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Weaver S, McGaugh SE, Kono TJY, Macip-Rios R, Gluesenkamp AG. Assessing genomic and ecological differentiation among subspecies of the Rough-footed Mud Turtle, Kinosternon hirtipes. J Hered 2022; 113:538-551. [PMID: 35922036 DOI: 10.1093/jhered/esac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Combining genetic and ecological measures of differentiation can provide compelling evidence for ecological and genetic divergence among lineages. The Rough-footed Mud Turtle, Kinosternon hirtipes, is distributed from the Trans-Pecos region of Texas to the highlands of Central Mexico and contains six described subspecies, five of which are extant. We use ddRAD sequencing and species distribution models to assess levels of ecological and genetic differentiation among these subspecies. We also predict changes in climatically suitable habitat under different climate change scenarios and assess levels of genetic diversity and inbreeding within each lineage. Our results show that there is strong genetic and ecological differentiation among multiple lineages within K. hirtipes, and that this differentiation appears to be the result of vicariance associated with the Trans-Mexican Volcanic Belt. We propose changes to subspecies designations to more accurately reflect the evolutionary relationships among populations and assess threats to each subspecies.
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Affiliation(s)
- Sam Weaver
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, Saint Paul, MN 55108, USA
| | - Suzanne E McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, Saint Paul, MN 55108, USA
| | - Thomas J Y Kono
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Lab, Saint Paul, MN 55108, USA
| | - Rodrigo Macip-Rios
- Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No.8701, Col. Ex Hacienda de San José de la Huerta, CP 58190 Morelia, Michoacán, México.,Laboratorio Nacional de Síntesis Ecológica, Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro No.8701, Col. Ex Hacienda de San José de la Huerta, CP 58190 Morelia, Michoacán, México
| | - Andrew G Gluesenkamp
- Center for Conservation and Research, San Antonio Zoo, 3903 N. St. Mary's Street, San Antonio, Texas 78212 USA
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Han Q, Kono TJY, Knutson CG, Parry NM, Seiler CL, Fox JG, Tannenbaum SR, Tretyakova NY. Multi-Omics Characterization of Inflammatory Bowel Disease-Induced Hyperplasia/Dysplasia in the Rag2-/-/ Il10-/- Mouse Model. Int J Mol Sci 2020; 22:ijms22010364. [PMID: 33396408 PMCID: PMC7795000 DOI: 10.3390/ijms22010364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/26/2022] Open
Abstract
Epigenetic dysregulation is hypothesized to play a role in the observed association between inflammatory bowel disease (IBD) and colon tumor development. In the present work, DNA methylome, hydroxymethylome, and transcriptome analyses were conducted in proximal colon tissues harvested from the Helicobacter hepaticus (H. hepaticus)-infected murine model of IBD. Reduced representation bisulfite sequencing (RRBS) and oxidative RRBS (oxRRBS) analyses identified 1606 differentially methylated regions (DMR) and 3011 differentially hydroxymethylated regions (DhMR). These DMR/DhMR overlapped with genes that are associated with gastrointestinal disease, inflammatory disease, and cancer. RNA-seq revealed pronounced expression changes of a number of genes associated with inflammation and cancer. Several genes including Duox2, Tgm2, Cdhr5, and Hk2 exhibited changes in both DNA methylation/hydroxymethylation and gene expression levels. Overall, our results suggest that chronic inflammation triggers changes in methylation and hydroxymethylation patterns in the genome, altering the expression of key tumorigenesis genes and potentially contributing to the initiation of colorectal cancer.
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Affiliation(s)
- Qiyuan Han
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Thomas J. Y. Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Charles G. Knutson
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Nicola M. Parry
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA;
| | - Christopher L. Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
| | - James G. Fox
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Steven R. Tannenbaum
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (C.G.K.); (J.G.F.); (S.R.T.)
| | - Natalia Y. Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA;
- Correspondence: ; Tel.: +1-612-626-3432
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Seiler CL, Song JUM, Kotandeniya D, Chen J, Kono TJY, Han Q, Colwell M, Auch B, Sarver AL, Upadhyaya P, Ren Y, Faulk C, De Flora S, La Maestra S, Chen Y, Kassie F, Tretyakova NY. Inhalation exposure to cigarette smoke and inflammatory agents induces epigenetic changes in the lung. Sci Rep 2020; 10:11290. [PMID: 32647312 PMCID: PMC7347915 DOI: 10.1038/s41598-020-67502-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 06/09/2020] [Indexed: 01/05/2023] Open
Abstract
Smoking-related lung tumors are characterized by profound epigenetic changes including scrambled patterns of DNA methylation, deregulated histone acetylation, altered gene expression levels, distorted microRNA profiles, and a global loss of cytosine hydroxymethylation marks. Here, we employed an enhanced version of bisulfite sequencing (RRBS/oxRRBS) followed by next generation sequencing to separately map DNA epigenetic marks 5-methyl-dC and 5-hydroxymethyl-dC in genomic DNA isolated from lungs of A/J mice exposed whole-body to environmental cigarette smoke for 10 weeks. Exposure to cigarette smoke significantly affected the patterns of cytosine methylation and hydroxymethylation in the lungs. Differentially hydroxymethylated regions were associated with inflammatory response/disease, organismal injury, and respiratory diseases and were involved in regulation of cellular development, function, growth, and proliferation. To identify epigenetic changes in the lung associated with exposure to tobacco carcinogens and inflammation, A/J mice were intranasally treated with the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), the inflammatory agent lipopolysaccharide (LPS), or both. NNK alone caused minimal epigenetic alterations, while exposure either to LPS or NNK/LPS in combination led to increased levels of global cytosine methylation and formylation, reduced cytosine hydroxymethylation, decreased histone acetylation, and altered expression levels of multiple genes. Our results suggest that inflammatory processes are responsible for epigenetic changes contributing to lung cancer development.
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Affiliation(s)
- Christopher L Seiler
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - J Ung Min Song
- Department of Veterinary Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - Delshanee Kotandeniya
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - Jianji Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Thomas J Y Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Qiyuan Han
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Mathia Colwell
- Department of Animal Science, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Benjamin Auch
- Genomics Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Aaron L Sarver
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - Pramod Upadhyaya
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - Yanan Ren
- Biostatistics Core, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Silvio De Flora
- Department of Health Sciences, University of Genoa, 16132, Genoa, Italy
| | | | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Fekadu Kassie
- Department of Veterinary Medicine, University of Minnesota, Minneapolis, MN, 55455, USA
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA
| | - Natalia Y Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
- Masonic Cancer Center, University of Minnesota, 2231 6th Street SE, 2-147 CCRB, Minneapolis, 55455, USA.
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Nashoba AR, Kono TJY. Selection and plasticity both account for interannual variation in life-history phenology in an annual prairie legume. Ecol Evol 2020; 10:940-951. [PMID: 32015856 PMCID: PMC6988531 DOI: 10.1002/ece3.5953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 11/28/2022] Open
Abstract
As the environment changes, so too must plant communities and populations if they are to persist. Life-history transitions and their timing are often the traits that are most responsive to changing environmental conditions. To compare the contributions of plasticity and natural selective response to variation in germination and flowering phenology, we performed a quantitative genetic study of phenotypic selection on Chamaecrista fasciculata (Fabaceae) across two consecutive years in a restored tallgrass prairie. The earliest dates of germination and flowering were recorded for two parental cohorts and one progeny cohort in an experimental garden. Environmental differences between years were the largest contributors to phenological variation in this population. In addition, there was substantial heritability for flowering time and statistically significant selection for advancement of flowering. Comparison between a progeny cohort and its preselection parental cohort indicated a change in mean flowering time consistent with the direction of selection. Selection on germination time was weaker than that on flowering time, while environmental effects on germination time were stronger. The response to selection on flowering time was detectable when accounting for the effect of the environment on phenotypic differences, highlighting the importance of controlling for year-to-year environmental variation in quantitative genetic studies.
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Affiliation(s)
- Amber R. Nashoba
- Department of Biological SciencesUniversity of AlaskaAnchorageAlaska
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5
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Kono TJY, Liu C, Vonderharr EE, Koenig D, Fay JC, Smith KP, Morrell PL. The Fate of Deleterious Variants in a Barley Genomic Prediction Population. Genetics 2019; 213:1531-1544. [PMID: 31653677 PMCID: PMC6893365 DOI: 10.1534/genetics.119.302733] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Targeted identification and purging of deleterious genetic variants has been proposed as a novel approach to animal and plant breeding. This strategy is motivated, in part, by the observation that demographic events and strong selection associated with cultivated species pose a "cost of domestication." This includes an increase in the proportion of genetic variants that are likely to reduce fitness. Recent advances in DNA resequencing and sequence constraint-based approaches to predict the functional impact of a mutation permit the identification of putatively deleterious SNPs (dSNPs) on a genome-wide scale. Using exome capture resequencing of 21 barley lines, we identified 3855 dSNPs among 497,754 total SNPs. We generated whole-genome resequencing data of Hordeum murinum ssp. glaucum as a phylogenetic outgroup to polarize SNPs as ancestral vs. derived. We also observed a higher proportion of dSNPs per synonymous SNPs (sSNPs) in low-recombination regions of the genome. Using 5215 progeny from a genomic prediction experiment, we examined the fate of dSNPs over three breeding cycles. Adjusting for initial frequency, derived alleles at dSNPs reduced in frequency or were lost more often than other classes of SNPs. The highest-yielding lines in the experiment, as chosen by standard genomic prediction approaches, carried fewer homozygous dSNPs than randomly sampled lines from the same progeny cycle. In the final cycle of the experiment, progeny selected by genomic prediction had a mean of 5.6% fewer homozygous dSNPs relative to randomly chosen progeny from the same cycle.
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Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Emily E Vonderharr
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Daniel Koenig
- Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Justin C Fay
- Department of Biology, University of Rochester, New York 14627
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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Seiler CL, Song JM, Fernandez J, Abrahante JE, Kono TJY, Chen Y, Ren Y, Kassie F, Tretyakova NY. Epigenetic Changes in Alveolar Type II Lung Cells of A/J Mice Following Intranasal Treatment with Lipopolysaccharide. Chem Res Toxicol 2019; 32:831-839. [PMID: 30942577 DOI: 10.1021/acs.chemrestox.9b00015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Lipopolysaccharide (LPS) is a bacterial endotoxin present in cigarette smoke. LPS is known to induce inflammation and to increase the size and the multiplicity of lung tumors induced by tobacco-specific nitrosamines. However, the means by which LPS contributes to pulmonary carcinogenesis are not known. One possible mechanism includes LPS-mediated epigenetic deregulation, which leads to aberrant expression of genes involved in DNA repair, tumor suppression, cell cycle progression, and cell growth. In the present work, epigenetic effects of LPS were examined in alveolar type II lung cells of A/J mice. Type II cells were selected because they serve as progenitors of lung adenocarcinomas in smoking induced lung cancer. A/J mice were intranasally treated with LPS, followed by isolation of alveolar type II cells from the lung using cell panning. Global levels of DNA methylation and histone acetylation were quantified by mass spectrometry, while genome-wide transcriptomic changes were characterized by RNA-Seq. LPS treatment was associated with epigenetic changes including decreased cytosine formylation and reduced histone H3K14 and H3K23 acetylation, as well as altered expression levels of genes involved in cell adhesion, inflammation, immune response, and epigenetic regulation. These results suggest that exposure to inflammatory agents in cigarette smoke leads to early epigenetic changes in the lung, which may collaborate with genetic changes to drive the development of lung cancer.
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Mazaheri M, Heckwolf M, Vaillancourt B, Gage JL, Burdo B, Heckwolf S, Barry K, Lipzen A, Ribeiro CB, Kono TJY, Kaeppler HF, Spalding EP, Hirsch CN, Robin Buell C, de Leon N, Kaeppler SM. Genome-wide association analysis of stalk biomass and anatomical traits in maize. BMC Plant Biol 2019; 19:45. [PMID: 30704393 PMCID: PMC6357476 DOI: 10.1186/s12870-019-1653-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 01/14/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Maize stover is an important source of crop residues and a promising sustainable energy source in the United States. Stalk is the main component of stover, representing about half of stover dry weight. Characterization of genetic determinants of stalk traits provide a foundation to optimize maize stover as a biofuel feedstock. We investigated maize natural genetic variation in genome-wide association studies (GWAS) to detect candidate genes associated with traits related to stalk biomass (stalk diameter and plant height) and stalk anatomy (rind thickness, vascular bundle density and area). RESULTS Using a panel of 942 diverse inbred lines, 899,784 RNA-Seq derived single nucleotide polymorphism (SNP) markers were identified. Stalk traits were measured on 800 members of the panel in replicated field trials across years. GWAS revealed 16 candidate genes associated with four stalk traits. Most of the detected candidate genes were involved in fundamental cellular functions, such as regulation of gene expression and cell cycle progression. Two of the regulatory genes (Zmm22 and an ortholog of Fpa) that were associated with plant height were previously shown to be involved in regulating the vegetative to floral transition. The association of Zmm22 with plant height was confirmed using a transgenic approach. Transgenic lines with increased expression of Zmm22 showed a significant decrease in plant height as well as tassel branch number, indicating a pleiotropic effect of Zmm22. CONCLUSION Substantial heritable variation was observed in the association panel for stalk traits, indicating a large potential for improving useful stalk traits in breeding programs. Genome-wide association analyses detected several candidate genes associated with multiple traits, suggesting common regulatory elements underlie various stalk traits. Results of this study provide insights into the genetic control of maize stalk anatomy and biomass.
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Affiliation(s)
- Mona Mazaheri
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
- Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706 USA
| | - Marlies Heckwolf
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
- Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706 USA
| | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy, Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
| | - Joseph L. Gage
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
| | - Brett Burdo
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
| | - Sven Heckwolf
- Department of Botany, University of Wisconsin, Madison, WI 53706 USA
| | - Kerrie Barry
- Department of Energy, Joint Genome Institute, Walnut Creek, California, 94598 USA
| | - Anna Lipzen
- Department of Energy, Joint Genome Institute, Walnut Creek, California, 94598 USA
| | - Camila Bastos Ribeiro
- Genótika Super Sementes. Colonizador Ênio Pipino - St. Industrial Sul, Sinop, MT 78550-098 Brazil
| | - Thomas J. Y. Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN 55108 USA
- Present address: Minnesota Supercomputing Institute, 117 Pleasant Street SE, Minneapolis, MN 55455 USA
| | - Heidi F. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
- Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706 USA
| | - Edgar P. Spalding
- Department of Botany, University of Wisconsin, Madison, WI 53706 USA
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN 55108 USA
| | - C. Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Energy, Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824 USA
| | - Natalia de Leon
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
- Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706 USA
| | - Shawn M. Kaeppler
- Department of Agronomy, University of Wisconsin, Madison, WI 53706 USA
- Department of Energy, Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53706 USA
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Passow CN, Kono TJY, Stahl BA, Jaggard JB, Keene AC, McGaugh SE. Nonrandom RNAseq gene expression associated with RNAlater and flash freezing storage methods. Mol Ecol Resour 2018; 19:456-464. [PMID: 30447171 DOI: 10.1111/1755-0998.12965] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/19/2018] [Accepted: 11/08/2018] [Indexed: 01/30/2023]
Abstract
RNA sequencing is a popular next-generation sequencing technique for assaying genome-wide gene expression profiles. Nonetheless, it is susceptible to biases that are introduced by sample handling prior gene expression measurements. Two of the most common methods for preserving samples in both field-based and laboratory conditions are submersion in RNAlater and flash freezing in liquid nitrogen. Flash freezing in liquid nitrogen can be impractical, particularly for field collections. RNAlater is a solution for stabilizing tissue for longer-term storage as it rapidly permeates tissue to protect cellular RNA. In this study, we assessed genome-wide expression patterns in 30-day-old fry collected from the same brood at the same time point that were flash-frozen in liquid nitrogen and stored at -80°C or submerged and stored in RNAlater at room temperature, simulating conditions of fieldwork. We show that sample storage is a significant factor influencing observed differential gene expression. In particular, genes with elevated GC content exhibit higher observed expression levels in liquid nitrogen flash-freezing relative to RNAlater storage. Further, genes with higher expression in RNAlater relative to liquid nitrogen experience disproportionate enrichment for functional categories, many of which are involved in RNA processing. This suggests that RNAlater may elicit a physiological response that has the potential to bias biological interpretations of expression studies. The biases introduced to observed gene expression arising from mimicking many field-based studies are substantial and should not be ignored.
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Affiliation(s)
- Courtney N Passow
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota
| | - Thomas J Y Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Bethany A Stahl
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - James B Jaggard
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Alex C Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Suzanne E McGaugh
- Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota
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Herman A, Brandvain Y, Weagley J, Jeffery WR, Keene AC, Kono TJY, Bilandžija H, Borowsky R, Espinasa L, O'Quin K, Ornelas-García CP, Yoshizawa M, Carlson B, Maldonado E, Gross JB, Cartwright RA, Rohner N, Warren WC, McGaugh SE. The role of gene flow in rapid and repeated evolution of cave-related traits in Mexican tetra, Astyanax mexicanus. Mol Ecol 2018; 27:4397-4416. [PMID: 30252986 DOI: 10.1111/mec.14877] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/08/2018] [Accepted: 08/19/2018] [Indexed: 12/13/2022]
Abstract
Understanding the molecular basis of repeatedly evolved phenotypes can yield key insights into the evolutionary process. Quantifying gene flow between populations is especially important in interpreting mechanisms of repeated phenotypic evolution, and genomic analyses have revealed that admixture occurs more frequently between diverging lineages than previously thought. In this study, we resequenced 47 whole genomes of the Mexican tetra from three cave populations, two surface populations and outgroup samples. We confirmed that cave populations are polyphyletic and two Astyanax mexicanus lineages are present in our data set. The two lineages likely diverged much more recently than previous mitochondrial estimates of 5-7 mya. Divergence of cave populations from their phylogenetically closest surface population likely occurred between ~161 and 191 k generations ago. The favoured demographic model for most population pairs accounts for divergence with secondary contact and heterogeneous gene flow across the genome, and we rigorously identified gene flow among all lineages sampled. Therefore, the evolution of cave-related traits occurred more rapidly than previously thought, and trogolomorphic traits are maintained despite gene flow with surface populations. The recency of these estimated divergence events suggests that selection may drive the evolution of cave-derived traits, as opposed to disuse and drift. Finally, we show that a key trogolomorphic phenotype QTL is enriched for genomic regions with low divergence between caves, suggesting that regions important for cave phenotypes may be transferred between caves via gene flow. Our study shows that gene flow must be considered in studies of independent, repeated trait evolution.
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Affiliation(s)
- Adam Herman
- Plant and Microbial Biology, Gortner Lab, University of Minnesota, Saint Paul, Minnesota.,Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Yaniv Brandvain
- Plant and Microbial Biology, Gortner Lab, University of Minnesota, Saint Paul, Minnesota
| | - James Weagley
- Ecology, Evolution, and Behavior, Gortner Lab, University of Minnesota, Saint Paul, Minnesota
| | - William R Jeffery
- Department of Biology, University of Maryland, College Park, Maryland
| | - Alex C Keene
- Department of Biological Sciences, Florida Atlantic University, Jupiter, Florida
| | - Thomas J Y Kono
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota
| | - Helena Bilandžija
- Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia.,Department of Biology, University of Maryland, College Park, Maryland
| | | | - Luis Espinasa
- School of Science, Marist College, Poughkeepsie, New York
| | - Kelly O'Quin
- Department of Biology, Centre College, Danville, Kentucky
| | - Claudia P Ornelas-García
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, Mexico
| | - Masato Yoshizawa
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, Hawaii
| | - Brian Carlson
- Department of Biology, College of Wooster, Wooster, Ohio
| | - Ernesto Maldonado
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Joshua B Gross
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio
| | - Reed A Cartwright
- The Biodesign Institute, Arizona State University, Tempe, Arizona.,School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri.,Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, Kansas
| | - Wesley C Warren
- McDonnell Genome Institute, Washington University, St Louis, Missouri
| | - Suzanne E McGaugh
- Department of Molecular Biology, Rudjer Boskovic Institute, Zagreb, Croatia
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10
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Kono TJY, Lei L, Shih CH, Hoffman PJ, Morrell PL, Fay JC. Comparative Genomics Approaches Accurately Predict Deleterious Variants in Plants. G3 (Bethesda) 2018; 8:3321-3329. [PMID: 30139765 PMCID: PMC6169392 DOI: 10.1534/g3.118.200563] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 08/10/2018] [Indexed: 12/11/2022]
Abstract
Recent advances in genome resequencing have led to increased interest in prediction of the functional consequences of genetic variants. Variants at phylogenetically conserved sites are of particular interest, because they are more likely than variants at phylogenetically variable sites to have deleterious effects on fitness and contribute to phenotypic variation. Numerous comparative genomic approaches have been developed to predict deleterious variants, but the approaches are nearly always assessed based on their ability to identify known disease-causing mutations in humans. Determining the accuracy of deleterious variant predictions in nonhuman species is important to understanding evolution, domestication, and potentially to improving crop quality and yield. To examine our ability to predict deleterious variants in plants we generated a curated database of 2,910 Arabidopsis thaliana mutants with known phenotypes. We evaluated seven approaches and found that while all performed well, their relative ranking differed from prior benchmarks in humans. We conclude that deleterious mutations can be reliably predicted in A. thaliana and likely other plant species, but that the relative performance of various approaches does not necessarily translate from one species to another.
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Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Li Lei
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Ching-Hua Shih
- Department of Genetics, Washington University, St. Louis, MO 63110
| | - Paul J Hoffman
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Peter L Morrell
- Department of Agronomy & Plant Genetics, University of Minnesota, St. Paul, MN 551085
| | - Justin C Fay
- Department of Genetics, Washington University, St. Louis, MO 63110
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11
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Brohammer AB, Kono TJY, Springer NM, McGaugh SE, Hirsch CN. The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines. Plant J 2018; 93:131-141. [PMID: 29124819 DOI: 10.1111/tpj.13765] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/14/2017] [Accepted: 10/27/2017] [Indexed: 05/22/2023]
Abstract
Maize is a diverse paleotetraploid species with considerable presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization. Differential fractionation refers to non-shared gene loss events between individuals following a whole-genome duplication event. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole-genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variably fractionated syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non-syntenic genes were six times more likely to be variable than syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large-scale presence/absence variation among syntenic genes.
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Affiliation(s)
- Alex B Brohammer
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
| | - Nathan M Springer
- Department of Plant and Microbial Biology, University of Minnesota, 1445 Gortner Avenue, St Paul, MN, 55108, USA
| | - Suzanne E McGaugh
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 1987 Upper Buford Circle, St Paul, MN, 55108, USA
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
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12
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Čermák T, Curtin SJ, Gil-Humanes J, Čegan R, Kono TJY, Konečná E, Belanto JJ, Starker CG, Mathre JW, Greenstein RL, Voytas DF. A Multipurpose Toolkit to Enable Advanced Genome Engineering in Plants. Plant Cell 2017; 29:1196-1217. [PMID: 28522548 PMCID: PMC5502448 DOI: 10.1105/tpc.16.00922] [Citation(s) in RCA: 331] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/25/2017] [Accepted: 05/16/2017] [Indexed: 05/18/2023]
Abstract
We report a comprehensive toolkit that enables targeted, specific modification of monocot and dicot genomes using a variety of genome engineering approaches. Our reagents, based on transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, are systematized for fast, modular cloning and accommodate diverse regulatory sequences to drive reagent expression. Vectors are optimized to create either single or multiple gene knockouts and large chromosomal deletions. Moreover, integration of geminivirus-based vectors enables precise gene editing through homologous recombination. Regulation of transcription is also possible. A Web-based tool streamlines vector selection and construction. One advantage of our platform is the use of the Csy-type (CRISPR system yersinia) ribonuclease 4 (Csy4) and tRNA processing enzymes to simultaneously express multiple guide RNAs (gRNAs). For example, we demonstrate targeted deletions in up to six genes by expressing 12 gRNAs from a single transcript. Csy4 and tRNA expression systems are almost twice as effective in inducing mutations as gRNAs expressed from individual RNA polymerase III promoters. Mutagenesis can be further enhanced 2.5-fold by incorporating the Trex2 exonuclease. Finally, we demonstrate that Cas9 nickases induce gene targeting at frequencies comparable to native Cas9 when they are delivered on geminivirus replicons. The reagents have been successfully validated in tomato (Solanum lycopersicum), tobacco (Nicotiana tabacum), Medicago truncatula, wheat (Triticum aestivum), and barley (Hordeum vulgare).
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Affiliation(s)
- Tomáš Čermák
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Shaun J Curtin
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Javier Gil-Humanes
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics of the CAS, CZ-61265 Brno, Czech Republic
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Eva Konečná
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Joseph J Belanto
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Colby G Starker
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Jade W Mathre
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Rebecca L Greenstein
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
| | - Daniel F Voytas
- Department of Genetics, Cell Biology, and Development and Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota 55455
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13
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Abstract
Populations continually incur new mutations with fitness effects ranging from lethal to adaptive. While the distribution of fitness effects of new mutations is not directly observable, many mutations likely either have no effect on organismal fitness or are deleterious. Historically, it has been hypothesized that a population may carry many mildly deleterious variants as segregating variation, which reduces the mean absolute fitness of the population. Recent advances in sequencing technology and sequence conservation-based metrics for inferring the functional effect of a variant permit examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding allows deleterious variants to persist and reach moderate frequency, potentially reducing crop productivity. In this study, we use exome resequencing of 15 barley accessions and genome resequencing of 8 soybean accessions to investigate the prevalence of deleterious single nucleotide polymorphisms (SNPs) in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach identifies known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also report the implementation of a SNP annotation tool BAD_Mutations that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.
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Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Mohsen Mohammadi
- Department of Agronomy and Plant Genetics, University of Minnesota Department of Agronomy, Purdue University
| | - Paul J Hoffman
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota
| | - Peter Tiffin
- Department of Plant Biology, University of Minnesota
| | | | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota
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14
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Campbell BW, Hofstad AN, Sreekanta S, Fu F, Kono TJY, O'Rourke JA, Vance CP, Muehlbauer GJ, Stupar RM. Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes. Theor Appl Genet 2016; 129:1725-38. [PMID: 27282876 PMCID: PMC4983299 DOI: 10.1007/s00122-016-2735-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/28/2016] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Three adjacent and distinct sequence rearrangements were identified at a NAP1 locus in a soybean mutant. Genetic dissection and validation revealed the function of this gene in soybean trichome development. A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequencing-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that co-segregated with the phenotype. Comparative genomic hybridization analysis of the mutant indicated that the chromosome 20 interval included a small structural variant within the coding region of a soybean ortholog (Glyma.20G019300) of Arabidopsis Nck-Associated Protein 1 (NAP1), a regulator of actin nucleation during trichome morphogenesis. Sequence analysis of the candidate allele revealed multiple rearrangements within the coding region, including two deletions (approximately 1-2 kb each), a translocation, and an inversion. Further analyses revealed that the mutant allele perfectly co-segregated with the phenotype, and a wild-type soybean NAP1 transgene functionally complemented an Arabidopsis nap1 mutant. In addition, mapping and exon sequencing of NAP1 in a spontaneous soybean gnarled trichome mutant (T31) identified a frame shift mutation resulting in a truncation of the coding region. These data indicate that the soybean NAP1 gene is essential for proper trichome development and show the utility of the soybean fast neutron population for forward genetic approaches for identifying genes.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Anna N Hofstad
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Suma Sreekanta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jamie A O'Rourke
- USDA-ARS, Corn Insects and Crop Genetics Research, Iowa State University, Ames, IA, 50011, USA
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
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15
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Durvasula A, Hoffman PJ, Kent TV, Liu C, Kono TJY, Morrell PL, Ross-Ibarra J. angsd-wrapper: utilities for analysing next-generation sequencing data. Mol Ecol Resour 2016; 16:1449-1454. [PMID: 27480660 DOI: 10.1111/1755-0998.12578] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/30/2016] [Accepted: 06/23/2016] [Indexed: 11/26/2022]
Abstract
High-throughput sequencing has changed many aspects of population genetics, molecular ecology and related fields, affecting both experimental design and data analysis. The software package angsd allows users to perform a number of population genetic analyses on high-throughput sequencing data. angsd uses probabilistic approaches which can directly make use of genotype likelihoods; thus, SNP calling is not required for comparative analyses. This takes advantage of all the sequencing data and produces more accurate results for samples with low sequencing depth. Here, we present angsd-wrapper, a set of wrapper scripts that provides a user-friendly interface for running angsd and visualizing results. angsd-wrapper supports multiple types of analyses including estimates of nucleotide sequence diversity neutrality tests, principal component analysis, estimation of admixture proportions for individual samples and calculation of statistics that quantify recent introgression. angsd-wrapper also provides interactive graphing of angsd results to enhance data exploration. We demonstrate the usefulness of angsd-wrapper by analysing resequencing data from populations of wild and domesticated Zea. angsd-wrapper is freely available from https://github.com/mojaveazure/angsd-wrapper.
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Affiliation(s)
- Arun Durvasula
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Paul J Hoffman
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Tyler V Kent
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
| | - Jeffrey Ross-Ibarra
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA. .,Center for Population Biology and Genome Center, University of California, Davis, Davis, CA, 95616, USA.
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16
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Nice LM, Steffenson BJ, Brown-Guedira GL, Akhunov ED, Liu C, Kono TJY, Morrell PL, Blake TK, Horsley RD, Smith KP, Muehlbauer GJ. Development and Genetic Characterization of an Advanced Backcross-Nested Association Mapping (AB-NAM) Population of Wild × Cultivated Barley. Genetics 2016; 203:1453-67. [PMID: 27182953 PMCID: PMC4937491 DOI: 10.1534/genetics.116.190736] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/02/2016] [Indexed: 12/29/2022] Open
Abstract
The ability to access alleles from unadapted germplasm collections is a long-standing problem for geneticists and breeders. Here we developed, characterized, and demonstrated the utility of a wild barley advanced backcross-nested association mapping (AB-NAM) population. We developed this population by backcrossing 25 wild barley accessions to the six-rowed malting barley cultivar Rasmusson. The 25 wild barley parents were selected from the 318 accession Wild Barley Diversity Collection (WBDC) to maximize allelic diversity. The resulting 796 BC2F4:6 lines were genotyped with 384 SNP markers, and an additional 4022 SNPs and 263,531 sequence variants were imputed onto the population using 9K iSelect SNP genotypes and exome capture sequence of the parents, respectively. On average, 96% of each wild parent was introgressed into the Rasmusson background, and the population exhibited low population structure. While linkage disequilibrium (LD) decay (r(2) = 0.2) was lowest in the WBDC (0.36 cM), the AB-NAM (9.2 cM) exhibited more rapid LD decay than comparable advanced backcross (28.6 cM) and recombinant inbred line (32.3 cM) populations. Three qualitative traits: glossy spike, glossy sheath, and black hull color were mapped with high resolution to loci corresponding to known barley mutants for these traits. Additionally, a total of 10 QTL were identified for grain protein content. The combination of low LD, negligible population structure, and high diversity in an adapted background make the AB-NAM an important tool for high-resolution gene mapping and discovery of novel allelic variation using wild barley germplasm.
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Affiliation(s)
- Liana M Nice
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108
| | - Gina L Brown-Guedira
- United States Department of Agriculture-Agricultural Research Service, North Carolina State University, Raleigh, North Carolina 27607
| | - Eduard D Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
| | - Chaochih Liu
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Thomas K Blake
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717
| | - Richard D Horsley
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58108
| | - Kevin P Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
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17
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Anderson JE, Michno JM, Kono TJY, Stec AO, Campbell BW, Curtin SJ, Stupar RM. Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants. BMC Biotechnol 2016; 16:41. [PMID: 27176220 PMCID: PMC4866027 DOI: 10.1186/s12896-016-0271-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/04/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The safety of mutagenized and genetically transformed plants remains a subject of scrutiny. Data gathered and communicated on the phenotypic and molecular variation induced by gene transfer technologies will provide a scientific-based means to rationally address such concerns. In this study, genomic structural variation (e.g. large deletions and duplications) and single nucleotide polymorphism rates were assessed among a sample of soybean cultivars, fast neutron-derived mutants, and five genetically transformed plants developed through Agrobacterium based transformation methods. RESULTS On average, the number of genes affected by structural variations in transgenic plants was one order of magnitude less than that of fast neutron mutants and two orders of magnitude less than the rates observed between cultivars. Structural variants in transgenic plants, while rare, occurred adjacent to the transgenes, and at unlinked loci on different chromosomes. DNA repair junctions at both transgenic and unlinked sites were consistent with sequence microhomology across breakpoints. The single nucleotide substitution rates were modest in both fast neutron and transformed plants, exhibiting fewer than 100 substitutions genome-wide, while inter-cultivar comparisons identified over one-million single nucleotide polymorphisms. CONCLUSIONS Overall, these patterns provide a fresh perspective on the genomic variation associated with high-energy induced mutagenesis and genetically transformed plants. The genetic transformation process infrequently results in novel genetic variation and these rare events are analogous to genetic variants occurring spontaneously, already present in the existing germplasm, or induced through other types of mutagenesis. It remains unclear how broadly these results can be applied to other crops or transformation methods.
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Affiliation(s)
- Justin E Anderson
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Jean-Michel Michno
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Adrian O Stec
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Benjamin W Campbell
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA
| | - Robert M Stupar
- Department of Agronomy & Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, 411 Borlaug Hall, St. Paul, MN 55108, USA.
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18
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Anderson JE, Kono TJY, Stupar RM, Kantar MB, Morrell PL. Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans. G3 (Bethesda) 2016; 6:835-43. [PMID: 26818076 PMCID: PMC4825654 DOI: 10.1534/g3.116.026914] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/22/2016] [Indexed: 01/04/2023]
Abstract
Natural populations across a species range demonstrate population structure owing to neutral processes such as localized origins of mutations and migration limitations. Selection also acts on a subset of loci, contributing to local adaptation. An understanding of the genetic basis of adaptation to local environmental conditions is a fundamental goal in basic biological research. When applied to crop wild relatives, this same research provides the opportunity to identify adaptive genetic variation that may be used to breed for crops better adapted to novel or changing environments. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses. The identification of potentially adaptive variants in this ex situ collection may permit a more targeted use of germplasm collections.
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Affiliation(s)
- Justin E Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Michael B Kantar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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19
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Kono TJY, Seth K, Poland JA, Morrell PL. SNPMeta: SNP annotation and SNP metadata collection without a reference genome. Mol Ecol Resour 2013; 14:419-25. [PMID: 24237904 DOI: 10.1111/1755-0998.12183] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 08/26/2013] [Accepted: 09/06/2013] [Indexed: 11/28/2022]
Abstract
The increase in availability of resequencing data is greatly accelerating SNP discovery and has facilitated the development of SNP genotyping assays. This, in turn, is increasing interest in annotation of individual SNPs. Currently, these data are only available through curation, or comparison to a reference genome. Many species lack a reference genome, but are still important genetic models or are significant species in agricultural production or natural ecosystems. For these species, it is possible to annotate SNPs through comparison with cDNA, or data from well-annotated genes in public repositories. We present SNPMeta, a tool which gathers information about SNPs by comparison with sequences present in GenBank databases. SNPMeta is able to annotate SNPs from contextual sequence in SNP assay designs, and SNPs discovered through genotyping by sequencing (GBS) approaches. However, SNPs discovered through GBS occur throughout the genome, rather than only in gene space, and therefore do not annotate at high rates. SNPMeta can therefore be used to annotate SNPs in nonmodel species or species that lack a reference genome. Annotations generated by SNPMeta are highly concordant with annotations that would be obtained from a reference genome.
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Affiliation(s)
- Thomas J Y Kono
- Department of Agronomy & Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
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