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Sapkota S, Chen LL, Yang S, Hyma KE, Cadle-Davidson L, Hwang CF. Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis-derived 'Norton'. Theor Appl Genet 2019; 132:137-147. [PMID: 30341491 DOI: 10.1007/s00122-018-3203-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 10/06/2018] [Indexed: 05/08/2023]
Abstract
A major QTL for downy mildew resistance was detected on chromosome 18 (Rpv27) in Vitis aestivalis-derived 'Norton' based on a high-resolution linkage map with SNP and SSR markers as well as 2 years of field and laboratory phenotyping data. Grapevine downy mildew caused by the oomycete Plasmopara viticola is one of the most widespread and destructive diseases, particularly in humid viticultural areas where it damages green tissues and defoliates vines. Traditional Vitis vinifera wine grape cultivars are susceptible to downy mildew whereas several North American and a few Asian cultivars possess various levels of resistance to this disease. To identify genetic determinants of downy mildew resistance in V. aestivalis-derived 'Norton,' a mapping population with 182 genotypes was developed from a cross between 'Norton' and V. vinifera 'Cabernet Sauvignon' from which a consensus map was constructed via 411 simple sequence repeat (SSR) markers. Using genotyping-by-sequencing, 3825 single nucleotide polymorphism (SNP) markers were also generated. Of these, 1665 SNP and 407 SSR markers were clustered into 19 linkage groups in 159 genotypes, spanning a genetic distance of 2203.5 cM. Disease progression in response to P. viticola was studied in this population for 2 years under both laboratory and field conditions, and strong correlations were observed among data sets (Spearman correlation coefficient = 0.57-0.79). A quantitative trait loci (QTL) analysis indicated a resistance locus on chromosome 18, here named Rpv27, explaining 33.8% of the total phenotypic variation. Flanking markers closely linked with the trait can be further used for marker-assisted selection in the development of new cultivars with resistance to downy mildew.
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Affiliation(s)
- Surya Sapkota
- State Fruit Experiment Station at Mountain Grove Campus, Darr College of Agriculture, Missouri State University, Springfield, MO, 65897, USA
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, NYS Agricultural Experiment Station, Cornell University, Geneva, NY, 14456, USA
| | - Li-Ling Chen
- State Fruit Experiment Station at Mountain Grove Campus, Darr College of Agriculture, Missouri State University, Springfield, MO, 65897, USA
| | - Shanshan Yang
- Bioinformatics Core Facility, The Biodesign Institute, Arizona State University, Tempe, AZ, 85287-5001, USA
| | - Katie E Hyma
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | | | - Chin-Feng Hwang
- State Fruit Experiment Station at Mountain Grove Campus, Darr College of Agriculture, Missouri State University, Springfield, MO, 65897, USA.
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Huang Z, Young ND, Reagon M, Hyma KE, Olsen KM, Jia Y, Caicedo AL. All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian
Oryza. Mol Ecol 2017; 26:3151-3167. [DOI: 10.1111/mec.14120] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 01/21/2017] [Accepted: 03/10/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Zhongyun Huang
- Department of Biology University of Massachusetts Amherst MA USA
| | - Nelson D. Young
- Department of Biology University of Massachusetts Amherst MA USA
| | - Michael Reagon
- Department of Biology Ohio State University Lima Lima OH USA
| | - Katie E. Hyma
- Department of Biology University of Massachusetts Amherst MA USA
| | | | - Yulin Jia
- Dale Bumpers National Rice Research Center USDA‐ARS Stuttgart AR USA
| | - Ana L. Caicedo
- Department of Biology University of Massachusetts Amherst MA USA
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Peris D, Moriarty RV, Alexander WG, Baker E, Sylvester K, Sardi M, Langdon QK, Libkind D, Wang QM, Bai FY, Leducq JB, Charron G, Landry CR, Sampaio JP, Gonçalves P, Hyma KE, Fay JC, Sato TK, Hittinger CT. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels 2017; 10:78. [PMID: 28360936 PMCID: PMC5369230 DOI: 10.1186/s13068-017-0763-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/18/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND Lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker's yeast Saccharomyces cerevisiae. Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in S. cerevisiae to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In other industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research. RESULTS To investigate the efficacy of this approach for traits relevant to lignocellulosic biofuel production, we generated synthetic hybrids by crossing engineered xylose-fermenting strains of S. cerevisiae with wild strains from various Saccharomyces species. These interspecies hybrids retained important parental traits, such as xylose consumption and stress tolerance, while displaying intermediate kinetic parameters and, in some cases, heterosis (hybrid vigor). Next, we exposed them to adaptive evolution in ammonia fiber expansion-pretreated corn stover hydrolysate and recovered strains with improved fermentative traits. Genome sequencing showed that the genomes of these evolved synthetic hybrids underwent rearrangements, duplications, and deletions. To determine whether the genus Saccharomyces contains additional untapped potential, we screened a genetically diverse collection of more than 500 wild, non-engineered Saccharomyces isolates and uncovered a wide range of capabilities for traits relevant to cellulosic biofuel production. Notably, Saccharomyces mikatae strains have high innate tolerance to hydrolysate toxins, while some Saccharomyces species have a robust native capacity to consume xylose. CONCLUSIONS This research demonstrates that hybridization is a viable method to combine industrially relevant traits from diverse yeast species and that members of the genus Saccharomyces beyond S. cerevisiae may offer advantageous genes and traits of interest to the lignocellulosic biofuel industry.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Ryan V. Moriarty
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - William G. Alexander
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - EmilyClare Baker
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Kayla Sylvester
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Maria Sardi
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Quinn K. Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, IPATEC (CONICET-UNComahue), Centro Regional Universitario Bariloche, Bariloche, Río Negro Argentina
| | - Qi-Ming Wang
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jean-Baptiste Leducq
- Departement des Sciences Biologiques, Université de Montréal, Montreal, QC Canada
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - Guillaume Charron
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - Christian R. Landry
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Katie E. Hyma
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Justin C. Fay
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
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Punnuri SM, Wallace JG, Knoll JE, Hyma KE, Mitchell SE, Buckler ES, Varshney RK, Singh BP. Development of a High-Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping-by-Sequencing Markers. Plant Genome 2016; 9. [PMID: 27898821 DOI: 10.3835/plantgenome2015.10.0106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Pearl millet [ (L.) R. Br; also (L.) Morrone] is an important crop throughout the world but better genomic resources for this species are needed to facilitate crop improvement. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping-by-sequencing (GBS) markers can be used to build high-density linkage maps, even in species lacking a reference genome. A recombinant inbred line (RIL) mapping population was developed from a cross between the lines 'Tift 99DB' and 'Tift 454'. DNA from 186 RILs, the parents, and the F was used for 96-plex KI GBS library development, which was further used for sequencing. The sequencing results showed that the average number of good reads per individual was 2.2 million, the pass filter rate was 88%, and the CV was 43%. High-quality GBS markers were developed with stringent filtering on sequence data from 179 RILs. The reference genetic map developed using 150 RILs contained 16,650 single-nucleotide polymorphisms (SNPs) and 333,567 sequence tags spread across all seven chromosomes. The overall average density of SNP markers was 23.23 SNP/cM in the final map and 1.66 unique linkage bins per cM covering a total genetic distance of 716.7 cM. The linkage map was further validated for its utility by using it in mapping quantitative trait loci (QTLs) for flowering time and resistance to leaf spot [ (Cke.) Sacc.]. This map is the densest yet reported for this crop and will be a valuable resource for the pearl millet community.
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Sardos J, Rouard M, Hueber Y, Cenci A, Hyma KE, van den Houwe I, Hribova E, Courtois B, Roux N. A Genome-Wide Association Study on the Seedless Phenotype in Banana (Musa spp.) Reveals the Potential of a Selected Panel to Detect Candidate Genes in a Vegetatively Propagated Crop. PLoS One 2016; 11:e0154448. [PMID: 27144345 PMCID: PMC4856271 DOI: 10.1371/journal.pone.0154448] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 04/13/2016] [Indexed: 11/19/2022] Open
Abstract
Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement.
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Affiliation(s)
- Julie Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
- * E-mail:
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Yann Hueber
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Alberto Cenci
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Katie E. Hyma
- Institute of Biotechnology, Genomic Diversity Facility, Cornell University, Ithaca, NY, 14853, United States of America
| | | | - Eva Hribova
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Nicolas Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
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Hyma KE, Barba P, Wang M, Londo JP, Acharya CB, Mitchell SE, Sun Q, Reisch B, Cadle-Davidson L. Heterozygous Mapping Strategy (HetMappS) for High Resolution Genotyping-By-Sequencing Markers: A Case Study in Grapevine. PLoS One 2015; 10:e0134880. [PMID: 26244767 PMCID: PMC4526651 DOI: 10.1371/journal.pone.0134880] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 07/14/2015] [Indexed: 02/07/2023] Open
Abstract
Genotyping by sequencing (GBS) provides opportunities to generate high-resolution genetic maps at a low genotyping cost, but for highly heterozygous species, missing data and heterozygote undercalling complicate the creation of GBS genetic maps. To overcome these issues, we developed a publicly available, modular approach called HetMappS, which functions independently of parental genotypes and corrects for genotyping errors associated with heterozygosity. For linkage group formation, HetMappS includes both a reference-guided synteny pipeline and a reference-independent de novo pipeline. The de novo pipeline can be utilized for under-characterized or high diversity families that lack an appropriate reference. We applied both HetMappS pipelines in five half-sib F1 families involving genetically diverse Vitis spp. Starting with at least 116,466 putative SNPs per family, the HetMappS pipelines identified 10,440 to 17,267 phased pseudo-testcross (Pt) markers and generated high-confidence maps. Pt marker density exceeded crossover resolution in all cases; up to 5,560 non-redundant markers were used to generate parental maps ranging from 1,047 cM to 1,696 cM. The number of markers used was strongly correlated with family size in both de novo and synteny maps (r = 0.92 and 0.91, respectively). Comparisons between allele and tag frequencies suggested that many markers were in tandem repeats and mapped as single loci, while markers in regions of more than two repeats were removed during map curation. Both pipelines generated similar genetic maps, and genetic order was strongly correlated with the reference genome physical order in all cases. Independently created genetic maps from shared parents exhibited nearly identical results. Flower sex was mapped in three families and correctly localized to the known sex locus in all cases. The HetMappS pipeline could have wide application for genetic mapping in highly heterozygous species, and its modularity provides opportunities to adapt portions of the pipeline to other family types, genotyping technologies or applications.
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Affiliation(s)
- Katie E. Hyma
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Paola Barba
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, United States of America
| | - Minghui Wang
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Jason P. Londo
- USDA-ARS Grape Genetics Research Unit, Geneva, New York, United States of America
| | - Charlotte B. Acharya
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Sharon E. Mitchell
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Qi Sun
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, United States of America
| | - Bruce Reisch
- Horticulture Section, School of Integrative Plant Science, Cornell University, Geneva, New York, United States of America
| | - Lance Cadle-Davidson
- USDA-ARS Grape Genetics Research Unit, Geneva, New York, United States of America
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Johnson JL, Wittgenstein H, Mitchell SE, Hyma KE, Temnykh SV, Kharlamova AV, Gulevich RG, Vladimirova AV, Fong HWF, Acland GM, Trut LN, Kukekova AV. Genotyping-By-Sequencing (GBS) Detects Genetic Structure and Confirms Behavioral QTL in Tame and Aggressive Foxes (Vulpes vulpes). PLoS One 2015; 10:e0127013. [PMID: 26061395 PMCID: PMC4465646 DOI: 10.1371/journal.pone.0127013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/09/2015] [Indexed: 12/22/2022] Open
Abstract
The silver fox (Vulpes vulpes) offers a novel model for studying the genetics of social behavior and animal domestication. Selection of foxes, separately, for tame and for aggressive behavior has yielded two strains with markedly different, genetically determined, behavioral phenotypes. Tame strain foxes are eager to establish human contact while foxes from the aggressive strain are aggressive and difficult to handle. These strains have been maintained as separate outbred lines for over 40 generations but their genetic structure has not been previously investigated. We applied a genotyping-by-sequencing (GBS) approach to provide insights into the genetic composition of these fox populations. Sequence analysis of EcoT22I genomic libraries of tame and aggressive foxes identified 48,294 high quality SNPs. Population structure analysis revealed genetic divergence between the two strains and more diversity in the aggressive strain than in the tame one. Significant differences in allele frequency between the strains were identified for 68 SNPs. Three of these SNPs were located on fox chromosome 14 within an interval of a previously identified behavioral QTL, further supporting the importance of this region for behavior. The GBS SNP data confirmed that significant genetic diversity has been preserved in both fox populations despite many years of selective breeding. Analysis of SNP allele frequencies in the two populations identified several regions of genetic divergence between the tame and aggressive foxes, some of which may represent targets of selection for behavior. The GBS protocol used in this study significantly expanded genomic resources for the fox, and can be adapted for SNP discovery and genotyping in other canid species.
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Affiliation(s)
- Jennifer L. Johnson
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States of America
| | - Helena Wittgenstein
- Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, United States of America
| | - Sharon E. Mitchell
- Institute of Biotechnology, Genomic Diversity Facility, Cornell University, Ithaca, NY, 14853, United States of America
| | - Katie E. Hyma
- Institute of Biotechnology, Genomic Diversity Facility, Cornell University, Ithaca, NY, 14853, United States of America
| | - Svetlana V. Temnykh
- Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, United States of America
| | - Anastasiya V. Kharlamova
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Rimma G. Gulevich
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | | | - Hiu Wa Flora Fong
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States of America
| | - Gregory M. Acland
- Baker Institute for Animal Health, Cornell University, College of Veterinary Medicine, Ithaca, NY, 14853, United States of America
| | - Lyudmila N. Trut
- Institute of Cytology and Genetics of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Anna V. Kukekova
- Department of Animal Sciences, College of ACES, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States of America
- * E-mail:
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Burgos NR, Singh V, Tseng TM, Black H, Young ND, Huang Z, Hyma KE, Gealy DR, Caicedo AL. The impact of herbicide-resistant rice technology on phenotypic diversity and population structure of United States weedy rice. Plant Physiol 2014; 166:1208-20. [PMID: 25122473 PMCID: PMC4226343 DOI: 10.1104/pp.114.242719] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 08/03/2014] [Indexed: 05/20/2023]
Abstract
The use of herbicide-resistant (HR) Clearfield rice (Oryza sativa) to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in Arkansas, where most U.S. rice is grown. To assess the impact of HR cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a history of Clearfield rice. Panicles from each weedy type were harvested and tested for resistance to imazethapyr. The majority of plants sampled had at least 20% resistant offspring. These resistant weeds were 97 to 199 cm tall and initiated flowering from 78 to 128 d, generally later than recorded for accessions collected prior to the widespread use of Clearfield rice (i.e. historical accessions). Whereas the majority (70%) of historical accessions had straw-colored hulls, only 30% of contemporary HR weedy rice had straw-colored hulls. Analysis of genotyping-by-sequencing data showed that HR weeds were not genetically structured according to hull color, whereas historical weedy rice was separated into straw-hull and black-hull populations. A significant portion of the local rice crop genome was introgressed into HR weedy rice, which was rare in historical weedy accessions. Admixture analyses showed that HR weeds tend to possess crop haplotypes in the portion of chromosome 2 containing the ACETOLACTATE SYNTHASE gene, which confers herbicide resistance to Clearfield rice. Thus, U.S. HR weedy rice is a distinct population relative to historical weedy rice and shows modifications in morphology and phenology that are relevant to weed management.
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Affiliation(s)
- Nilda Roma Burgos
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Vijay Singh
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Te Ming Tseng
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Howard Black
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Nelson D Young
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Zhongyun Huang
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Katie E Hyma
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - David R Gealy
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
| | - Ana L Caicedo
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas 72704 (N.R.B., V.S., T.M.T.);United States Department of Agriculture Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas 72160 (H.B., D.R.G.); andBiology Department, University of Massachusetts, Amherst, Massachusetts 01003 (N.D.Y., Z.H., K.E.H., A.L.C.)
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Girma G, Hyma KE, Asiedu R, Mitchell SE, Gedil M, Spillane C. Next-generation sequencing based genotyping, cytometry and phenotyping for understanding diversity and evolution of Guinea yams. Theor Appl Genet 2014; 127:1783-94. [PMID: 24981608 DOI: 10.1007/s00122-014-2339-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/22/2014] [Indexed: 05/24/2023]
Abstract
Genotyping by sequencing (GBS) is used to understand the origin and domestication of guinea yams, including the contribution of wild relatives and polyploidy events to the cultivated guinea yams. Patterns of genetic diversity within and between two cultivated guinea yams (Dioscorea rotundata and D. cayenensis) and five wild relatives (D. praehensilis, D. mangenotiana, D. abyssinica, D. togoensis and D. burkilliana) were investigated using next-generation sequencing (genotyping by sequencing, GBS). Additionally, the two cultivated species were assessed for intra-specific morphological and ploidy variation. In guinea yams, ploidy level is correlated with species identity. Using flow cytometry a single ploidy level was inferred across D. cayenensis (3x, N = 21), D. praehensilis (2x, N = 7), and D. mangenotiana (3x, N = 5) accessions, whereas both diploid and triploid (or aneuploid) accessions were present in D. rotundata (N = 11 and N = 32, respectively). Multi-dimensional scaling and maximum parsimony analyses of 2,215 SNPs revealed that wild guinea yam populations form discrete genetic groupings according to species. D. togoensis and D. burkilliana were most distant from the two cultivated yam species, whereas D. abyssinica, D. mangenotiana, and D. praehensilis were closest to cultivated yams. In contrast, cultivated species were genetically less clearly defined at the intra-specific level. While D. cayenensis formed a single genetic group, D. rotundata comprised three separate groups consisting of; (1) a set of diploid individuals genetically similar to D. praehensilis, (2) a set of diploid individuals genetically similar to D. cayenensis, and (3) a set of triploid individuals. The current study demonstrates the utility of GBS for assessing yam genomic diversity. Combined with morphological and biological data, GBS provides a powerful tool for testing hypotheses regarding the evolution, domestication and breeding of guinea yams.
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Affiliation(s)
- Gezahegn Girma
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Hyma KE, Fay JC. Mixing of vineyard and oak-tree ecotypes of Saccharomyces cerevisiae in North American vineyards. Mol Ecol 2013; 22:2917-30. [PMID: 23286354 DOI: 10.1111/mec.12155] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 10/15/2012] [Accepted: 10/19/2012] [Indexed: 12/21/2022]
Abstract
Humans have had a significant impact on the distribution and abundance of Saccharomyces cerevisiae through its widespread use in beer, bread and wine production. Yet, similar to other Saccharomyces species, S. cerevisiae has also been isolated from habitats unrelated to fermentations. Strains of S. cerevisiae isolated from grapes, wine must and vineyards worldwide are genetically differentiated from strains isolated from oak-tree bark, exudate and associated soil in North America. However, the causes and consequences of this differentiation have not yet been resolved. Historical differentiation of these two groups may have been influenced by geographic, ecological or human-associated barriers to gene flow. Here, we make use of the relatively recent establishment of vineyards across North America to identify and characterize any active barriers to gene flow between these two groups. We examined S. cerevisiae strains isolated from grapes and oak trees within three North American vineyards and compared them to those isolated from oak trees outside of vineyards. Within vineyards, we found evidence of migration between grapes and oak trees and potential gene flow between the divergent oak-tree and vineyard groups. Yet, we found no vineyard genotypes on oak trees outside of vineyards. In contrast, Saccharomyces paradoxus isolated from the same sources showed population structure characterized by isolation by distance. The apparent absence of ecological or genetic barriers between sympatric vineyard and oak-tree populations of S. cerevisiae implies that vineyards play an important role in the mixing between these two groups.
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Affiliation(s)
- Katie E Hyma
- Evolution, Ecology and Population Biology Program, Washington University, St. Louis, MO 63130, USA.
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Hyma KE, Caicedo AL. Shedding light on the evolution of plasticity in natural populations. Mol Ecol 2012; 20:3491-3. [PMID: 21884290 DOI: 10.1111/j.1365-294x.2011.05215.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Plasticity allows for changes in phenotype in response to environmental cues, often facilitating local adaptation to seasonal environments. Phenotypic plasticity alone, however, may not always be sufficient to ensure adaptation to new localities. In particular, changing cues associated with shifting seasonal regimes may no longer induce appropriate phenotypic responses in new environments (Nicotra et al. 2010). Plastic responses must thus evolve to avoid being maladaptive. To date, the extent to which plastic responses can change and the genetic mechanisms by which this can happen have remained elusive. In this issue of Molecular Ecology, Blackman et al. (2011a) harness natural variation in flowering time among populations of the wild sunflower, Helianthus annuus, to demonstrate that plasticity has indeed evolved in this species. Remarkably, they are able to detect changes in gene expression that are associated with both a loss of plasticity and a reversal of the plastic response. These changes occur in two separate, but integrated, regulatory pathways controlling the transition to flowering, suggesting that complex regulatory networks that incorporate multiple environmental and developmental cues may facilitate the evolution of plastic responses. This study leverages knowledge from plant genetic models to provide a surprising level of insight into the evolution of an adaptive trait in a non-model species. Through discoveries of the roles of gene duplication and network modularity in the evolution of plastic responses, the study raises questions about the degree to which species-specific network architectures may act as a constraint to the potential of adaptation.
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Affiliation(s)
- Katie E Hyma
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
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Hyma KE, Saerens SM, Verstrepen KJ, Fay JC. Divergence in wine characteristics produced by wild and domesticated strains of Saccharomyces cerevisiae. FEMS Yeast Res 2011; 11:540-51. [PMID: 22093681 PMCID: PMC3262967 DOI: 10.1111/j.1567-1364.2011.00746.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 07/14/2011] [Accepted: 07/19/2011] [Indexed: 01/23/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae is the primary species used by wine makers to convert sugar into alcohol during wine fermentation. Saccharomyces cerevisiae is found in vineyards, but is also found in association with oak trees and other natural sources. Although wild strains of S. cerevisiae as well as other Saccharomyces species are also capable of wine fermentation, a genetically distinct group of S. cerevisiae strains is primarily used to produce wine, consistent with the idea that wine making strains have been domesticated for wine production. In this study, we demonstrate that humans can distinguish between wines produced using wine strains and wild strains of S. cerevisiae as well as its sibling species, Saccharomyces paradoxus. Wine strains produced wine with fruity and floral characteristics, whereas wild strains produced wine with earthy and sulfurous characteristics. The differences that we observe between wine and wild strains provides further evidence that wine strains have evolved phenotypes that are distinct from their wild ancestors and relevant to their use in wine production.
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Affiliation(s)
- Katie E Hyma
- Evolution, Ecology and Population Biology Program, Washington University, St. Louis, MO, USA.
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Hyma KE, Lacher DW, Nelson AM, Bumbaugh AC, Janda JM, Strockbine NA, Young VB, Whittam TS. Evolutionary genetics of a new pathogenic Escherichia species: Escherichia albertii and related Shigella boydii strains. J Bacteriol 2005; 187:619-28. [PMID: 15629933 PMCID: PMC543563 DOI: 10.1128/jb.187.2.619-628.2005] [Citation(s) in RCA: 159] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A bacterium originally described as Hafnia alvei induces diarrhea in rabbits and causes epithelial damage similar to the attachment and effacement associated with enteropathogenic Escherichia coli. Subsequent studies identified similar H. alvei-like strains that are positive for an intimin gene (eae) probe and, based on DNA relatedness, are classified as a distinct Escherichia species, Escherichia albertii. We determined sequences for multiple housekeeping genes in five E. albertii strains and compared these sequences to those of strains representing the major groups of pathogenic E. coli and Shigella. A comparison of 2,484 codon positions in 14 genes revealed that E. albertii strains differ, on average, at approximately 7.4% of the nucleotide sites from pathogenic E. coli strains and at 15.7% from Salmonella enterica serotype Typhimurium. Interestingly, E. albertii strains were found to be closely related to strains of Shigella boydii serotype 13 (Shigella B13), a distant relative of E. coli representing a divergent lineage in the genus Escherichia. Analysis of homologues of intimin (eae) revealed that the central conserved domains are similar in E. albertii and Shigella B13 and distinct from those of eae variants found in pathogenic E. coli. Sequence analysis of the cytolethal distending toxin gene cluster (cdt) also disclosed three allelic groups corresponding to E. albertii, Shigella B13, and a nontypeable isolate serologically related to S. boydii serotype 7. Based on the synonymous substitution rate, the E. albertii-Shigella B13 lineage is estimated to have split from an E. coli-like ancestor approximately 28 million years ago and formed a distinct evolutionary branch of enteric pathogens that has radiated into groups with distinct virulence properties.
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Affiliation(s)
- Katie E Hyma
- Microbial Evolution Laboratory, 165 Food Safety & Toxicology Building, Michigan State University, East Lansing, MI 48824, USA
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