, Bierne N, Broquet T, Wincker P, Perdereau A, Arnaud-Haond S, Gagnaire PA, Jollivet D, Hourdez S, Bonhomme F. Subtle limits to connectivity revealed by outlier loci within two divergent metapopulations of the deep-sea hydrothermal gastropod Ifremeria nautilei. Mol Ecol 2022; 31:2796-2813. [PMID: 35305041 DOI: 10.1111/mec.16430] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 11/30/2022]
Abstract
Hydrothermal vents form archipelagos of ephemeral deep-sea habitats that raise interesting questions about the evolution and dynamics of the associated endemic fauna, constantly subject to extinction-recolonization processes. These metal-rich environments are coveted for the mineral resources they harbor, thus raising recent conservation concerns. The evolutionary fate and demographic resilience of hydrothermal species strongly depend on the degree of connectivity among and within their fragmented metapopulations. In the deep sea, however, assessing connectivity is difficult and usually requires indirect genetic approaches. Improved detection of fine-scale genetic connectivity is now possible based on genome-wide screening for genetic differentiation. Here, we explored population connectivity in the hydrothermal vent snail Ifremeria nautilei across its species range encompassing five distinct back-arc basins in the Southwest Pacific. The global analysis, based on 10 570 single nucleotide polymorphism (SNP) markers derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), depicted two semi-isolated and homogeneous genetic clusters. Demo-genetic modeling suggests that these two groups began to diverge about 70 000 generations ago, but continue to exhibit weak and slightly asymmetrical gene flow. Furthermore, a careful analysis of outlier loci showed subtle limitations to connectivity between neighboring basins within both groups. This finding indicates that migration is not strong enough to totally counterbalance drift or local selection, hence questioning the potential for demographic resilience at this latter geographical scale. These results illustrate the potential of large genomic datasets to understand fine-scale connectivity patterns in hydrothermal vents and the deep sea.
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Affiliation(s)
- Adrien Tran Lu Y
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Stéphanie Ruault
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Claire Daguin-Thiébaut
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Jade Castel
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Nicolas Bierne
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Thomas Broquet
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Patrick Wincker
- Génomique Métabolique, Génoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Aude Perdereau
- Génomique Métabolique, Génoscope, Institut de Biologie François Jacob, CEA, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Sophie Arnaud-Haond
- MARBEC, Marine Biodiversity Exploitation and Conservation, Univ Montpellier, CNRS, IFREMER, IRD, Sète, France
| | | | - Didier Jollivet
- Sorbonne Université, CNRS, UMR 7144, 'Dynamique de la Diversité Marine' (DyDiv) Lab, Station biologique de Roscoff, Place G. Teissier, 29680, Roscoff, France
| | - Stéphane Hourdez
- Sorbonne Université, CNRS, UMR 8222, Laboratoire d'Ecogéochimie des Environnements Benthiques, Observatoire Océanologique de Banyuls, Avenue Pierre Fabre, 66650, Banyuls-sur-Mer, France
| | - François Bonhomme
- ISEM, Institut des Sciences de l'Evolution, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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16
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Yang F, Cai L, Dao Z, Sun W. Genomic Data Reveals Population Genetic and Demographic History of Magnolia fistulosa (Magnoliaceae), a Plant Species With Extremely Small Populations in Yunnan Province, China. Front Plant Sci 2022; 13:811312. [PMID: 35251084 PMCID: PMC8892343 DOI: 10.3389/fpls.2022.811312] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/13/2022] [Indexed: 05/11/2023]
Abstract
Elucidating the genetic background of threatened species is fundamental to their management and conservation, and investigating the demographic history of these species is helpful in the determination of the threats facing them. The woody species of the genus Magnolia (Magnoliaceae) have high economic, scientific and ecological values. Although nearly half of all Magnolia species have been evaluated as threatened, to date there has been no population genetic study employing Next Generation Sequencing (NGS) technology in this genus. In the present study, we investigate the conservation genomics of Magnolia fistulosa, a threatened species endemic to the limestone area along the Sino-Vietnamese border, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. To increase the reliability of our statistical inferences, we employed two approaches, Stacks and ipyrad, for SNP calling. A total of 15,272 and 18,960, respectively, putatively neutral SNPs were generated by Stacks and ipyrad. Relatively high genetic diversity and large population divergence were detected in M. fistulosa. Although higher absolute values were calculated using the ipyrad data set, the two data sets showed the same trends in genetic diversity (π, H e), population differentiation (F ST) and inbreeding coefficients (F IS). A change in the effective population size of M. fistulosa within the last 1 Ma was detected, including a population decline about 0.5-0.8 Ma ago, a bottleneck event about 0.2-0.3 Ma ago, population fluctuations during the last glacial stage, and the recovery of effective population size after the last glacial maximum. Our findings not only lay the foundation for the future conservation of this species, but also provide new insights into the evolutionary history of the genus Magnolia in southeastern Yunnan, China.
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Affiliation(s)
- Fengmao Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhiling Dao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species With Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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17
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Palacio-Mejía JD, Grabowski PP, Ortiz EM, Silva-Arias GA, Haque T, Des Marais DL, Bonnette J, Lowry DB, Juenger TE. Geographic patterns of genomic diversity and structure in the C 4 grass Panicum hallii across its natural distribution. AoB Plants 2021; 13:plab002. [PMID: 33708370 PMCID: PMC7937184 DOI: 10.1093/aobpla/plab002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/05/2021] [Indexed: 06/01/2023]
Abstract
Geographic patterns of within-species genomic diversity are shaped by evolutionary processes, life history and historical and contemporary factors. New genomic approaches can be used to infer the influence of such factors on the current distribution of infraspecific lineages. In this study, we evaluated the genomic and morphological diversity as well as the genetic structure of the C4 grass Panicum hallii across its complex natural distribution in North America. We sampled extensively across the natural range of P. hallii in Mexico and the USA to generate double-digestion restriction-associated DNA (ddRAD) sequence data for 423 individuals from 118 localities. We used these individuals to study the divergence between the two varieties of P. hallii, P. hallii var. filipes and P. hallii var. hallii as well as the genetic diversity and structure within these groups. We also examined the possibility of admixture in the geographically sympatric zone shared by both varieties, and assessed distribution shifts related with past climatic fluctuations. There is strong genetic and morphological divergence between the varieties and consistent genetic structure defining seven genetic clusters that follow major ecoregions across the range. South Texas constitutes a hotspot of genetic diversity with the co-occurrence of all genetic clusters and admixture between the two varieties. It is likely a recolonization and convergence point of populations that previously diverged in isolation during fragmentation events following glaciation periods.
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Affiliation(s)
| | - Paul P Grabowski
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Edgardo M Ortiz
- Ecology & Ecosystem Management, Plant Biodiversity Research, Technical University of Munich, Freising, Germany
| | - Gustavo Adolfo Silva-Arias
- Professorship for Population Genetics, Department of Life Science Systems, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Taslima Haque
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - David L Des Marais
- Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jason Bonnette
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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18
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Hu L, Yang R, Wang YH, Gong X. The natural hybridization between species Ligularia nelumbifolia and Cremanthodium stenoglossum (Senecioneae, Asteraceae) suggests underdeveloped reproductive isolation and ambiguous intergeneric boundary. AoB Plants 2021; 13:plab012. [PMID: 33796247 PMCID: PMC7994929 DOI: 10.1093/aobpla/plab012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Natural hybridization is frequent in plants and is considered an important factor facilitating speciation. The natural intergeneric hybridization between Ligularia and Cremanthodium was previously confirmed using a couple of DNA markers. However, the mechanism of this intergeneric hybridization and the role of reproductive isolation in the process of hybridization remain unclear. Here we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to further quantify the occurrence of hybridization, the genetic structure of the hybrid population and the role of reproductive isolation between Ligularia nelumbifolia and Cremanthodium stenoglossum. The results based on the ddRAD-seq SNP data sets indicated that hybridization between L. nelumbifolia and C. stenoglossum was restricted to F1s, and no gene introgression was identified between these two species. STRUCTURE analysis and maximum likelihood (ML) tree results showed a slightly larger genetic contribution of L. nelumbifolia to putative hybrid F1s. We deduced that the reproductive isolation between these two parent species is not well-developed but still strong enough to maintain the genetic integrity of the species, and that their F1s are sterile or with low fertility. Given the poorly resolved phylogenetic relationship between Ligularia and Cremanthodium, the occurrence of natural hybridization between L. nelumbifolia and C. stenoglossum may provide new insights into the re-circumscription and re-delimitation of these two genera.
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Affiliation(s)
- Li Hu
- Plant Science Institute, School of Life Sciences, Yunnan University, Kunming 650201, Yunnan, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue-Hua Wang
- Plant Science Institute, School of Life Sciences, Yunnan University, Kunming 650201, Yunnan, China
| | - Xun Gong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Zhang G, Li J, Zhang J, Liang X, Wang T, Yin S. A high-density SNP-based genetic map and several economic traits-related loci in Pelteobagrus vachelli. BMC Genomics 2020; 21:700. [PMID: 33028208 PMCID: PMC7542894 DOI: 10.1186/s12864-020-07115-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 09/29/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND A high-density genetic linkage map is essential for QTL fine mapping, comparative genome analysis, identification of candidate genes and marker-assisted selection in aquaculture species. Pelteobagrus vachelli is a very popular commercial species in Asia. However, some specific characters hindered achievement of the traditional selective breeding based on phenotypes, such as lack of large-scale genomic resource and short of markers tightly associated with growth, sex determination and hypoxia tolerance related traits. RESULTS By making use of 5059 ddRAD markers in P. vachelli, a high-resolution genetic linkage map was successfully constructed. The map' length was 4047.01 cM by using an interval of 0.11 cm, which is an average marker standard. Comparative genome mapping revealed that a high proportion (83.2%) of markers with a one-to-one correspondence were observed between P. vachelli and P. fulvidraco. Based on the genetic map, 8 significant genome-wide QTLs for 4 weight, 1 body proportion, 2 sex determination, and 1 hypoxia tolerance related traits were detected on 4 LGs. Some SNPs from these significant genome-wide QTLs were observably associated with these phenotypic traits in other individuals by Kompetitive Allele Specific PCR. In addition, two candidate genes for weight, Sipa1 and HSD11B2, were differentially expressed between fast-, medium- and slow-growing P. vachelli. Sema7a, associated with hypoxia tolerance, was induced after hypoxia exposure and reoxygenation. CONCLUSIONS We mapped a set of suggestive and significant QTLs as well as candidate genes for 12 growth, 1 sex determination and 1 hypoxia tolerance related traits based on a high-density genetic linkage map by making use of SNP markers for P. fulvidraco. Our results have offered a valuable method about the much more efficient production of all-male, fast growth and hypoxia tolerance P. vachelli for the aquaculture industry.
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Affiliation(s)
- Guosong Zhang
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Key laboratory for physiology biochemistry and application, Heze University, Heze, 274015, Shandong, China
| | - Jie Li
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Jiajia Zhang
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Xia Liang
- Key laboratory for physiology biochemistry and application, Heze University, Heze, 274015, Shandong, China
| | - Tao Wang
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
- Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China
| | - Shaowu Yin
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
- Co-Innovation Center for Marine Bio-Industry Technology, Lian Yungang, 222005, China.
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Liu D, Zhang L, Wang J, Ma Y. Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs. Front Genet 2020; 11:757. [PMID: 33101354 PMCID: PMC7500208 DOI: 10.3389/fgene.2020.00757] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Though it is well-acknowledged that next generation sequencing (NGS) technologies can provide further insights into plant conservation management than traditional molecular markers, studies employing NGS to address conservation genomics and subsequent conservation strategies for threatened plants are still rare. Rhododendron is the largest genus of woody plants in China, and many species are threatened, however, to date there has been no conservation genetic research using NGS in this genus. In the present study, we investigated the conservation genetics of R. cyanocarpum, a threatened species endemic to the Cangshan Mountains in Yunnan, China, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. Due to the availability of sufficient SNPs, we were able to distinguish between neutral and putatively selected SNPs and were able to further investigate the genetic diversity, population structure, and differentiation in R. cyanocarpum, as well as make an estimation of its demographic history. A total of 6,584 SNPs were obtained, of which 5,729 were neutral (detected using Tajima’s D). In terms of the 5,729 neutral SNPs, R. cyanocarpum had a higher genetic diversity (π = 0.0702 ± 0.0017, He = 0.0675 ± 0.0016) than other plant species assessed using Rad-seq methods, while population differentiation (Fst from 0.0314 to 0.0452) was weak. Interestingly, contrasting patterns of population structure were revealed from all neutral and selected SNPs, with distinct genetic clusters forming for all SNPs and neutral SNPs, but no distinct subgroups for selected ones. Moreover, we were able to detect changes in effective population size (Ne) of R. cyanocarpum from 150,000 years ago, including a bottleneck event ca. 60,000 years ago, followed by recovery of Ne over a short period, and a subsequent gradual decline in Ne to date. Implications for conserving R. cyanocarpum based on these main results are then discussed.
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Affiliation(s)
- Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lu Zhang
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming, China
| | - Jihua Wang
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Torello Marinoni D, Nishio S, Valentini N, Shirasawa K, Acquadro A, Portis E, Alma A, Akkak A, Pavese V, Cavalet-Giorsa E, Botta R. Development of High-Density Genetic Linkage Maps and Identification of Loci for Chestnut Gall Wasp Resistance in Castanea spp. Plants (Basel) 2020; 9:plants9081048. [PMID: 32824716 PMCID: PMC7465717 DOI: 10.3390/plants9081048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 11/29/2022]
Abstract
Castanea sativa is an important multipurpose species in Europe for nut and timber production as well as for its role in the landscape and in the forest ecosystem. This species has low tolerance to chestnut gall wasp (Dryocosmus kuriphilus Yasumatsu), which is a pest that was accidentally introduced into Europe in early 2000 and devastated forest and orchard trees. Resistance to the gall wasp was found in the hybrid cultivar ‘Bouche de Bétizac’ (C. sativa × C. crenata) and studied by developing genetic linkage maps using a population derived from a cross between ‘Bouche de Bétizac’ and the susceptible cultivar ‘Madonna’ (C. sativa). The high-density genetic maps were constructed using double-digest restriction site-associated DNA-seq and simple sequence repeat markers. The map of ‘Bouche de Bétizac’ consisted of 1459 loci and spanned 809.6 cM; the map of ‘Madonna’ consisted of 1089 loci and spanned 753.3 cM. In both maps, 12 linkage groups were identified. A single major QTL was recognized on the ‘Bouche de Bétizac’ map, explaining up to 67–69% of the phenotypic variance of the resistance trait (Rdk1). The Rdk1 quantitative trait loci (QTL) region included 11 scaffolds and two candidate genes putatively involved in the resistance response were identified. This study will contribute to C. sativa breeding programs and to the study of Rdk1 genes.
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Affiliation(s)
- Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
- Correspondence:
| | - Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO, 2-1 Fujimoto, Tsukuba, Ibaraki 305-8605, Japan;
| | - Nadia Valentini
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan;
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Alberto Alma
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Aziz Akkak
- Dipartimento di Scienze Agrarie, degli Alimenti e dell’Ambiente, Università degli Studi di Foggia, Via Napoli 25, 71121 Foggia, Italy;
| | - Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Emile Cavalet-Giorsa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari—DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy; (N.V.); (A.A.); (E.P.); (A.A.); (V.P.); (E.C.-G.); (R.B.)
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Natarajan S, Hossain MR, Kim HT, Denison MIJ, Ferdous MJ, Jung HJ, Park JI, Nou IS. ddRAD-seq derived genome-wide SNPs, high density linkage map and QTLs for fruit quality traits in strawberry ( Fragaria x ananassa). 3 Biotech 2020; 10:353. [PMID: 32760641 DOI: 10.1007/s13205-020-02291-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 06/07/2020] [Indexed: 12/31/2022] Open
Abstract
Understanding the genetic determinants are essential for improving the fruit quality traits of strawberry. In this study, we focused on mapping the loci for fruit-length (FL), -diameter (FD), -weight (FW) and -soluble solid content (SSC) using the genome-wide single nucleotide polymorphisms (SNPs) identified via ddRAD-sequencing of the F1 population raised from Maehyang (♀) X Festival (♂). A total of 12,698 high quality SNPs were identified of which 1554 SNPs that showed significant Mendelian segregation (p < 0.05) were mapped to 53 linkage groups (LG) spanning a total of 2937.93 cM with an average marker density of 2.14 cM/locus. Six QTLs for FL and four QTLs for each of FD, FW and SSC were identified that explained 24–35%, 21–42%, 24–54% and 23–50% of overall phenotypic variations, respectively. The genes that lie within these QTL regions were extracted and discussed thoroughly. In addition, a high resolution melting marker (MF154) were designed based on the SNP A1723G of the UDP-glucose 4-epimerase GEPI48-like gene FAN_iscf00021287. The marker detected the high vs low sugar containing F1 plants and commercial cultivars with 81.39% and 86.95% detection accuracy, respectively. These SNPs, linkage map, QTLs and candidate genes will be helpful in understanding and improving the fruit quality traits of strawberry.
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Zhou M, Yang G, Sun G, Guo Z, Gong X, Pan Y. Resolving complicated relationships of the Panax bipinnatifidus complex in southwestern China by RAD-seq data. Mol Phylogenet Evol 2020; 149:106851. [PMID: 32438045 DOI: 10.1016/j.ympev.2020.106851] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 11/26/2022]
Abstract
The P. binpinnatifidus complex included most of the Panax species distributed in Sino-Himalaya regions except for P. pseudoginseng, P. stipuleanatus and P. notoginseng. However, the delimitation and identification of these taxa within the species complex are very difficult due to the existence of morphological intermediates, and their evolutionary relationships remain unresolved despite several studies have been carried out based on traditional DNA markers. The taxonomic uncertainty hinders the identification, conservation and exploration of these wild populations of Panax. To study this species complex, we employed ddRAD-seq data of these taxa from 18 different localities of southwestern China, using two RAD analysis pipelines, STACKS and pyRAD. Based on the results of phylogenetic analysis, the species complex was divided into four clades with high supports, which largely agreed with morphologically described species. Two clades, corresponding to P. vietnamensis and P. zingiberensis, respectively, were sister groups, indicating that these two species had a closer genetic relationship; the third clade was consisted of samples with bamboo-like rhizomes named as P. wangianus clade, and the fourth one with moniliform rhizomes was named as P. bipinnatifidus clade. The population genetic structure analysis and D-statistics test showed the localized admixture among these species, which indicated that introgression had occurred among the related lineages continuously distributed in southeastern Yunnan and adjacent regions.
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Affiliation(s)
- Mingmei Zhou
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqian Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Guiling Sun
- Institute of Plant Stress Biology, State Key Laboratory of Cotton Biology, Henan University, Henan 475001, China
| | - Zhenhua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xun Gong
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Yuezhi Pan
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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24
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Jouraku A, Kuwazaki S, Miyamoto K, Uchiyama M, Kurokawa T, Mori E, Mori MX, Mori Y, Sonoda S. Ryanodine receptor mutations (G4946E and I4790K) differentially responsible for diamide insecticide resistance in diamondback moth, Plutella xylostella L. Insect Biochem Mol Biol 2020; 118:103308. [PMID: 31863874 DOI: 10.1016/j.ibmb.2019.103308] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/10/2019] [Accepted: 12/16/2019] [Indexed: 06/10/2023]
Abstract
This study examined diamondback moth (Plutella xylostella) strains showing high-level resistance to cyantraniliprole (KA17 strain) and to flubendiamide and chlorantraniliprole (KU13 strain). The LC50 value of the KA17 strain against cyantraniliprole was ca. 100-fold higher than that of the KU13 strain. The KA17 strain also exhibited high-level resistance to chlorantraniliprole and flubendiamide equivalent to those in the KU13 strain. The KU13 strain showed a higher LC50 value against cyantraniliprole than the susceptible strains. However, the LC50 value of the KU13 strain against cyantraniliprole was below the agriculturally recommended concentration. Subsequent QTL analysis using ddRAD-seq identified the resistance responsible regions of the KA17 and KU13 strains with different diamide resistance profiles. Ryanodine receptor (RyR) gene was included in the identified regions. Single nucleotide polymorphism calling in the RyR gene using RNA-seq found previously reported G4946E (amino acid mutation from glycine to glutamic acid at amino acid position 4946) and novel I4790K (amino acid mutation from isoleucine to lysine at amino acid position 4790) mutations, respectively, in the RyR of the KU13 and KA17 strains. Functional significance of I4790K in the resistance was confirmed in calcium imaging of the human embryonic kidney 293T cell line expressing Bombyx mori RyR with the mutation. This reporting is the first describing I4790K as a fundamental mechanism responsible for the resistance to the diamides including cyantraniliprole. From this study, we also report up-regulated expression of some degradation enzymes and that of the RyR gene in the KA17 and KU13 strains based on results of RNA-seq data analysis.
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Affiliation(s)
- Akiya Jouraku
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan
| | - Seigo Kuwazaki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan
| | - Kazuhisa Miyamoto
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8634, Japan
| | - Makoto Uchiyama
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Tatsuki Kurokawa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Emiko Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Masayuki X Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Yasuo Mori
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Shoji Sonoda
- School of Agriculture, Utsunomiya University, Utsunomiya, Tochigi, 321-8505, Japan.
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Severn-Ellis AA, Scheben A, Neik TX, Saad NSM, Pradhan A, Batley J. Genotyping for Species Identification and Diversity Assessment Using Double-Digest Restriction Site-Associated DNA Sequencing ( ddRAD-Seq). Methods Mol Biol 2020; 2107:159-87. [PMID: 31893447 DOI: 10.1007/978-1-0716-0235-5_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genotyping-by-sequencing (GBS) is a powerful approach for studying the genetic diversity of legume species. By using restriction enzymes or other methods to generate a reduced representation of the genome for sequencing, GBS can provide genome-wide single nucleotide polymorphisms (SNP) for diversity analysis at high throughput and low cost. Here we describe a novel double-digest restriction site-associated DNA sequencing (ddRAD-seq) approach. We also describe the downstream bioinformatic analysis of the sequencing data, including alignment to a reference genome, de novo assembly, SNP calling, phylogenetic analysis, and structure analysis.
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Guo C, Guo ZH, Li DZ. Phylogenomic analyses reveal intractable evolutionary history of a temperate bamboo genus (Poaceae: Bambusoideae). Plant Divers 2019; 41:213-219. [PMID: 31528780 PMCID: PMC6742490 DOI: 10.1016/j.pld.2019.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/24/2019] [Accepted: 05/25/2019] [Indexed: 06/10/2023]
Abstract
Shibataea is a genus of temperate bamboos (Poaceae: Bambusoideae) endemic to China, but little is known about its phylogenetic position and interspecific relationships. To elucidate the phylogenetic relationship of the bamboo genus Shibataea, we performed genome-scale phylogenetic analysis of all seven species and one variety of the genus using double digest restriction-site associated DNA sequencing (ddRAD-seq) and whole plastid genomes generated using genome skimming. Our phylogenomic analyses based on ddRAD-seq and plastome data congruently recovered Shibataea as monophyletic. The nuclear data resolved S. hispida as the earliest diverged species, followed by S. chinensis, while the rest of Shibataea can be further divided into two clades. However, the plastid and nuclear topologies conflict significantly. By comparing the results of network analysis and topologies reconstructed from different datasets, we identify S. kumasasa as the most admixed species, which may be caused by incomplete lineage sorting (ILS) or interspecific gene flow with four sympatric species. This study highlights the power of ddRAD and plastome data in resolving complex relationships in the intractable bamboo genus.
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Affiliation(s)
- Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
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Raggi L, Caproni L, Carboni A, Negri V. Genome-Wide Association Study Reveals Candidate Genes for Flowering Time Variation in Common Bean ( Phaseolus vulgaris L.). Front Plant Sci 2019; 10:962. [PMID: 31428109 PMCID: PMC6689981 DOI: 10.3389/fpls.2019.00962] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/10/2019] [Indexed: 05/13/2023]
Abstract
The common bean is one of the most important staples in many areas of the world. Extensive phenotypic and genetic characterization of unexplored bean germplasm are still needed to unlock the breeding potential of this crop. Dissecting genetic control of flowering time is of pivotal importance to foster common bean breeding and to develop new varieties able to adapt to changing climatic conditions. Indeed, flowering time strongly affects yield and plant adaptation ability. The aim of this study was to investigate the genetic control of days to flowering using a whole genome association approach on a panel of 192 highly homozygous common bean genotypes purposely developed from landraces using Single Seed Descent. The phenotypic characterization was carried out at two experimental sites throughout two growing seasons, using a randomized partially replicated experimental design. The same plant material was genotyped using double digest Restriction-site Associated DNA sequencing producing, after a strict quality control, a dataset of about 50 k Single Nucleotide Polymorphisms (SNPs). The Genome-Wide Association Study revealed significant and meaningful associations between days to flowering and several SNP markers; seven genes are proposed as the best candidates to explain the detected associations.
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Affiliation(s)
- Lorenzo Raggi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| | - Leonardo Caproni
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| | - Andrea Carboni
- CREA Research Centre for Cereal and Industrial Crops, Bologna, Italy
| | - Valeria Negri
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
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Li BJ, Zhu ZX, Gu XH, Lin HR, Xia JH. QTL Mapping for Red Blotches in Malaysia Red Tilapia (Oreochromis spp.). Mar Biotechnol (NY) 2019; 21:384-395. [PMID: 30863905 DOI: 10.1007/s10126-019-09888-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Body color is an interesting economic trait in fish. Red tilapia with red blotches may decrease its commercial values. Conventional selection of pure red color lines is a time-consuming and labor-intensive process. To accelerate selection of pure lines through marker-assisted selection, in this study, double-digest restriction site-associated DNA sequencing (ddRAD-seq) technology was applied to genotype a full-sib mapping family of Malaysia red tilapia (Oreochromis spp.) (N = 192). Genome-wide significant quantitative trait locus (QTL)-controlling red blotches were mapped onto two chromosomes (chrLG5 and chrLG15) explaining 9.7% and 8.2% of phenotypic variances by a genome-wide association study (GWAS) and linkage-based QTL mapping. Six SNPs from the chromosome chrLG5 (four), chrLG15 (one), and unplaced supercontig GL831288-1 (one) were significantly associated to the red blotch trait in GWAS analysis. We developed nine microsatellite markers and validated significant correlations between genotypes and blotch data (p < 0.05). Our study laid a foundation for exploring a genetic mechanism of body colors and carrying out genetic improvement for color quality in tilapia.
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Affiliation(s)
- Bi Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Zong Xian Zhu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Xiao Hui Gu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Hao Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
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DaCosta JM, Miller MJ, Mortensen JL, Reed JM, Curry RL, Sorenson MD. Phylogenomics clarifies biogeographic and evolutionary history, and conservation status of West Indian tremblers and thrashers (Aves: Mimidae). Mol Phylogenet Evol 2019; 136:196-205. [PMID: 30999037 DOI: 10.1016/j.ympev.2019.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/26/2019] [Accepted: 04/14/2019] [Indexed: 01/06/2023]
Abstract
The West Indian avifauna has provided fundamental insights into island biogeography, taxon cycles, and the evolution of avian behavior. Our interpretations, however, should rely on robust hypotheses of evolutionary relationships and consistent conclusions about taxonomic status in groups with many endemic island populations. Here we present a phylogenetic study of the West Indian thrashers, tremblers, and allies, an assemblage of at least 5 species found on 29 islands, including what is considered the Lesser Antilles' only avian radiation. We improve on previous phylogenetic studies of this group by using double-digest restriction site-associated DNA sequencing (ddRAD-seq) to broadly sample loci scattered across the nuclear genome. A variety of analyses, based on either nucleotide variation in 2223 loci recovered in all samples or at 13,282 loci confidently scored as present or absent in all samples, converged on a single well-supported phylogenetic hypothesis. Results indicate that the resident West Indian taxa form a monophyletic group, exclusive of the Neotropical-Nearctic migratory Gray Catbird Dumetella carolinensis, which breeds in North America; this outcome differs from earlier studies suggesting that Gray Catbird was nested within a clade of island resident species. Thus, our findings imply a single colonization of the West Indies without the need to invoke a subsequent 'reverse colonization' of the mainland by West Indian taxa. Additionally, our study is the first to sample both endemic subspecies of the endangered White-breasted Thrasher Ramphocinclus brachyurus. We find that these subspecies have a long history of evolutionary independence with no evidence of gene flow, and are as genetically divergent from each other as other genera in the group. These findings support recognition of R. brachyurus (restricted to Martinique) and the Saint Lucia Thrasher R. sanctaeluciae as two distinct, single-island endemic species, and indicate the need to re-evaluate conservation plans for these taxa. Our results demonstrate the utility of phylogenomic datasets for generating robust systematic hypotheses.
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Affiliation(s)
- Jeffrey M DaCosta
- Department of Biology, Boston University, Boston, MA, USA; Biology Department, Boston College, Chestnut Hill, MA, USA
| | - Matthew J Miller
- Department of Biology, Villanova University, Villanova, PA, USA; Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK, USA.
| | - Jennifer L Mortensen
- Department of Biology, Tufts University, Medford, MA, USA; Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - J Michael Reed
- Department of Biology, Tufts University, Medford, MA, USA
| | - Robert L Curry
- Department of Biology, Villanova University, Villanova, PA, USA
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Laila R, Park JI, Robin AHK, Natarajan S, Vijayakumar H, Shirasawa K, Isobe S, Kim HT, Nou IS. Mapping of a novel clubroot resistance QTL using ddRAD-seq in Chinese cabbage (Brassica rapa L.). BMC Plant Biol 2019; 19:13. [PMID: 30621588 PMCID: PMC6325862 DOI: 10.1186/s12870-018-1615-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 12/21/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plasmodiophora brassicae is a soil-borne plant pathogen that causes clubroot disease, which results in crop yield loss in cultivated Brassica species. Here, we investigated whether a quantitative trait locus (QTL) in B. rapa might confer resistance to a Korean P. brassicae pathotype isolate, Seosan. We crossed resistant and susceptible parental lines and analyzed the segregation pattern in a F2 population of 348 lines. We identified and mapped a novel clubroot resistance QTL using the same mapping population that included susceptible Chinese cabbage and resistant turnip lines. Forty-five resistant and 45 susceptible F2 lines along with their parental lines were used for double digest restriction site-associated DNA sequencing (ddRAD-seq). High resolution melting (HRM)-based validation of SNP positions was conducted to confirm the novel locus. RESULTS A 3:1 ratio was observed for resistant: susceptible genotypes, which is in accordance with Mendelian segregation. ddRAD-seq identified a new locus, CRs, on chromosome A08 that was different from the clubroot resistance (CR) locus, Crr1. HRM analysis validated SNP positions and constricted CRs region. Four out of seventeen single nucleotide polymorphisms (SNPs) positions were within a 0.8-Mb region that included three NBS-LRR candidate genes but not Crr1. CONCLUSION The newly identified CRs locus is a novel clubroot resistance locus, as the cultivar Akimeki bears the previously known Crr1 locus but remains susceptible to the Seosan isolate. These results could be exploited to develop molecular markers to detect Seosan-resistant genotypes and develop resistant Chinese cabbage cultivars.
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Affiliation(s)
- Rawnak Laila
- Department of Horticulture, Sunchon National University, Suncheon, 57922 Republic of Korea
| | - Jong-In Park
- Department of Horticulture, Sunchon National University, Suncheon, 57922 Republic of Korea
| | - Arif Hasan Khan Robin
- Department of Horticulture, Sunchon National University, Suncheon, 57922 Republic of Korea
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, 2202, Mymensingh, Bangladesh
| | - Sathishkumar Natarajan
- Department of Horticulture, Sunchon National University, Suncheon, 57922 Republic of Korea
| | | | | | | | - Hoy-Taek Kim
- Department of Horticulture, Sunchon National University, Suncheon, 57922 Republic of Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, Suncheon, 57922 Republic of Korea
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Kobayashi H, Haino Y, Iwasaki T, Tezuka A, Nagano AJ, Shimada S. ddRAD-seq based phylogeographic study of Sargassum thunbergii (Phaeophyceae, Heterokonta) around Japanese coast. Mar Environ Res 2018; 140:104-113. [PMID: 29895505 DOI: 10.1016/j.marenvres.2018.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Using genome-wide SNP data obtained from high-throughput techniques based on double digest restriction site-associated DNA sequencing (ddRAD-seq), we elucidated the migration history and genetic diversity of the Japanese population of the ecologically important brown seaweed Sargassum thunbergii (Mertens ex Roth) Kuntze. STRUCTURE and NeighborNet analyses showed a clear genetic differentiation among populations of four geographic regions: Kyushu (POP1); Sea of Japan (POP2); Hokkaido and Tohoku (POP3); and Pacific coast from Kyushu to Kanto (POP4). Approximate Bayesian Computation (ABC) analysis indicated that POP4 diverged first, followed by the separation between POP2 (the largest effective population size) and POP3; POP1 was the last to form, shaped by the mixture of POP2 (73%) and POP4 (27%). High genetic diversity was detected in POP1 and POP2, whereas low genetic diversity was detected in POP3 and POP4. These results indicated that S. thunbergii populations of Kyushu and the Sea of Japan might have been maintained as large and stable populations gathered different lineages from China, Korea and/or Japan.
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Affiliation(s)
- Honoka Kobayashi
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan
| | - Yuka Haino
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan
| | - Takaya Iwasaki
- Faculty of Science, Kanagawa University, Tsuchiya 2946, Hiratsuka, Kanagawa, 259-1293, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu, Shiga, 520-2194, Japan
| | - Satoshi Shimada
- Faculty of Core Research, Natural Science Division, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan.
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Hosoya S, Kikuchi K, Nagashima H, Onodera J, Sugimoto K, Satoh K, Matsuzaki K, Yasugi M, Nagano AJ, Kumagayi A, Ueda K, Kurokawa T. Assessment of genetic diversity in Coho salmon (Oncorhynchus kisutch) populations with no family records using ddRAD-seq. BMC Res Notes 2018; 11:548. [PMID: 30071886 PMCID: PMC6071332 DOI: 10.1186/s13104-018-3663-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Selective breeding for desirable traits is becoming popular in aquaculture. In Miyagi prefecture, Japan, a selectively bred population of Coho salmon (Oncorhynchus kisutch) has been established with the original, randomly breeding population maintained separately. Since they have been bred without family records, the genetic diversity within these populations remains unknown. In this study, we estimated the genetic diversity and key quantitative genetic parameters such as heritability and genomic breeding value for body size traits by means of genomic best linear unbiased prediction to assess the genetic health of these populations. RESULTS Ninety-nine and 83 females from the selective and random groups, respectively, were genotyped at 2350 putative SNPs by means of double digest restriction associated DNA sequencing. The genetic diversity in the selectively bred group was low, as were the estimated heritability and prediction accuracy for length and weight (h2 = 0.26-0.28; accuracy = 0.34), compared to the randomly bred group (h2 = 0.50-0.60; accuracy = 0.51-0.54). Although the tested sample size was small, these results suggest that further selection is difficult for the selectively bred population, while there is some potential for the randomly bred group, especially with the aid of genomic information.
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Affiliation(s)
- Sho Hosoya
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, 2971-4 Bentenjima, Maisaka, Hamamatsu, Shizuoka, 431-0214, Japan.
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, University of Tokyo, 2971-4 Bentenjima, Maisaka, Hamamatsu, Shizuoka, 431-0214, Japan
| | - Hiroshi Nagashima
- Miyagi Prefecture Fisheries Technology Institute, Freshwater Fisheries Experimental Station, Taiwa, Miyagi, 981-3625, Japan
| | - Junichi Onodera
- Miyagi Prefecture Fisheries Technology Institute, Freshwater Fisheries Experimental Station, Taiwa, Miyagi, 981-3625, Japan
| | - Kouichi Sugimoto
- Miyagi Prefecture Fisheries Technology Institute, Freshwater Fisheries Experimental Station, Taiwa, Miyagi, 981-3625, Japan
| | - Kou Satoh
- Miyagi Prefecture Fisheries Technology Institute, Freshwater Fisheries Experimental Station, Taiwa, Miyagi, 981-3625, Japan
| | - Keisuke Matsuzaki
- Miyagi Prefecture Fisheries Technology Institute, Freshwater Fisheries Experimental Station, Taiwa, Miyagi, 981-3625, Japan
| | - Masaki Yasugi
- Center for Ecological Research, Kyoto University, Hirano 509-3-2, Otsu, Shiga, 520-2113, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Hirano 509-3-2, Otsu, Shiga, 520-2113, Japan.,JST CREST, Honcho 4-1-8, Kawaguchi, Saitama, 332-0012, Japan.,Faculty of Agriculture, Ryukoku University, Yokotani 1-5, Seta Ohe-cho, Otsu-shi, Shiga, 520-2194, Japan
| | - Akira Kumagayi
- Miyagi Prefecture Fisheries Technology Institute, Freshwater Fisheries Experimental Station, Taiwa, Miyagi, 981-3625, Japan
| | - Kenichi Ueda
- Miyagi Prefecture Fisheries Technology Institute, Freshwater Fisheries Experimental Station, Taiwa, Miyagi, 981-3625, Japan
| | - Tadahide Kurokawa
- Kushiro Laboratory, Hokkaido National Fisheries Research Institute, Japan Fisheries Research and Education Agency, 116 Katsurakoi, Kushiro-shi, Hokkaido, 085-0802, Japan.
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Ba H, Li Z, Yang Y, Li C. Development of Diagnostic SNP Markers To Monitor Hybridization Between Sika Deer ( Cervus nippon) and Wapiti ( Cervus elaphus). G3 Genes|Genomes|Genetics 2018; 8:2173-2179. [PMID: 29789312 PMCID: PMC6027871 DOI: 10.1534/g3.118.200417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Sika deer (Cervus Nippon) and wapiti (Cervus elaphus) are closely related species and their hybridization can result in significant allele-shift of their gene pool. Additive genetic effects and putative heterotic effects of their hybridization on growth performance could confer considerable economic advantage in deer farming. Here, we used double-digest restriction site-associated DNA sequencing technology (ddRAD-seq) and detected ∼320,000 genome-wide SNPs from 30 captive individuals: 7 sika deer, 6 wapiti and 17 F1 hybrids (reciprocal cross). By screening observed heterozygosity of each SNP across four taxonomic groups, we report for the first time a resource of 2,015 putative diagnostic SNP markers (species-specific SNPs for sika deer and wapiti), which can be used to design tools for assessing or monitoring the degree of hybridization between sika deer and wapiti. These ddRAD-seq data and SNP datasets are also valuable resources for genome-wide studies, including trait discovery for breeders of domestic deer.
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Affiliation(s)
- Hengxing Ba
- State Key Laboratory for Molecular Biology of Special Wild Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, No. 4899, Juye Street, Jingyue District, Changchun, Jilin province, 130112, P.R. China
| | - Zhipeng Li
- State Key Laboratory for Molecular Biology of Special Wild Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, No. 4899, Juye Street, Jingyue District, Changchun, Jilin province, 130112, P.R. China
| | - Yifeng Yang
- State Key Laboratory for Molecular Biology of Special Wild Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, No. 4899, Juye Street, Jingyue District, Changchun, Jilin province, 130112, P.R. China
| | - Chunyi Li
- State Key Laboratory for Molecular Biology of Special Wild Economic Animals, Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, No. 4899, Juye Street, Jingyue District, Changchun, Jilin province, 130112, P.R. China
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Buckley SJ, Domingos FMCB, Attard CRM, Brauer CJ, Sandoval-Castillo J, Lodge R, Unmack PJ, Beheregaray LB. Phylogenomic history of enigmatic pygmy perches: implications for biogeography, taxonomy and conservation. R Soc Open Sci 2018; 5:172125. [PMID: 30110415 PMCID: PMC6030323 DOI: 10.1098/rsos.172125] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 04/30/2018] [Indexed: 06/08/2023]
Abstract
Pygmy perches (Percichthyidae) are a group of poorly dispersing freshwater fishes that have a puzzling biogeographic disjunction across southern Australia. Current understanding of pygmy perch phylogenetic relationships suggests past east-west migrations across a vast expanse of now arid habitat in central southern Australia, a region lacking contemporary rivers. Pygmy perches also represent a threatened group with confusing taxonomy and potentially cryptic species diversity. Here, we present the first study of the evolutionary history of pygmy perches based on genome-wide information. Data from 13 991 ddRAD loci and a concatenated sequence of 1 075 734 bp were generated for all currently described and potentially cryptic species. Phylogenetic relationships, biogeographic history and cryptic diversification were inferred using a framework that combines phylogenomics, species delimitation and estimation of divergence times. The genome-wide phylogeny clarified the biogeographic history of pygmy perches, demonstrating multiple east-west events of divergence within the group across the Australian continent. These results also resolved discordance between nuclear and mitochondrial data from a previous study. In addition, we propose three cryptic species within a southwestern species complex. The finding of potentially new species demonstrates that pygmy perches may be even more susceptible to ecological and demographic threats than previously thought. Our results have substantial implications for improving conservation legislation of pygmy perch lineages, especially in southwestern Western Australia.
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Affiliation(s)
- Sean J. Buckley
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Fabricius M. C. B. Domingos
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
- Instituto de Ciências Biológicas e da Saúde, Universidade Federal de Mato Grosso, Pontal do Araguaia, MT 78698-000, Brazil
| | - Catherine R. M. Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Chris J. Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Ryan Lodge
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - Peter J. Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory 2601, Australia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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Guo Y, Yang G, Chen Y, Li D, Guo Z. A comparison of different methods for preserving plant molecular materials and the effect of degraded DNA on ddRAD sequencing. Plant Divers 2018; 40:106-116. [PMID: 30175291 PMCID: PMC6114257 DOI: 10.1016/j.pld.2018.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 05/26/2023]
Abstract
Obtaining high-quality plant materials for experiments is challenging for many research projects. Therefore, it is of special importance to determine the best method for preserving biological macromolecules like DNA, which degrade over time. Although some research has demonstrated that DNA degradation has little effect on traditional molecular markers, the effects of DNA degradation on ddRAD-seq, a popular reduced-representation sequencing technology, have not been adequately investigated. In this study, we first chose six woody bamboo species (Bambusoideae, Poaceae) to explore appropriate methods for preserving molecular materials with two DNA extraction approaches. Then we sequenced twenty-one bamboos and examined the effects of DNA quality on data generation using the ddRAD-seq technique (MiddRAD-seq). Finally, we reconstructed phylogenies of twenty woody bamboo species. We found that the integrity of dry-powdered DNA was preserved longer than that of TE-dissolved DNA, regardless of whether the DNA was extracted by a modified CTAB protocol or DNAsecure plant kit. The ddRAD-seq data were robust, except when DNA was severely degraded. In addition, we resolved the phylogenetic positions of the sampled Phyllostachys spp. Our results suggest that dry-powdered DNA is the most appropriate preservation method for plant molecular materials. Furthermore, a moderate level of DNA degradation has little effect on reduced representation sequencing techniques represented by ddRAD-seq.
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Affiliation(s)
- Ying Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - GuoQian Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunmei Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dezhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Zhenhua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Liu X, Karrenberg S. Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation. Mol Ecol 2018; 27:3889-3904. [PMID: 29577481 DOI: 10.1111/mec.14562] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 01/22/2018] [Accepted: 01/31/2018] [Indexed: 01/02/2023]
Abstract
The evolution of reproductive barriers and their underlying genetic architecture is of central importance for the formation of new species. Reproductive barriers can be controlled either by few large-effect loci suggesting strong selection on key traits, or by many small-effect loci, consistent with gradual divergence or with selection on polygenic or multiple traits. Genetic coupling between reproductive barrier loci further promotes divergence, particularly divergence with ongoing gene flow. In this study, we investigated the genetic architectures of ten morphological, phenological and life history traits associated with reproductive barriers between the hybridizing sister species Silene dioica and S. latifolia; both are dioecious with XY-sex determination. We used quantitative trait locus (QTL) mapping in two reciprocal F2 crosses. One to six QTLs per trait, including nine major QTLs (PVE > 20%), were detected on 11 of the 12 linkage groups. We found strong evidence for coupling of QTLs for uncorrelated traits and for an important role of sex chromosomes in the genetic architectures of reproductive barrier traits. Unexpectedly, QTLs detected in the two F2 crosses differed largely, despite limited phenotypic differences between them and sufficient statistical power. The widely dispersed genetic architectures of traits associated with reproductive barriers suggest gradual divergence or multifarious selection. Coupling of the underlying QTLs likely promoted divergence with gene flow in this system. The low congruence of QTLs between the two crosses further points to variable and possibly redundant genetic architectures of traits associated with reproductive barriers, with important implications for the evolutionary dynamics of divergence and speciation.
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Affiliation(s)
- Xiaodong Liu
- Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Sophie Karrenberg
- Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
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Ortego J, Gugger PF, Sork VL. Genomic data reveal cryptic lineage diversification and introgression in Californian golden cup oaks (section Protobalanus). New Phytol 2018; 218:804-818. [PMID: 29274282 DOI: 10.1111/nph.14951] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 11/14/2017] [Indexed: 05/15/2023]
Abstract
Here we study hybridization, introgression and lineage diversification in the widely distributed canyon live oak (Quercus chrysolepis) and the relict island oak (Q. tomentella), two Californian golden cup oaks with an intriguing biogeographical history. We employed restriction-site-associated DNA sequencing and integrated phylogenomic and population genomic analyses to study hybridization and reconstruct the evolutionary past of these taxa. Our analyses revealed the presence of two cryptic lineages within Q. chrysolepis. One of these lineages shares its most recent common ancestor with Q. tomentella, supporting the paraphyly of Q. chrysolepis. The split of these lineages was estimated to take place during the late Pliocene or the early Pleistocene, a time corresponding well with the common presence of Q. tomentella in the fossil records of continental California. Analyses also revealed historical hybridization among lineages, high introgression from Q. tomentella into Q. chrysolepis in their current area of sympatry, and widespread admixture between the two lineages of Q. chrysolepis in contact zones. Our results support that the two lineages of Q. chrysolepis behave as a single functional species phenotypically and ecologically well differentiated from Q. tomentella, a situation that can be only accommodated considering hybridization and speciation as a continuum with diffuse limits.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio 26, Seville, E-41092, Spain
| | - Paul F Gugger
- Appalachian Laboratory, University of Maryland Center for Environmental Science, 301 Braddock Road, Frostburg, MD, 21532, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
- Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
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Allen L, Sanders KL, Thomson VA. Molecular evidence for the first records of facultative parthenogenesis in elapid snakes. R Soc Open Sci 2018; 5:171901. [PMID: 29515892 PMCID: PMC5830781 DOI: 10.1098/rsos.171901] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 01/18/2018] [Indexed: 09/29/2023]
Abstract
Parthenogenesis is a form of asexual reproduction by which embryos develop from unfertilized eggs. Parthenogenesis occurs in reptiles; however, it is not yet known to occur in the widespread elapid snakes (Elapidae), which include well-known taxa such as cobras, mambas, taipans and sea snakes. Here, we describe the production of viable parthenogens in two species of Australo-Papuan elapids with divergent reproductive modes: the oviparous coastal/Papuan taipan (Oxyuranus scutellatus) and the viviparous southern death adder (Acanthophis antarcticus). Analyses of nuclear SNP data excluded paternity for putative fathers and convincingly demonstrated asexual reproduction, thus representing the first evidence of facultative parthenogenesis in Elapidae. Our finding has broad implications for understanding the evolution of reproductive diversity in snakes, as well as managing the conservation of genetic diversity in wild and captive populations.
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Affiliation(s)
- L. Allen
- Venom Supplies, PO Box 547, Tanunda, South Australia 5352, Australia
- School of Biological Sciences, and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - K. L. Sanders
- School of Biological Sciences, and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - V. A. Thomson
- School of Biological Sciences, and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
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Attard CRM, Brauer CJ, Sandoval-Castillo J, Faulks LK, Unmack PJ, Gilligan DM, Beheregaray LB. Ecological disturbance influences adaptive divergence despite high gene flow in golden perch (Macquaria ambigua): Implications for management and resilience to climate change. Mol Ecol 2017; 27:196-215. [PMID: 29165848 DOI: 10.1111/mec.14438] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 10/31/2017] [Accepted: 11/04/2017] [Indexed: 01/01/2023]
Abstract
Populations that are adaptively divergent but maintain high gene flow may have greater resilience to environmental change as gene flow allows the spread of alleles that have already been tested elsewhere. In addition, populations naturally subjected to ecological disturbance may already hold resilience to future environmental change. Confirming this necessitates ecological genomic studies of high dispersal, generalist species. Here we perform one such study on golden perch (Macquaria ambigua) in the Murray-Darling Basin (MDB), Australia, using a genome-wide SNP data set. The MDB spans across arid to wet and temperate to subtropical environments, with low to high ecological disturbance in the form of low to high hydrological variability. We found high gene flow across the basin and three populations with low neutral differentiation. Genotype-environment association analyses detected adaptive divergence predominantly linked to an arid region with highly variable riverine flow, and candidate loci included functions related to fat storage, stress and molecular or tissue repair. The high connectivity of golden perch in the MDB will likely allow locally adaptive traits in its most arid and hydrologically variable environment to spread and be selected in localities that are predicted to become arid and hydrologically variable in future climates. High connectivity in golden perch is likely due to their generalist life history and efforts of fisheries management. Our study adds to growing evidence of adaptation in the face of gene flow and highlights the importance of considering ecological disturbance and adaptive divergence in biodiversity management.
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Affiliation(s)
- Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Leanne K Faulks
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia.,Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Nagano, Japan
| | - Peter J Unmack
- Institute for Applied Ecology, University of Canberra, Canberra, ACT, Australia
| | - Dean M Gilligan
- New South Wales Department of Primary Industries, Batemans Bay Fisheries Centre, Batemans Bay, NSW, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
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Ba H, Jia B, Wang G, Yang Y, Kedem G, Li C. Genome-Wide SNP Discovery and Analysis of Genetic Diversity in Farmed Sika Deer ( Cervus nippon) in Northeast China Using Double-Digest Restriction Site-Associated DNA Sequencing. G3 (Bethesda) 2017; 7:3169-76. [PMID: 28751500 DOI: 10.1534/g3.117.300082] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Sika deer are an economically valuable species owing to their use in traditional Chinese medicine, particularly their velvet antlers. Sika deer in northeast China are mostly farmed in enclosure. Therefore, genetic management of farmed sika deer would benefit from detailed knowledge of their genetic diversity. In this study, we generated over 1.45 billion high-quality paired-end reads (288 Gbp) across 42 unrelated individuals using double-digest restriction site-associated DNA sequencing (ddRAD-seq). A total of 96,188 (29.63%) putative biallelic SNP loci were identified with an average sequencing depth of 23×. Based on the analysis, we found that the majority of the loci had a deficit of heterozygotes (FIS >0) and low values of Hobs, which could be due to inbreeding and Wahlund effects. We also developed a collection of high-quality SNP probes that will likely be useful in a variety of applications in genotyping for cervid species in the future.
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Black AN, Seears HA, Hollenbeck CM, Samollow PB. Rapid genetic and morphologic divergence between captive and wild populations of the endangered Leon Springs pupfish, Cyprinodon bovinus. Mol Ecol 2017; 26:2237-2256. [PMID: 28133827 DOI: 10.1111/mec.14028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 12/20/2016] [Accepted: 12/28/2016] [Indexed: 12/17/2022]
Abstract
The Leon Springs pupfish (Cyprinodon bovinus) is an endangered species currently restricted to a single desert spring and a separate captive habitat in southwestern North America. Following establishment of the captive population from wild stock in 1976, the wild population has undergone natural population size fluctuations, intentional culling to purge genetic contamination from an invasive congener (Cyprinodon variegatus) and augmentation/replacement of wild fish from the captive stock. A severe population decline following the most recent introduction of captive fish prompted us to examine whether the captive and wild populations have differentiated during the short time they have been isolated from one another. If so, the development of divergent genetic and/or morphologic traits between populations could contribute to a diminished ability of fish from one location to thrive in the other. Examination of genomewide single nucleotide polymorphisms and morphologic variation revealed no evidence of residual C. variegatus characteristics in contemporary C. bovinus samples. However, significant genetic and morphologic differentiation was detected between the wild and captive populations, some of which might reflect local adaptation. Our results indicate that genetic and physical characteristics can diverge rapidly between isolated subdivisions of managed populations, potentially compromising the value of captive stock for future supplementation efforts. In the case of C. bovinus, our findings underscore the need to periodically inoculate the captive population with wild genetic material to help mitigate genetic, and potentially morphologic, divergence between them and also highlight the utility of parallel morphologic and genomic evaluation to inform conservation management planning.
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Affiliation(s)
- Andrew N Black
- Hatfield Marine Science Center, Coastal Oregon Marine Experiment Station, Oregon State University, 2030 SE Marine Science Drive, Newport, OR, 97365, USA
| | - Heidi A Seears
- Department of Biology, University of Virginia, Gilmer Hall, Charlottesville, VA, 22904, USA
| | - Christopher M Hollenbeck
- Marine Genomics Laboratory, Department of Life Sciences, Texas A&M University, Corpus Christi, TX, 78412, USA
| | - Paul B Samollow
- Department of Veterinary Integrative Biosciences and Program in Genetics, Texas A&M University, College Station, TX, 77843, USA
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Antoniou A, Kasapidis P, Kotoulas G, Mylonas CC, Magoulas A. Genetic diversity of Atlantic Bluefin tuna in the Mediterranean Sea: insights from genome-wide SNPs and microsatellites. ACTA ACUST UNITED AC 2017; 24:3. [PMID: 28239596 PMCID: PMC5314471 DOI: 10.1186/s40709-017-0062-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/28/2017] [Indexed: 11/25/2022]
Abstract
Background Elucidating the patterns of the Atlantic Bluefin tuna [ABFT, Thunnus thynnus (Linnaeus, 1758)] population structure constitutes a challenging task of great importance. Most of the unique challenges stem from its biology, as well as the attributes of the marine realm in which it disperses. Accurate information is urgently needed for stock assessment, and the identification of critical features to the persistence and adaptation of populations in order to formulate and adopt effective strategies for ABFT conservation and management. Conclusions of a great number of ABFT genetic studies on the Mediterranean Sea stock structure are rather controversial and not yet conclusive. In this study, ABFT genomic diversity was investigated in the Mediterranean Sea, which is the most important area for the species’ reproduction. Results Analyzing genome-wide SNPs and microsatellites from ABFT samples collected throughout the Mediterranean Sea did not provide strong evidence of genetic structure, pointing towards the existence of a single panmictic unit. An alternative view would recognize a failure to reject the null hypothesis of a panmictic unit as an effect of the study’s sampling design, the type of markers used, and the effectiveness/suitability of analysis methods in respect to the species biological characteristics or any combination of the above. Conclusions Unravelling the drivers of ABFT population diversity would require the consideration of important aspects of the species spawning behavior for the determination of the appropriate sampling design. Novel approaches and methods of analysis that will bring together experts in genetics/-omics, ecology and oceanography are deemed necessary. Analyzing ABFT genetic data under the discipline of seascape genetics could provide the analysis framework under which major abiotic and biotic forces controlling ABFT recruitment could be identified, elucidating the complicated population dynamics of the species, while multiple and continuous fisheries monitoring should in all cases be considered as a prerequisite in order to achieve efficient and long-term ABFT conservation.
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Affiliation(s)
- Aglaia Antoniou
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Panagiotis Kasapidis
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Constantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research, Gournes Pediados, P.O. Box 2214, 71003 Heraklion, Crete, Greece
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Fritz ML, Paa S, Baltzegar J, Gould F. Application of a dense genetic map for assessment of genomic responses to selection and inbreeding in Heliothis virescens. Insect Mol Biol 2016; 25:385-400. [PMID: 27097739 DOI: 10.1111/imb.12234] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Adaptation of pest species to laboratory conditions and selection for resistance to toxins in the laboratory are expected to cause inbreeding and genetic bottlenecks that reduce genetic variation. Heliothis virescens, a major cotton pest, has been colonized in the laboratory many times, and a few laboratory colonies have been selected for Bacillus thuringiensis (Bt) resistance. We developed 350-bp double-digest restriction-site associated DNA-sequencing (ddRAD-seq) molecular markers to examine and compare changes in genetic variation associated with laboratory adaptation, artificial selection and inbreeding in this nonmodel insect species. We found that allelic and nucleotide diversity declined dramatically in laboratory-reared H. virescens as compared with field-collected populations. The declines were primarily a result of the loss of low frequency alleles present in field-collected H. virescens. A further, albeit modest decline in genetic diversity was observed in a Bt-selected population. The greatest decline was seen in H. virescens that were sib-mated for 10 generations, in which more than 80% of loci were fixed for a single allele. To determine which regions of the genome were resistant to fixation in our sib-mated line, we generated a dense intraspecific linkage map containing three PCR-based and 659 ddRAD-seq markers. Markers that retained polymorphism were observed in small clusters spread over multiple linkage groups, but this clustering was not statistically significant. Overall, we have confirmed and extended the general expectations for reduced genetic diversity in laboratory colonies, provided tools for further genomic analyses and produced highly homozygous genomic DNA for future whole genome sequencing of H. virescens.
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Affiliation(s)
- M L Fritz
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, USA
| | - S Paa
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
| | - J Baltzegar
- Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, USA
| | - F Gould
- Department of Entomology, North Carolina State University, Raleigh, NC, USA
- Department of Biological Sciences, Program in Genetics, North Carolina State University, Raleigh, NC, USA
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DaCosta JM, Sorenson MD. ddRAD-seq phylogenetics based on nucleotide, indel, and presence-absence polymorphisms: Analyses of two avian genera with contrasting histories. Mol Phylogenet Evol 2015; 94:122-35. [PMID: 26279345 DOI: 10.1016/j.ympev.2015.07.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 07/22/2015] [Accepted: 07/29/2015] [Indexed: 11/16/2022]
Abstract
Genotype-by-sequencing (GBS) methods have revolutionized the field of molecular ecology, but their application in molecular phylogenetics remains somewhat limited. In addition, most phylogenetic studies based on large GBS data sets have relied on analyses of concatenated data rather than species tree methods that explicitly account for genealogical stochasticity among loci. We explored the utility of "double-digest" restriction site-associated DNA sequencing (ddRAD-seq) for phylogenetic analyses of the Lagonosticta firefinches (family Estrildidae) and the Vidua brood parasitic finches (family Viduidae). As expected, the number of homologous loci shared among samples was negatively correlated with genetic distance due to the accumulation of restriction site polymorphisms. Nonetheless, for each genus, we obtained data sets of ∼3000 loci shared in common among all samples, including a more distantly related outgroup taxon. For all samples combined, we obtained >1000 homologous loci despite ∼20my divergence between estrildid and parasitic finches. In addition to nucleotide polymorphisms, the ddRAD-seq data yielded large sets of indel and locus presence-absence polymorphisms, all of which had higher consistency indices than mtDNA sequence data in the context of concatenated parsimony analyses. Species tree methods, using individual gene trees or single nucleotide polymorphisms as input, generated results broadly consistent with analyses of concatenated data, particularly for Lagonosticta, which appears to have a well resolved, bifurcating history. Results for Vidua were also generally consistent across methods and data sets, although nodal support and results from different species tree methods were more variable. Lower gene tree congruence in Vidua is likely the result of its unique evolutionary history, which includes rapid speciation by host shift and occasional hybridization and introgression due to incomplete reproductive isolation. We conclude that ddRAD-seq is a cost-effective method for generating robust phylogenetic data sets, particularly for analyses of closely related species and genera.
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Henning F, Lee HJ, Franchini P, Meyer A. Genetic mapping of horizontal stripes in Lake Victoria cichlid fishes: benefits and pitfalls of using RAD markers for dense linkage mapping. Mol Ecol 2014; 23:5224-40. [PMID: 25039588 DOI: 10.1111/mec.12860] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/02/2014] [Accepted: 07/12/2014] [Indexed: 01/25/2023]
Abstract
The genetic dissection of naturally occurring phenotypes sheds light on many fundamental and longstanding questions in speciation and adaptation and is a central research topic in evolutionary biology. Until recently, forward-genetic approaches were virtually impossible to apply to nonmodel organisms, but the development of next-generation sequencing techniques eases this difficulty. Here, we use the ddRAD-seq method to map a colour trait with a known adaptive function in cichlid fishes, well-known textbook examples for rapid rates of speciation and astonishing phenotypic diversification. A suite of phenotypic key innovations is related to speciation and adaptation in cichlids, among which body coloration features prominently. The focal trait of this study, horizontal stripes, evolved in parallel in several cichlid radiations and is associated with piscivorous foraging behaviour. We conducted interspecific crosses between Haplochromis sauvagei and H. nyererei and constructed a linkage map with 867 SNP markers distributed on 22 linkage groups and total size of 1130.63 cM. Lateral stripes are inherited as a Mendelian trait and map to a single genomic interval that harbours a paralog of a gene with known function in stripe patterning. Dorsolateral and mid-lateral stripes were always coinherited and are thus under the same genetic control. Additionally, we directly quantify the genotyping error rates in RAD markers and offer guidelines for identifying and dealing with errors. Uncritical marker selection was found to severely impact linkage map construction. Fortunately, by applying appropriate quality control steps, a genotyping accuracy of >99.9% can be reached, thus allowing for efficient linkage mapping of evolutionarily relevant traits.
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Affiliation(s)
- Frederico Henning
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Universitätsstraße 10, Konstanz, 78457, Germany
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