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Migicovsky Z, Douglas GM, Myles S. Genotyping-by-sequencing of Canada’s apple biodiversity collection. Front Genet 2022; 13:934712. [PMID: 36092877 PMCID: PMC9452695 DOI: 10.3389/fgene.2022.934712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Zoë Migicovsky
- Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | | | - Sean Myles
- Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- *Correspondence: Sean Myles,
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2
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Davies T, Watts S, McClure K, Migicovsky Z, Myles S. Phenotypic divergence between the cultivated apple (Malus domestica) and its primary wild progenitor (Malus sieversii). PLoS One 2022; 17:e0250751. [PMID: 35320270 PMCID: PMC8942233 DOI: 10.1371/journal.pone.0250751] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 02/22/2022] [Indexed: 11/18/2022] Open
Abstract
An understanding of the relationship between the cultivated apple (Malus domestica) and its primary wild progenitor species (M. sieversii) not only provides an understanding of how apples have been improved in the past, but may be useful for apple improvement in the future. We measured 10 phenotypes in over 1000 unique apple accessions belonging to M. domestica and M. sieversii from Canada's Apple Biodiversity Collection. Using principal components analysis (PCA), we determined that M. domestica and M. sieversii differ significantly in phenotypic space and are nearly completely distinguishable as two separate groups. We found that M. domestica had a shorter juvenile phase than M. sieversii and that cultivated trees produced flowers and ripe fruit later than their wild progenitors. Cultivated apples were also 3.6 times heavier, 43% less acidic, and had 68% less phenolic content than wild apples. Using historical records, we found that apple breeding over the past 200 years has resulted in a trend towards apples that have higher soluble solids, are less bitter, and soften less during storage. Our results quantify the significant changes in phenotype that have taken place since apple domestication, and provide evidence that apple breeding has led to continued phenotypic divergence of the cultivated apple from its wild progenitor species.
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Affiliation(s)
- Thomas Davies
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Sophie Watts
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Kendra McClure
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Zoë Migicovsky
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- * E-mail:
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3
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Watts S, McElroy M, Migicovsky Z, Maassen H, van Velzen R, Myles S. Cannabis labelling is associated with genetic variation in terpene synthase genes. Nat Plants 2021; 7:1330-1334. [PMID: 34650264 PMCID: PMC8516649 DOI: 10.1038/s41477-021-01003-y] [Citation(s) in RCA: 15] [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: 04/13/2021] [Accepted: 08/03/2021] [Indexed: 05/17/2023]
Abstract
Analysis of over 100 Cannabis samples quantified for terpene and cannabinoid content and genotyped for over 100,000 single nucleotide polymorphisms indicated that Sativa- and Indica-labelled samples were genetically indistinct on a genome-wide scale. Instead, we found that Cannabis labelling was associated with variation in a small number of terpenes whose concentrations are controlled by genetic variation at tandem arrays of terpene synthase genes.
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Affiliation(s)
- Sophie Watts
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, Nova Scotia, Canada
| | - Michel McElroy
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, Nova Scotia, Canada
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, Nova Scotia, Canada
| | - Hugo Maassen
- Bedrocan International, Veendam, the Netherlands
| | - Robin van Velzen
- Bedrocan International, Veendam, the Netherlands
- Biosystematics Group, Wageningen University, Wageningen, the Netherlands
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Truro, Nova Scotia, Canada.
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4
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Migicovsky Z, Yeats TH, Watts S, Song J, Forney CF, Burgher-MacLellan K, Somers DJ, Gong Y, Zhang Z, Vrebalov J, van Velzen R, Giovannoni JG, Rose JKC, Myles S. Apple Ripening Is Controlled by a NAC Transcription Factor. Front Genet 2021; 12:671300. [PMID: 34239539 PMCID: PMC8258254 DOI: 10.3389/fgene.2021.671300] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 02/23/2021] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
Softening is a hallmark of ripening in fleshy fruits, and has both desirable and undesirable implications for texture and postharvest stability. Accordingly, the timing and extent of pre-harvest ripening and associated textural changes following harvest are key targets for improving fruit quality through breeding. Previously, we identified a large effect locus associated with harvest date and firmness in apple (Malus domestica) using genome-wide association studies (GWAS). Here, we present additional evidence that polymorphisms in or around a transcription factor gene, NAC18.1, may cause variation in these traits. First, we confirmed our previous findings with new phenotype and genotype data from ∼800 apple accessions. In this population, we compared a genetic marker within NAC18.1 to markers targeting three other firmness-related genes currently used by breeders (ACS1, ACO1, and PG1), and found that the NAC18.1 marker was the strongest predictor of both firmness at harvest and firmness after 3 months of cold storage. By sequencing NAC18.1 across 18 accessions, we revealed two predominant haplotypes containing the single nucleotide polymorphism (SNP) previously identified using GWAS, as well as dozens of additional SNPs and indels in both the coding and promoter sequences. NAC18.1 encodes a protein that is orthogolous to the NON-RIPENING (NOR) transcription factor, a regulator of ripening in tomato (Solanum lycopersicum). We introduced both NAC18.1 transgene haplotypes into the tomato nor mutant and showed that both haplotypes complement the nor ripening deficiency. Taken together, these results indicate that polymorphisms in NAC18.1 may underlie substantial variation in apple firmness through modulation of a conserved ripening program.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Trevor H Yeats
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Sophie Watts
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Jun Song
- Agriculture and Agri-Food Canada, Kentville, NS, Canada
| | | | | | - Daryl J Somers
- Vineland Research and Innovation Centre, Vineland Station, ON, Canada
| | - Yihui Gong
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Zhaoqi Zhang
- College of Horticulture, South China Agriculture University, Guangzhou, China
| | - Julia Vrebalov
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States.,Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Robin van Velzen
- Biosystematics Group, Wageningen University, Wageningen, Netherlands
| | - James G Giovannoni
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States.,United States Department of Agriculture, Robert W. Holley Center, Cornell University, Ithaca, NY, United States
| | - Jocelyn K C Rose
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
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5
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Migicovsky Z, Cousins P, Jordan LM, Myles S, Striegler RK, Verdegaal P, Chitwood DH. Grapevine rootstocks affect growth-related scion phenotypes. Plant Direct 2021; 5:e00324. [PMID: 34095741 PMCID: PMC8156960 DOI: 10.1002/pld3.324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 05/19/2023]
Abstract
Grape growers use rootstocks to provide protection against pests and pathogens and to modulate viticulture performance such as shoot growth. Our study examined two grapevine scion varieties ('Chardonnay' and 'Cabernet Sauvignon') grafted to 15 different rootstocks and determined the effect of rootstocks on eight traits important to viticulture. We assessed the vines across five years and identified both year and variety as contributing strongly to trait variation. The effect of rootstock was relatively consistent across years and varieties, explaining between 8.99% and 9.78% of the variation in growth-related traits including yield, pruning weight, berry weight and Ravaz index (yield to pruning weight ratio). Increases in yield due to rootstock were generally the result of increases in berry weight, likely due to increased water uptake by vines grafted to a particular rootstock. We demonstrated a greater than 50% increase in yield, pruning weight, or Ravaz index by choosing the optimal rootstock, indicating that rootstock choice is crucial for grape growers looking to improve vine performance.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food and Environmental SciencesFaculty of AgricultureDalhousie UniversityTruroNSCanada
| | | | | | - Sean Myles
- Department of Plant, Food and Environmental SciencesFaculty of AgricultureDalhousie UniversityTruroNSCanada
| | | | - Paul Verdegaal
- University of California Cooperative ExtensionSan Joaquin ValleyStocktonCAUSA
| | - Daniel H. Chitwood
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
- Department of Computational Mathematics, Science and EngineeringMichigan State UniversityEast LansingMIUSA
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6
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Karimi K, Farid AH, Myles S, Miar Y. Detection of selection signatures for response to Aleutian mink disease virus infection in American mink. Sci Rep 2021; 11:2944. [PMID: 33536540 PMCID: PMC7859209 DOI: 10.1038/s41598-021-82522-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 01/21/2021] [Indexed: 02/06/2023] Open
Abstract
Aleutian disease (AD) is the most significant health issue for farmed American mink. The objective of this study was to identify the genomic regions subjected to selection for response to infection with Aleutian mink disease virus (AMDV) in American mink using genotyping by sequencing (GBS) data. A total of 225 black mink were inoculated with AMDV and genotyped using a GBS assay based on the sequencing of ApeKI-digested libraries. Five AD-characterized phenotypes were used to assign animals to pairwise groups. Signatures of selection were detected using integrated measurement of fixation index (FST) and nucleotide diversity (θπ), that were validated by haplotype-based (hap-FLK) test. The total of 99 putatively selected regions harbouring 63 genes were detected in different groups. The gene ontology revealed numerous genes related to immune response (e.g. TRAF3IP2, WDR7, SWAP70, CBFB, and GPR65), liver development (e.g. SULF2, SRSF5) and reproduction process (e.g. FBXO5, CatSperβ, CATSPER4, and IGF2R). The hapFLK test supported two strongly selected regions that contained five candidate genes related to immune response, virus–host interaction, reproduction and liver regeneration. This study provided the first map of putative selection signals of response to AMDV infection in American mink, bringing new insights into genomic regions controlling the AD phenotypes.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - A Hossain Farid
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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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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8
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Karimi K, Farid AH, Myles S, Miar Y. PSXII-24 Identification of selection signatures for response of American mink to Aleutian mink disease virus infection. J Anim Sci 2020. [DOI: 10.1093/jas/skaa278.443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Aleutian disease (AD) is one of the most important health problems in the mink industry worldwide, leading to economic losses. We used a set of single nucleotide polymorphisms (SNPs) to detect the genomic regions potentially under selection for response to Aleutian mink disease virus (AMDV) infection in black American mink. A total of 191 mink which were inoculated with a local strain of AMDV and survived until pelting were genotyped using genotyping-by-sequencing technique. The presence of viral DNA in the spleen samples were tested by polymerase chain reaction. After filtering, 47,800 SNPs at 171 individuals were used for further analyses. Signatures of selection for response to AMDV infection were detected using fixation index (FST) and nucleotide diversity (θπ) statistics measured between negative and positive groups. The overlap of top 1% SNPs obtained from both FST and θπ scores were considered as potential selection signs. This measurement identified a total of 21 candidate regions containing 11 genes which were likely subjected to selection for viral clearance. Several identified genes were those that modulate immune system (TCF4), reproductive process (CATSPERB, MAS1 and IGF2R), response to stimulus (WNT11 and MAS1), and functions of heart (TENM4 and WNT11) and liver (IGF2R). In addition, gene ontology showed that 63.6% of detected genes (seven) were involved in binding activities (GO:0005488). These genes can be used in molecular assessment of viral clearance in American mink. The results indicated that selection for viral clearance and thus AD tolerant animals can be a feasible strategy to deal with the global AMDV infection on mink farms.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University
| | - A Hossain Farid
- Department of Animal Science and Aquaculture, Dalhousie University
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Dalhousie University
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University
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9
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Karimi K, Farid AH, Sargolzaei M, Myles S, Miar Y. Linkage Disequilibrium, Effective Population Size and Genomic Inbreeding Rates in American Mink Using Genotyping-by-Sequencing Data. Front Genet 2020; 11:223. [PMID: 32231688 PMCID: PMC7083153 DOI: 10.3389/fgene.2020.00223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 09/02/2019] [Accepted: 02/26/2020] [Indexed: 12/11/2022] Open
Abstract
Knowledge of linkage disequilibrium (LD) patterns is necessary to determine the minimum density of markers required for genomic studies and to infer historical changes as well as inbreeding events in the populations. In this study, we used genotyping-by-sequencing (GBS) approach to detect single nucleotide polymorphisms (SNPs) across American mink genome and further to estimate LD, effective population size (Ne), and inbreeding rates based on excess of homozygosity (FHOM) and runs of homozygosity (ROH). A GBS assay was constructed based on the sequencing of ApeKI-digested libraries from 285 American mink using Illumina HiSeq Sequencer. Data of 13,321 SNPs located on 46 scaffolds was used to perform LD analysis. The average LD (r2 ± SD) between adjacent SNPs was 0.30 ± 0.35 over all scaffolds with an average distance of 51 kb between markers. The average r2 < 0.2 was observed at inter-marker distances of >40 kb, suggesting that at least 60,000 informative SNPs would be required for genomic selection in American mink. The Ne was estimated to be 116 at five generations ago. In addition, the most rapid decline of population size was observed between 100 and 200 generations ago. Our results showed that short extensions of homozygous genotypes (500 kb to 1 Mb) were abundant across the genome and accounted for 33% of all ROH identified. The average inbreeding coefficient based on ROH longer than 1 Mb was 0.132 ± 0.042. The estimations of FHOM ranged from −0.44 to 0.34 among different samples with an average of 0.15 over all individuals. This study provided useful insights to determine the density of SNP panel providing enough statistical power and accuracy in genomic studies of American mink. Moreover, these results confirmed that GBS approach can be considered as a useful tool for genomic studies in American mink.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - A Hossain Farid
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada.,Select Sires Inc., Plain City, OH, United States
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
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10
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Karimi K, Farid AH, Sargolzaei M, Myles S, Miar Y. PSVIII-31 Genome-wide estimation of linkage disequilibrium using American mink genotyping-by-sequencing data. J Anim Sci 2019. [DOI: 10.1093/jas/skz258.543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Linkage disequilibrium (LD) has been defined as the correlation between alleles at different loci in the genome. The LD levels can be influenced by the evolutionary processes and historical events in populations. The main objective of this study was to estimate the LD levels at different distances of American mink genome using genotyping-by-sequencing (GBS) data. A total of 285 American mink (Neovison vison) were sequenced based on GBS libraries prepared by digesting the genomic DNA with the restriction enzyme ApeKI. After quality control, 13,321 single nucleotide polymorphism (SNP) markers located on 46 Scaffolds were used to determine the extension of LD in the genome. The average r2 was computed for all syntenic SNP pairwise at inter-marker distances from 0 up to 1 Mb. The average r2 between adjacent SNPs was 0.29, ranged from 0.18 to 0.53 across all scaffolds. In addition, the average distance between adjacent markers was 51 kb. The average r2 above 0.3 was observed in less than 1 kb distances and declined with increase in distances between markers. The average r2 was estimated to be less than 0.2 for markers more than 10 kb apart. Furthermore, the average LD level was decreased to 0.08 for inter-marker distances between 0.9 and 1 Mb. The results of this study can be used to determine the optimum maker density required for obtaining enough accuracy and power in both genomic selection and genome-wide association studies.
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Affiliation(s)
- Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University
| | - A Hossain Farid
- Department of Animal Science and Aquaculture, Dalhousie University
| | | | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Dalhousie University
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University
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11
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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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12
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Peace CP, Bianco L, Troggio M, van de Weg E, Howard NP, Cornille A, Durel CE, Myles S, Migicovsky Z, Schaffer RJ, Costes E, Fazio G, Yamane H, van Nocker S, Gottschalk C, Costa F, Chagné D, Zhang X, Patocchi A, Gardiner SE, Hardner C, Kumar S, Laurens F, Bucher E, Main D, Jung S, Vanderzande S. Apple whole genome sequences: recent advances and new prospects. Hortic Res 2019; 6:59. [PMID: 30962944 PMCID: PMC6450873 DOI: 10.1038/s41438-019-0141-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/15/2019] [Accepted: 03/15/2019] [Indexed: 05/19/2023]
Abstract
In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.
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Affiliation(s)
- Cameron P. Peace
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Luca Bianco
- Computational Biology, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Michela Troggio
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - Eric van de Weg
- Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands
| | - Nicholas P. Howard
- Department of Horticultural Science, University of Minnesota, St. Paul, MN 55108 USA
- Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität, 26129 Oldenburg, Germany
| | - Amandine Cornille
- GQE – Le Moulon, Institut National de la Recherche Agronomique, University of Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Charles-Eric Durel
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS B2N 5E3 Canada
| | - Robert J. Schaffer
- The New Zealand Institute for Plant and Food Research Ltd, Motueka, 7198 New Zealand
- School of Biological Sciences, University of Auckland, Auckland, 1142 New Zealand
| | - Evelyne Costes
- AGAP, INRA, CIRAD, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Gennaro Fazio
- Plant Genetic Resources Unit, USDA ARS, Geneva, NY 14456 USA
| | - Hisayo Yamane
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan
| | - Steve van Nocker
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Chris Gottschalk
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Fabrizio Costa
- Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, San Michele all’Adige, TN 38010 Italy
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, 100193 Beijing, China
| | | | - Susan E. Gardiner
- The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Palmerston North Research Centre, Palmerston North, 4474 New Zealand
| | - Craig Hardner
- Queensland Alliance of Agriculture and Food Innovation, University of Queensland, St Lucia, 4072 Australia
| | - Satish Kumar
- New Cultivar Innovation, Plant and Food Research, Havelock North, 4130 New Zealand
| | - Francois Laurens
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
| | - Etienne Bucher
- Institut National de la Recherche Agronomique, Institut de Recherche en Horticulture et Semences, UMR 1345, 49071 Beaucouzé, France
- Agroscope, 1260 Changins, Switzerland
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Stijn Vanderzande
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
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McClure KA, Gong Y, Song J, Vinqvist-Tymchuk M, Campbell Palmer L, Fan L, Burgher-MacLellan K, Zhang Z, Celton JM, Forney CF, Migicovsky Z, Myles S. Genome-wide association studies in apple reveal loci of large effect controlling apple polyphenols. Hortic Res 2019; 6:107. [PMID: 31645962 PMCID: PMC6804656 DOI: 10.1038/s41438-019-0190-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 05/03/2023]
Abstract
Apples are a nutritious food source with significant amounts of polyphenols that contribute to human health and wellbeing, primarily as dietary antioxidants. Although numerous pre- and post-harvest factors can affect the composition of polyphenols in apples, genetics is presumed to play a major role because polyphenol concentration varies dramatically among apple cultivars. Here we investigated the genetic architecture of apple polyphenols by combining high performance liquid chromatography (HPLC) data with ~100,000 single nucleotide polymorphisms (SNPs) from two diverse apple populations. We found that polyphenols can vary in concentration by up to two orders of magnitude across cultivars, and that this dramatic variation was often predictable using genetic markers and frequently controlled by a small number of large effect genetic loci. Using GWAS, we identified candidate genes for the production of quercitrin, epicatechin, catechin, chlorogenic acid, 4-O-caffeoylquinic acid and procyanidins B1, B2, and C1. Our observation that a relatively simple genetic architecture underlies the dramatic variation of key polyphenols in apples suggests that breeders may be able to improve the nutritional value of apples through marker-assisted breeding or gene editing.
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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
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - YuiHui Gong
- College of Horticulture, South China Agriculture University, Guangzhou, 510642 China
| | - Jun Song
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Melinda Vinqvist-Tymchuk
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Leslie Campbell Palmer
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Lihua Fan
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Karen Burgher-MacLellan
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - ZhaoQi Zhang
- College of Horticulture, South China Agriculture University, Guangzhou, 510642 China
| | - Jean-Marc Celton
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Charles F. Forney
- Agriculture and Agri-Food Canada, Kentville Research and Development Centre, Kentville, NS B4N 1J5 Canada
| | - Zoë Migicovsky
- 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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Poole R, Jarrom D, Myles S. #24 Health Technology Wales – Assessing Value, Optimising Use (poster presentation). Int J Surg 2018. [DOI: 10.1016/j.ijsu.2018.10.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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15
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Larsen B, Gardner K, Pedersen C, Ørgaard M, Migicovsky Z, Myles S, Toldam-Andersen TB. Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing. PLoS One 2018; 13:e0201889. [PMID: 30110387 PMCID: PMC6093671 DOI: 10.1371/journal.pone.0201889] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 07/24/2018] [Indexed: 12/20/2022] Open
Abstract
In recent years, new genome-wide marker systems have provided highly informative alternatives to low density marker systems for evaluating plant populations. To date, most apple germplasm collections have been genotyped using low-density markers such as simple sequence repeats (SSRs), whereas only a few have been explored using high-density genome-wide marker information. We explored the genetic diversity of the Pometum gene bank collection (University of Copenhagen, Denmark) of 349 apple accessions using over 15,000 genome-wide single nucleotide polymorphisms (SNPs) and 15 SSR markers, in order to compare the strength of the two approaches for describing population structure. We found that 119 accessions shared a putative clonal relationship with at least one other accession in the collection, resulting in the identification of 272 (78%) unique accessions. Of these unique accessions, over half (52%) share a first-degree relationship with at least one other accession. There is therefore a high degree of clonal and family relatedness in the Danish apple gene bank. We find significant genetic differentiation between Malus domestica and its supposed primary wild ancestor, M. sieversii, as well as between accessions of Danish origin and all others. Using the GBS approach allowed us to estimate ploidy levels, which were in accordance with flow cytometry results. Overall, we found strong concordance between analyses based on the genome-wide SNPs and the 15 SSR loci. However, we argue that GBS is superior to traditional SSR approaches because it allows detection of a much more detailed population structure and can be further exploited in genome-wide association studies (GWAS). Finally, we compare GBS with SSR for the purpose of identifying clones and pedigree relations in a diverse apple gene bank and discuss the advantages and constraints of the two approaches.
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Affiliation(s)
- Bjarne Larsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
- * E-mail:
| | - Kyle Gardner
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Faculty of Agriculture, Agricultural Campus, Truro, NS, Canada
| | - Carsten Pedersen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Marian Ørgaard
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Faculty of Agriculture, Agricultural Campus, Truro, NS, Canada
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Dalhousie University, Faculty of Agriculture, Agricultural Campus, Truro, NS, Canada
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Li M, An H, Angelovici R, Bagaza C, Batushansky A, Clark L, Coneva V, Donoghue MJ, Edwards E, Fajardo D, Fang H, Frank MH, Gallaher T, Gebken S, Hill T, Jansky S, Kaur B, Klahs PC, Klein LL, Kuraparthy V, Londo J, Migicovsky Z, Miller A, Mohn R, Myles S, Otoni WC, Pires JC, Rieffer E, Schmerler S, Spriggs E, Topp CN, Van Deynze A, Zhang K, Zhu L, Zink BM, Chitwood DH. Topological Data Analysis as a Morphometric Method: Using Persistent Homology to Demarcate a Leaf Morphospace. Front Plant Sci 2018; 9:553. [PMID: 29922307 PMCID: PMC5996898 DOI: 10.3389/fpls.2018.00553] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/09/2018] [Indexed: 05/18/2023]
Abstract
Current morphometric methods that comprehensively measure shape cannot compare the disparate leaf shapes found in seed plants and are sensitive to processing artifacts. We explore the use of persistent homology, a topological method applied as a filtration across simplicial complexes (or more simply, a method to measure topological features of spaces across different spatial resolutions), to overcome these limitations. The described method isolates subsets of shape features and measures the spatial relationship of neighboring pixel densities in a shape. We apply the method to the analysis of 182,707 leaves, both published and unpublished, representing 141 plant families collected from 75 sites throughout the world. By measuring leaves from throughout the seed plants using persistent homology, a defined morphospace comparing all leaves is demarcated. Clear differences in shape between major phylogenetic groups are detected and estimates of leaf shape diversity within plant families are made. The approach predicts plant family above chance. The application of a persistent homology method, using topological features, to measure leaf shape allows for a unified morphometric framework to measure plant form, including shapes, textures, patterns, and branching architectures.
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Affiliation(s)
- Mao Li
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Clement Bagaza
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Albert Batushansky
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Lynn Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Viktoriya Coneva
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Michael J. Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Erika Edwards
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
| | - Diego Fajardo
- National Center for Genome Resources (NCGR), Santa Fe, NM, United States
| | - Hui Fang
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | | | - Timothy Gallaher
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Sarah Gebken
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Theresa Hill
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Shelley Jansky
- Vegetable Crops Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, United States
| | - Baljinder Kaur
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Phillip C. Klahs
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
| | - Laura L. Klein
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Vasu Kuraparthy
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Jason Londo
- Grape Genetics Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Geneva, NY, United States
| | - Zoë Migicovsky
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Allison Miller
- Department of Biology, Saint Louis University, St. Louis, MO, United States
| | - Rebekah Mohn
- Department of Plant and Microbial Biology, University of Minnesota – Twin Cities, St. Paul, MN, United States
| | - Sean Myles
- Department of Plant, Food, and Environmental Sciences, Dalhousie University, Truro, NS, Canada
| | - Wagner C. Otoni
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
| | - J. C. Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Edmond Rieffer
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Sam Schmerler
- Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, United States
- American Museum of Natural History, New York, NY, United States
| | - Elizabeth Spriggs
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | | | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Kuang Zhang
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Linglong Zhu
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Braden M. Zink
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Daniel H. Chitwood
- Independent Researcher, Santa Rosa, CA, United States
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
- Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, United States
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17
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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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18
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McElroy MS, Navarro AJR, Mustiga G, Stack C, Gezan S, Peña G, Sarabia W, Saquicela D, Sotomayor I, Douglas GM, Migicovsky Z, Amores F, Tarqui O, Myles S, Motamayor JC. Prediction of Cacao ( Theobroma cacao) Resistance to Moniliophthora spp. Diseases via Genome-Wide Association Analysis and Genomic Selection. Front Plant Sci 2018; 9:343. [PMID: 29662497 PMCID: PMC5890178 DOI: 10.3389/fpls.2018.00343] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Accepted: 02/28/2018] [Indexed: 05/21/2023]
Abstract
Cacao (Theobroma cacao) is a globally important crop, and its yield is severely restricted by disease. Two of the most damaging diseases, witches' broom disease (WBD) and frosty pod rot disease (FPRD), are caused by a pair of related fungi: Moniliophthora perniciosa and Moniliophthora roreri, respectively. Resistant cultivars are the most effective long-term strategy to address Moniliophthora diseases, but efficiently generating resistant and productive new cultivars will require robust methods for screening germplasm before field testing. Marker-assisted selection (MAS) and genomic selection (GS) provide two potential avenues for predicting the performance of new genotypes, potentially increasing the selection gain per unit time. To test the effectiveness of these two approaches, we performed a genome-wide association study (GWAS) and GS on three related populations of cacao in Ecuador genotyped with a 15K single nucleotide polymorphism (SNP) microarray for three measures of WBD infection (vegetative broom, cushion broom, and chirimoya pod), one of FPRD (monilia pod) and two productivity traits (total fresh weight of pods and % healthy pods produced). GWAS yielded several SNPs associated with disease resistance in each population, but none were significantly correlated with the same trait in other populations. Genomic selection, using one population as a training set to estimate the phenotypes of the remaining two (composed of different families), varied among traits, from a mean prediction accuracy of 0.46 (vegetative broom) to 0.15 (monilia pod), and varied between training populations. Simulations demonstrated that selecting seedlings using GWAS markers alone generates no improvement over selecting at random, but that GS improves the selection process significantly. Our results suggest that the GWAS markers discovered here are not sufficiently predictive across diverse germplasm to be useful for MAS, but that using all markers in a GS framework holds substantial promise in accelerating disease-resistance in cacao.
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Affiliation(s)
- Michel S. McElroy
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Alberto J. R. Navarro
- MARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United States
| | - Guiliana Mustiga
- MARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United States
| | - Conrad Stack
- MARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United States
| | - Salvador Gezan
- School of Forest Resources and Conservation, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL, United States
| | - Geover Peña
- Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | - Widem Sarabia
- Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | - Diego Saquicela
- Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | | | - Gavin M. Douglas
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Freddy Amores
- Facultad de Ciencias Agrarias, Universidad Técnica Estatal de Quevedo, Quevedo, Ecuador
| | - Omar Tarqui
- Instituto Nacional de Investigaciones Agropecuarias, Quito, Ecuador
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Juan C. Motamayor
- MARS, Incorporated c/o United States Department of Agriculture – Agricultural Research Service, Miami, FL, United States
- *Correspondence: Juan C. Motamayor,
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Money D, Migicovsky Z, Gardner K, Myles S. LinkImputeR: user-guided genotype calling and imputation for non-model organisms. BMC Genomics 2017; 18:523. [PMID: 28693460 PMCID: PMC5504746 DOI: 10.1186/s12864-017-3873-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [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: 12/21/2016] [Accepted: 06/20/2017] [Indexed: 11/24/2022] Open
Abstract
Background Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use only of genotypes that are successfully inferred after having passed a certain read depth threshold. Because of this, any read information for genotypes that did not pass the threshold, and were thus set to missing, is ignored. Most genomic studies also choose read depth thresholds and quality filters without investigating their effects on the size and quality of the resulting genotype data. Moreover, almost all genotype imputation methods require ordered markers and are therefore of limited utility in non-model organisms. Results Here we introduce LinkImputeR, a software program that exploits the read count information that is normally ignored, and makes use of all available DNA sequence information for the purposes of genotype calling and imputation. It is specifically designed for non-model organisms since it requires neither ordered markers nor a reference panel of genotypes. Using next-generation DNA sequence (NGS) data from apple, cannabis and grape, we quantify the effect of varying read count and missingness thresholds on the quantity and quality of genotypes generated from LinkImputeR. We demonstrate that LinkImputeR can increase the number of genotype calls by more than an order of magnitude, can improve genotyping accuracy by several percent and can thus improve the power of downstream analyses. Moreover, we show that the effects of quality and read depth filters can differ substantially between data sets and should therefore be investigated on a per-study basis. Conclusions By exploiting DNA sequence data that is normally ignored during genotype calling and imputation, LinkImputeR can significantly improve both the quantity and quality of genotype data generated from NGS technologies. It enables the user to quickly and easily examine the effects of varying thresholds and filters on the number and quality of the resulting genotype calls. In this manner, users can decide on thresholds that are most suitable for their purposes. We show that LinkImputeR can significantly augment the value and utility of NGS data sets, especially in non-model organisms with poor genomic resources. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3873-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Money
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada.
| | - Zoë Migicovsky
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Kyle Gardner
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
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20
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Migicovsky Z, Myles S. Exploiting Wild Relatives for Genomics-assisted Breeding of Perennial Crops. Front Plant Sci 2017; 8:460. [PMID: 28421095 PMCID: PMC5379136 DOI: 10.3389/fpls.2017.00460] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/16/2017] [Indexed: 05/18/2023]
Abstract
Perennial crops are vital contributors to global food production and nutrition. However, the breeding of new perennial crops is an expensive and time-consuming process due to the large size and lengthy juvenile phase of many species. Genomics provides a valuable tool for improving the efficiency of breeding by allowing progeny possessing a trait of interest to be selected at the seed or seedling stage through marker-assisted selection (MAS). The benefits of MAS to a breeder are greatest when the targeted species takes a long time to reach maturity and is expensive to grow and maintain. Thus, MAS holds particular promise in perennials since they are often costly and time-consuming to grow to maturity and evaluate. Well-characterized germplasm that breeders can tap into for improving perennials is often limited in genetic diversity. Wild relatives are a largely untapped source of desirable traits including disease resistance, fruit quality, and rootstock characteristics. This review focuses on the use of genomics-assisted breeding in perennials, especially as it relates to the introgression of useful traits from wild relatives. The identification of genetic markers predictive of beneficial phenotypes derived from wild relatives is hampered by genomic tools designed for domesticated species that are often ill-suited for use in wild relatives. There is therefore an urgent need for better genomic resources from wild relatives. A further barrier to exploiting wild diversity through genomics is the phenotyping bottleneck: well-powered genetic mapping requires accurate and cost-effective characterization of large collections of diverse wild germplasm. While genomics will always be used in combination with traditional breeding methods, it is a powerful tool for accelerating the speed and reducing the costs of breeding while harvesting the potential of wild relatives for improving perennial crops.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University,Truro, NS, Canada
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Migicovsky Z, Li M, Chitwood DH, Myles S. Morphometrics Reveals Complex and Heritable Apple Leaf Shapes. Front Plant Sci 2017; 8:2185. [PMID: 29354142 PMCID: PMC5758599 DOI: 10.3389/fpls.2017.02185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/12/2017] [Indexed: 05/19/2023]
Abstract
Apple (Malus spp.) is a widely grown and valuable fruit crop. Leaf shape is important for flowering in apple and may also be an early indicator for other agriculturally valuable traits. We examined 9,000 leaves from 869 unique apple accessions using linear measurements and comprehensive morphometric techniques. We identified allometric variation as the result of differing length-to-width aspect ratios between accessions and species of apple. The allometric variation was due to variation in the width of the leaf blade, not the length. Aspect ratio was highly correlated with the first principal component (PC1) of morphometric variation quantified using elliptical Fourier descriptors (EFDs) and persistent homology (PH). While the primary source of variation was aspect ratio, subsequent PCs corresponded to complex shape variation not captured by linear measurements. After linking the morphometric information with over 122,000 genome-wide single nucleotide polymorphisms (SNPs), we found high SNP heritability values even at later PCs, indicating that comprehensive morphometrics can capture complex, heritable phenotypes. Thus, techniques such as EFDs and PH are capturing heritable biological variation that would be missed using linear measurements alone.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
- *Correspondence: Zoë Migicovsky
| | - Mao Li
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Daniel H. Chitwood
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
- Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Sean Myles
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
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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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24
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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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25
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Migicovsky Z, Sawler J, Money D, Eibach R, Miller AJ, Luby JJ, Jamieson AR, Velasco D, von Kintzel S, Warner J, Wührer W, Brown PJ, Myles S. Genomic ancestry estimation quantifies use of wild species in grape breeding. BMC Genomics 2016; 17:478. [PMID: 27357509 PMCID: PMC4928267 DOI: 10.1186/s12864-016-2834-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/13/2016] [Indexed: 11/24/2022] Open
Abstract
Background Grapes are one of the world’s most valuable crops and most are made into wine. Grapes belong to the genus Vitis, which includes over 60 inter-fertile species. The most common grape cultivars derive their entire ancestry from the species Vitis vinifera, but wild relatives have also been exploited to create hybrid cultivars, often with increased disease resistance. Results We evaluate the genetic ancestry of some of the most widely grown commercial hybrids from North America and Europe. Using genotyping-by-sequencing (GBS), we generated 2482 SNPs and 56 indels from 7 wild Vitis, 7 V. vinifera, and 64 hybrid cultivars. We used a principal component analysis (PCA) based ancestry estimation procedure and verified its accuracy with both empirical and simulated data. V. vinifera ancestry ranged from 11 % to 76 % across hybrids studied. Approximately one third (22/64) of the hybrids have ancestry estimates consistent with F1 hybridization: they derive half of their ancestry from wild Vitis and half from V. vinifera. Conclusions Our results suggest that hybrid grape breeding is in its infancy. The distribution of V. vinifera ancestry across hybrids also suggests that backcrosses to wild Vitis species have been more frequent than backcrosses to V. vinifera during hybrid grape breeding. This pattern is unusual in crop breeding, as it is most common to repeatedly backcross to elite, or domesticated, germplasm. We anticipate our method can be extended to facilitate marker-assisted selection in order to introgress beneficial wild Vitis traits, while allowing for offspring with the highest V. vinifera content to be selected at the seedling stage. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2834-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zoë Migicovsky
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Jason Sawler
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.,Anandia Labs, 2259 Lower Mall, Vancouver, BC, Canada
| | - Daniel Money
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada
| | - Rudolph Eibach
- JKI Institute for Grapevine Breeding, Geilweilerhof, Germany
| | - Allison J Miller
- Department of Biology, Saint Louis University, Saint Louis, MO, USA
| | - James J Luby
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, USA
| | - Andrew R Jamieson
- Agriculture & Agri-Food Canada, Atlantic Food & Horticulture Research Centre, Kentville, NS, Canada
| | | | | | - John Warner
- Warner Vineyards, 391 Thorpe Rd, RR#2, Centreville, NS, Canada
| | - Walter Wührer
- Wührer Vineyards, 187 Highway 221, RR#1, Kingston, NS, Canada
| | - Patrick J Brown
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada.
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26
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Goto-Yamamoto N, Sawler J, Myles S. Genetic Analysis of East Asian Grape Cultivars Suggests Hybridization with Wild Vitis. PLoS One 2015; 10:e0140841. [PMID: 26488600 PMCID: PMC4619069 DOI: 10.1371/journal.pone.0140841] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/29/2015] [Indexed: 11/18/2022] Open
Abstract
Koshu is a grape cultivar native to Japan and is one of the country’s most important cultivars for wine making. Koshu and other oriental grape cultivars are widely believed to belong to the European domesticated grape species Vitis vinifera. To verify the domesticated origin of Koshu and four other cultivars widely grown in China and Japan, we genotyped 48 ancestry informative single nucleotide polymorphisms (SNPs) and estimated wild and domesticated ancestry proportions. Our principal components analysis (PCA) based ancestry estimation revealed that Koshu is 70% V. vinifera, and that the remaining 30% of its ancestry is most likely derived from wild East Asian Vitis species. Partial sequencing of chloroplast DNA suggests that Koshu’s maternal line is derived from the Chinese wild species V. davidii or a closely related species. Our results suggest that many traditional East Asian grape cultivars such as Koshu were generated from hybridization events with wild grape species.
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Affiliation(s)
- Nami Goto-Yamamoto
- National Research Institute of Brewing, Higashi-Hiroshima, Japan
- * E-mail: (NG); (SM)
| | - Jason Sawler
- Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
- Anandia Labs, 2259 Lower Mall, Vancouver, British Columbia, Canada
| | - Sean Myles
- Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
- * E-mail: (NG); (SM)
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27
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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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28
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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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29
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Chitwood DH, Ranjan A, Martinez CC, Headland LR, Thiem T, Kumar R, Covington MF, Hatcher T, Naylor DT, Zimmerman S, Downs N, Raymundo N, Buckler ES, Maloof JN, Aradhya M, Prins B, Li L, Myles S, Sinha NR. A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. Plant Physiol 2014; 164:259-72. [PMID: 24285849 PMCID: PMC3875807 DOI: 10.1104/pp.113.229708] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/25/2013] [Indexed: 05/18/2023]
Abstract
Terroir, the unique interaction between genotype, environment, and culture, is highly refined in domesticated grape (Vitis vinifera). Toward cultivating terroir, the science of ampelography tried to distinguish thousands of grape cultivars without the aid of genetics. This led to sophisticated phenotypic analyses of natural variation in grape leaves, which within a palmate-lobed framework exhibit diverse patterns of blade outgrowth, hirsuteness, and venation patterning. Here, we provide a morphometric analysis of more than 1,200 grape accessions. Elliptical Fourier descriptors provide a global analysis of leaf outlines and lobe positioning, while a Procrustes analysis quantitatively describes venation patterning. Correlation with previous ampelography suggests an important genetic component, which we confirm with estimates of heritability. We further use RNA-Seq of mutant varieties and perform a genome-wide association study to explore the genetic basis of leaf shape. Meta-analysis reveals a relationship between leaf morphology and hirsuteness, traits known to correlate with climate in the fossil record and extant species. Together, our data demonstrate a genetic basis for the intricate diversity present in grape leaves. We discuss the possibility of using grape leaves as a breeding target to preserve terroir in the face of anticipated climate change, a major problem facing viticulture.
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30
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Sawler J, Reisch B, Aradhya MK, Prins B, Zhong GY, Schwaninger H, Simon C, Buckler E, Myles S. Genomics assisted ancestry deconvolution in grape. PLoS One 2013; 8:e80791. [PMID: 24244717 PMCID: PMC3823699 DOI: 10.1371/journal.pone.0080791] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 10/07/2013] [Indexed: 11/19/2022] Open
Abstract
The genus Vitis (the grapevine) is a group of highly diverse, diploid woody perennial vines consisting of approximately 60 species from across the northern hemisphere. It is the world’s most valuable horticultural crop with ~8 million hectares planted, most of which is processed into wine. To gain insights into the use of wild Vitis species during the past century of interspecific grape breeding and to provide a foundation for marker-assisted breeding programmes, we present a principal components analysis (PCA) based ancestry estimation method to calculate admixture proportions of hybrid grapes in the United States Department of Agriculture grape germplasm collection using genome-wide polymorphism data. We find that grape breeders have backcrossed to both the domesticated V. vinifera and wild Vitis species and that reasonably accurate genome-wide ancestry estimation can be performed on interspecific Vitis hybrids using a panel of fewer than 50 ancestry informative markers (AIMs). We compare measures of ancestry informativeness used in selecting SNP panels for two-way admixture estimation, and verify the accuracy of our method on simulated populations of admixed offspring. Our method of ancestry deconvolution provides a first step towards selection at the seed or seedling stage for desirable admixture profiles, which will facilitate marker-assisted breeding that aims to introgress traits from wild Vitis species while retaining the desirable characteristics of elite V. vinifera cultivars.
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Affiliation(s)
- Jason Sawler
- Department of Plant and Animals Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Bruce Reisch
- Department of Horticulture, Cornell University, Ithaca, New York, United States of America
| | - Mallikarjuna K. Aradhya
- National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, University of California, Davis, Davis, California, United States of America
| | - Bernard Prins
- National Clonal Germplasm Repository, United States Department of Agriculture, Agricultural Research Service, University of California, Davis, Davis, California, United States of America
| | - Gan-Yuan Zhong
- United States Department of Agriculture, Agricultural Research Service, Grape Genetics Research Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, New York, United States of America
- United States Department of Agriculture, Agricultural Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, New York, United States of America
| | - Heidi Schwaninger
- United States Department of Agriculture, Agricultural Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, New York, United States of America
| | - Charles Simon
- United States Department of Agriculture, Agricultural Research Service, Plant Genetic Resources Unit, New York State Agricultural Experiment Station, Cornell University, Geneva, New York, United States of America
| | - Edward Buckler
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
- United States Department of Agriculture, Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America
| | - Sean Myles
- Department of Plant and Animals Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
- * E-mail:
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31
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McCouch S, Baute GJ, Bradeen J, Bramel P, Bretting PK, Buckler E, Burke JM, Charest D, Cloutier S, Cole G, Dempewolf H, Dingkuhn M, Feuillet C, Gepts P, Grattapaglia D, Guarino L, Jackson S, Knapp S, Langridge P, Lawton-Rauh A, Lijua Q, Lusty C, Michael T, Myles S, Naito K, Nelson RL, Pontarollo R, Richards CM, Rieseberg L, Ross-Ibarra J, Rounsley S, Hamilton RS, Schurr U, Stein N, Tomooka N, van der Knaap E, van Tassel D, Toll J, Valls J, Varshney RK, Ward J, Waugh R, Wenzl P, Zamir D. Agriculture: Feeding the future. Nature 2013; 499:23-4. [PMID: 23823779 DOI: 10.1038/499023a] [Citation(s) in RCA: 240] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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32
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Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Myles S, Martinez-Zapater JM, Zyprian E, Moreira FM, Grando MS. Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC Plant Biol 2013; 13:39. [PMID: 23497049 PMCID: PMC3610244 DOI: 10.1186/1471-2229-13-39] [Citation(s) in RCA: 150] [Impact Index Per Article: 13.6] [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: 10/26/2012] [Accepted: 02/27/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples. RESULTS We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability. CONCLUSIONS The comprehensive molecular characterization of our grape germplasm collection contributes to the knowledge about levels and distribution of genetic diversity in the existing resources of Vitis and provides insights into genetic subdivision within the European germplasm. Genotypic and phenotypic information compared in this study may efficiently guide further exploration of this diversity for facilitating its practical use.
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Affiliation(s)
- Francesco Emanuelli
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Silvia Lorenzi
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Lukasz Grzeskowiak
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Valentina Catalano
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Marco Stefanini
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Michela Troggio
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
| | - Sean Myles
- Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada
| | - José M Martinez-Zapater
- Instituto de Ciencias de la Vid y del Vino (CSIC, UR, Gobierno de La Rioja), C/ Madre de dios 51, Logroño, 26006, Spain
| | - Eva Zyprian
- JKI Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, 76833, Germany
| | - Flavia M Moreira
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
- Instituto Federal de Santa Catarina, Rua José Lino Kretzer 608 - Praia Comprida, São José, Santa Catarina, 88130-310, Brasil
| | - M Stella Grando
- Department of Genomics and Biology of Fruit Crops, IASMA Research and Innovation Centre, Fondazione Edmund Mach - Via E. Mach 1, San Michele all'Adige, TN, 38010, Italy
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Kenny EE, Timpson NJ, Sikora M, Yee MC, Moreno-Estrada A, Eng C, Huntsman S, Burchard EG, Stoneking M, Bustamante CD, Myles S. Melanesian blond hair is caused by an amino acid change in TYRP1. Science 2012; 336:554. [PMID: 22556244 DOI: 10.1126/science.1217849] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Naturally blond hair is rare in humans and found almost exclusively in Europe and Oceania. Here, we identify an arginine-to-cysteine change at a highly conserved residue in tyrosinase-related protein 1 (TYRP1) as a major determinant of blond hair in Solomon Islanders. This missense mutation is predicted to affect catalytic activity of TYRP1 and causes blond hair through a recessive mode of inheritance. The mutation is at a frequency of 26% in the Solomon Islands, is absent outside of Oceania, represents a strong common genetic effect on a complex human phenotype, and highlights the importance of examining genetic associations worldwide.
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Affiliation(s)
- Eimear E Kenny
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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Gunnarsdóttir ED, Nandineni MR, Li M, Myles S, Gil D, Pakendorf B, Stoneking M. Erratum: Corrigendum: Larger mitochondrial DNA than Y-chromosome differences between matrilocal and patrilocal groups from Sumatra. Nat Commun 2012. [DOI: 10.1038/ncomms1401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Mahanil S, Ramming D, Cadle-Davidson M, Owens C, Garris A, Myles S, Cadle-Davidson L. Development of marker sets useful in the early selection of Ren4 powdery mildew resistance and seedlessness for table and raisin grape breeding. Theor Appl Genet 2012; 124:23-33. [PMID: 21904846 DOI: 10.1007/s00122-011-1684-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2011] [Accepted: 08/12/2011] [Indexed: 05/02/2023]
Abstract
The single, dominant powdery mildew resistance locus Ren4 from Vitis romanetii prevents hyphal growth by Erysiphe necator. Previously, we showed that when introgressed into V. vinifera in the modified BC(2) population 03-3004, Ren4 was linked with the simple sequence repeat marker VMC7f2 on chromosome 18-a marker that is associated with multiple disease resistance and seedlessness. However, in the current study, this marker was monomorphic in related breeding populations 05-3010 and 07-3553. To enhance marker-assisted selection at this locus, we developed multiplexed SNP markers using three approaches: conversion of bulked segregant analysis AFLP markers, sequencing of candidate genes and regions flanking known V. vinifera SNPs, and hybridization to the Vitis9KSNP genotyping array. The Vitis9KSNP array was more cost-efficient than all other approaches tested for marker discovery and genotyping, enabling the genotyping of 1317 informative SNPs within the span of 1 week and at a cost of 11 cents per SNP. From a total of 1,446 high quality, informative markers segregating in 03-3004, we developed a haplotype signature of 15 multiplexed SNP markers linked with Ren4 in 03-3004, 5 of which were linked in 05-3010, and 6 of which were linked in 07-3553. Two of these populations segregated for seedlessness, which was tightly linked with Ren4 in 03-3004 (2 cM) but not in 05-3010 (22 cM). Chromosomal rearrangements were detected among these three populations and the reference genome PN40024. Since this is the first application of the Vitis9KSNP array in a breeding program, some suggestions are provided for application of genotyping arrays. Our results provide novel markers for tracking and pyramiding this unique resistance gene and for further functional characterization of this region on chromosome 18 encoding multiple disease resistance and seedlessness.
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Affiliation(s)
- Siraprapa Mahanil
- USDA-ARS Grape Genetics Research Unit, 630 W. North St, Geneva, NY 14456, USA
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Brown PJ, Upadyayula N, Mahone GS, Tian F, Bradbury PJ, Myles S, Holland JB, Flint-Garcia S, McMullen MD, Buckler ES, Rocheford TR. Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genet 2011; 7:e1002383. [PMID: 22125498 PMCID: PMC3219606 DOI: 10.1371/journal.pgen.1002383] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 09/29/2011] [Indexed: 11/20/2022] Open
Abstract
We compared the genetic architecture of thirteen maize morphological traits in a large population of recombinant inbred lines. Four traits from the male inflorescence (tassel) and three traits from the female inflorescence (ear) were measured and studied using linkage and genome-wide association analyses and compared to three flowering and three leaf traits previously studied in the same population. Inflorescence loci have larger effects than flowering and leaf loci, and ear effects are larger than tassel effects. Ear trait models also have lower predictive ability than tassel, flowering, or leaf trait models. Pleiotropic loci were identified that control elongation of ear and tassel, consistent with their common developmental origin. For these pleiotropic loci, the ear effects are larger than tassel effects even though the same causal polymorphisms are likely involved. This implies that the observed differences in genetic architecture are not due to distinct features of the underlying polymorphisms. Our results support the hypothesis that genetic architecture is a function of trait stability over evolutionary time, since the traits that changed most during the relatively recent domestication of maize have the largest effects. Genetic architecture is of broad interest in evolutionary biology, plant and animal breeding, and medicine, because it influences both the response to selection and the success of trait mapping. Results from the most rigorously studied genetic systems suggest a similar genetic architecture across all species and traits studied, with many loci of small effect. A few strongly selected traits in domesticated organisms show unusual genetic architecture, for reasons that are unclear. We compare maize inflorescence, flowering, and leaf traits and show that inflorescence traits have distinct genetic architectures characterized by larger effects. Female inflorescences (ears) have larger effects than male inflorescences (tassels) even though the two structures have similar developmental origins. Analysis of pleiotropic loci shows that these larger effects are not inherent features of the underlying polymorphisms. Rather, maize inflorescences appear to be exceptionally labile, with female inflorescences more labile than male inflorescences. These results support the canalization hypothesis, which predicts that rapidly changing traits will have larger effects. We suggest that maize inflorescence traits, and ear traits in particular, have larger effects than flowering or leaf traits as a result of strong directional selection during maize domestication.
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Affiliation(s)
- Patrick J. Brown
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- * E-mail: (PJ Brown); (TR Rocheford)
| | - Narasimham Upadyayula
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Gregory S. Mahone
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Feng Tian
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Peter J. Bradbury
- United States Department of Agriculture – Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America
| | - Sean Myles
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - James B. Holland
- United States Department of Agriculture – Agricultural Research Service and Department of Crop Science, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Sherry Flint-Garcia
- United States Department of Agriculture – Agricultural Research Service and Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Michael D. McMullen
- United States Department of Agriculture – Agricultural Research Service and Division of Plant Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- United States Department of Agriculture – Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Torbert R. Rocheford
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
- * E-mail: (PJ Brown); (TR Rocheford)
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Delfin F, Myles S, Choi Y, Hughes D, Illek R, van Oven M, Pakendorf B, Kayser M, Stoneking M. Bridging Near and Remote Oceania: mtDNA and NRY Variation in the Solomon Islands. Mol Biol Evol 2011; 29:545-64. [DOI: 10.1093/molbev/msr186] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Myles S, Boyko AR, Owens CL, Brown PJ, Grassi F, Aradhya MK, Prins B, Reynolds A, Chia JM, Ware D, Bustamante CD, Buckler ES. Genetic structure and domestication history of the grape. Proc Natl Acad Sci U S A 2011; 108:3530-5. [PMID: 21245334 PMCID: PMC3048109 DOI: 10.1073/pnas.1009363108] [Citation(s) in RCA: 321] [Impact Index Per Article: 24.7] [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] [Indexed: 01/17/2023] Open
Abstract
The grape is one of the earliest domesticated fruit crops and, since antiquity, it has been widely cultivated and prized for its fruit and wine. Here, we characterize genome-wide patterns of genetic variation in over 1,000 samples of the domesticated grape, Vitis vinifera subsp. vinifera, and its wild relative, V. vinifera subsp. sylvestris from the US Department of Agriculture grape germplasm collection. We find support for a Near East origin of vinifera and present evidence of introgression from local sylvestris as the grape moved into Europe. High levels of genetic diversity and rapid linkage disequilibrium (LD) decay have been maintained in vinifera, which is consistent with a weak domestication bottleneck followed by thousands of years of widespread vegetative propagation. The considerable genetic diversity within vinifera, however, is contained within a complex network of close pedigree relationships that has been generated by crosses among elite cultivars. We show that first-degree relationships are rare between wine and table grapes and among grapes from geographically distant regions. Our results suggest that although substantial genetic diversity has been maintained in the grape subsequent to domestication, there has been a limited exploration of this diversity. We propose that the adoption of vegetative propagation was a double-edged sword: Although it provided a benefit by ensuring true breeding cultivars, it also discouraged the generation of unique cultivars through crosses. The grape currently faces severe pathogen pressures, and the long-term sustainability of the grape and wine industries will rely on the exploitation of the grape's tremendous natural genetic diversity.
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Affiliation(s)
- Sean Myles
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
- Department of Biology, Acadia University, Wolfville, NS, Canada B4P 2R6
- Department of Plant and Animal Sciences, Nova Scotia Agricultural College, Truro, NS, Canada B2N 5E3
| | - Adam R. Boyko
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Christopher L. Owens
- Grape Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Cornell University, Geneva, NY 14456
| | - Patrick J. Brown
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
| | - Fabrizio Grassi
- Botanical Garden, Department of Biology, University of Milan, 20133 Milan, Italy
| | - Mallikarjuna K. Aradhya
- National Clonal Germplasm Repository, United States Department of Agriculture-Agricultural Research Service, University of California, Davis, CA 95616
| | - Bernard Prins
- National Clonal Germplasm Repository, United States Department of Agriculture-Agricultural Research Service, University of California, Davis, CA 95616
| | - Andy Reynolds
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Jer-Ming Chia
- Cold Spring Harbor Laboratory, United States Department of Agriculture-Agricultural Research Service, Cold Spring Harbor, NY 11724; and
| | - Doreen Ware
- Cold Spring Harbor Laboratory, United States Department of Agriculture-Agricultural Research Service, Cold Spring Harbor, NY 11724; and
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, NY14853
| | - Carlos D. Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Cornell University, Ithaca, NY14853
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Myles S, Lea RA, Ohashi J, Chambers GK, Weiss JG, Hardouin E, Engelken J, Macartney-Coxson DP, Eccles DA, Naka I, Kimura R, Inaoka T, Matsumura Y, Stoneking M. Testing the thrifty gene hypothesis: the Gly482Ser variant in PPARGC1A is associated with BMI in Tongans. BMC Med Genet 2011; 12:10. [PMID: 21244673 PMCID: PMC3025936 DOI: 10.1186/1471-2350-12-10] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 01/18/2011] [Indexed: 12/03/2022]
Abstract
Background The thrifty gene hypothesis posits that, in populations that experienced periods of feast and famine, natural selection favoured individuals carrying thrifty alleles that promote the storage of fat and energy. Polynesians likely experienced long periods of cold stress and starvation during their settlement of the Pacific and today have high rates of obesity and type 2 diabetes (T2DM), possibly due to past positive selection for thrifty alleles. Alternatively, T2DM risk alleles may simply have drifted to high frequency in Polynesians. To identify thrifty alleles in Polynesians, we previously examined evidence of positive selection on T2DM-associated SNPs and identified a T2DM risk allele at unusually high frequency in Polynesians. We suggested that the risk allele of the Gly482Ser variant in the PPARGC1A gene was driven to high frequency in Polynesians by positive selection and therefore possibly represented a thrifty allele in the Pacific. Methods Here we examine whether PPARGC1A is a thrifty gene in Pacific populations by testing for an association between Gly482Ser genotypes and BMI in two Pacific populations (Maori and Tongans) and by evaluating the frequency of the risk allele of the Gly482Ser variant in a sample of worldwide populations. Results We find that the Gly482Ser variant is associated with BMI in Tongans but not in Maori. In a sample of 58 populations worldwide, we also show that the 482Ser risk allele reaches its highest frequency in the Pacific. Conclusion The association between Gly482Ser genotypes and BMI in Tongans together with the worldwide frequency distribution of the Gly482Ser risk allele suggests that PPARGC1A remains a candidate thrifty gene in Pacific populations.
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Affiliation(s)
- Sean Myles
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, USA.
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Cohen D, Alam F, Dunstan F, Myles S, Hughes D, Routledge P. 062 Abolition of prescription co-payments in Wales: an observational study on dispensing rates. Br J Soc Med 2010. [DOI: 10.1136/jech.2010.120956.62] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
Researchers from diverse backgrounds are converging on the view that human evolution has been shaped by gene-culture interactions. Theoretical biologists have used population genetic models to demonstrate that cultural processes can have a profound effect on human evolution, and anthropologists are investigating cultural practices that modify current selection. These findings are supported by recent analyses of human genetic variation, which reveal that hundreds of genes have been subject to recent positive selection, often in response to human activities. Here, we collate these data, highlighting the considerable potential for cross-disciplinary exchange to provide novel insights into how culture has shaped the human genome.
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Affiliation(s)
- Kevin N Laland
- School of Biology, University of St Andrews, Bute Building, Westburn Lane, St Andrews, Fife KY16 9TS, UK.
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Abstract
Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating the genetic mapping of agriculturally important phenotypes. The first step in optimizing the design of genetic mapping studies involves large-scale polymorphism discovery and a subsequent genome-wide assessment of the population structure and pattern of linkage disequilibrium (LD) in the species of interest. In the present study, we provide such an assessment for the grapevine (genus Vitis), the world's most economically important fruit crop. Reduced representation libraries (RRLs) from 17 grape DNA samples (10 cultivated V. vinifera and 7 wild Vitis species) were sequenced with sequencing-by-synthesis technology. We developed heuristic approaches for SNP calling, identified hundreds of thousands of SNPs and validated a subset of these SNPs on a 9K genotyping array. We demonstrate that the 9K SNP array provides sufficient resolution to distinguish among V. vinifera cultivars, between V. vinifera and wild Vitis species, and even among diverse wild Vitis species. We show that there is substantial sharing of polymorphism between V. vinifera and wild Vitis species and find that genetic relationships among V. vinifera cultivars agree well with their proposed geographic origins using principal components analysis (PCA). Levels of LD in the domesticated grapevine are low even at short ranges, but LD persists above background levels to 3 kb. While genotyping arrays are useful for assessing population structure and the decay of LD across large numbers of samples, we suggest that whole-genome sequencing will become the genotyping method of choice for genome-wide genetic mapping studies in high-diversity plant species. This study demonstrates that we can move quickly towards genome-wide studies of crop species using next-generation sequencing. Our study sets the stage for future work in other high diversity crop species, and provides a significant enhancement to current genetic resources available to the grapevine genetic community.
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Affiliation(s)
- Sean Myles
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
| | - Jer-Ming Chia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Bonnie Hurwitz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Charles Simon
- New York State Agricultural Experiment Station, Geneva, New York, United States of America
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, United States of America
| | - Gan Yuan Zhong
- New York State Agricultural Experiment Station, Geneva, New York, United States of America
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, United States of America
| | - Edward Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, United States of America
- * E-mail: (EB); (DW)
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, United States of America
- * E-mail: (EB); (DW)
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Myles S, Peiffer J, Brown PJ, Ersoz ES, Zhang Z, Costich DE, Buckler ES. Association mapping: critical considerations shift from genotyping to experimental design. Plant Cell 2009; 21:2194-202. [PMID: 19654263 PMCID: PMC2751942 DOI: 10.1105/tpc.109.068437] [Citation(s) in RCA: 433] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2009] [Revised: 07/06/2009] [Accepted: 07/13/2009] [Indexed: 05/18/2023]
Abstract
The goal of many plant scientists' research is to explain natural phenotypic variation in terms of simple changes in DNA sequence. Traditionally, linkage mapping has been the most commonly employed method to reach this goal: experimental crosses are made to generate a family with known relatedness, and attempts are made to identify cosegregation of genetic markers and phenotypes within this family. In vertebrate systems, association mapping (also known as linkage disequilibrium mapping) is increasingly being adopted as the mapping method of choice. Association mapping involves searching for genotype-phenotype correlations in unrelated individuals and often is more rapid and cost-effective than traditional linkage mapping. We emphasize here that linkage and association mapping are complementary approaches and are more similar than is often assumed. Unlike in vertebrates, where controlled crosses can be expensive or impossible (e.g., in humans), the plant scientific community can exploit the advantages of both controlled crosses and association mapping to increase statistical power and mapping resolution. While the time and money required for the collection of genotype data were critical considerations in the past, the increasing availability of inexpensive DNA sequencing and genotyping methods should prompt researchers to shift their attention to experimental design. This review provides thoughts on finding the optimal experimental mix of association mapping using unrelated individuals and controlled crosses to identify the genes underlying phenotypic variation.
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Affiliation(s)
- Sean Myles
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853-2703, USA.
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Hillmer AM, Freudenberg J, Myles S, Herms S, Tang K, Hughes DA, Brockschmidt FF, Ruan Y, Stoneking M, Nöthen MM. Recent positive selection of a human androgen receptor/ectodysplasin A2 receptor haplotype and its relationship to male pattern baldness. Hum Genet 2009; 126:255-64. [PMID: 19373488 PMCID: PMC3774421 DOI: 10.1007/s00439-009-0668-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Accepted: 04/06/2009] [Indexed: 12/12/2022]
Abstract
Genetic variants in the human androgen receptor gene (AR) are associated with male pattern baldness (androgenetic alopecia, AGA) in Europeans. Previous observations of long-range linkage disequilibrium at the AR locus are consistent with the hypothesis of recent positive selection. Here, we further investigate this signature and its relationship to the AGA risk haplotype. The haplotype homozygosity suggests that the AGA risk haplotype was driven to high frequency by positive selection in Europeans although a low meiotic recombination rate contributed to the high haplotype homozygosity. Further, we find high levels of population differentiation as measured by F(ST) and a series of fixed derived alleles along an extended region centromeric to AR in the Asian HapMap sample. The predominant AGA risk haplotype also carries the putatively functional variant 57K in the flanking ectodysplasin A2 receptor gene (EDA2R). It is therefore probable that the AGA risk haplotype rose to high frequency in combination with this EDA2R variant, possibly by hitchhiking on a positively selected 57K haplotype.
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Affiliation(s)
- Axel M Hillmer
- Department of Genomics, Life and Brain Center, University of Bonn, Bonn, Germany.
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Myles S, Stoneking M, Timpson N. An assessment of the portability of ancestry informative markers between human populations. BMC Med Genomics 2009; 2:45. [PMID: 19619313 PMCID: PMC2719660 DOI: 10.1186/1755-8794-2-45] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 07/20/2009] [Indexed: 12/20/2022] Open
Abstract
Background Recent work has shown that population stratification can have confounding effects on genetic association studies and statistical methods have been developed to correct for these effects. Subsets of markers that are highly-differentiated between populations, ancestry-informative markers (AIMs), have been used to correct for population stratification. Often AIMs are discovered in one set of populations and then employed in a different set of populations. The underlying assumption in these cases is that the population under study has the same substructure as the population in which the AIMs were discovered. The present study assesses this assumption and evaluates the portability between worldwide populations of 10 SNPs found to be highly-differentiated within Britain (BritAIMs). Methods We genotyped 10 BritAIMs in ~1000 individuals from 53 populations worldwide. We assessed the degree to which these 10 BritAIMs capture population stratification in other groups of populations by use of the Fst statistic. We used Fst values from 2750 random markers typed in the same set of individuals as an empirical distribution to which the Fst values of the 10 BritAIMs were compared. Results Allele frequency differences between continental groups for the BritAIMs are not unusually high. This is also the case for comparisons within continental groups distantly related to Britain. However, two BritAIMs show high Fst between European populations and two BritAIMs show high Fst between populations from the Middle East. Overall the median Fst across all BritAIMs is not unusually high compared to the empirical distribution. Conclusion We find that BritAIMs are generally not useful to distinguish between continental groups or within continental groups distantly related to Britain. Moreover, our analyses suggest that the portability of AIMs across geographical scales (e.g. between Europe and Britain) can be limited and should therefore be taken into consideration in the design and interpretation of genetic association studies.
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Affiliation(s)
- Sean Myles
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY 14853-2703, USA.
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Silander K, Tang H, Myles S, Jakkula E, Timpson NJ, Cavalli-Sforza L, Peltonen L. Worldwide patterns of haplotype diversity at 9p21.3, a locus associated with type 2 diabetes and coronary heart disease. Genome Med 2009; 1:51. [PMID: 19463184 PMCID: PMC2689443 DOI: 10.1186/gm51] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2009] [Revised: 03/27/2009] [Accepted: 05/12/2009] [Indexed: 11/10/2022] Open
Abstract
A 100 kb region on 9p21.3 harbors two major disease susceptibility loci: one for type 2 diabetes (T2D) and one for coronary heart disease (CHD). The single nucleotide polymorphisms (SNPs) associated with these two diseases in Europeans reside on two adjacent haplotype blocks with independent effects on disease. To help delimit the regions that likely harbor the disease-causing variants in populations of non-European origin, we studied the haplotype diversity and allelic history of the 9p21.3 region using 938 unrelated individuals from 51 populations (Human Genome Diversity Panel). We used SNP data from Illumina's 650Y SNP arrays supplemented with five additional SNPs within the region of interest. Haplotype frequencies were analyzed with the EM algorithm implemented in PLINK. For the T2D locus, the TT risk haplotype of SNPs rs10811661 and rs10757283 was present at similar frequencies in all global populations, while a shared 6-SNP haplotype that carries the protective C allele of rs10811661 was found at a frequency of 2.9% in Africans and 41.3% in East Asians and was associated with low haplotype diversity. For the CHD locus, all populations shared a core risk haplotype spanning >17.5 kb, which shows dramatic increase in frequency between African (11.5%) and Middle Eastern (63.7%) populations. Interestingly, two SNPs (rs2891168 and rs10757278) tagging this CHD risk haplotype are most strongly associated with CHD disease status according to independent clinical fine-mapping studies. The large variation in linkage disequilibrium patterns identified between the populations demonstrates the importance of allelic background data when selecting SNPs for replication in global populations. Intriguingly, the protective allele for T2D and the risk allele for CHD show an increase in frequency in non-Africans compared to Africans, implying different population histories for these two adjacent disease loci.
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Affiliation(s)
- Kaisa Silander
- Institute of Molecular Medicine FIMM, University of Helsinki, and Unit of Public Health Genomics, National Institute for Health and Welfare, Tukholmankatu 8, 00290 Helsinki, Finland.
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Shaw C, McNamara R, Abrams K, Cannings-John R, Hood K, Longo M, Myles S, O'Mahony S, Roe B, Williams K. Systematic review of respite care in the frail elderly. Health Technol Assess 2009; 13:1-224, iii. [DOI: 10.3310/hta13200] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- C Shaw
- Department of Care Sciences, University of Glamorgan, Pontypridd, UK
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Myles S, Davison D, Barrett J, Stoneking M, Timpson N. Worldwide population differentiation at disease-associated SNPs. BMC Med Genomics 2008; 1:22. [PMID: 18533027 PMCID: PMC2440747 DOI: 10.1186/1755-8794-1-22] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Accepted: 06/04/2008] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Recent genome-wide association (GWA) studies have provided compelling evidence of association between genetic variants and common complex diseases. These studies have made use of cases and controls almost exclusively from populations of European ancestry and little is known about the frequency of risk alleles in other populations. The present study addresses the transferability of disease associations across human populations by examining levels of population differentiation at disease-associated single nucleotide polymorphisms (SNPs). METHODS We genotyped ~1000 individuals from 53 populations worldwide at 25 SNPs which show robust association with 6 complex human diseases (Crohn's disease, type 1 diabetes, type 2 diabetes, rheumatoid arthritis, coronary artery disease and obesity). Allele frequency differences between populations for these SNPs were measured using Fst. The Fst values for the disease-associated SNPs were compared to Fst values from 2750 random SNPs typed in the same set of individuals. RESULTS On average, disease SNPs are not significantly more differentiated between populations than random SNPs in the genome. Risk allele frequencies, however, do show substantial variation across human populations and may contribute to differences in disease prevalence between populations. We demonstrate that, in some cases, risk allele frequency differences are unusually high compared to random SNPs and may be due to the action of local (i.e. geographically-restricted) positive natural selection. Moreover, some risk alleles were absent or fixed in a population, which implies that risk alleles identified in one population do not necessarily account for disease prevalence in all human populations. CONCLUSION Although differences in risk allele frequencies between human populations are not unusually large and are thus likely not due to positive local selection, there is substantial variation in risk allele frequencies between populations which may account for differences in disease prevalence between human populations.
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Affiliation(s)
- Sean Myles
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
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Bryk J, Hardouin E, Pugach I, Hughes D, Strotmann R, Stoneking M, Myles S. Positive selection in East Asians for an EDAR allele that enhances NF-kappaB activation. PLoS One 2008; 3:e2209. [PMID: 18493316 PMCID: PMC2374902 DOI: 10.1371/journal.pone.0002209] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 04/07/2008] [Indexed: 12/18/2022] Open
Abstract
Genome-wide scans for positive selection in humans provide a promising approach to establish links between genetic variants and adaptive phenotypes. From this approach, lists of hundreds of candidate genomic regions for positive selection have been assembled. These candidate regions are expected to contain variants that contribute to adaptive phenotypes, but few of these regions have been associated with phenotypic effects. Here we present evidence that a derived nonsynonymous substitution (370A) in EDAR, a gene involved in ectodermal development, was driven to high frequency in East Asia by positive selection prior to 10,000 years ago. With an in vitro transfection assay, we demonstrate that 370A enhances NF-kappaB activity. Our results suggest that 370A is a positively selected functional genetic variant that underlies an adaptive human phenotype.
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Affiliation(s)
- Jarosław Bryk
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Emilie Hardouin
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Irina Pugach
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David Hughes
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rainer Strotmann
- Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sean Myles
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- * E-mail:
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Myles S, Tang K, Somel M, Green RE, Kelso J, Stoneking M. Identification and analysis of genomic regions with large between-population differentiation in humans. Ann Hum Genet 2008; 72:99-110. [PMID: 18184145 DOI: 10.1111/j.1469-1809.2007.00390.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The primary aim of genetic association and linkage studies is to identify genetic variants that contribute to phenotypic variation within human populations. Since the overwhelming majority of human genetic variation is found within populations, these methods are expected to be effective and can likely be extrapolated from one human population to another. However, they may lack power in detecting the genetic variants that contribute to phenotypes that differ greatly between human populations. Phenotypes that show large differences between populations are expected to be associated with genomic regions exhibiting large allele frequency differences between populations. Thus, from genome-wide polymorphism data genomic regions with large allele frequency differences between populations can be identified, and evaluated as candidates for large between-population phenotypic differences. Here we use allele frequency data from approximately 1.5 million SNPs from three human populations, and present an algorithm that identifies genomic regions containing SNPs with extreme Fst. We demonstrate that our candidate regions have reduced heterozygosity in Europeans and Chinese relative to African-Americans, and are likely enriched with genes that have experienced positive natural selection. We identify genes that are likely responsible for phenotypes known to differ dramatically between human populations and present several candidates worthy of future investigation. Our list of high Fst genomic regions is a first step in identifying the genetic variants that contribute to large phenotypic differences between populations, many of which have likely experienced positive natural selection. Our approach based on between population differences can compliment traditional within population linkage and association studies to uncover novel genotype-phenotype relationships.
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Affiliation(s)
- S Myles
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig,
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