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Calleja-Rodriguez A, Pan J, Funda T, Chen Z, Baison J, Isik F, Abrahamsson S, Wu HX. Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine. BMC Genomics 2020; 21:796. [PMID: 33198692 PMCID: PMC7667760 DOI: 10.1186/s12864-020-07188-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots pine (Pinus sylvestris L.), a genomic prediction study was conducted with 694 individuals representing 183 full-sib families that were genotyped with genotyping-by-sequencing (GBS) and phenotyped for growth and wood quality traits. 8719 SNPs were used to compare different genomic with pedigree prediction models. Additionally, four prediction efficiency methods were used to evaluate the impact of genomic breeding value estimations by assigning diverse ratios of training and validation sets, as well as several subsets of SNP markers. RESULTS Genomic Best Linear Unbiased Prediction (GBLUP) and Bayesian Ridge Regression (BRR) combined with expectation maximization (EM) imputation algorithm showed slightly higher prediction efficiencies than Pedigree Best Linear Unbiased Prediction (PBLUP) and Bayesian LASSO, with some exceptions. A subset of approximately 6000 SNP markers, was enough to provide similar prediction efficiencies as the full set of 8719 markers. Additionally, prediction efficiencies of genomic models were enough to achieve a higher selection response, that varied between 50-143% higher than the traditional pedigree-based selection. CONCLUSIONS Although prediction efficiencies were similar for genomic and pedigree models, the relative selection response was doubled for genomic models by assuming that earlier selections can be done at the seedling stage, reducing the progeny testing time, thus shortening the breeding cycle length roughly by 50%.
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Affiliation(s)
- Ainhoa Calleja-Rodriguez
- Skogforsk (The Forestry Research Institute of Sweden), Box 3, Sävar, SE 918 21 Sweden
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
| | - Jin Pan
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
| | - Tomas Funda
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
- Department of Genetics and Breeding, Faculty of Agrobiology and Natural Resources, Czech University of Life Sciences Prague, Prague, 165 00 Czech Republic
- Key Laboratory of Forest Genetics and Biotechnology, Nanjing Forestry University, Nanjing, 210037 China
| | - Zhiqiang Chen
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
| | - John Baison
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
- RAGT Seeds, Essex, CB 101TA United Kingdom
| | - Fikret Isik
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695 USA
| | - Sara Abrahamsson
- Skogforsk (The Forestry Research Institute of Sweden), Box 3, Sävar, SE 918 21 Sweden
| | - Harry X. Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, SE - 901 83 Sweden
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, 100083 China
- National Research Collection Australia, CSIRO, Canberra, ACT 2601 Australia
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Xu Y, Liu X, Fu J, Wang H, Wang J, Huang C, Prasanna BM, Olsen MS, Wang G, Zhang A. Enhancing Genetic Gain through Genomic Selection: From Livestock to Plants. PLANT COMMUNICATIONS 2020; 1:100005. [PMID: 33404534 PMCID: PMC7747995 DOI: 10.1016/j.xplc.2019.100005] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Although long-term genetic gain has been achieved through increasing use of modern breeding methods and technologies, the rate of genetic gain needs to be accelerated to meet humanity's demand for agricultural products. In this regard, genomic selection (GS) has been considered most promising for genetic improvement of the complex traits controlled by many genes each with minor effects. Livestock scientists pioneered GS application largely due to livestock's significantly higher individual values and the greater reduction in generation interval that can be achieved in GS. Large-scale application of GS in plants can be achieved by refining field management to improve heritability estimation and prediction accuracy and developing optimum GS models with the consideration of genotype-by-environment interaction and non-additive effects, along with significant cost reduction. Moreover, it would be more effective to integrate GS with other breeding tools and platforms for accelerating the breeding process and thereby further enhancing genetic gain. In addition, establishing an open-source breeding network and developing transdisciplinary approaches would be essential in enhancing breeding efficiency for small- and medium-sized enterprises and agricultural research systems in developing countries. New strategies centered on GS for enhancing genetic gain need to be developed.
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Affiliation(s)
- Yunbi Xu
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- CIMMYT-China Tropical Maize Research Center, Foshan University, Foshan 528231, China
- CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai 201400, China
| | - Xiaogang Liu
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junjie Fu
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hongwu Wang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiankang Wang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Changling Huang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Boddupalli M. Prasanna
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Michael S. Olsen
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Guoying Wang
- Institute of Crop Science/CIMMYT-China, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Aimin Zhang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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Lu M, Krutovsky KV, Nelson CD, Koralewski TE, Byram TD, Loopstra CA. Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.). BMC Genomics 2016; 17:730. [PMID: 27624183 PMCID: PMC5022155 DOI: 10.1186/s12864-016-3081-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/09/2016] [Indexed: 01/06/2023] Open
Abstract
Background Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated single nucleotide polymorphisms (SNPs) and to genotype the sampled trees. Results The exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723 exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 % of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were located in coding regions (CDS), 5 % in 5’ or 3’ untranslated regions (UTRs) and 42 % in non-target and non-coding regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD) decayed very rapidly, with the correlation coefficient (r2) between pairs of SNPs linked within single scaffolds decaying to half maximum (r2 = 0.22) within 55 bp, to r2 = 0.1 within 192 bp, and to r2 = 0.05 within 451 bp. Population structure analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and eastern parts of the loblolly pine range included in our sample of trees. Conclusions The obtained results demonstrated the efficiency of exome capture for genotyping species such as loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a valuable resource for future genetic and genomic research in loblolly pine. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3081-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mengmeng Lu
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
| | - Konstantin V Krutovsky
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA. .,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA. .,Department of Forest Genetics and Forest Tree Breeding, Georg-August-University of Göttingen, Göttingen, 37077, Germany. .,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina Str, Moscow, 119333, Russia. .,Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk, 660036, Russia.
| | - C Dana Nelson
- USDA Forest Service, Southern Research Station, Southern Institute of Forest Genetics, 23332 Success Road, Saucier, MS, 39574, USA.,University of Kentucky, Forest Health Research and Education Center, 730 Rose Street, Lexington, KY, 40546, USA
| | - Tomasz E Koralewski
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA
| | - Thomas D Byram
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Texas A&M Forest Service, 2585 TAMU, College Station, TX, 77843-2585, USA
| | - Carol A Loopstra
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX, 77843-2138, USA.,Molecular and Environmental Plant Sciences Program, Texas A&M University, 2474 TAMU, College Station, TX, 77843-2474, USA
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Kole C, Muthamilarasan M, Henry R, Edwards D, Sharma R, Abberton M, Batley J, Bentley A, Blakeney M, Bryant J, Cai H, Cakir M, Cseke LJ, Cockram J, de Oliveira AC, De Pace C, Dempewolf H, Ellison S, Gepts P, Greenland A, Hall A, Hori K, Hughes S, Humphreys MW, Iorizzo M, Ismail AM, Marshall A, Mayes S, Nguyen HT, Ogbonnaya FC, Ortiz R, Paterson AH, Simon PW, Tohme J, Tuberosa R, Valliyodan B, Varshney RK, Wullschleger SD, Yano M, Prasad M. Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects. FRONTIERS IN PLANT SCIENCE 2015; 6:563. [PMID: 26322050 PMCID: PMC4531421 DOI: 10.3389/fpls.2015.00563] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/08/2015] [Indexed: 05/19/2023]
Abstract
Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of QueenslandSt Lucia, QLD, Australia
| | - David Edwards
- School of Agriculture and Food Sciences, University of QueenslandBrisbane, QLD, Australia
| | - Rishu Sharma
- Department of Plant Pathology, Faculty of Agriculture, Bidhan Chandra Krishi ViswavidyalayaMohanpur, India
| | - Michael Abberton
- Genetic Resources Centre, International Institute of Tropical AgricultureIbadan, Nigeria
| | - Jacqueline Batley
- Centre for Integrated Legume Research, University of QueenslandBrisbane, QLD, Australia
| | - Alison Bentley
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - John Bryant
- CLES, Hatherly Laboratories, University of ExeterExeter, UK
| | - Hongwei Cai
- Forage Crop Research Institute, Japan Grassland Agriculture and Forage Seed AssociationNasushiobara, Japan
- Department of Plant Genetics and Breeding, College of Agronomy and Biotechnology, China Agricultural UniversityBeijing, China
| | - Mehmet Cakir
- Faculty of Science and Engineering, School of Biological Sciences and Biotechnology, Murdoch UniversityMurdoch, WA, Australia
| | - Leland J. Cseke
- Department of Biological Sciences, The University of Alabama in HuntsvilleHuntsville, AL, USA
| | - James Cockram
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | | | - Ciro De Pace
- Department of Agriculture, Forests, Nature and Energy, University of TusciaViterbo, Italy
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten NationenBonn, Germany
| | - Shelby Ellison
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | - Paul Gepts
- Section of Crop and Ecosystem Sciences, Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Andy Greenland
- The John Bingham Laboratory, National Institute of Agricultural BotanyCambridge, UK
| | - Anthony Hall
- Department of Botany and Plant Sciences, University of CaliforniaRiverside, Riverside, USA
| | - Kiyosumi Hori
- Agrogenomics Research Center, National Institute of Agrobiological SciencesTsukuba, Japan
| | | | - Mike W. Humphreys
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Massimo Iorizzo
- Department of Horticulture, University of WisconsinMadison, WI, USA
| | | | - Athole Marshall
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityWales, UK
| | - Sean Mayes
- Biotechnology and Crop Genetics, Crops for the FutureSemenyih, Malaysia
| | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesSundvagen, Sweden
| | | | - Philipp W. Simon
- Department of Horticulture, USDA-ARS, University of WisconsinMadison, WI, USA
| | - Joe Tohme
- Agrobiodiversity and Biotechnology Project, Centro International de Agricultura TropicalCali, Columbia
| | | | - Babu Valliyodan
- National Center for Soybean Biotechnology and Division of Plant Science, University of MissouriColumbia, MO, USA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics, International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Stan D. Wullschleger
- Oak Ridge National Laboratory, Environmental Sciences Division, Climate Change Science InstituteOak Ridge, TN, USA
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop ScienceTsukuba, Japan
| | - Manoj Prasad
- Department of Plant Molecular Genetics and Genomics, National Institute of Plant Genome ResearchNew Delhi, India
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5
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Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One 2014; 9:e90581. [PMID: 24599324 PMCID: PMC3944147 DOI: 10.1371/journal.pone.0090581] [Citation(s) in RCA: 177] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/31/2014] [Indexed: 12/21/2022] Open
Abstract
MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).
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Affiliation(s)
- Wan-Ping Lee
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Michael P. Stromberg
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Alistair Ward
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Chip Stewart
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Erik P. Garrison
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Gabor T. Marth
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
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6
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Lee WP, Stromberg MP, Ward A, Stewart C, Garrison EP, Marth GT. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PLoS One 2014; 9:e90581. [PMID: 24599324 DOI: 10.1371/journal.pone.009058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/31/2014] [Indexed: 05/27/2023] Open
Abstract
MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies, including Illumina, Applied Biosystems SOLiD, Roche 454, Ion Torrent and Pacific BioSciences SMRT. Indeed, MOSAIK was the only aligner to provide consistent mappings for all the generated data (sequencing technologies, low-coverage and exome) in the 1000 Genomes Project. To provide highly accurate alignments, MOSAIK employs a hash clustering strategy coupled with the Smith-Waterman algorithm. This method is well-suited to capture mismatches as well as short insertions and deletions. To support the growing interest in larger structural variant (SV) discovery, MOSAIK provides explicit support for handling known-sequence SVs, e.g. mobile element insertions (MEIs) as well as generating outputs tailored to aid in SV discovery. All variant discovery benefits from an accurate description of the read placement confidence. To this end, MOSAIK uses a neural-network based training scheme to provide well-calibrated mapping quality scores, demonstrated by a correlation coefficient between MOSAIK assigned and actual mapping qualities greater than 0.98. In order to ensure that studies of any genome are supported, a training pipeline is provided to ensure optimal mapping quality scores for the genome under investigation. MOSAIK is multi-threaded, open source, and incorporated into our command and pipeline launcher system GKNO (http://gkno.me).
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Affiliation(s)
- Wan-Ping Lee
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Michael P Stromberg
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Alistair Ward
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Chip Stewart
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America; Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Erik P Garrison
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
| | - Gabor T Marth
- Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America
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