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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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2
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Huang K, Dunn DW, Li Z, Zhang P, Dai Y, Li B. Inference of individual ploidy level using codominant markers. Mol Ecol Resour 2019; 19:1218-1229. [DOI: 10.1111/1755-0998.13032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 04/18/2019] [Accepted: 05/01/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Kang Huang
- 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
| | - Zhonghu Li
- 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
| | - Yu Dai
- 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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Liu B, Mo WJ, Zhang D, De Storme N, Geelen D. Cold Influences Male Reproductive Development in Plants: A Hazard to Fertility, but a Window for Evolution. PLANT & CELL PHYSIOLOGY 2019; 60:7-18. [PMID: 30602022 DOI: 10.1093/pcp/pcy209] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/11/2018] [Indexed: 05/16/2023]
Abstract
Being sessile organisms, plants suffer from various abiotic stresses including low temperature. In particular, male reproductive development of plants is extremely sensitive to cold which may dramatically reduce viable pollen shed and plant fertility. Cold stress disrupts stamen development and prominently interferes with the tapetum, with the stress-responsive hormones ABA and gibberellic acid being greatly involved. In particular, low temperature stress delays and/or inhibits programmed cell death of the tapetal cells which consequently damages pollen development and causes male sterility. On the other hand, studies in Arabidopsis and crops have revealed that ectopically decreased temperature has an impact on recombination and cytokinesis during meiotic cell division, implying a putative role for temperature in manipulating plant genomic diversity and architecture during the evolution of plants. Here, we review the current understanding of the physiological impact of cold stress on the main male reproductive development processes including tapetum development, male meiosis and gametogenesis. Moreover, we provide insights into the genetic factors and signaling pathways that are involved, with putative mechanisms being discussed.
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Affiliation(s)
- Bing Liu
- College of Life Sciences, South-Central University for Nationalities, Wuhan, China
- School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Wen-Juan Mo
- Experiment Center of Forestry in North China, Chinese Academy of Forestry, Beijing, China
| | - Dabing Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Nico De Storme
- Department of Plants and Crops, unit HortiCell, Faculty of Bioscience Engineering, University of Ghent, Ghent, Belgium
| | - Danny Geelen
- Department of Plants and Crops, unit HortiCell, Faculty of Bioscience Engineering, University of Ghent, Ghent, Belgium
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Bourke PM, Voorrips RE, Visser RGF, Maliepaard C. Tools for Genetic Studies in Experimental Populations of Polyploids. FRONTIERS IN PLANT SCIENCE 2018; 9:513. [PMID: 29720992 PMCID: PMC5915555 DOI: 10.3389/fpls.2018.00513] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 04/04/2018] [Indexed: 05/19/2023]
Abstract
Polyploid organisms carry more than two copies of each chromosome, a condition rarely tolerated in animals but which occurs relatively frequently in the plant kingdom. One of the principal challenges faced by polyploid organisms is to evolve stable meiotic mechanisms to faithfully transmit genetic information to the next generation upon which the study of inheritance is based. In this review we look at the tools available to the research community to better understand polyploid inheritance, many of which have only recently been developed. Most of these tools are intended for experimental populations (rather than natural populations), facilitating genomics-assisted crop improvement and plant breeding. This is hardly surprising given that a large proportion of domesticated plant species are polyploid. We focus on three main areas: (1) polyploid genotyping; (2) genetic and physical mapping; and (3) quantitative trait analysis and genomic selection. We also briefly review some miscellaneous topics such as the mode of inheritance and the availability of polyploid simulation software. The current polyploid analytic toolbox includes software for assigning marker genotypes (and in particular, estimating the dosage of marker alleles in the heterozygous condition), establishing chromosome-scale linkage phase among marker alleles, constructing (short-range) haplotypes, generating linkage maps, performing genome-wide association studies (GWAS) and quantitative trait locus (QTL) analyses, and simulating polyploid populations. These tools can also help elucidate the mode of inheritance (disomic, polysomic or a mixture of both as in segmental allopolyploids) or reveal whether double reduction and multivalent chromosomal pairing occur. An increasing number of polyploids (or associated diploids) are being sequenced, leading to publicly available reference genome assemblies. Much work remains in order to keep pace with developments in genomic technologies. However, such technologies also offer the promise of understanding polyploid genomes at a level which hitherto has remained elusive.
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Affiliation(s)
| | | | | | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
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5
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de Oliveira AA, Pastina MM, de Souza VF, da Costa Parrella RA, Noda RW, Simeone MLF, Schaffert RE, de Magalhães JV, Damasceno CMB, Margarido GRA. Genomic prediction applied to high-biomass sorghum for bioenergy production. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:49. [PMID: 29670457 PMCID: PMC5893689 DOI: 10.1007/s11032-018-0802-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 03/13/2018] [Indexed: 05/18/2023]
Abstract
The increasing cost of energy and finite oil and gas reserves have created a need to develop alternative fuels from renewable sources. Due to its abiotic stress tolerance and annual cultivation, high-biomass sorghum (Sorghum bicolor L. Moench) shows potential as a bioenergy crop. Genomic selection is a useful tool for accelerating genetic gains and could restructure plant breeding programs by enabling early selection and reducing breeding cycle duration. This work aimed at predicting breeding values via genomic selection models for 200 sorghum genotypes comprising landrace accessions and breeding lines from biomass and saccharine groups. These genotypes were divided into two sub-panels, according to breeding purpose. We evaluated the following phenotypic biomass traits: days to flowering, plant height, fresh and dry matter yield, and fiber, cellulose, hemicellulose, and lignin proportions. Genotyping by sequencing yielded more than 258,000 single-nucleotide polymorphism markers, which revealed population structure between subpanels. We then fitted and compared genomic selection models BayesA, BayesB, BayesCπ, BayesLasso, Bayes Ridge Regression and random regression best linear unbiased predictor. The resulting predictive abilities varied little between the different models, but substantially between traits. Different scenarios of prediction showed the potential of using genomic selection results between sub-panels and years, although the genotype by environment interaction negatively affected accuracies. Functional enrichment analyses performed with the marker-predicted effects suggested several interesting associations, with potential for revealing biological processes relevant to the studied quantitative traits. This work shows that genomic selection can be successfully applied in biomass sorghum breeding programs.
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Affiliation(s)
- Amanda Avelar de Oliveira
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP 13418-900 Brazil
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Klein LL, Miller AJ, Ciotir C, Hyma K, Uribe-Convers S, Londo J. High-throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections. AMERICAN JOURNAL OF BOTANY 2018; 105:215-226. [PMID: 29578297 DOI: 10.1002/ajb2.1033] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 01/04/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY Grapes are one of the most economically important berry crops worldwide, with the vast majority of production derived from the domesticated Eurasian species Vitis vinifera. Expansion of production into new areas, development of new cultivars, and concerns about adapting grapevines for changing climates necessitate the use of wild grapevine species in breeding programs. Diversity within Vitis has long been a topic of study; however, questions remain regarding relationships between species. Furthermore, the identity of some living accessions is unclear. METHODS This study generated 11,020 single nucleotide polymorphism (SNP) markers for more than 300 accessions in the USDA-ARS grape germplasm repository using genotyping-by-sequencing. Resulting data sets were used to reconstruct evolutionary relationships among several North American and Eurasian Vitis species, and to suggest taxonomic labels for previously unidentified and misidentified germplasm accessions based on genetic distance. KEY RESULTS Maximum likelihood analyses of SNP data support the monophyly of Vitis, subg. Vitis, a Eurasian subg. Vitis clade, and a North American subg. Vitis clade. Data delineate species groups within North America. In addition, analysis of genetic distance suggested taxonomic identities for 20 previously unidentified Vitis accessions and for 28 putatively misidentified accessions. CONCLUSIONS This work advances understanding of Vitis evolutionary relationships and provides the foundation for ongoing germplasm enhancement. It supports conservation and breeding efforts by contributing to a growing genetic framework for identifying novel genetic variation and for incorporating new, unsampled populations into the germplasm repository system.
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Affiliation(s)
- Laura L Klein
- Department of Biology, Saint Louis University, St. Louis, MO, 63110, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, St. Louis, MO, 63110, USA
| | - Claudia Ciotir
- Department of Biology, Saint Louis University, St. Louis, MO, 63110, USA
| | - Katie Hyma
- Cornell University, Institute for Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Simon Uribe-Convers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason Londo
- United States Department of Agriculture, Agricultural Research Service, Grape Genetics Research Unit, Geneva, NY, 14425, USA
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7
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SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data. Bioinformatics 2017; 34:407-415. [DOI: 10.1093/bioinformatics/btx587] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022] Open
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8
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Genetic structure, diversity, and hybridization in populations of the rare arctic relict Euphrasia hudsoniana (Orobanchaceae) and its invasive congener Euphrasia stricta. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0995-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Christmas MJ, Biffin E, Breed MF, Lowe AJ. Targeted capture to assess neutral genomic variation in the narrow-leaf hopbush across a continental biodiversity refugium. Sci Rep 2017; 7:41367. [PMID: 28145488 PMCID: PMC5286450 DOI: 10.1038/srep41367] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 12/20/2016] [Indexed: 11/09/2022] Open
Abstract
The Adelaide geosyncline, a mountainous region in central southern Australia, is purported to be an important continental refugium for Mediterranean and semi-arid Australian biota, yet few population genetic studies have been conducted to test this theory. Here, we focus on a plant species distributed widely throughout the region, the narrow-leaf hopbush, Dodonaea viscosa ssp. angustissima, and examine its genetic diversity and population structure. We used a hybrid-capture target enrichment technique to selectively sequence over 700 genes from 89 individuals across 17 sampling locations. We compared 815 single nucleotide polymorphisms among individuals and populations to investigate population genetic structure. Three distinct genetic clusters were identified; a Flinders/Gammon ranges cluster, an Eastern cluster, and a Kangaroo Island cluster. Higher genetic diversity was identified in the Flinders/Gammon Ranges cluster, indicating that this area is likely to have acted as a refugium during past climate oscillations. We discuss these findings and consider the historical range dynamics of these populations. We also provide methodological considerations for population genomics studies that aim to use novel genomic approaches (such as target capture methods) on non-model systems. The application of our findings to restoration of this species across the region are also considered.
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Affiliation(s)
- Matthew J. Christmas
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, SA 5005, Australia
| | - Ed Biffin
- State Herbarium of South Australia, Hackney Road, Adelaide, SA 5000, Australia
| | - Martin F. Breed
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, SA 5005, Australia
| | - Andrew J. Lowe
- Environment Institute and School of Biological Sciences, The University of Adelaide, North Terrace, SA 5005, Australia
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Salazar JA, Pacheco I, Shinya P, Zapata P, Silva C, Aradhya M, Velasco D, Ruiz D, Martínez-Gómez P, Infante R. Genotyping by Sequencing for SNP-Based Linkage Analysis and Identification of QTLs Linked to Fruit Quality Traits in Japanese Plum ( Prunus salicina Lindl.). FRONTIERS IN PLANT SCIENCE 2017; 8:476. [PMID: 28443103 PMCID: PMC5386982 DOI: 10.3389/fpls.2017.00476] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 03/20/2017] [Indexed: 05/21/2023]
Abstract
Marker-assisted selection (MAS) in stone fruit (Prunus species) breeding is currently difficult to achieve due to the polygenic nature of the most relevant agronomic traits linked to fruit quality. Genotyping by sequencing (GBS), however, provides a large quantity of useful data suitable for fine mapping using Single Nucleotide Polymorphisms (SNPs) from a reference genome. In this study, GBS was used to genotype 272 seedlings of three F1 Japanese plum (Prunus salicina Lindl) progenies derived from crossing "98-99" (as a common female parent) with "Angeleno," "September King," and "September Queen" as male parents. Raw sequences were aligned to the Peach genome v1, and 42,909 filtered SNPs were obtained after sequence alignment. In addition, 153 seedlings from the "98-99" × "Angeleno" cross were used to develop a genetic map for each parent. A total of 981 SNPs were mapped (479 for "98-99" and 502 for "Angeleno"), covering a genetic distance of 688.8 and 647.03 cM, respectively. Fifty five seedlings from this progeny were phenotyped for different fruit quality traits including ripening time, fruit weight, fruit shape, chlorophyll index, skin color, flesh color, over color, firmness, and soluble solids content in the years 2015 and 2016. Linkage-based QTL analysis allowed the identification of genomic regions significantly associated with ripening time (LG4 of both parents and both phenotyping years), fruit skin color (LG3 and LG4 of both parents and both years), chlorophyll degradation index (LG3 of both parents in 2015) and fruit weight (LG7 of both parents in 2016). These results represent a promising situation for GBS in the identification of SNP variants associated to fruit quality traits, potentially applicable in breeding programs through MAS, in a highly heterozygous crop species such as Japanese plum.
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Affiliation(s)
- Juan A. Salazar
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
| | - Igor Pacheco
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de Alimentos, Universidad de ChileSantiago, Chile
| | - Paulina Shinya
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
| | - Patricio Zapata
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
| | - Claudia Silva
- Laboratorio de Bioinformática y Expresión Génica, Instituto de Nutrición y Tecnología de Alimentos, Universidad de ChileSantiago, Chile
| | | | | | - David Ruiz
- National Clonal Germplasm Repository, ARS, USDADavis, CA, USA
| | | | - Rodrigo Infante
- Departamento de Producción Agrícola, Universidad de ChileSantiago, Chile
- *Correspondence: Rodrigo Infante
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Barker MS, Husband BC, Pires JC. Spreading Winge and flying high: The evolutionary importance of polyploidy after a century of study. AMERICAN JOURNAL OF BOTANY 2016; 103:1139-45. [PMID: 27480249 DOI: 10.3732/ajb.1600272] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 05/10/2023]
Affiliation(s)
- Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, Arizona 85721 USA
| | - Brian C Husband
- Department of Integrative Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 USA
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