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Šarhanová P, Majeský Ľ, Sochor M. A novel strategy to study apomixis, automixis, and autogamy in plants. PLANT REPRODUCTION 2024:10.1007/s00497-024-00499-6. [PMID: 38431531 DOI: 10.1007/s00497-024-00499-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/02/2024] [Indexed: 03/05/2024]
Abstract
KEY MESSAGE The combination of a flow cytometric seed screen and genotyping of each single seed offers a cost-effective approach to detecting complex reproductive pathways in flowering plants. Reproduction may be seen as one of the driving forces of evolution. Flow cytometric seed screen and genotyping of parents and progeny are commonly employed techniques to discern various modes of reproduction in flowering plants. Nevertheless, both methods possess limitations constraining their individual capacity to investigate reproductive modes thoroughly. We implemented both methods in a novel manner to analyse reproduction pathways using a carefully selected material of parental individuals and their seed progeny. The significant advantage of this approach lies in its ability to apply both methods to a single seed. The introduced methodology provides valuable insights into discerning the levels of apomixis, sexuality, and selfing in complex Rubus taxa. The results may be explained by the occurrence of automixis in Rubus, which warrants further investigation. The approach showcased its effectiveness in a different apomictic system, specifically in Taraxacum. Our study presents a comprehensive methodological approach for determining the mode of reproduction where flow cytometry loses its potential. It provides a reliable and cost-effective method with significant potential in biosystematics, population genetics, and crop breeding.
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Affiliation(s)
- Petra Šarhanová
- Department of Botany and Zoology, Masaryk University, Kotlářská 267/2, 611 37, Brno, Czech Republic.
| | - Ľuboš Majeský
- Faculty of Science, Department of Botany, Palacký University in Olomouc, Šlechtitelů 27, 783 71, Olomouc-Holice, Czech Republic
| | - Michal Sochor
- Centre of the Region Haná for Biotechnological and Agricultural Research, Crop Research Institute, Šlechtitelů 29, 78371, Olomouc, Czech Republic
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Zhang J, Hieno A, Otsubo K, Feng W, Kageyama K. Population Genetic Analysis of Phytophthora colocasiae from Taro in Japan Using SSR Markers. J Fungi (Basel) 2023; 9:jof9040391. [PMID: 37108846 PMCID: PMC10145753 DOI: 10.3390/jof9040391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/14/2023] [Accepted: 03/21/2023] [Indexed: 04/29/2023] Open
Abstract
Phytophthora colocasiae is an important pathogen that causes great economic losses in taro production in tropical and subtropical regions, especially in Japan. Understanding the genetic variations in P. colocasiae populations and their transmission patterns in Japan is essential for effective disease control. Here, the genetic diversity of 358 P. colocasiae isolates, including 348 from Japan, 7 from China, and 3 from Indonesia, was assessed using 11 simple sequence repeat (SSR) primer pairs with high polymorphism. The phylogenetic tree of the SSR locus showed that the isolates from Japan could be divided into 14 groups, with group A being the dominant group. Among foreign isolates, only six from mainland China were similar to those from Japan and clustered in groups B and E. Analysis of molecular variance (AMOVA), principal components analysis (PCA), and cluster analysis (K = 3) results revealed a moderate level of genetic diversity, mainly within individuals. Populations showed high heterozygosity, a lack of regional differentiation, and frequent gene flow. Analysis of mating types and ploidy levels revealed that A2 and self-fertile (SF) A2 types and tetraploids were dominant across populations. Explanations and hypotheses for the results can provide more effective strategies for disease management of taro leaf blight.
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Affiliation(s)
- Jing Zhang
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Kayoko Otsubo
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Wenzhuo Feng
- Key Laboratory of Agricultural Microbiology, College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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Feng X, Zhu R, Jia Y, Tong J, Yu X, Pang M, Liu C, Sui X, Chen Y. Genetic diversity and population structure of the invasive populations of goldfish Carassius auratus complex in Tibet. Biol Invasions 2023. [DOI: 10.1007/s10530-023-03027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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Slonecki TJ, Rutter WB, Olukolu BA, Yencho GC, Jackson DM, Wadl PA. Genetic diversity, population structure, and selection of breeder germplasm subsets from the USDA sweetpotato ( Ipomoea batatas) collection. FRONTIERS IN PLANT SCIENCE 2023; 13:1022555. [PMID: 36816486 PMCID: PMC9932972 DOI: 10.3389/fpls.2022.1022555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/28/2022] [Indexed: 06/18/2023]
Abstract
Sweetpotato (Ipomoea batatas) is the sixth most important food crop and plays a critical role in maintaining food security worldwide. Support for sweetpotato improvement research in breeding and genetics programs, and maintenance of sweetpotato germplasm collections is essential for preserving food security for future generations. Germplasm collections seek to preserve phenotypic and genotypic diversity through accession characterization. However, due to its genetic complexity, high heterogeneity, polyploid genome, phenotypic plasticity, and high flower production variability, sweetpotato genetic characterization is challenging. Here, we characterize the genetic diversity and population structure of 604 accessions from the sweetpotato germplasm collection maintained by the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Plant Genetic Resources Conservation Unit (PGRCU) in Griffin, Georgia, United States. Using the genotyping-by-sequencing platform (GBSpoly) and bioinformatic pipelines (ngsComposer and GBSapp), a total of 102,870 polymorphic SNPs with hexaploid dosage calls were identified from the 604 accessions. Discriminant analysis of principal components (DAPC) and Bayesian clustering identified six unique genetic groupings across seven broad geographic regions. Genetic diversity analyses using the hexaploid data set revealed ample genetic diversity among the analyzed collection in concordance with previous analyses. Following population structure and diversity analyses, breeder germplasm subsets of 24, 48, 96, and 384 accessions were established using K-means clustering with manual selection to maintain phenotypic and genotypic diversity. The genetic characterization of the PGRCU sweetpotato germplasm collection and breeder germplasm subsets developed in this study provide the foundation for future association studies and serve as precursors toward phenotyping studies aimed at linking genotype with phenotype.
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Affiliation(s)
- Tyler J. Slonecki
- United States Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States
| | - William B. Rutter
- United States Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States
| | - Bode A. Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - G. Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC, United States
| | - D. Michael Jackson
- United States Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States
| | - Phillip A. Wadl
- United States Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States
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Xiang N, Lu B, Yuan T, Yang T, Guo J, Wu Z, Liu H, Liu X, Qin R. De Novo Transcriptome Assembly and EST-SSR Marker Development and Application in Chrysosplenium macrophyllum. Genes (Basel) 2023; 14:genes14020279. [PMID: 36833206 PMCID: PMC9956384 DOI: 10.3390/genes14020279] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Chrysosplenium macrophyllum Oliv., belonging to the family Saxifragaceae, is a traditional and unique Chinese herbal medicine. However, the lack of adequate molecular markers has hampered the progress regarding population genetics and evolution within this species. In this research, we used the DNBSEQ-T7 Sequencer (MGI) sequencing assay to analyze the transcriptome profiles of C. macrophyllum. SSR markers were developed on the basis of transcriptomic sequences and further validated on C. macrophyllum and other Chrysosplenium species. The genetic diversity and structure of the 12 populations were analyzed by using polymorphic expressed sequence tag simple sequence repeat (EST-SSR) markers. A potential pool of 3127 non-redundant EST-SSR markers were identified for C. macrophyllum in this study. The developed EST-SSR markers had high amplification rates and cross-species transferability in Chrysosplenium. Our results also showed that the natural populations of C. macrophyllum had a high level of genetic diversity. Genetic distance, principal component analysis, and popular structure analysis revealed that all 60 samples clustered into two major groups that were consistent with their geographical origins. This study provided a batch of highly polymorphic EST-SSR molecular markers that were developed via transcriptome sequencing. These markers will be of great significance for the study of the genetic diversity and evolutionary history of C. macrophyllum and other Chrysosplenium species.
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Affiliation(s)
- Niyan Xiang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Bojie Lu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Tao Yuan
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Tiange Yang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Jiani Guo
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
| | - Zhihua Wu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Xing Liu
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa 850000, China
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Correspondence: (X.L.); (R.Q.)
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
- Correspondence: (X.L.); (R.Q.)
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Huang K, Li W, Yang B, Wang D, He S, Shen Y, Ao J, Li Y, Cui Y, Kong Y, Li W, Li N, Dunn DW, Li B. vcfpop: Performing population genetics analyses for autopolyploids and aneuploids based on next-generation sequencing data sets. Mol Ecol Resour 2022. [PMID: 36458971 DOI: 10.1111/1755-0998.13744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Polyploids are cells or organisms with a genome consisting of more than two sets of homologous chromosomes. Polyploid plants have important traits that facilitate speciation and are thus often model systems for evolutionary, molecular ecology and agricultural studies. However, due to their unusual mode of inheritance and double-reduction, diploid models of population genetic analysis cannot properly be applied to autopolyploids. To overcome this problem, we developed a software package entitled vcfpop to perform a variety of population genetic analyses for autopolyploids, such as parentage analysis, analysis of molecular variance, principal coordinates analysis, hierarchical clustering analysis and Bayesian clustering. We used three data sets to evaluate the capability of vcfpop to analyse large data sets on a desktop computer. This software is freely available at http://github.com/huangkang1987/vcfpop.
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Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wenkai Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Bing Yang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Dan Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Shujun He
- Shaanxi Key Laboratory for Animal Conservation, Institute of Zoology, Shaanxi Academy of Sciences, Xi'an, China
| | - Yujia Shen
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Jincuo Ao
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Yuhang Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Yunxia Cui
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Yuchen Kong
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Wei Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Nianlong Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
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Population Structure of White Sturgeon (Acipenser transmontanus) in the Columbia River Inferred from Single-Nucleotide Polymorphisms. DIVERSITY 2022. [DOI: 10.3390/d14121045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
White sturgeon (Acipenser transmontanus) are the largest freshwater fish in North America, with reproducing populations in the Sacramento-San Joaquin, Fraser, and Columbia River Basins. Of these, the Columbia River is the largest, but it is also highly fragmented by hydroelectric dams, and many segments are characterized by declining abundance and persistent recruitment failure. Efforts to conserve and supplement these fish requires an understanding of their spatial genetic structure. Here, we assembled a large set of samples from throughout the Columbia River Basin, along with representative collections from adjacent basins, and genotyped them using a panel of 325 single-nucleotide markers. Results from individual- and group-based analyses of these data indicate that white sturgeon in the uppermost Columbia River Basin, in the Kootenai and upper Snake Rivers, are the most distinct, while the remaining populations downstream in the basin can be described as a genetic gradient consistent with an isolation-by-distance effect. Notably, the population in the lowest reaches of the Columbia River is more distinct from the middle or upper reaches than from outside basins, and suggests historically a higher or more recent gene exchange through coastal routes than with populations in the interior Columbia Basin. Nonetheless, proximal reaches were generally only marginally or non-significantly divergent, suggesting that transplanting larvae or juveniles from nearby sources poses relatively little risk of outbreeding depression. Indeed, we inferred examples of dispersal between reaches via close-kin mark-recapture and genetic mark-recapture that indicate movement between nearby reaches is not unusual. Samples from the Kootenai and upper Snake Rivers exhibited notably lower genetic diversity than the remaining samples as a result of population bottlenecks, genetic drift, and/or historical divergence. Conservation actions, such as supplementation, are underway to maintain population viability and will require balanced efforts to increase demographic abundance while maintaining genetic diversity.
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Wang J, Feng L, Mu S, Dong A, Gan J, Wen Z, Meng J, Li M, Wu R, Sun L. Asymptotic tests for Hardy-Weinberg equilibrium in hexaploids. HORTICULTURE RESEARCH 2022; 9:uhac104. [PMID: 35795385 PMCID: PMC9250657 DOI: 10.1093/hr/uhac104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Hexaploids, a group of organisms containing three complete sets of chromosomes in a single nucleus, are of utmost importance to evolutionary studies and breeding programs. Many studies have focused on hexaploid linkage analysis and QTL mapping in controlled crosses, but little methodology has been developed to reveal how hexaploids diversify and evolve in natural populations. We formulate a general framework for studying the pattern of genetic variation in autohexaploid populations through testing deviation from Hardy-Weinberg equilibrium (HWE) at individual molecular markers. We confirm that hexaploids cannot reach exact HWE but can approach asymptotic HWE at 8-9 generations of random mating. We derive a statistical algorithm for testing HWE and the occurrence of double reduction for autopolyploids, a phenomenon that affects population variation during long evolutionary processes. We perform computer simulation to validate the statistical behavior of our test procedure and demonstrate its usefulness by analyzing a real data set for autohexaploid chrysanthemum. When extended to allohexaploids, our test procedure will provide a generic tool for illustrating the genome structure of hexaploids in the quest to infer their evolutionary status and design association studies of complex traits.
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Affiliation(s)
- Jing Wang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Li Feng
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuaicheng Mu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ang Dong
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jinwen Gan
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhenying Wen
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Juan Meng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Mingyu Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Center for Statistical Genetics, Departments of Public Health Sciences and Statistics, The Pennsylvania State University, Hershey, PA 17033, USA
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Wang Z, Hu G, Li Z, Zhong C, Yao X. Characterizing Tetraploid Populations of Actinidia chinensis for Kiwifruit Genetic Improvement. PLANTS 2022; 11:plants11091154. [PMID: 35567155 PMCID: PMC9102457 DOI: 10.3390/plants11091154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 11/24/2022]
Abstract
Understanding genetic diversity and structure in natural populations and their suitable habitat response to environmental changes is critical for the protection and utilization of germplasm resources. We evaluated the genetic diversity and structure of 24 A. chinensis populations using simple sequence repeat (SSR) molecular markers. The potential suitable distribution of tetraploid A. chinensis estimated under the current climate and predicted for the future climate was generated with ecological niche modeling (ENM). The results indicated that the polyploid populations of A.chinensis have high levels of genetic diversity and that there are distinct eastern and western genetic clusters. The population structure of A. chinensis can be explained by an isolation-by-distance model. The results also revealed that potentially suitable areas of tetraploids will likely be gradually lost and the habitat will likely be increasingly fragmented in the future. This study provides an extensive overview of tetraploid A. chinensis across its distribution range, contributing to a better understanding of its germplasm resources. These results can also provide the scientific basis for the protection and sustainable utilization of kiwifruit wild resources.
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Affiliation(s)
- Zhi Wang
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
- CAS Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China; (G.H.); (Z.L.)
| | - Guangming Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China; (G.H.); (Z.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuozhou Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China; (G.H.); (Z.L.)
| | - Caihong Zhong
- CAS Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China; (G.H.); (Z.L.)
- Correspondence: (C.Z.); (X.Y.); Tel.: +86-27-8770884 (C.Z. & X.Y.); Fax: +86-27-87510567 (C.Z. & X.Y.)
| | - Xiaohong Yao
- CAS Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan 430074, China; (G.H.); (Z.L.)
- Correspondence: (C.Z.); (X.Y.); Tel.: +86-27-8770884 (C.Z. & X.Y.); Fax: +86-27-87510567 (C.Z. & X.Y.)
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Huang K, Dunn DW, Li W, Wang D, Li B. Linkage disequilibrium under polysomic inheritance. Heredity (Edinb) 2022; 128:11-20. [PMID: 34983965 PMCID: PMC8733019 DOI: 10.1038/s41437-021-00482-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 10/13/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023] Open
Abstract
Linkage disequilibrium (LD) is the non-random association of alleles at different loci. Squared LD coefficients r2 (for phased genotypes) and [Formula: see text] (for unphased genotypes) will converge to constants that are determined by the sample size, the recombination frequency, the effective population size and the mating system. LD can therefore be used for gene mapping and the estimation of effective population size. However, current methods work only with diploids. To resolve this problem, we here extend the linkage disequilibrium measures to include polysomic inheritance. We derive the values of r2 and [Formula: see text] at equilibrium state for various mating systems and different ploidy levels. For unlinked loci, [Formula: see text] for monoecious and dioecious (with random pairing) mating systems or [Formula: see text] for dioecious mating systems (with lifetime pairing), where f is the number of females in a half-sib family and η is a constant related to the ploidy level. We simulate the application of estimating Ne using unphased genotypes. We find that estimating Ne in polyploids requires similar sample sizes and numbers of loci as in diploids, with the main source of bias due to using 0.5 as the recombination frequency.
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Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T1Z4, Canada
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Wenkai Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Dan Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, 710069, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
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Yadav S, Ross EM, Aitken KS, Hickey LT, Powell O, Wei X, Voss-Fels KP, Hayes BJ. A linkage disequilibrium-based approach to position unmapped SNPs in crop species. BMC Genomics 2021; 22:773. [PMID: 34715779 PMCID: PMC8555328 DOI: 10.1186/s12864-021-08116-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High-density SNP arrays are now available for a wide range of crop species. Despite the development of many tools for generating genetic maps, the genome position of many SNPs from these arrays is unknown. Here we propose a linkage disequilibrium (LD)-based algorithm to allocate unassigned SNPs to chromosome regions from sparse genetic maps. This algorithm was tested on sugarcane, wheat, and barley data sets. We calculated the algorithm's efficiency by masking SNPs with known locations, then assigning their position to the map with the algorithm, and finally comparing the assigned and true positions. RESULTS In the 20-fold cross-validation, the mean proportion of masked mapped SNPs that were placed by the algorithm to a chromosome was 89.53, 94.25, and 97.23% for sugarcane, wheat, and barley, respectively. Of the markers that were placed in the genome, 98.73, 96.45 and 98.53% of the SNPs were positioned on the correct chromosome. The mean correlations between known and new estimated SNP positions were 0.97, 0.98, and 0.97 for sugarcane, wheat, and barley. The LD-based algorithm was used to assign 5920 out of 21,251 unpositioned markers to the current Q208 sugarcane genetic map, representing the highest density genetic map for this species to date. CONCLUSIONS Our LD-based approach can be used to accurately assign unpositioned SNPs to existing genetic maps, improving genome-wide association studies and genomic prediction in crop species with fragmented and incomplete genome assemblies. This approach will facilitate genomic-assisted breeding for many orphan crops that lack genetic and genomic resources.
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Affiliation(s)
- Seema Yadav
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, Queensland, 4067, Australia.
| | - Elizabeth M Ross
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, Queensland, 4067, Australia
| | - Karen S Aitken
- Agriculture and Food, CSIRO, Queensland Bioscience Precinct, St. Lucia, Brisbane, Queensland, 4067, Australia
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, Queensland, 4067, Australia
| | - Owen Powell
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, Queensland, 4067, Australia
| | - Xianming Wei
- Sugar Research Australia, Mackay, QLD, 4741, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, Queensland, 4067, Australia
| | - Ben J Hayes
- Queensland Alliance for Agriculture and Food Innovation, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, Queensland, 4067, Australia.
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12
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Dieterich Mabin ME, Brunet J, Riday H, Lehmann L. Self-Fertilization, Inbreeding, and Yield in Alfalfa Seed Production. FRONTIERS IN PLANT SCIENCE 2021; 12:700708. [PMID: 34295346 PMCID: PMC8290836 DOI: 10.3389/fpls.2021.700708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/04/2021] [Indexed: 06/13/2023]
Abstract
Selfing (self-pollination) is the ultimate form of inbreeding, or mating among close relatives. Selfing can create yield loss when inbreeding depression, defined as a lower survival and reproduction of inbred relative to outbred progeny, is present. To determine the impact of selfing in alfalfa (Medicago sativa L.), we quantified the selfing rate of 32 alfalfa seed production fields located in three regions, namely, the Pacific Northwest (PNW), the Central Valley of California (CEV), and the Imperial Valley of California (IMP). Selfing rates (the proportion of selfed seeds) varied between 5.3 and 30% with an average of 12.2% over the 32 seed production fields. In both the parents and their progeny, we observed an excess of heterozygotes relative to Hardy-Weinberg expectations. We detected notable levels of inbreeding in parents (0.231 ± 0.007 parental inbreeding coefficient) and progeny (0.229 ± 0.005). There were a 15% decrease in the number of seeds per stem (seed set) and a 13% decline in the number of seeds per pod in selfed relative to outcrossed stems, but negligible inbreeding depression for pods per raceme and seed weight. The number of racemes on selfed stems increased significantly in fields with greater selfing rates, supporting the presence of geitonogamous or among flower selfing. Despite the significant level of inbreeding depression, seed set did not decrease in fields with higher selfing rates, where the greater number of racemes on the selfed stems increased the seed set. The effects of the field selfing rate on the seed yield metrics were mostly indirect with direct effects of the number of racemes per stem. Available data indicate that the majority of selfing in alfalfa is pollinator-mediated, and thus, eliminating selfing in alfalfa seed production would require the selection of self-incompatible varieties, which, by eliminating inbreeding depression, would provide a 15% potential increase in seed yield and an increase in future hay yield.
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Affiliation(s)
- Molly E. Dieterich Mabin
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Madison, WI, United States
| | - Johanne Brunet
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service, Madison, WI, United States
| | - Heathcliffe Riday
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service, Madison, WI, United States
| | - Lauren Lehmann
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service, Madison, WI, United States
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13
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Development of novel microsatellite marker panel in threatened tetraploid mahseer, Tor tor (Hamilton 1822) for insights into its genetic diversity and population structure. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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14
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Delomas TA, Willis SC, Parker BL, Miller D, Anders P, Schreier A, Narum S. Genotyping single nucleotide polymorphisms and inferring ploidy by amplicon sequencing for polyploid, ploidy-variable organisms. Mol Ecol Resour 2021; 21:2288-2298. [PMID: 34008918 DOI: 10.1111/1755-0998.13431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 11/30/2022]
Abstract
Whole genome duplication is hypothesized to have played a critical role in the evolution of several major taxa, including vertebrates, and while many lineages have rediploidized, some retain polyploid genomes. Additionally, variation in ploidy can occur naturally or be artificially induced within select plant and animal species. Modern genetic techniques have not been widely applied to polyploid or ploidy-variable species, in part due to the difficulty of obtaining genotype data from polyploids. In this study, we demonstrate a strategy for developing an amplicon sequencing panel of single nucleotide polymorphisms for high-throughput genotyping of polyploid organisms. We then develop a method to infer ploidy of individuals from amplicon sequencing data that is generalized to apply to any ploidy and does not require prior identification of heterozygous genotypes. Combining these two techniques will allow researchers to both infer ploidy and generate ploidy-aware genotypes with the same amplicon sequencing panel. We demonstrate this approach with white sturgeon Acipenser transmontanus, a ploidy-variable (octoploid, decaploid and dodecaploid) imperiled species under conservation management in the Pacific Northwest and obtained a panel of 325 loci. These loci were validated by examining inheritance in known-cross families, and the ploidy inference method was validated with known ploidy samples. We provide scripts that adapt existing pipelines to genotype polyploids and an R package for application of the ploidy inference method. We expect that these techniques will empower studies of genetic variation and inheritance in polyploid organisms that vary in ploidy level, either naturally or as a result of artificial propagation practices.
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Affiliation(s)
- Thomas A Delomas
- Pacific States Marine Fisheries Commission/Idaho Department of Fish and Game, Eagle Fish Genetics Laboratory, Eagle, ID, USA
| | - Stuart C Willis
- Hagerman Genetics Lab, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
| | - Blaine L Parker
- Columbia River Inter-Tribal Fish Commission, Portland, OR, USA
| | | | | | - Andrea Schreier
- Genomic Variation Laboratory, Department of Animal Science, University of California Davis, Davis, CA, USA
| | - Shawn Narum
- Hagerman Genetics Lab, Columbia River Inter-Tribal Fish Commission, Hagerman, ID, USA
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15
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Gerard D. Pairwise linkage disequilibrium estimation for polyploids. Mol Ecol Resour 2021; 21:1230-1242. [PMID: 33559321 DOI: 10.1111/1755-0998.13349] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/18/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
Abstract
Many tasks in statistical genetics involve pairwise estimation of linkage disequilibrium (LD). The study of LD in diploids is mature. However, in polyploids, the field lacks a comprehensive characterization of LD. Polyploids also exhibit greater levels of genotype uncertainty than diploids, yet no methods currently exist to estimate LD in polyploids in the presence of such genotype uncertainty. Furthermore, most LD estimation methods do not quantify the level of uncertainty in their LD estimates. Our study contains three major contributions. (i) We characterize haplotypic and composite measures of LD in polyploids. These composite measures of LD turn out to be functions of common statistical measures of association. (ii) We derive procedures to estimate haplotypic and composite LD in polyploids in the presence of genotype uncertainty. We do this by estimating LD directly from genotype likelihoods, which may be obtained from many genotyping platforms. (iii) We derive standard errors of all LD estimators that we discuss. We validate our methods on both real and simulated data. Our methods are implemented in the R package ldsep, available on the Comprehensive R Archive Network https://cran.r-project.org/package=ldsep.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, DC, USA
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16
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Huang K, Huber G, Ritland K, Dunn DW, Li B. Performing parentage analysis for polysomic inheritances based on allelic phenotypes. G3-GENES GENOMES GENETICS 2021; 11:6080682. [PMID: 33585871 PMCID: PMC8022955 DOI: 10.1093/g3journal/jkaa064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/09/2020] [Indexed: 11/26/2022]
Abstract
Polyploidy poses several problems for parentage analysis. We present a new polysomic inheritance model for parentage analysis based on genotypes or allelic phenotypes to solve these problems. The effects of five factors are simultaneously accommodated in this model: (1) double-reduction, (2) null alleles, (3) negative amplification, (4) genotyping errors and (5) self-fertilization. To solve genotyping ambiguity (unknown allele dosage), we developed a new method to establish the likelihood formulas for allelic phenotype data and to simultaneously include the effects of our five chosen factors. We then evaluated and compared the performance of our new method with three established methods by using both simulated data and empirical data from the cultivated blueberry (Vaccinium corymbosum). We also developed and compared the performance of two additional estimators to estimate the genotyping error rate and the sample rate. We make our new methods freely available in the software package polygene, at http://github.com/huangkang1987/polygene.
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Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China.,Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Gwendolyn Huber
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Kermit Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an 710069, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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17
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Wang C, Ma X, Tang L. Isolation and characterization of twelve polymorphic microsatellite markers in the endangered Hopea hainanensis (Dipterocarpaceae). Ecol Evol 2021; 11:4-10. [PMID: 33437410 PMCID: PMC7790650 DOI: 10.1002/ece3.7077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 11/02/2020] [Accepted: 11/10/2020] [Indexed: 12/22/2022] Open
Abstract
Microsatellite markers were isolated and characterized for Hopea hainanensis Merrill & Chun, an endangered tree species with scattered distribution in Hainan Island and northern Vietnam. Twenty-six microsatellite markers were developed based on next-generation sequencing data and were genotyped by capillary electrophoresis on an ABI 3730xl DNA Analyzer. Twelve markers were found to be polymorphic in H. hainanensis. GENODIVE analyses indicated that the number of alleles ranged from 2 to 6 per locus, and the observed and expected heterozygosity varied from 0 to 0.755 and from 0.259 to 0.779, respectively. Primer transferability was tested with Hopea chinensis Hand.-Mazz. and Hopea reticulata Tardieu, in which 3 and 7 microsatellite markers were found to be polymorphic, separately. The results showed that H. reticulata and H. hainanensis had similar levels of genetic diversity. A neighbor joining dendrogram clustered all individuals into two major groups, one of which was exclusively constituted by H. hainanensis, while the other consisted of two subgroups, corresponding to H. reticulata and H. chinensis, respectively. The 12 polymorphic microsatellite markers could be applied to study genetic diversity, population differentiation, mating system, and fine-scale spatial genetic structures of H. hainanensis as well as its close relatives, facilitating the conservation and restoration of these endangered but valuable Hopea species.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Tropical Biological Resources of Ministry of EducationSchool of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of EducationSchool of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Liang Tang
- College of Ecology and EnvironmentHainan UniversityHaikouChina
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18
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Abstract
A suitable pairwise relatedness estimation is key to genetic studies. Several methods are proposed to compute relatedness in autopolyploids based on molecular data. However, unlike diploids, autopolyploids still need further studies considering scenarios with many linked molecular markers with known dosage. In this study, we provide guidelines for plant geneticists and breeders to access trustworthy pairwise relatedness estimates. To this end, we simulated populations considering different ploidy levels, meiotic pairings patterns, number of loci and alleles, and inbreeding levels. Analysis were performed to access the accuracy of distinct methods and to demonstrate the usefulness of molecular marker in practical situations. Overall, our results suggest that at least 100 effective biallelic molecular markers are required to have good pairwise relatedness estimation if methods based on correlation is used. For this number of loci, current methods based on multiallelic markers show lower performance than biallelic ones. To estimate relatedness in cases of inbreeding or close relationships (as parent-offspring, full-sibs, or half-sibs) is more challenging. Methods to estimate pairwise relatedness based on molecular markers, for different ploidy levels or pedigrees were implemented in the AGHmatrix R package.
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19
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Wang C, Ma X, Ren M, Tang L. Genetic diversity and population structure in the endangered tree Hopea hainanensis (Dipterocarpaceae) on Hainan Island, China. PLoS One 2020; 15:e0241452. [PMID: 33253236 PMCID: PMC7703895 DOI: 10.1371/journal.pone.0241452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/15/2020] [Indexed: 11/29/2022] Open
Abstract
Hopea hainanensis Merrill & Chun (Dipterocarpaceae) is an endangered tree species restricted to Hainan Island, China and a small part of Northern Vietnam. On Hainan Island, it is an important indicator species for tropical forests. However, because of its highly valued timber, H. hainanensis has suffered from overexploitation, leading to a sharp population decline. To facilitate the conservation of this species, genetic diversity and population structure were assessed using 12 SSR markers for 10 populations sampled across Hainan Island. Compared to non-threatened Hopea species, H. hainanensis exhibited reduced overall genetic diversity and increased population differentiation (AMOVA: FST = 0.23). Bayesian model-based clustering and principal coordinate analysis consistently assigned H. hainanensis individuals into three genetic groups, which were found to be widespread and overlapping geographically. A Mantel test found no correlation between genetic and geographical distances (r = 0.040, p = 0.418). The observed genetic structure suggests that long-distance gene flow occurred among H. hainanensis populations prior to habitat fragmentation. A recent population bottleneck was revealed, which may cause rapid loss of genetic diversity and increased differentiation across populations. Based on these findings, appropriate strategies for the long-term conservation of the endangered species H. hainanensis are proposed.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Xiang Ma
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Life and Pharmaceutical Sciences, Hainan University, Haikou, China
| | - Mingxun Ren
- College of Ecology and Environment, Hainan University, Haikou, China
| | - Liang Tang
- College of Ecology and Environment, Hainan University, Haikou, China
- * E-mail:
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20
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Huang K, Wang T, Dunn DW, Zhang P, Sun H, Li B. A generalized framework for AMOVA with multiple hierarchies and ploidies. Integr Zool 2020; 16:33-52. [PMID: 32648364 DOI: 10.1111/1749-4877.12460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The analysis of molecular variance (AMOVA) is a widely used statistical method in population genetics and molecular ecology. The classic framework of AMOVA only supports haploid and diploid data, in which the number of hierarchies ranges from two to four. In practice, natural populations can be classified into more hierarchies, and polyploidy is frequently observed in extant species. The ploidy level may even vary within the same species, and/or within the same individual. We generalized the framework of AMOVA such that it can be used for any number of hierarchies and any level of ploidy. Based on this framework, we present four methods to account for data that are multilocus genotypic and allelic phenotypic (with unknown allele dosage). We use simulated datasets and an empirical dataset to evaluate the performance of our framework. We make freely available our methods in a new software package, polygene, which is freely available at https://github.com/huangkang1987/polygene.
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Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China.,Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, Canada
| | - Tiantian Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Derek W Dunn
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Pei Zhang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Hongjuan Sun
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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21
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Ackiss AS, Balao F. Diving in uncharted waters: An updated genetics toolkit highlights the challenges of polyploidy in landscape genomics analyses. Mol Ecol Resour 2020; 20:841-843. [PMID: 32492285 DOI: 10.1111/1755-0998.13203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/06/2020] [Accepted: 05/27/2020] [Indexed: 12/14/2022]
Abstract
As molecular ecologists, we have by necessity become adept at working across computational platforms. A diverse community of scientists has developed a broad array of analytical resources spanning command line to graphical user interface across Linux, Mac, and Windows environments and a dizzying array of program-specific input formats. In light of this, we often explore our data like free divers - filling our lungs with air and descending for a short period of time into one part of our data set before resurfacing, reformatting, and preparing for our next analysis. In this issue of Molecular Ecology Resources, Meirmans (2020) presents an updated version of GenoDive, a program with a toolkit that provides users with the opportunity to stay a while and delve deeper into the diverse portfolio of information provided by a genomic data set. The comprehensive nature of GenoDive coupled with its unique capability to handle both diploid and polyploid data also provides an opportunity to reflect on the unevenness of resources available for the analysis of polyploid versus diploid data. Since new updates include the addition of plug-ins for genotype-environment association analyses, we limit the observations presented here to the common tools used for landscape genomics analyses.
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Affiliation(s)
- Amanda S Ackiss
- Wisconsin Cooperative Fishery Research Unit, College of Natural Resources, University of Wisconsin-Stevens Point, Stevens Point, WI, USA
| | - Francisco Balao
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Sevilla, Spain
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22
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Huang K, Dunn DW, Ritland K, Li B. polygene: Population genetics analyses for autopolyploids based on allelic phenotypes. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13338] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation College of Life Sciences Northwest University Xi’an China
- Department of Forest and Conservation Sciences University of British Columbia Vancouver Canada
| | - Derek W. Dunn
- Shaanxi Key Laboratory for Animal Conservation College of Life Sciences Northwest University Xi’an China
| | - Kermit Ritland
- Department of Forest and Conservation Sciences University of British Columbia Vancouver Canada
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation College of Life Sciences Northwest University Xi’an China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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