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Achakkagari SR, Kyriakidou M, Gardner KM, De Koeyer D, De Jong H, Strömvik MV, Tai HH. Genome sequencing of adapted diploid potato clones. Front Plant Sci 2022; 13:954933. [PMID: 36003817 PMCID: PMC9394749 DOI: 10.3389/fpls.2022.954933] [Citation(s) in RCA: 1] [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] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Cultivated potato is a vegetatively propagated crop, and most varieties are autotetraploid with high levels of heterozygosity. Reducing the ploidy and breeding potato at the diploid level can increase efficiency for genetic improvement including greater ease of introgression of diploid wild relatives and more efficient use of genomics and markers in selection. More recently, selfing of diploids for generation of inbred lines for F1 hybrid breeding has had a lot of attention in potato. The current study provides genomics resources for nine legacy non-inbred adapted diploid potato clones developed at Agriculture and Agri-Food Canada. De novo genome sequence assembly using 10× Genomics and Illumina sequencing technologies show the genome sizes ranged from 712 to 948 Mbp. Structural variation was identified by comparison to two references, the potato DMv6.1 genome and the phased RHv3 genome, and a k-mer based analysis of sequence reads showed the genome heterozygosity range of 1 to 9.04% between clones. A genome-wide approach was taken to scan 5 Mb bins to visualize patterns of heterozygous deleterious alleles. These were found dispersed throughout the genome including regions overlapping segregation distortions. Novel variants of the StCDF1 gene conferring earliness of tuberization were found among these clones, which all produce tubers under long days. The genomes will be useful tools for genome design for potato breeding.
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Affiliation(s)
| | - Maria Kyriakidou
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Kyle M. Gardner
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - David De Koeyer
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Hielke De Jong
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Martina V. Strömvik
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Helen H. Tai
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
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2
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Hoopes G, Meng X, Hamilton JP, Achakkagari SR, de Alves Freitas Guesdes F, Bolger ME, Coombs JJ, Esselink D, Kaiser NR, Kodde L, Kyriakidou M, Lavrijssen B, van Lieshout N, Shereda R, Tuttle HK, Vaillancourt B, Wood JC, de Boer JM, Bornowski N, Bourke P, Douches D, van Eck HJ, Ellis D, Feldman MJ, Gardner KM, Hopman JCP, Jiang J, De Jong WS, Kuhl JC, Novy RG, Oome S, Sathuvalli V, Tan EH, Ursum RA, Vales MI, Vining K, Visser RGF, Vossen J, Yencho GC, Anglin NL, Bachem CWB, Endelman JB, Shannon LM, Strömvik MV, Tai HH, Usadel B, Buell CR, Finkers R. Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol Plant 2022; 15:520-536. [PMID: 35026436 DOI: 10.1016/j.molp.2022.01.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [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: 06/19/2021] [Revised: 10/19/2021] [Accepted: 01/07/2022] [Indexed: 05/11/2023]
Abstract
Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations are predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The StCDF1 locus controls maturity, and analysis of six tetraploid genomes revealed that 12 allelic variants of StCDF1 are correlated with maturity in a dosage-dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.
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Affiliation(s)
- Genevieve Hoopes
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
| | - John P Hamilton
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Sai Reddy Achakkagari
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | | | - Marie E Bolger
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, 52428 Jülich, Germany
| | - Joseph J Coombs
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Danny Esselink
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Natalie R Kaiser
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; Bayer Crop Science, Woodland, CA 95695, USA
| | - Linda Kodde
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Maria Kyriakidou
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Brian Lavrijssen
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Natascha van Lieshout
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Rachel Shereda
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Heather K Tuttle
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
| | | | - Joshua C Wood
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Nolan Bornowski
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Peter Bourke
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - David Douches
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Herman J van Eck
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Dave Ellis
- International Potato Center, 1895 Avenida La Molina, Lima, Peru
| | | | - Kyle M Gardner
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, Fredericton, NB E3B 4Z7, Canada
| | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Walter S De Jong
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-1901, USA
| | - Joseph C Kuhl
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Richard G Novy
- USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, USA
| | - Stan Oome
- HZPC Research B.V., Edisonweg 5, 8501 XG Joure, the Netherlands
| | - Vidyasagar Sathuvalli
- Department of Crop and Soil Science, Oregon State University, Hermiston, OR 97838, USA
| | - Ek Han Tan
- School of Biology and Ecology, University of Maine, 5735 Hitchner Hall Orono, ME 04469, USA
| | - Remco A Ursum
- HZPC Research B.V., Edisonweg 5, 8501 XG Joure, the Netherlands
| | - M Isabel Vales
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-2133, USA
| | - Kelly Vining
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Jack Vossen
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695-7609, USA
| | - Noelle L Anglin
- International Potato Center, 1895 Avenida La Molina, Lima, Peru; USDA-ARS, Small Grains and Potato Germplasm Research, Aberdeen, ID 83210, USA
| | - Christian W B Bachem
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Laura M Shannon
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108, USA
| | - Martina V Strömvik
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Helen H Tai
- Agriculture and Agri-Food Canada Fredericton Research and Development Centre, Fredericton, NB E3B 4Z7, Canada
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, 52428 Jülich, Germany; Institute for Biological Data Science, Heinrich Heine University, Düsseldorf, 40225 Düsseldorf, Germany
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA.
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, Plant Breeding, 6708 PB Wageningen, the Netherlands.
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Migicovsky Z, Gardner KM, Richards C, Thomas Chao C, Schwaninger HR, Fazio G, Zhong GY, Myles S. Genomic consequences of apple improvement. Hortic Res 2021; 8:9. [PMID: 33384408 PMCID: PMC7775473 DOI: 10.1038/s41438-020-00441-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/09/2020] [Indexed: 05/10/2023]
Abstract
The apple (Malus domestica) is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years. Here, we genetically characterise over 1000 apple accessions from the United States Department of Agriculture (USDA) germplasm collection using over 30,000 single-nucleotide polymorphisms (SNPs). We confirm the close genetic relationship between modern apple cultivars and their primary progenitor species, Malus sieversii from Central Asia, and find that cider apples derive more of their ancestry from the European crabapple, Malus sylvestris, than do dessert apples. We determine that most of the USDA collection is a large complex pedigree: over half of the collection is interconnected by a series of first-degree relationships. In addition, 15% of the accessions have a first-degree relationship with one of the top 8 cultivars produced in the USA. With the exception of 'Honeycrisp', the top 8 cultivars are interconnected to each other via pedigree relationships. The cultivars 'Golden Delicious' and 'Red Delicious' were found to have over 60 first-degree relatives, consistent with their repeated use by apple breeders. We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased firmness. Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will benefit from increased exploitation of its tremendous natural genetic diversity.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Kyle M Gardner
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, Fredericton, NB, Canada
| | | | - C Thomas Chao
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, USA
| | | | - Gennaro Fazio
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, USA
| | - Gan-Yuan Zhong
- USDA-ARS, Grape Genetics Research Unit, Geneva, NY, USA.
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
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Larsen B, Migicovsky Z, Jeppesen AA, Gardner KM, Toldam-Andersen TB, Myles S, Ørgaard M, Petersen MA, Pedersen C. Genome-Wide Association Studies in Apple Reveal Loci for Aroma Volatiles, Sugar Composition, and Harvest Date. Plant Genome 2019; 12. [PMID: 31290918 DOI: 10.3835/plantgenome2018.12.0104] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Understanding the genetic architecture of fruit quality traits is crucial to target breeding of apple ( L.) cultivars. We linked genotype and phenotype information by combining genotyping-by-sequencing (GBS) generated single nucleotide polymorphism (SNP) markers with fruit flavor volatile data, sugar and acid content, and historical trait data from a gene bank collection. Using gas chromatography-mass spectrometry (GC-MS) analysis of apple juice samples, we identified 49 fruit volatile organic compounds (VOCs). We found a very variable content of VOCs, especially for the esters, among 149 apple cultivars. We identified convincing associations for the acetate esters especially butyl acetate and hexyl acetate on chromosome 2 in a region of several alcohol acyl-transferases including AAT1. For sucrose content and for fructose and sucrose in percentage of total sugars, we revealed significant SNP associations. Here, we suggest a vacuolar invertase close to significant SNPs for this association as candidate gene. Harvest date was in strong SNP association with a NAC transcription factor gene and sequencing identified two haplotypes associated with harvest date. The study shows that SNP marker characterization of a gene bank collection can be successfully combined with new and historical trait data for association studies. Suggested candidate genes may contribute to an improved understanding of the genetic basis for important traits and simultaneously provide tools for targeted breeding using marker-assisted selection (MAS).
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5
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McClure KA, Gardner KM, Douglas GM, Song J, Forney CF, DeLong J, Fan L, Du L, Toivonen PMA, Somers DJ, Rajcan I, Myles S. A Genome-Wide Association Study of Apple Quality and Scab Resistance. Plant Genome 2018; 11:170075. [PMID: 29505632 DOI: 10.3835/plantgenome2017.08.0075] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The apple ( × Borkh.) is an economically and culturally important crop grown worldwide. Growers of this long-lived perennial must produce fruit of adequate quality while also combatting abiotic and biotic stress. Traditional apple breeding can take up to 20 yr from initial cross to commercial release, but genomics-assisted breeding can help accelerate this process. To advance genomics-assisted breeding in apple, we performed genome-wide association studies (GWAS) and genomic prediction in a collection of 172 apple accessions by linking over 55,000 single nucleotide polymorphisms (SNPs) with 10 phenotypes collected over 2 yr. Genome-wide association studies revealed several known loci for skin color, harvest date and firmness at harvest. Several significant GWAS associations were detected for resistance to a major fungal pathogen, apple scab ( [Cke.] Wint.), but we demonstrate that these hits likely represent a single ancestral source. Using genomic prediction, we show that most phenotypes are sufficiently predictable using genome-wide SNPs to be candidates for genomic selection. Finally, we detect a signal for firmness retention after storage on chromosome 10 and show that it may not stem from variation in , a gene repeatedly identified in bi-parental mapping studies and widely believed to underlie a major QTL for firmness on chromosome 10. We provide evidence that this major QTL is more likely due to variation in a neighboring ethylene response factor (ERF) gene. The present study showcases the superior mapping resolution of GWAS compared to bi-parental linkage mapping by identifying a novel candidate gene underlying a well-studied, major QTL involved in apple firmness.
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6
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Migicovsky Z, Sawler J, Gardner KM, Aradhya MK, Prins BH, Schwaninger HR, Bustamante CD, Buckler ES, Zhong GY, Brown PJ, Myles S. Patterns of genomic and phenomic diversity in wine and table grapes. Hortic Res 2017; 4:17035. [PMID: 28791127 PMCID: PMC5539807 DOI: 10.1038/hortres.2017.35] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/16/2017] [Indexed: 05/18/2023]
Abstract
Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
| | - Jason Sawler
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
- Anandia Labs, Vancouver,
BC
V6T 1Z4, Canada
| | - Kyle M Gardner
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
- Agriculture and Agri-Food Canada, Fredericton
Research and Development Centre, Fredericton, NB,
Canada
E3B 4Z7
| | - Mallikarjuna K Aradhya
- National Clonal Germplasm Repository, United
States Department of Agriculture-Agricultural Research Service, University of
California, Davis, CA
95616, USA
| | - Bernard H Prins
- National Clonal Germplasm Repository, United
States Department of Agriculture-Agricultural Research Service, University of
California, Davis, CA
95616, USA
| | - Heidi R Schwaninger
- United States Department of Agriculture,
Agricultural Research Service, Grape Genetics Research Unit, New York State Agricultural
Experiment Station, Cornell University, Geneva, NY
14456, USA
| | | | - Edward S Buckler
- Department of Plant Breeding and Genetics,
Cornell University, Ithaca, NY
14853, USA
| | - Gan-Yuan Zhong
- United States Department of Agriculture,
Agricultural Research Service, Grape Genetics Research Unit, New York State Agricultural
Experiment Station, Cornell University, Geneva, NY
14456, USA
- United States Department of Agriculture,
Agricultural Research Service, Plant Genetic Resources Unit, New York State Agricultural
Experiment Station, Cornell University, Geneva, NY
14456, USA
| | - Patrick J Brown
- Department of Crop Science, University of
Illinois, Urbana, IL
61801, USA
| | - Sean Myles
- Department of Plant, Food and Environmental
Sciences, Faculty of Agriculture, Dalhousie University, Truro,
NS
B2N 5E3, Canada
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McClure KA, Gardner KM, Toivonen PMA, Hampson CR, Song J, Forney CF, DeLong J, Rajcan I, Myles S. QTL analysis of soft scald in two apple populations. Hortic Res 2016; 3:16043. [PMID: 27651916 PMCID: PMC5022660 DOI: 10.1038/hortres.2016.43] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 08/13/2016] [Accepted: 08/14/2016] [Indexed: 05/29/2023]
Abstract
The apple (Malus×domestica Borkh.) is one of the world's most widely grown and valuable fruit crops. With demand for apples year round, storability has emerged as an important consideration for apple breeding programs. Soft scald is a cold storage-related disorder that results in sunken, darkened tissue on the fruit surface. Apple breeders are keen to generate new cultivars that do not suffer from soft scald and can thus be marketed year round. Traditional breeding approaches are protracted and labor intensive, and therefore marker-assisted selection (MAS) is a valuable tool for breeders. To advance MAS for storage disorders in apple, we used genotyping-by-sequencing (GBS) to generate high-density genetic maps in two F1 apple populations, which were then used for quantitative trait locus (QTL) mapping of soft scald. In total, 900 million DNA sequence reads were generated, but after several data filtering steps, only 2% of reads were ultimately used to create two genetic maps that included 1918 and 2818 single-nucleotide polymorphisms. Two QTL associated with soft scald were identified in one of the bi-parental populations originating from parent 11W-12-11, an advanced breeding line. This study demonstrates the utility of next-generation DNA sequencing technologies for QTL mapping in F1 populations, and provides a basis for the advancement of MAS to improve storability of apples.
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Affiliation(s)
- Kendra A McClure
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia B2N 5E3, Canada
- Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Kyle M Gardner
- Agriculture and Agri-Food Canada, Fredericton Research and Development Centre, Fredericton, New Brunswick E3B 4Z7, Canada
| | - Peter MA Toivonen
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Cheryl R Hampson
- Agriculture and Agri-Food Canada, Summerland Research and Development Centre, Summerland, British Columbia V0H 1Z0, Canada
| | - Jun Song
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, Nova Scotia, Canada B4N 1J5
| | - Charles F Forney
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, Nova Scotia, Canada B4N 1J5
| | - John DeLong
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, Nova Scotia, Canada B4N 1J5
| | - Istvan Rajcan
- Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia B2N 5E3, Canada
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Migicovsky Z, Gardner KM, Money D, Sawler J, Bloom JS, Moffett P, Chao CT, Schwaninger H, Fazio G, Zhong GY, Myles S. Genome to Phenome Mapping in Apple Using Historical Data. Plant Genome 2016; 9. [PMID: 27898813 DOI: 10.3835/plantgenome2015.11.0113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Apple ( X Borkh.) is one of the world's most valuable fruit crops. Its large size and long juvenile phase make it a particularly promising candidate for marker-assisted selection (MAS). However, advances in MAS in apple have been limited by a lack of phenotype and genotype data from sufficiently large samples. To establish genotype-phenotype relationships and advance MAS in apple, we extracted over 24,000 phenotype scores from the USDA-Germplasm Resources Information Network (GRIN) database and linked them with over 8000 single nucleotide polymorphisms (SNPs) from 689 apple accessions from the USDA apple germplasm collection clonally preserved in Geneva, NY. We find significant genetic differentiation between Old World and New World cultivars and demonstrate that the genetic structure of the domesticated apple also reflects the time required for ripening. A genome-wide association study (GWAS) of 36 phenotypes confirms the association between fruit color and the MYB1 locus, and we also report a novel association between the transcription factor, NAC18.1, and harvest date and fruit firmness. We demonstrate that harvest time and fruit size can be predicted with relatively high accuracies ( > 0.46) using genomic prediction. Rapid decay of linkage disequilibrium (LD) in apples means millions of SNPs may be required for well-powered GWAS. However, rapid LD decay also promises to enable extremely high resolution mapping of causal variants, which holds great potential for advancing MAS.
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Sawler J, Stout JM, Gardner KM, Hudson D, Vidmar J, Butler L, Page JE, Myles S. The Genetic Structure of Marijuana and Hemp. PLoS One 2015; 10:e0133292. [PMID: 26308334 PMCID: PMC4550350 DOI: 10.1371/journal.pone.0133292] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 06/25/2015] [Indexed: 11/18/2022] Open
Abstract
Despite its cultivation as a source of food, fibre and medicine, and its global status as the most used illicit drug, the genus Cannabis has an inconclusive taxonomic organization and evolutionary history. Drug types of Cannabis (marijuana), which contain high amounts of the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC), are used for medical purposes and as a recreational drug. Hemp types are grown for the production of seed and fibre, and contain low amounts of THC. Two species or gene pools (C. sativa and C. indica) are widely used in describing the pedigree or appearance of cultivated Cannabis plants. Using 14,031 single-nucleotide polymorphisms (SNPs) genotyped in 81 marijuana and 43 hemp samples, we show that marijuana and hemp are significantly differentiated at a genome-wide level, demonstrating that the distinction between these populations is not limited to genes underlying THC production. We find a moderate correlation between the genetic structure of marijuana strains and their reported C. sativa and C. indica ancestry and show that marijuana strain names often do not reflect a meaningful genetic identity. We also provide evidence that hemp is genetically more similar to C. indica type marijuana than to C. sativa strains.
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Affiliation(s)
- Jason Sawler
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada
- Anandia Labs, 2259 Lower Mall, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Jake M. Stout
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Kyle M. Gardner
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada
| | - Darryl Hudson
- The DOC Solutions, 213 West 32nd St, Hamilton, Ontario, L9C 5H3, Canada
| | - John Vidmar
- Alberta Innovates-Technology Futures, P.O. Bag 4000, Vegreville, Alberta, T9C 1T4, Canada
| | - Laura Butler
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada
| | - Jonathan E. Page
- Anandia Labs, 2259 Lower Mall, Vancouver, British Columbia, V6T 1Z4, Canada
- Botany Department, University of British Columbia, #3529–6270 University Blvd, Vancouver, British Columbia, V6T 1Z4, Canada
- * E-mail: (JEP); (SM)
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada
- * E-mail: (JEP); (SM)
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10
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Abstract
Perennial crops represent important fresh and processed food sources worldwide, but advancements in breeding perennials are often impeded due to their very nature. The perennial crops we rely on most for food take several years to reach production maturity and require large spaces to grow, which make breeding new cultivars costly compared with most annual crops. Because breeding perennials is inefficient and expensive, they are often grown in monocultures consisting of small numbers of elite cultivars that are vegetatively propagated for decades or even centuries. This practice puts many perennial crops at risk for calamity since they remain stationary in the face of evolving pest and disease pressures. Although there is tremendous genetic diversity available to them, perennial crop breeders often struggle to generate commercially successful cultivars in a timely and cost-effective manner because of the high costs of breeding. Moreover, consumers often expect the same cultivars to be available indefinitely, and there is often little or no incentive for growers and retailers to take the risk of adopting new cultivars. While genomics studies linking DNA variants to commercially important traits have been performed in diverse perennial crops, the translation of these studies into accelerated breeding of improved cultivars has been limited. Here we explain the "perennial problem" in detail and demonstrate how modern genomics tools can significantly improve the cost effectiveness of breeding perennial crops and thereby prevent crucial food sources from succumbing to the perils of perpetual propagation.
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Affiliation(s)
- Kendra A McClure
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Jason Sawler
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Kyle M Gardner
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Daniel Money
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
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11
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Oliver RE, Tinker NA, Lazo GR, Chao S, Jellen EN, Carson ML, Rines HW, Obert DE, Lutz JD, Shackelford I, Korol AB, Wight CP, Gardner KM, Hattori J, Beattie AD, Bjørnstad Å, Bonman JM, Jannink JL, Sorrells ME, Brown-Guedira GL, Mitchell Fetch JW, Harrison SA, Howarth CJ, Ibrahim A, Kolb FL, McMullen MS, Murphy JP, Ohm HW, Rossnagel BG, Yan W, Miclaus KJ, Hiller J, Maughan PJ, Redman Hulse RR, Anderson JM, Islamovic E, Jackson EW. SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species. PLoS One 2013; 8:e58068. [PMID: 23533580 PMCID: PMC3606164 DOI: 10.1371/journal.pone.0058068] [Citation(s) in RCA: 65] [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: 10/17/2012] [Accepted: 01/30/2013] [Indexed: 11/19/2022] Open
Abstract
A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources.
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Affiliation(s)
- Rebekah E. Oliver
- General Mills Crop Biosciences, Kannapolis, North Carolina, United States of America
| | - Nicholas A. Tinker
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- * E-mail:
| | - Gerard R. Lazo
- Western Regional Research Center, Genomics and Gene Discovery, United States Department of Agriculture - Agricultural Research Service, Albany, California, United States of America
| | - Shiaoman Chao
- Biosciences Research Lab, United States Department of Agriculture - Agricultural Research Service, Fargo, North Dakota, United States of America
| | - Eric N. Jellen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Martin L. Carson
- Cereal Disease Laboratory, United States Department of Agriculture - Agricultural Research Service, Saint Paul, Minnesota, United States of America
| | - Howard W. Rines
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Donald E. Obert
- Limagrain Cereal Seeds, Lafayette, Indiana, United States of America
| | - Joseph D. Lutz
- General Mills Crop Biosciences, Kannapolis, North Carolina, United States of America
| | - Irene Shackelford
- Small Grains and Potato Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service, Aberdeen, Idaho, United States of America
| | - Abraham B. Korol
- Department of Evolutionary and Environmental Biology and Institute of Evolution, University of Haifa, Haifa, Israel
| | - Charlene P. Wight
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Kyle M. Gardner
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jiro Hattori
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Aaron D. Beattie
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Åsmund Bjørnstad
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - J. Michael Bonman
- Small Grains and Potato Germplasm Research Unit, United States Department of Agriculture - Agricultural Research Service, Aberdeen, Idaho, United States of America
| | - Jean-Luc Jannink
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture - Agricultural Research Service, Ithaca, New York, United States of America
| | - Mark E. Sorrells
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Gina L. Brown-Guedira
- Eastern Regional Small Grains Genotyping Laboratory, North Carolina State University, United States Department of Agriculture - Agricultural Research Service, Raleigh, North Carolina, United States of America
| | | | - Stephen A. Harrison
- School of Plant, Environmental and Soil Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Catherine J. Howarth
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion, United Kingdom
| | - Amir Ibrahim
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Frederic L. Kolb
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Michael S. McMullen
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - J. Paul Murphy
- Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Herbert W. Ohm
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Brian G. Rossnagel
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Weikai Yan
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Kelci J. Miclaus
- JMP, SAS Institute Incorporated, Cary, North Carolina, United States of America
| | - Jordan Hiller
- JMP, SAS Institute Incorporated, Cary, North Carolina, United States of America
| | - Peter J. Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Rachel R. Redman Hulse
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, Utah, United States of America
| | - Joseph M. Anderson
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Emir Islamovic
- Department of Plant and Environmental Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Eric W. Jackson
- General Mills Crop Biosciences, Kannapolis, North Carolina, United States of America
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12
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Abstract
We applied QTL mapping to fitness variation of Avena barbata under well-watered greenhouse conditions. One hundred eighty recombinant inbred lines were assayed for flowering time, total size, mass allocation, and fitness. Composite Interval Mapping identified two to five loci affecting these traits. These were well supported in more powerful Multiple and Bayesian interval mapping analyses that indicated that additional QTL, as well as epistatic interactions also affect the traits. The posterior distribution of the number of QTL peaked at five to eight additive loci and one to two interactions, but the specific locations of the additional loci could not be determined with certainty. In most cases in which loci for separate traits mapped to similar locations, explicit tests supported pleiotropy over close linkage of separate loci. Alleles that hastened first flowering generally reduced vegetative mass, increased reproductive mass, and were associated with high fitness. Because effects on mass allocation generally cancelled one another, few loci affected total plant size. Only one QTL affected vegetative mass independent of reproductive mass and this locus had little effect on fitness. Thus selection acts to shift the mass allocation toward greater reproductive allocation, because the correlated decrease in vegetative mass poses only a minor fitness cost.
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Affiliation(s)
- Robert G Latta
- Department of Biology, Dalhousie University, Halifax, NS, Canada.
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13
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Abstract
We examined heritable variation for quantitative traits within and between naturally occurring mesic and xeric ecotypes of the slender wild oat (Avena barbata), and in 188 recombinant inbred lines derived from a cross between the ecotypes. We measured a suite of seedling and adult traits in the greenhouse, as well as performance-related traits in field sites native to the two ecotypes. Although the ecotypes were genetically diverged for most traits, few traits showed significant heritable variation within either ecotype. In contrast, considerable heritable variation was released in the recombinant progeny of the cross, and transgressive segregation was apparent in all traits. Heritabilities were substantially greater in the greenhouse than in the field, and this was associated with an increase in environmental variance in the field, rather than a decrease in genetic variance. Strong genetic correlations were evident among the recombinants, such that 22 measured traits could be well represented by only seven underlying factors, which accounted for 80% of the total variation. The primary axis of variation in the greenhouse described a trade-off between vegetative and reproductive allocation, mediated by the date of first flowering, and fitness was strongly correlated with this trade-off. Other factors in the greenhouse described variation in size and in seedling traits. Lack of correlation among these factors represents the release of multivariate trait variation through recombination. In the field, a separate axis of variation in overall performance was found for each year/site combination. Performance was significantly correlated across field environments, but not significantly correlated between greenhouse and field.
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Affiliation(s)
- K M Gardner
- Department of Biology, Dalhousie University, Halifax, NS, Canada
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14
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Abstract
We review genetic correlations among quantitative traits in light of their underlying quantitative trait loci (QTL). We derive an expectation of genetic correlation from the effects of underlying loci and test whether published genetic correlations can be explained by the QTL underlying the traits. While genetically correlated traits shared more QTL (33%) on average than uncorrelated traits (11%), the actual number of shared QTL shared was small. QTL usually predicted the sign of the correlation with good accuracy, but the quantitative prediction was poor. Approximately 25% of trait pairs in the data set had at least one QTL with antagonistic effects. Yet a significant minority (20%) of such trait pairs have net positive genetic correlations due to such antagonistic QTL 'hidden' within positive genetic correlations. We review the evidence on whether shared QTL represent single pleiotropic loci or closely linked monotropic genes, and argue that strict pleiotropy can be viewed as one end of a continuum of recombination rates where r=0. QTL studies of genetic correlation will likely be insufficient to predict evolutionary trajectories over long time spans in large panmictic populations, but will provide important insights into the trade-offs involved in population and species divergence.
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Affiliation(s)
- Kyle M Gardner
- Department of Biology, Dalhousie University, 1355 Oxford Street, Halifax, Nova Scotia, Canada B3H 4J1
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15
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Latta RG, Gardner KM, Johansen-Morris AD. Hybridization, recombination, and the genetic basis of fitness variation across environments in Avena barbata. Genetica 2006; 129:167-77. [PMID: 17006737 DOI: 10.1007/s10709-006-9012-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Accepted: 04/21/2005] [Indexed: 12/01/2022]
Abstract
We created Recombinant Inbred Lines (RILs) derived from a cross between ecotypes of Avena barbata associated with moist (mesic) and dry (xeric) habitats in California. Traits which were correlated with fitness across RILs mapped to the same Quantitative Trait Loci (QTLs) as fitness. However, different QTL affected fitness in different environments so that fitness was weakly correlated across environments. Recombination released considerable heritable variation both in fitness, and in ecologically relevant traits. Many traits showed transgressive segregation caused by recombination of QTL associated in repulsion phase in the parents. In addition, some traits were uncorrelated, allowing novel combinations of those traits to be created. Recombination also created heritable variation in reaction norms for at least one trait (root allocation). Altogether these results suggest that recombination can combine the most selectively advantageous genes and traits of the parents to produce broadly adapted genotypes that are capable of outperforming the parents. Indeed, two of the RILs showed higher fitness than the parental ecotypes across a range of environmental treatments in the greenhouse, but their superiority was less pronounced in the field. Although late-generation recombinants exhibited hybrid breakdown, being less fit, on average, than the mid-parent, early generation hybrids appear to exhibit hybrid vigour through the expression of dominance effects in the heterozyotes. This vigour may offset the effects of hybrid breakdown in the early generations following a cross, enhancing the opportunity for recombination to create broadly adapted genotypes. We discuss the implications of these findings to the evolution of colonizing species.
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Affiliation(s)
- Robert G Latta
- Department of Biology, Dalhousie University, 1355 Oxford St, Halifax, Nova Scotia, Canada, B3H 4J1.
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16
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Abstract
We constructed recombinant inbred lines of a cross between naturally occurring ecotypes of Avena barbata (Pott ex Link), Poaceae, associated with contrasting moisture environments. These lines were assessed for fitness in common garden reciprocal transplant experiments in two contrasting field sites in each of two years, as well as a novel, benign greenhouse environment. An AFLP (amplified fragment length polymorphism) linkage map of 129 markers spanned 644 cM in 19 linkage groups, which is smaller, with more linkage groups, than expected. Therefore parts of the A. barbata genome remain unmapped, possibly because they lack variation between the ecotypes. Nevertheless, we identified QTL (quantitative trait loci) under selection in both native environments and in the greenhouse. Across years at the same site, the same loci remain under selection, for the same alleles. Across sites, an overlapping set of loci are under selection with either (i) the same alleles favoured at both sites or (ii) loci under selection at one site and neutral at the other. QTL under selection in the greenhouse were generally unlinked to those under selection in the field because selection acted on a different trait. We found little evidence that selection favours alternate alleles in alternate environments, which would be necessary if genotype by environment interaction were to maintain genetic variation in A. barbata. Additive effect QTL were best able to explain the genetic variation among recombinant inbred lines for the greenhouse environment where heritability was highest, and past selection had not eliminated variation.
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Affiliation(s)
- Kyle M Gardner
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, Canada B3H 4J1
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17
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Muir KT, Kook KA, Stern C, Gardner KM. Analysis of amiodarone and desethylamiodarone in serum and tears by reversed-phase high-performance liquid chromatography. J Chromatogr 1986; 374:394-9. [PMID: 3958097 DOI: 10.1016/s0378-4347(00)83298-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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18
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Abstract
We compared the distribution of HLA-ABC (class I) and HLA-DR (class II) antigens on fresh human donor corneal tissue, donor corneas following a 72-hour storage in McCarey-Kaufman (M-K) medium, and corneal buttons from patients with allograft rejection and with chronic herpetic stromal keratitis. Incubation in M-K media had little or no effect on the distribution of HLA antigens as compared with fresh tissue. In contrast to control corneas, both HLA class I and II antigens were detected on corneal endothelial cells, cells in the stroma, and on basal epithelial cells in rejected allografts. Corneal endothelium in herpetic buttons did not express detectable HLA antigens. HLA-DR positive Langerhan's cells were demonstrated in the central corneal epithelium of rejected allografts, as well as in herpetic corneas, but not in control corneas except at the limbus. Based upon these observations, a theory of corneal allograft rejection in humans is proposed based upon the induction of class I HLA-ABC and class II HLA-DR antigens on cells in the donor button by a factor(s) associated with cellular inflammation.
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20
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Gardner KM, Straatsma BR, Pettit TH. Neodymium: YAG laser posterior capsulotomy: the first 100 cases at UCLA. Ophthalmic Surg 1985; 16:24-8. [PMID: 3838376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Initial anatomic success was reported in 97 of the first 100 neodymium: YAG laser posterior capsulotomies performed at the Jules Stein Eye Institute. Visual acuity improved in 90 patients, was unchanged in five, and decreased in five. In the five patients with decreased visual acuity after posterior capsulotomy, the decrease was unrelated to capsulotomy and caused by progression of preexisting retinal disease. Our experience suggests that attention to patient evaluation and surgical technique can help minimize complications and assure best results.
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21
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Pepose JS, Nestor MS, Gardner KM, Foos RY, Pettit TH. Composition of cellular infiltrates in rejected human corneal allografts. Graefes Arch Clin Exp Ophthalmol 1985; 222:128-33. [PMID: 3884454 DOI: 10.1007/bf02173536] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We utilized the leu series of monoclonal antibodies and an indirect immunoperoxidase technique to quantitate the cellular infiltrates in seven rejected human corneal allografts and compared them to nine identically processed corneas from patients with chronic herpetic stromal keratitis and to three control corneas. The cellular infiltrates in the rejected allografts were of mixed composition, comprised predominantly of leu-1 positive T-lymphocytes and leu-M3 positive macrophages. Both helper and cytotoxic-suppressor T-cells were identified in the stromal lesions. Statistically significant differences were noted in the absolute number of mononuclear cells and macrophages seen infiltrating the rejected corneal allografts compared to the herpetic corneas. We discuss the implications of these findings with regard to possible mechanisms underlying corneal allograft rejection in man.
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Abstract
Cataract disrupts the crystalline lens, a transparent, elastic, avascular, biconvex structure composed of a capsule, lens epithelium, and lens fiber cells. Many factors contribute to the progression of lens opacity, but aging is most frequently associated with cataract. As aging-related cataract develops, many biochemical and biophysical changes occur, most notably a marked increase in the insolubilization of the crystallin and extensive oxidation damage to many of the lens constituents. Cataract management should include ophthalmologic history and examination, medical evaluation, optical correction, control of ocular and systemic disease that may contribute to cataract, discontinuation of cataractogenic drugs, and periodic reexamination. Surgery is indicated when cataract is associated with vision decrease interfering with activities important to the patient, intraocular inflammation or glaucoma, or interference with management of posterior segment disease. More than 600 000 cataract operations are done in the United States each year; in 1982 an estimated 496 000 cataract operations were combined with intraocular lens implantation.
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Abstract
We use a new model for describing the flexure of hydrogel lenses in situ to evaluate toric hydrogel lenses. The mathematical development of the model precludes use of prism ballasted lenses (because of differential thickness in the vertical meridian and possible lenticulation in the midperiphery), and so double-thin zone lenses were used here. Our results suggest that such lenses (low-minus power) align almost perfectly with the anterior corneal surface creating minimal tear layers.
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Abstract
We have developed a computer program which allows analysis of soft contact lens flexure without assuming a priori that the posterior surface of the lens aligns with the central anterior cornea. Such analysis leads to the conclusion that thin low-minus lenses entrap tear layers of low volume (about 5.5 microliter) and minimum power, whereas low-plus lens systems can develop tear layers of greater volume (about 9.5 microliter), and significant power (about -2.00 D). The later finding supports clinical impressions that plus lenses "lose" power when placed on the eye. In some cases our data suggest that the lens posterior surface closely aligns with the anterior cornea, whereas in other cases such alignment is unlikely. It also appears that mathematical models for the simultaneous flexure of front and back radii of soft lenses may be described for specific lens designs. This current study suggests that delta r2 congruent to 2 delta r1 describes the relation for low-plus lenses, and delta r2 congruent to 0.75 delta r1 is the relation for low-minus lenses.
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Gardner KM, DiDario B, De Voldre B. Toward better control: a medical record department management reporting system. Top Health Rec Manage 1983; 3:53-8. [PMID: 10258909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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