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Pasqualetto G, Palmieri L, Martens S, Bus VGM, Chagné D, Wiedow C, Malnoy MA, Gardiner SE. Molecular characterization of intergeneric hybrids between Malus and Pyrus. HORTICULTURE RESEARCH 2022; 10:uhac239. [PMID: 36643755 PMCID: PMC9832871 DOI: 10.1093/hr/uhac239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Apple (Malus) and pear (Pyrus) are economically important fruit crops well known for their unique textures, flavours, and nutritional qualities. Both genera are characterised by a distinct pattern of secondary metabolites, which directly affect not only resistance to certain diseases, but also have significant impacts on the flavour and nutritional value of the fruit. The identical chromosome numbers, similar genome size, and their recent divergence date, together with DNA markers have shown that apple and pear genomes are highly co-linear. This study utilized comparative genomic approaches, including simple sequence repeats, high resolution single nucleotide polymorphism melting analysis, and single nucleotide polymorphism chip analysis to identify genetic differences among hybrids of Malus and Pyrus, and F2 offspring. This research has demonstrated and validated that these three marker types, along with metabolomics analysis are very powerful tools to detect and confirm hybridity of progeny derived from crosses between apple and pear in both cross directions. Furthermore, this work analysed the genus-specific metabolite patterns and the resistance to fire blight (Erwinia amylovora) in progeny. The findings of this work will enhance and accelerate the breeding of novel tree fruit crops that benefit producers and consumers, by enabling marker assisted selection of desired traits introgressed between pear and apple.
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Affiliation(s)
- Giulia Pasqualetto
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, UD 33100, Italy
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - Luisa Palmieri
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
| | - Stefan Martens
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
| | - Vincent G M Bus
- The New Zealand Institute for Plant and Food Research Ltd (PFR), Hawke’s Bay Research Centre, Havelock North, New Zealand
| | - David Chagné
- PFR, Fitzherbert Science Centre, Palmerston North, New Zealand
| | - Claudia Wiedow
- PFR, Fitzherbert Science Centre, Palmerston North, New Zealand
| | - Mickael A Malnoy
- Research and Innovation Centre, Edmund Mach Foundation, San Michele all'Adige, TN 38010, Italy
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Button-Simons KA, Kumar S, Carmago N, Haile MT, Jett C, Checkley LA, Kennedy SY, Pinapati RS, Shoue DA, McDew-White M, Li X, Nosten FH, Kappe SH, Anderson TJC, Romero-Severson J, Ferdig MT, Emrich SJ, Vaughan AM, Cheeseman IH. The power and promise of genetic mapping from Plasmodium falciparum crosses utilizing human liver-chimeric mice. Commun Biol 2021; 4:734. [PMID: 34127785 PMCID: PMC8203791 DOI: 10.1038/s42003-021-02210-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 04/30/2021] [Indexed: 12/30/2022] Open
Abstract
Genetic crosses are most powerful for linkage analysis when progeny numbers are high, parental alleles segregate evenly and numbers of inbred progeny are minimized. We previously developed a novel genetic crossing platform for the human malaria parasite Plasmodium falciparum, an obligately sexual, hermaphroditic protozoan, using mice carrying human hepatocytes (the human liver-chimeric FRG NOD huHep mouse) as the vertebrate host. We report on two genetic crosses-(1) an allopatric cross between a laboratory-adapted parasite (NF54) of African origin and a recently patient-derived Asian parasite, and (2) a sympatric cross between two recently patient-derived Asian parasites. We generated 144 unique recombinant clones from the two crosses, doubling the number of unique recombinant progeny generated in the previous 30 years. The allopatric African/Asian cross has minimal levels of inbreeding and extreme segregation distortion, while in the sympatric Asian cross, inbred progeny predominate and parental alleles segregate evenly. Using simulations, we demonstrate that these progeny provide the power to map small-effect mutations and epistatic interactions. The segregation distortion in the allopatric cross slightly erodes power to detect linkage in several genome regions. We greatly increase the power and the precision to map biomedically important traits with these new large progeny panels.
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Affiliation(s)
- Katrina A Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nelly Carmago
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Meseret T Haile
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Catherine Jett
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Lisa A Checkley
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Spencer Y Kennedy
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Douglas A Shoue
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Marina McDew-White
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - François H Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine Research Building, University of Oxford Old Road Campus, Oxford, UK
| | - Stefan H Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Timothy J C Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | | | - Michael T Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | | | - Ashley M Vaughan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ian H Cheeseman
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, USA.
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Delame M, Prado E, Blanc S, Robert-Siegwald G, Schneider C, Mestre P, Rustenholz C, Merdinoglu D. Introgression reshapes recombination distribution in grapevine interspecific hybrids. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1073-1087. [PMID: 30535509 DOI: 10.1007/s00122-018-3260-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/03/2018] [Indexed: 05/25/2023]
Abstract
In grapevine interspecific hybrids, meiotic recombination is suppressed in homeologous regions and enhanced in homologous regions of recombined chromosomes, whereas crossover rate remains unchanged when chromosome pairs are entirely homeologous. Vitis rotundifolia, an American species related to the cultivated European grapevine Vitis vinifera, has a high level of resistance to several grapevine major diseases and is consequently a valuable resource for grape breeding. However, crosses between both species most often lead to very few poorly fertile hybrids. In this context, identifying genetic and genomic features that make cross-breeding between both species difficult is essential. To this end, three mapping populations were generated by pseudo-backcrosses using V. rotundifolia as the donor parent and several V. vinifera cultivars as the recurrent parents. Genotyping-by-sequencing was used to establish high-density genetic linkage maps and to determine the genetic composition of the chromosomes of each individual. A good collinearity of the SNP positions was observed between parental maps, confirming the synteny between both species, except on lower arm of chromosome 7. Interestingly, recombination rate in V. rotundifolia × V. vinifera interspecific hybrids depends on the length of the introgressed region. It is similar to grapevine for chromosome pairs entirely homeologous. Conversely, for chromosome pairs partly homeologous, recombination is suppressed in the homeologous regions, whereas it is enhanced in the homologous ones. This balance leads to the conservation of the total genetic length of each chromosome between V. vinifera and hybrid maps, whatever the backcross level and the proportion of homeologous region. Altogether, these results provide new insight to optimize the use of V. rotundifolia in grape breeding and, more generally, to improve the introgression of gene of interest from wild species related to crops.
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Affiliation(s)
- Marion Delame
- SVQV UMR-A 1131, INRA, Université de Strasbourg, 68000, Colmar, France
- Direction des Formations Doctorales, AgroParisTech, 19 avenue du Maine, 75015, Paris, France
| | - Emilce Prado
- SVQV UMR-A 1131, INRA, Université de Strasbourg, 68000, Colmar, France
| | - Sophie Blanc
- SVQV UMR-A 1131, INRA, Université de Strasbourg, 68000, Colmar, France
| | | | | | - Pere Mestre
- SVQV UMR-A 1131, INRA, Université de Strasbourg, 68000, Colmar, France
| | | | - Didier Merdinoglu
- SVQV UMR-A 1131, INRA, Université de Strasbourg, 68000, Colmar, France.
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Giesbers AKJ, den Boer E, Ulen JJWEH, van Kaauwen MPW, Visser RGF, Niks RE, Jeuken MJW. Patterns of Transmission Ratio Distortion in Interspecific Lettuce Hybrids Reveal a Sex-Independent Gametophytic Barrier. Genetics 2019; 211:263-276. [PMID: 30401697 PMCID: PMC6325705 DOI: 10.1534/genetics.118.301566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 10/30/2018] [Indexed: 11/18/2022] Open
Abstract
Interspecific crosses can result in progeny with reduced vitality or fertility due to genetic incompatibilities between species, a phenomenon known as hybrid incompatibility (HI). HI is often caused by a bias against deleterious allele combinations, which results in transmission ratio distortion (TRD). Here, we determined the genome-wide distribution of HI between wild lettuce, Lactuca saligna, and cultivated lettuce, L. sativa, in a set of backcross inbred lines (BILs) with single introgression segments from L. saligna introgressed into a L. sativa genetic background. Almost all BILs contained an introgression segment in a homozygous state except a few BILs, for which we were able to obtain only a single heterozygous introgression. Their inbred progenies displayed severe TRD with a bias toward the L. sativa allele and complete nontransmission of the homozygous L. saligna introgression, i.e., absolute HI. These HI might be caused by deleterious heterospecific allele combinations at two loci. We used an multilocus segregating interspecific F2 population to identify candidate conspecific loci that can nullify the HI in BILs. Segregation analysis of developed double-introgression progenies showed nullification of three HI and proved that these HI are explained by nuclear pairwise incompatibilities. One of these digenic HI showed 29% reduced seed set and its pattern of TRD pointed to a sex-independent gametophytic barrier. Namely, this HI was caused by complete nontransmission of one heterospecific allele combination at the haploid stage, surprisingly in both male and female gametophytes. Our study shows that two-locus incompatibility systems contribute to reproductive barriers among Lactuca species.
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Affiliation(s)
- Anne K J Giesbers
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Erik den Boer
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | | | | | - Richard G F Visser
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Rients E Niks
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Marieke J W Jeuken
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
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Gramlich S, Wagner ND, Hörandl E. RAD-seq reveals genetic structure of the F 2-generation of natural willow hybrids (Salix L.) and a great potential for interspecific introgression. BMC PLANT BIOLOGY 2018; 18:317. [PMID: 30509159 PMCID: PMC6276181 DOI: 10.1186/s12870-018-1552-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/21/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Hybridization of species with porous genomes can eventually lead to introgression via repeated backcrossing. The potential for introgression between species is reflected by the extent of segregation distortion in later generation hybrids. Here we studied a population of hybrids between Salix purpurea and S. helvetica that has emerged within the last 30 years on a glacier forefield in the European Alps due to secondary contact of the parental species. We used 5758 biallelic SNPs produced by RAD sequencing with the aim to ascertain the predominance of backcrosses (F1 hybrid x parent) or F2 hybrids (F1 hybrid x F1 hybrid) among hybrid offspring. Further, the SNPs were used to study segregation distortion in the second hybrid generation. RESULTS The analyses in STRUCTURE and NewHybrids revealed that the population consisted of parents and F1 hybrids, whereas hybrid offspring consisted mainly of backcrosses to either parental species, but also some F2 hybrids. Although there was a clear genetic differentiation between S. purpurea and S. helvetica (FST = 0.24), there was no significant segregation distortion in the backcrosses or the F2 hybrids. Plant height of the backcrosses resembled the respective parental species, whereas F2 hybrids were more similar to the subalpine S. helvetica. CONCLUSIONS The co-occurrence of the parental species and the hybrids on the glacier forefield, the high frequency of backcrossing, and the low resistance to gene flow via backcrossing make a scenario of introgression in this young hybrid population highly likely, potentially leading to the transfer of adaptive traits. We further suggest that this willow hybrid population may serve as a model for the evolutionary processes initiated by recent global warming.
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Affiliation(s)
- Susanne Gramlich
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
| | - Natascha Dorothea Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University Goettingen, Untere Karspüle 2, 37073 Goettingen, Germany
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Ma GJ, Song QJ, Markell SG, Qi LL. High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R 15 , in sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1423-1432. [PMID: 29564500 DOI: 10.1007/s00122-018-3087-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 03/12/2018] [Indexed: 06/08/2023]
Abstract
A novel rust resistance gene, R 15 , derived from the cultivated sunflower HA-R8 was assigned to linkage group 8 of the sunflower genome using a genotyping-by-sequencing approach. SNP markers closely linked to R 15 were identified, facilitating marker-assisted selection of resistance genes. The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environmentally friendly host plant resistance. The inbred line HA-R8 carries a gene conferring resistance to all known races of the rust pathogen in North America and can be used as a broad-spectrum resistance resource. Based on phenotypic assessments of 140 F2 individuals derived from a cross of HA 89 with HA-R8, rust resistance in the population was found to be conferred by a single dominant gene (R 15 ) originating from HA-R8. Genotypic analysis with the currently available SSR markers failed to find any association between rust resistance and any markers. Therefore, we used genotyping-by-sequencing (GBS) analysis to achieve better genomic coverage. The GBS data showed that R 15 was located at the top end of linkage group (LG) 8. Saturation with 71 previously mapped SNP markers selected within this region further showed that it was located in a resistance gene cluster on LG8, and mapped to a 1.0-cM region between three co-segregating SNP makers SFW01920, SFW00128, and SFW05824 as well as the NSA_008457 SNP marker. These closely linked markers will facilitate marker-assisted selection and breeding in sunflower.
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Affiliation(s)
- G J Ma
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - Q J Song
- Soybean Genomics and Improvement Laboratory, USDA-Agricultural Research Service, Beltsville, MD, 20705-2350, USA
| | - S G Markell
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA
| | - L L Qi
- Red River Valley Agricultural Research Center, USDA-Agricultural Research Service, Fargo, ND, 58102-2765, USA.
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Larcombe MJ, Costa E Silva J, Tilyard P, Gore P, Potts BM. On the persistence of reproductive barriers in Eucalyptus: the bridging of mechanical barriers to zygote formation by F1 hybrids is counteracted by intrinsic post-zygotic incompatibilities. ANNALS OF BOTANY 2016; 118:431-44. [PMID: 27401540 PMCID: PMC4998977 DOI: 10.1093/aob/mcw115] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/04/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Many previous studies conclude that pre-zygotic barriers such as mechanical isolation account for most reproductive isolation between pairs of taxa. However, the inheritance and persistence of barriers such as these after the first generation of hybridization is rarely quantified, even though it is a vital consideration in understanding gene flow potential. There is an asymmetrical pre-zygotic mechanical barrier to hybridization between Eucalyptus nitens and Eucalyptus globulus, which completely prevents small-flowered E. nitens pollen from mating with large E. globulus flowers, while the reverse cross is possible. We aimed to determine the relative importance of pre- and post-zygotic barriers in preventing gene flow following secondary contact between E. nitens and E. globulus, including the inheritance of barriers in advanced-generation hybrids. METHODS Experimental crossing was used to produce outcrossed E. nitens, E. globulus and their F1, F2, BCg and BCn hybrids. The strength and inheritance of a suite of pre- and post-zygotic barriers were assessed, including 20-year survival, growth and reproductive capacity. KEY RESULTS The mechanical barrier to hybridization was lost or greatly reduced in the F1 hybrid. In contrast, intrinsic post-zygotic barriers were strong and persistent. Line-cross analysis indicated that the outbreeding depression in the hybrids was best explained by epistatic loss. CONCLUSIONS The removal of strong mechanical barriers between E. nitens and E. globulus allows F1 hybrids to act as a bridge for bi-directional gene flow between these species. However, strong and persistent post-zygotic barriers exist, meaning that wherever F1 hybridization does occur, intrinsic post-zygotic barriers will be responsible for most reproductive isolation in this system. This potential transient nature of mechanical barriers to zygote formation due to additive inheritance in hybrids appears under-appreciated, and highlights the often important role that intrinsic post-mating barriers play in maintaining species boundaries at zones of secondary contact.
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Affiliation(s)
- Matthew J Larcombe
- Department of Botany, University of Otago, PO Box 56, Dunedin 9011, New Zealand
| | - João Costa E Silva
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Paul Tilyard
- School of Biological Sciences, and ARC Centre for Forest Value, 10 University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
| | - Peter Gore
- seedEnergy Pty Ltd, 2 Derwent Avenue, Margate, Tasmania 7054, Australia
| | - Brad M Potts
- School of Biological Sciences, and ARC Centre for Forest Value, 10 University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
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Bodénès C, Chancerel E, Ehrenmann F, Kremer A, Plomion C. High-density linkage mapping and distribution of segregation distortion regions in the oak genome. DNA Res 2016; 23:115-24. [PMID: 27013549 PMCID: PMC4833419 DOI: 10.1093/dnares/dsw001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/05/2016] [Indexed: 11/14/2022] Open
Abstract
We developed the densest single-nucleotide polymorphism (SNP)-based linkage genetic map to date for the genus Quercus An 8k gene-based SNP array was used to genotype more than 1,000 full-sibs from two intraspecific and two interspecific full-sib families of Quercus petraea and Quercus robur A high degree of collinearity was observed between the eight parental maps of the two species. A composite map was then established with 4,261 SNP markers spanning 742 cM over the 12 linkage groups (LGs) of the oak genome. Nine genomic regions from six LGs displayed highly significant distortions of segregation. Two main hypotheses concerning the mechanisms underlying segregation distortion are discussed: genetic load vs. reproductive barriers. Our findings suggest a predominance of pre-zygotic to post-zygotic barriers.
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Affiliation(s)
- Catherine Bodénès
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France Université de Bordeaux, UMR1202 BIOGECO, F-33610 Talence, France
| | - Emilie Chancerel
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France Université de Bordeaux, UMR1202 BIOGECO, F-33610 Talence, France
| | - François Ehrenmann
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France Université de Bordeaux, UMR1202 BIOGECO, F-33610 Talence, France
| | - Antoine Kremer
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France Université de Bordeaux, UMR1202 BIOGECO, F-33610 Talence, France
| | - Christophe Plomion
- INRA, UMR1202 BIOGECO, F-33610 Cestas, France Université de Bordeaux, UMR1202 BIOGECO, F-33610 Talence, France
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Liu S, Li Y, Qin Z, Geng X, Bao L, Kaltenboeck L, Kucuktas H, Dunham R, Liu Z. High-density interspecific genetic linkage mapping provides insights into genomic incompatibility between channel catfish and blue catfish. Anim Genet 2015; 47:81-90. [PMID: 26537786 DOI: 10.1111/age.12372] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2015] [Indexed: 02/01/2023]
Abstract
Catfish is the leading aquaculture species in the United States. The interspecific hybrid catfish produced by mating female channel catfish with male blue catfish outperform both of their parent species in a number of traits. However, mass production of the hybrids has been difficult because of reproductive isolation. Investigations of genome structure and organization of the hybrids provide insights into the genetic basis for maintenance of species divergence in the face of gene flow, thereby helping develop strategies for introgression and efficient production of the hybrids for aquaculture. In this study, we constructed a high-density genetic linkage map using the hybrid catfish system with the catfish 250K SNP array. A total of 26,238 SNPs were mapped to 29 linkage groups, with 12,776 unique marker positions. The linkage map spans approximately 3240 cM with an average intermarker distance of 0.25 cM. A fraction of markers (986 of 12,776) exhibited significant deviation from the expected Mendelian ratio of segregation, and they were clustered in major genomic blocks across 15 LGs, most notably LG9 and LG15. The distorted markers exhibited significant bias for maternal alleles among the backcross progenies, suggesting strong selection against the blue catfish alleles. The clustering of distorted markers within genomic blocks should lend insights into speciation as marked by incompatibilities between the two species. Such findings should also have profound implications for understanding the genomic evolution of closely related species as well as the introgression of hybrid production programs in aquaculture.
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Affiliation(s)
- S Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - Y Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - Z Qin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - X Geng
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - L Bao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - L Kaltenboeck
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - H Kucuktas
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - R Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
| | - Z Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, USA
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10
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Hudson CJ, Freeman JS, Myburg AA, Potts BM, Vaillancourt RE. Genomic patterns of species diversity and divergence in Eucalyptus. THE NEW PHYTOLOGIST 2015; 206:1378-1390. [PMID: 25678438 DOI: 10.1111/nph.13316] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 12/19/2014] [Indexed: 06/04/2023]
Abstract
We examined genome-wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range-wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW ) and divergence (FST ), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1-5.3% of markers and were widely distributed throughout the genome. Marker divergence (FST and SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology.
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Affiliation(s)
- Corey J Hudson
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
- Tasmanian Alkaloids, PO Box 130, Westbury, TAS 7303, Australia
| | - Jules S Freeman
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
- National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
- Faculty of Science, Health, Education and Engineering, and Collaborative Research Network, University of the Sunshine Coast, Locked Bag 4, Maroochydore, QLD, 4558, Australia
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Brad M Potts
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
- National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
| | - René E Vaillancourt
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
- National Centre for Future Forest Industries, University of Tasmania, Private Bag 55, Hobart, TAS, 7001, Australia
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11
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Zhou W, Tang Z, Hou J, Hu N, Yin T. Genetic Map Construction and Detection of Genetic Loci Underlying Segregation Distortion in an Intraspecific Cross of Populus deltoides. PLoS One 2015; 10:e0126077. [PMID: 25942445 PMCID: PMC4420497 DOI: 10.1371/journal.pone.0126077] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/25/2015] [Indexed: 11/18/2022] Open
Abstract
Based on a two-way pseudo-testcross strategy, high density and complete coverage linkage maps were constructed for the maternal and paternal parents of an intraspecific F2 pedigree of Populus deltoides. A total of 1,107 testcross markers were obtained, and the mapping population consisted of 376 progeny. Among these markers, 597 were from the mother, and were assigned into 19 linkage groups, spanning a total genetic distance of 1,940.3 cM. The remaining 519 markers were from the father, and were also were mapped into 19 linkage groups, covering 2,496.3 cM. The genome coverage of both maps was estimated as greater than 99.9% at 20 cM per marker, and the numbers of linkage groups of both maps were in accordance with the 19 haploid chromosomes in Populus. Marker segregation distortion was observed in large contiguous blocks on some of the linkage groups. Subsequently, we mapped the segregation distortion loci in this mapping pedigree. Altogether, eight segregation distortion loci with significant logarithm of odds supports were detected. Segregation distortion indicated the uneven transmission of the alternate alleles from the mapping parents. The corresponding genome regions might contain deleterious genes or be associated with hybridization incompatibility. In addition to the detection of segregation distortion loci, the established genetic maps will serve as a basic resource for mapping genetic loci controlling traits of interest in future studies.
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Affiliation(s)
- Wencai Zhou
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
- Jiangxi Academy of Forestry, Nanchang 330032, China
| | - Zaixiang Tang
- Department of Epidemiology and Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou 215123, China
| | - Jing Hou
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Nan Hu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Tongming Yin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, China
- * E-mail:
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12
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Larcombe MJ, Holland B, Steane DA, Jones RC, Nicolle D, Vaillancourt RE, Potts BM. Patterns of Reproductive Isolation inEucalyptus—A Phylogenetic Perspective. Mol Biol Evol 2015; 32:1833-46. [DOI: 10.1093/molbev/msv063] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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13
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Dumas P, Legeai F, Lemaitre C, Scaon E, Orsucci M, Labadie K, Gimenez S, Clamens AL, Henri H, Vavre F, Aury JM, Fournier P, Kergoat GJ, d'Alençon E. Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species? Genetica 2015; 143:305-16. [PMID: 25694156 PMCID: PMC4419160 DOI: 10.1007/s10709-015-9829-2] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 02/09/2015] [Indexed: 12/11/2022]
Abstract
The moth Spodoptera frugiperda is a well-known pest of crops throughout the Americas, which consists of two strains adapted to different host-plants: the first feeds preferentially on corn, cotton and sorghum whereas the second is more associated with rice and several pasture grasses. Though morphologically indistinguishable, they exhibit differences in their mating behavior, pheromone compositions, and show development variability according to the host-plant. Though the latter suggest that both strains are different species, this issue is still highly controversial because hybrids naturally occur in the wild, not to mention the discrepancies among published results concerning mating success between the two strains. In order to clarify the status of the two host-plant strains of S. frugiperda, we analyze features that possibly reflect the level of post-zygotic isolation: (1) first generation (F1) hybrid lethality and sterility; (2) patterns of meiotic segregation of hybrids in reciprocal second generation (F2), as compared to the meiosis of the two parental strains. We found a significant reduction of mating success in F1 in one direction of the cross and a high level of microsatellite markers showing transmission ratio distortion in the F2 progeny. Our results support the existence of post-zygotic reproductive isolation between the two laboratory strains and are in accordance with the marked level of genetic differentiation that was recovered between individuals of the two strains collected from the field. Altogether these results provide additional evidence in favor of a sibling species status for the two strains.
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Affiliation(s)
- Pascaline Dumas
- UM - UMR 1333 DGIMI, Université Montpellier, Place Eugène Bataillon, 34095, Montpellier, France,
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14
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Sequencing, assembling, and correcting draft genomes using recombinant populations. G3-GENES GENOMES GENETICS 2014; 4:669-79. [PMID: 24531727 PMCID: PMC4059239 DOI: 10.1534/g3.114.010264] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Current de novo whole-genome sequencing approaches often are inadequate for organisms lacking substantial preexisting genetic data. Problems with these methods are manifest as: large numbers of scaffolds that are not ordered within chromosomes or assigned to individual chromosomes, misassembly of allelic sequences as separate loci when the individual(s) being sequenced are heterozygous, and the collapse of recently duplicated sequences into a single locus, regardless of levels of heterozygosity. Here we propose a new approach for producing de novo whole-genome sequences—which we call recombinant population genome construction—that solves many of the problems encountered in standard genome assembly and that can be applied in model and nonmodel organisms. Our approach takes advantage of next-generation sequencing technologies to simultaneously barcode and sequence a large number of individuals from a recombinant population. The sequences of all recombinants can be combined to create an initial de novo assembly, followed by the use of individual recombinant genotypes to correct assembly splitting/collapsing and to order and orient scaffolds within linkage groups. Recombinant population genome construction can rapidly accelerate the transformation of nonmodel species into genome-enabled systems by simultaneously producing a high-quality genome assembly and providing genomic tools (e.g., high-confidence single-nucleotide polymorphisms) for immediate applications. In populations segregating for important functional traits, this approach also enables simultaneous mapping of quantitative trait loci. We demonstrate our method using simulated Illumina data from a recombinant population of Caenorhabditis elegans and show that the method can produce a high-fidelity, high-quality genome assembly for both parents of the cross.
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15
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McAdam EL, Freeman JS, Whittock SP, Buck EJ, Jakse J, Cerenak A, Javornik B, Kilian A, Wang CH, Andersen D, Vaillancourt RE, Carling J, Beatson R, Graham L, Graham D, Darby P, Koutoulis A. Quantitative trait loci in hop (Humulus lupulus L.) reveal complex genetic architecture underlying variation in sex, yield and cone chemistry. BMC Genomics 2013; 14:360. [PMID: 23718194 PMCID: PMC3680207 DOI: 10.1186/1471-2164-14-360] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hop (Humulus lupulus L.) is cultivated for its cones, the secondary metabolites of which contribute bitterness, flavour and aroma to beer. Molecular breeding methods, such as marker assisted selection (MAS), have great potential for improving the efficiency of hop breeding. The success of MAS is reliant on the identification of reliable marker-trait associations. This study used quantitative trait loci (QTL) analysis to identify marker-trait associations for hop, focusing on traits related to expediting plant sex identification, increasing yield capacity and improving bittering, flavour and aroma chemistry. RESULTS QTL analysis was performed on two new linkage maps incorporating transferable Diversity Arrays Technology (DArT) markers. Sixty-three QTL were identified, influencing 36 of the 50 traits examined. A putative sex-linked marker was validated in a different pedigree, confirming the potential of this marker as a screening tool in hop breeding programs. An ontogenetically stable QTL was identified for the yield trait dry cone weight; and a QTL was identified for essential oil content, which verified the genetic basis for variation in secondary metabolite accumulation in hop cones. A total of 60 QTL were identified for 33 secondary metabolite traits. Of these, 51 were pleiotropic/linked, affecting a substantial number of secondary metabolites; nine were specific to individual secondary metabolites. CONCLUSIONS Pleiotropy and linkage, found for the first time to influence multiple hop secondary metabolites, have important implications for molecular selection methods. The selection of particular secondary metabolite profiles using pleiotropic/linked QTL will be challenging because of the difficulty of selecting for specific traits without adversely changing others. QTL specific to individual secondary metabolites, however, offer unequalled value to selection programs. In addition to their potential for selection, the QTL identified in this study advance our understanding of the genetic control of traits of current economic and breeding significance in hop and demonstrate the complex genetic architecture underlying variation in these traits. The linkage information obtained in this study, based on transferable markers, can be used to facilitate the validation of QTL, crucial to the success of MAS.
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Affiliation(s)
- Erin L McAdam
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart TAS 7001, Australia
| | - Jules S Freeman
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart TAS 7001, Australia
- Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore 4558 QLD, Australia
| | - Simon P Whittock
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart TAS 7001, Australia
- Hop Products Australia, 26 Cambridge Road, Bellerive 7018 TAS, Australia
| | - Emily J Buck
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 11 600, Palmerston North 4442, New Zealand
| | - Jernej Jakse
- Agronomy Department, Centre for Plant Biotechnology and Breeding, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana 1000, Slovenia
| | - Andreja Cerenak
- Slovenian Institute of Hop Research and Brewing, Cesta Zalskega Tabora 2, Zalec 3310, Slovenia
| | - Branka Javornik
- Agronomy Department, Centre for Plant Biotechnology and Breeding, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana 1000, Slovenia
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, PO Box 7141, Yarralumla 2600ACT, Australia
| | - Cai-Hong Wang
- Department of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Dave Andersen
- The New Zealand Institute for Plant & Food Research Limited, Old Mill Road, Motueka 7120, New Zealand
| | - René E Vaillancourt
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart TAS 7001, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, PO Box 7141, Yarralumla 2600ACT, Australia
| | - Ron Beatson
- The New Zealand Institute for Plant & Food Research Limited, Old Mill Road, Motueka 7120, New Zealand
| | - Lawrence Graham
- The New Zealand Institute for Plant & Food Research Limited, Old Mill Road, Motueka 7120, New Zealand
| | - Donna Graham
- The New Zealand Institute for Plant & Food Research Limited, Old Mill Road, Motueka 7120, New Zealand
| | - Peter Darby
- Wye Hops Ltd., China Farm, Upper Harbledown, Canterbury, Kent CT2 9AR, UK
| | - Anthony Koutoulis
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart TAS 7001, Australia
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16
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Investigating incipient speciation in Arabidopsis lyrata from patterns of transmission ratio distortion. Genetics 2013; 194:697-708. [PMID: 23666938 DOI: 10.1534/genetics.113.152561] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Our understanding of the development of intrinsic reproductive isolation is still largely based on theoretical models and thorough empirical studies on a small number of species. Theory suggests that reproductive isolation develops through accumulation of epistatic genic incompatibilities, also known as Bateson-Dobzhansky-Muller (BDM) incompatibilities. We can detect these from marker transmission ratio distortion (TRD) in hybrid progenies of crosses between species or populations, where TRD is expected to result from selection against heterospecific allele combinations in hybrids. TRD may also manifest itself because of intragenomic conflicts or competition between gametes or zygotes. We studied early stage speciation in Arabidopsis lyrata by investigating patterns of TRD across the genome in F2 progenies of three reciprocal crosses between four natural populations. We found that the degree of TRD increases with genetic distance between crossed populations, but also that reciprocal progenies may differ substantially in their degree of TRD. Chromosomes AL6 and especially AL1 appear to be involved in many single- and two-locus distortions, but the location and source of TRD vary between crosses and between reciprocal progenies. We also found that the majority of single- and two-locus TRD appears to have a gametic, as opposed to zygotic, origin. Thus, while theory on BDM incompatibilities is typically illustrated with derived nuclear alleles proving incompatible in hybrid zygotes, our results suggest a prominent role for distortions emerging before zygote formation.
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17
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Transmission ratio distortion in an interspecific cross between Fusarium circinatum and Fusarium subglutinans. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0066-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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A hybrid genetic linkage map of two ecologically and morphologically divergent Midas cichlid fishes (Amphilophus spp.) obtained by massively parallel DNA sequencing (ddRADSeq). G3-GENES GENOMES GENETICS 2013; 3:65-74. [PMID: 23316439 PMCID: PMC3538344 DOI: 10.1534/g3.112.003897] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/05/2012] [Indexed: 12/30/2022]
Abstract
Cichlid fishes are an excellent model system for studying speciation and the formation of adaptive radiations because of their tremendous species richness and astonishing phenotypic diversity. Most research has focused on African rift lake fishes, although Neotropical cichlid species display much variability as well. Almost one dozen species of the Midas cichlid species complex (Amphilophus spp.) have been described so far and have formed repeated adaptive radiations in several Nicaraguan crater lakes. Here we apply double-digest restriction-site associated DNA sequencing to obtain a high-density linkage map of an interspecific cross between the benthic Amphilophus astorquii and the limnetic Amphilophus zaliosus, which are sympatric species endemic to Crater Lake Apoyo, Nicaragua. A total of 755 RAD markers were genotyped in 343 F2 hybrids. The map resolved 25 linkage groups and spans a total distance of 1427 cM with an average marker spacing distance of 1.95 cM, almost matching the total number of chromosomes (n = 24) in these species. Regions of segregation distortion were identified in five linkage groups. Based on the pedigree of parents to F2 offspring, we calculated a genome-wide mutation rate of 6.6 × 10−8 mutations per nucleotide per generation. This genetic map will facilitate the mapping of ecomorphologically relevant adaptive traits in the repeated phenotypes that evolved within the Midas cichlid lineage and, as the first linkage map of a Neotropical cichlid, facilitate comparative genomic analyses between African cichlids, Neotropical cichlids and other teleost fishes.
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Genomic characterization of DArT markers based on high-density linkage analysis and physical mapping to the Eucalyptus genome. PLoS One 2012; 7:e44684. [PMID: 22984541 PMCID: PMC3439404 DOI: 10.1371/journal.pone.0044684] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 08/06/2012] [Indexed: 01/07/2023] Open
Abstract
Diversity Arrays Technology (DArT) provides a robust, high throughput, cost-effective method to query thousands of sequence polymorphisms in a single assay. Despite the extensive use of this genotyping platform for numerous plant species, little is known regarding the sequence attributes and genome-wide distribution of DArT markers. We investigated the genomic properties of the 7,680 DArT marker probes of a Eucalyptus array, by sequencing them, constructing a high density linkage map and carrying out detailed physical mapping analyses to the Eucalyptus grandis reference genome. A consensus linkage map with 2,274 DArT markers anchored to 210 microsatellites and a framework map, with improved support for ordering, displayed extensive collinearity with the genome sequence. Only 1.4 Mbp of the 75 Mbp of still unplaced scaffold sequence was captured by 45 linkage mapped but physically unaligned markers to the 11 main Eucalyptus pseudochromosomes, providing compelling evidence for the quality and completeness of the current Eucalyptus genome assembly. A highly significant correspondence was found between the locations of DArT markers and predicted gene models, while most of the 89 DArT probes unaligned to the genome correspond to sequences likely absent in E. grandis, consistent with the pan-genomic feature of this multi-Eucalyptus species DArT array. These comprehensive linkage-to-physical mapping analyses provide novel data regarding the genomic attributes of DArT markers in plant genomes in general and for Eucalyptus in particular. DArT markers preferentially target the gene space and display a largely homogeneous distribution across the genome, thereby providing superb coverage for mapping and genome-wide applications in breeding and diversity studies. Data reported on these ubiquitous properties of DArT markers will be particularly valuable to researchers working on less-studied crop species who already count on DArT genotyping arrays but for which no reference genome is yet available to allow such detailed characterization.
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20
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Burkart-Waco D, Josefsson C, Dilkes B, Kozloff N, Torjek O, Meyer R, Altmann T, Comai L. Hybrid incompatibility in Arabidopsis is determined by a multiple-locus genetic network. PLANT PHYSIOLOGY 2012; 158:801-12. [PMID: 22135429 PMCID: PMC3271768 DOI: 10.1104/pp.111.188706] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 11/21/2011] [Indexed: 05/24/2023]
Abstract
The cross between Arabidopsis thaliana and the closely related species Arabidopsis arenosa results in postzygotic hybrid incompatibility, manifested as seed death. Ecotypes of A. thaliana were tested for their ability to produce live seed when crossed to A. arenosa. The identified genetic variation was used to map quantitative trait loci (QTLs) encoded by the A. thaliana genome that affect the frequency of postzygotic lethality and the phenotypes of surviving seeds. Seven QTLs affecting the A. thaliana component of this hybrid incompatibility were identified by crossing a Columbia × C24 recombinant inbred line population to diploid A. arenosa pollen donors. Additional epistatic loci were identified based on their pairwise interaction with one or several of these QTLs. Epistatic interactions were detected for all seven QTLs. The two largest additive QTLs were subjected to fine-mapping, indicating the action of at least two genes in each. The topology of this network reveals a large set of minor-effect loci from the maternal genome controlling hybrid growth and viability at different developmental stages. Our study establishes a framework that will enable the identification and characterization of genes and pathways in A. thaliana responsible for hybrid lethality in the A. thaliana × A. arenosa interspecific cross.
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21
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Hunter B, Bomblies K. Progress and Promise in using Arabidopsis to Study Adaptation, Divergence, and Speciation. THE ARABIDOPSIS BOOK 2010; 8:e0138. [PMID: 22303263 PMCID: PMC3244966 DOI: 10.1199/tab.0138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Fundamental questions remain to be answered on how lineages split and new species form. The Arabidopsis genus, with several increasingly well characterized species closely related to the model system A. thaliana, provides a rare opportunity to address key questions in speciation research. Arabidopsis species, and in some cases populations within a species, vary considerably in their habitat preferences, adaptations to local environments, mating system, life history strategy, genome structure and chromosome number. These differences provide numerous open doors for understanding the role these factors play in population divergence and how they may cause barriers to arise among nascent species. Molecular tools available in A. thaliana are widely applicable to its relatives, and together with modern comparative genomic approaches they will provide new and increasingly mechanistic insights into the processes underpinning lineage divergence and speciation. We will discuss recent progress in understanding the molecular basis of local adaptation, reproductive isolation and genetic incompatibility, focusing on work utilizing the Arabidopsis genus, and will highlight several areas in which additional research will provide meaningful insights into adaptation and speciation processes in this genus.
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Affiliation(s)
- Ben Hunter
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA, USA
| | - Kirsten Bomblies
- Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Ave., Cambridge, MA, USA
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Tang S, Okashah RA, Knapp SJ, Arnold ML, Martin NH. Transmission ratio distortion results in asymmetric introgression in Louisiana Iris. BMC PLANT BIOLOGY 2010; 10:48. [PMID: 20298609 PMCID: PMC2923522 DOI: 10.1186/1471-2229-10-48] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Accepted: 03/18/2010] [Indexed: 05/03/2023]
Abstract
BACKGROUND Linkage maps are useful tools for examining both the genetic architecture of quantitative traits and the evolution of reproductive incompatibilities. We describe the generation of two genetic maps using reciprocal interspecific backcross 1 (BC1) mapping populations from crosses between Iris brevicaulis and Iris fulva. These maps were constructed using expressed sequence tag (EST)- derived codominant microsatellite markers. Such a codominant marker system allowed for the ability to link the two reciprocal maps, and compare patterns of transmission ratio distortion observed between the two. RESULTS Linkage mapping resulted in markers that coalesced into 21 linkage groups for each of the reciprocal backcross maps, presumably corresponding to the 21 haploid chromosomes of I. brevicaulis and I. fulva. The composite map was 1190.0-cM long, spanned 81% of the I. brevicaulis and I. fulva genomes, and had a mean density of 4.5 cM per locus. Transmission ratio distortion (TRD) was observed in 138 (48.5%) loci distributed in 19 of the 21 LGs in BCIB, BCIF, or both BC1 mapping populations. Of the distorted markers identified, I. fulva alleles were detected at consistently higher-than-expected frequencies in both mapping populations. CONCLUSIONS The observation that I. fulva alleles are overrepresented in both mapping populations suggests that I. fulva alleles are favored to introgress into I. brevicaulis genetic backgrounds, while I. brevicaulis alleles would tend to be prevented from introgressing into I. fulva. These data are consistent with the previously observed patterns of introgression in natural hybrid zones, where I. fulva alleles have been consistently shown to introgress across species boundaries.
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Affiliation(s)
- Shunxue Tang
- Center for Applied Genetic Technologies, The University of Georgia, Athens, GA 30602, USA
- Dow AgroSciences LLC, Indianapolis, IN 46268, USA
| | - Rebecca A Okashah
- Center for Applied Genetic Technologies, The University of Georgia, Athens, GA 30602, USA
| | - Steven J Knapp
- Center for Applied Genetic Technologies, The University of Georgia, Athens, GA 30602, USA
| | - Michael L Arnold
- Department of Genetics, The University of Georgia, Athens, GA 30602, USA
| | - Noland H Martin
- Department of Biology, Texas State University - San Marcos, San Marcos, TX 78666, USA
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McKinnon GE, Smith JJ, Potts BM. Recurrent nuclear DNA introgression accompanies chloroplast DNA exchange between two eucalypt species. Mol Ecol 2010; 19:1367-80. [PMID: 20298471 DOI: 10.1111/j.1365-294x.2010.04579.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Numerous studies within plant genera have found geographically structured sharing of chloroplast (cp) DNA among sympatric species, consistent with introgressive hybridization. Current research is aimed at understanding the extent, direction and significance of nuclear (nr) DNA exchange that accompanies putative cpDNA exchange. Eucalyptus is a complex tree genus for which cpDNA sharing has been established between multiple species. Prior phylogeographic analysis has indicated cpDNA introgression into the widespread forest species Eucalyptus globulus from its rare congener E. cordata. In this study, we use AFLP markers to characterize corresponding nrDNA introgression, on both a broad and fine spatial scale. Using 388 samples we examine (i) the fine-scale spatial structure of cp and nrDNA introgression from E. cordata into E. globulus at a site in natural forest and (ii) broad-scale patterns of AFLP marker introgression at six additional mixed populations. We show that while E. globulus and E. cordata retain strongly differentiated nuclear gene pools overall, leakage of nrDNA occurs at mixed populations, with some AFLP markers being transferred to E. globulus recurrently at different sites. On the fine scale, different AFLP fragments show varying distances of introgression into E. globulus, while introgression of cpDNA is extensive. The frequency of E. cordata markers in E. globulus is correlated with spatial proximity to E. cordata, but departs from expectations based on AFLP marker frequency in E. cordata, indicating that selection may be governing the persistence of introgressed fragments in E. globulus.
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Affiliation(s)
- G E McKinnon
- School of Plant Science, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia.
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Croxford AE, Rogers T, Caligari PDS, Wilkinson MJ. High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar. THE NEW PHYTOLOGIST 2008; 180:594-607. [PMID: 18684160 DOI: 10.1111/j.1469-8137.2008.02588.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
* The provision of sequence-tagged site (STS) anchor points allows meaningful comparisons between mapping studies but can be a time-consuming process for nonmodel species or orphan crops. * Here, the first use of high-resolution melt analysis (HRM) to generate STS markers for use in linkage mapping is described. This strategy is rapid and low-cost, and circumvents the need for labelled primers or amplicon fractionation. * Using white lupin (Lupinus albus, x = 25) as a case study, HRM analysis was applied to identify 91 polymorphic markers from expressed sequence tag (EST)-derived and genomic libraries. Of these, 77 generated STS anchor points in the first fully resolved linkage map of the species. The map also included 230 amplified fragment length polymorphisms (AFLP) loci, spanned 1916 cM (84.2% coverage) and divided into the expected 25 linkage groups. * Quantitative trait loci (QTL) analyses performed on the population revealed genomic regions associated with several traits, including the agronomically important time to flowering (tf), alkaloid synthesis and stem height (Ph). Use of HRM-STS markers also allowed us to make direct comparisons between our map and that of the related crop, Lupinus angustifolius, based on the conversion of RFLP, microsatellite and single nucleotide polymorphism (SNP) markers into HRM markers.
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Affiliation(s)
- Adam E Croxford
- Institute of Biological, Environmental and Rural Sciences, Edward Llwyd Building, Aberystwyth University, SY23 3DA, UK
| | - Tom Rogers
- KG Fruits Ltd, Tatlingbury Oast, Five Oak Green, Tonbridge, Kent TN12 6RG, UK
| | - Peter D S Caligari
- Instituto de Biología Vegetal y Biotecnología, Universidad de Talca, 2 Norte 685 Talca, Chile
| | - Michael J Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Edward Llwyd Building, Aberystwyth University, SY23 3DA, UK
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López-Fernández H, Bolnick DI. What causes partial F1 hybrid viability? Incomplete penetrance versus genetic variation. PLoS One 2007; 2:e1294. [PMID: 18074018 PMCID: PMC2121587 DOI: 10.1371/journal.pone.0001294] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 11/16/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Interspecific hybrid crosses often produce offspring with reduced but non-zero survivorship. In this paper we ask why such partial inviability occurs. This partial inviability could arise from incomplete penetrance of lethal Dobzhansky-Muller incompatibilities (DMIs) shared by all members of a hybrid cross. Alternatively, siblings may differ with respect to the presence or number of DMIs, leading to genotype-dependent variation in viability and hence non-Mendelian segregation of parental alleles in surviving F1 hybrids. METHODOLOGY/PRINCIPAL FINDINGS We used amplified fragment length polymorphisms (AFLPs) to test for segregation distortion in one hybrid cross between green and longear sunfish (Lepomis cyanellus and L. megalotis). Hybrids showed partial viability, and twice as much segregation distortion (36.8%) of AFLPs as an intraspecific control cross (18.8%). Incomplete penetrance of DMIs, which should cause genotype-independent mortality, is insufficient to explain the observed segregation distortion. CONCLUSIONS/SIGNIFICANCE We conclude that F1 hybrid sunfish are polymorphic for DMIs, either due to sex-linked DMI loci (causing Haldane's Rule), or polymorphic autosomal DMI loci. Because few AFLP markers were sex-linked (2%), the most parsimonious conclusion is that parents may have been heterozygous for loci causing hybrid inviability.
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Affiliation(s)
- Hernán López-Fernández
- Section of Ecology, Evolutionary Biology and Systematics, Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Daniel I. Bolnick
- Section of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America
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26
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Leppälä J, Bechsgaard JS, Schierup MH, Savolainen O. Transmission ratio distortion in Arabidopsis lyrata: effects of population divergence and the S-locus. Heredity (Edinb) 2007; 100:71-8. [DOI: 10.1038/sj.hdy.6801066] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Goodwillie C, Ritland C, Ritland K. THE GENETIC BASIS OF FLORAL TRAITS ASSOCIATED WITH MATING SYSTEM EVOLUTION IN LEPTOSIPHON (POLEMONIACEAE): AN ANALYSIS OF QUANTITATIVE TRAIT LOCI. Evolution 2007. [DOI: 10.1111/j.0014-3820.2006.tb01131.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Carol Goodwillie
- Department of Biology, East Caroline University, Greenville, North Carolina 27858
| | - Carol Ritland
- Faculty of Forestry, The University of British Columbia, Vancounver, British Columbia V6T IZ4, Canada
| | - Kermit Ritland
- Faculty of Forestry, The University of British Columbia, Vancounver, British Columbia V6T IZ4, Canada
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Rogers SM, Isabel N, Bernatchez L. Linkage maps of the dwarf and Normal lake whitefish (Coregonus clupeaformis) species complex and their hybrids reveal the genetic architecture of population divergence. Genetics 2007; 175:375-98. [PMID: 17110497 PMCID: PMC1774998 DOI: 10.1534/genetics.106.061457] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2006] [Accepted: 10/24/2006] [Indexed: 01/22/2023] Open
Abstract
Elucidating the genetic architecture of population divergence may reveal the evolution of reproductive barriers and the genomic regions implicated in the process. We assembled genetic linkage maps for the dwarf and Normal lake whitefish species complex and their hybrids. A total of 877 AFLP loci and 30 microsatellites were positioned. The homology of mapped loci between families supported the existence of 34 linkage groups (of 40n expected) exhibiting 83% colinearity among linked loci between these two families. Classes of AFLP markers were not randomly distributed among linkage groups. Both AFLP and microsatellites exhibited deviations from Mendelian expectations, with 30.4% exhibiting significant segregation distortion across 28 linkage groups of the four linkage maps in both families (P < 0.00001). Eight loci distributed over seven homologous linkage groups were significantly distorted in both families and the level of distortion, when comparing homologous loci of the same phase between families, was correlated (Spearman R = 0.378, P = 0.0021). These results suggest that substantial divergence incurred during allopatric glacial separation and subsequent sympatric ecological specialization has resulted in several genomic regions that are no longer complementary between dwarf and Normal populations issued from different evolutionary glacial lineages.
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Affiliation(s)
- S M Rogers
- Québec Océan, Département de Biologie, Université Laval, Sainte-Foy, Québec G1K 7P4, Canada.
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Harrison JS, Edmands S. Chromosomal basis of viability differences in Tigriopus californicus interpopulation hybrids. J Evol Biol 2006; 19:2040-51. [PMID: 17040401 DOI: 10.1111/j.1420-9101.2006.01145.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Crosses between populations of Tigriopus californicus result in backcross and F2 hybrid breakdown for a variety of fitness related measures. The magnitude of this hybrid breakdown is correlated with evolutionary divergence. We assessed the chromosomal basis of viability differences in nonrecombinant backcross hybrids using markers mapped to individual chromosomes. To assess effects of evolutionary divergence we crossed one population to three different populations: two distantly related (approximately 18% mitochondrial COI sequence divergence) and one closely related (approximately 1% mitochondrial COI sequence divergence). We found that all three interpopulation crosses resulted in significant deviations from expected Mendelian ratios at a majority of the loci studied. In all but one case, deviations were due to a deficit of parental homozygotes. This pattern implies that populations of T. californicus carry a significant genetic load, and that a combination of beneficial dominance and deleterious homozygote-heterozygote interactions significantly affects hybrid viability. Pairwise tests of linkage disequilibrium detected relatively few significant interactions. For the two divergent crosses, effects of individual chromosomes were highly concordant. These two crosses also showed higher heterozygote excess in females than males across the vast majority of chromosomes.
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Affiliation(s)
- J S Harrison
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093-0202, USA.
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30
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Rogers SM, Bernatchez L. The genetic basis of intrinsic and extrinsic post-zygotic reproductive isolation jointly promoting speciation in the lake whitefish species complex (Coregonus clupeaformis). J Evol Biol 2006; 19:1979-94. [PMID: 17040396 DOI: 10.1111/j.1420-9101.2006.01150.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Understanding the genetic architecture of reproductive barriers and the evolutionary forces that drove their divergence represents a considerable challenge towards understanding speciation. The objective of this study was to determine the genetic basis of intrinsic and extrinsic post-zygotic isolation in diverging populations of dwarf and normal lake whitefish with allopatric glacial origins. We found that the rate of embryonic mortality was 5.3-6.5 times higher in dwarf-normal hybrid backcrosses during development than in F1 dwarf and normal crosses. When comparing embryos that died during development against larvae that successfully hatched, patterns of Mendelian segregation at 101 loci whose linkage is known identified 13 loci distributed over seven linkage groups that exhibited significant shifts in segregation ratios leading to significant segregation distortion at these loci in the surviving progeny. Controlled crosses and quantitative trait loci analysis revealed a significant genetic basis for developmental time until emergence, a trait critical to fish larval survival in nature. Hatching backcross progeny exhibited asynchronous emergence and transgressive segregation, suggesting that extrinsic post-zygotic isolation may select against hybridization in specific environmental contexts. Evidence of a genetic basis for increased embryonic mortality followed by asynchronous emergence indicated that intrinsic and extrinsic mechanisms are not mutually exclusive in the formation and maintenance of reproductive isolation, but may be jointly promoting population divergence and ultimately speciation.
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Affiliation(s)
- S M Rogers
- Québec Océan, Department de Biologie, Université Laval, Ste-Foy, QC, Canada.
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31
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Abstract
For whole-genome analysis in a basal chordate (protochordate), we used F1 pseudo-testcross mapping strategy and amplified fragment length polymorphism (AFLP) markers to construct primary linkage maps of the ascidian tunicate Ciona intestinalis. Two genetic maps consisted of 14 linkage groups, in agreement with the haploid chromosome number, and contained 276 and 125 AFLP loci derived from crosses between British and Neapolitan individuals. The two maps covered 4218.9 and 2086.9 cM, respectively, with an average marker interval of 16.1 and 18.9 cM. We observed a high recombinant ratio, ranging from 25 to 49 kb/cM, which can explain the high degree of polymorphism in this species. Some AFLP markers were converted to sequence tagged sites (STSs) by sequence determination, in order to create anchor markers for the fragmental physical map. Our recombination tools provide basic knowledge of genetic status and whole genome organization, and genetic markers to assist positional cloning in C. intestinalis.
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Affiliation(s)
- Shungo Kano
- Laboratory of Biochemistry and Molecular Biology, Stazione Zoologica A. Dohrn, Naples 80121, Italy.
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Brondani RPV, Williams ER, Brondani C, Grattapaglia D. A microsatellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus. BMC PLANT BIOLOGY 2006; 6:20. [PMID: 16995939 PMCID: PMC1599733 DOI: 10.1186/1471-2229-6-20] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2006] [Accepted: 09/22/2006] [Indexed: 05/11/2023]
Abstract
BACKGROUND Eucalypts are the most widely planted hardwood trees in the world occupying globally more than 18 million hectares as an important source of carbon neutral renewable energy and raw material for pulp, paper and solid wood. Quantitative Trait Loci (QTLs) in Eucalyptus have been localized on pedigree-specific RAPD or AFLP maps seriously limiting the value of such QTL mapping efforts for molecular breeding. The availability of a genus-wide genetic map with transferable microsatellite markers has become a must for the effective advancement of genomic undertakings. This report describes the development of a novel set of 230 EMBRA microsatellites, the construction of the first comprehensive microsatellite-based consensus linkage map for Eucalyptus and the consolidation of existing linkage information for other microsatellites and candidate genes mapped in other species of the genus. RESULTS The consensus map covers approximately 90% of the recombining genome of Eucalyptus, involves 234 mapped EMBRA loci on 11 linkage groups, an observed length of 1,568 cM and a mean distance between markers of 8.4 cM. A compilation of all microsatellite linkage information published in Eucalyptus allowed us to establish the homology among linkage groups between this consensus map and other maps published for E. globulus. Comparative mapping analyses also resulted in the linkage group assignment of other 41 microsatellites derived from other Eucalyptus species as well as candidate genes and QTLs for wood and flowering traits published in the literature. This report significantly increases the availability of microsatellite markers and mapping information for species of Eucalyptus and corroborates the high conservation of microsatellite flanking sequences and locus ordering between species of the genus. CONCLUSION This work represents an important step forward for Eucalyptus comparative genomics, opening stimulating perspectives for evolutionary studies and molecular breeding applications. The generalized use of an increasingly larger set of interspecific transferable markers and consensus mapping information, will allow faster and more detailed investigations of QTL synteny among species, validation of expression-QTL across variable genetic backgrounds and positioning of a growing number of candidate genes co-localized with QTLs, to be tested in association mapping experiments.
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Affiliation(s)
- Rosana PV Brondani
- EMBRAPA Recursos Genéticos e Biotecnologia, CP 02372, 70770-970 DF Brasilia, Brazil
- Department of Cell Biology, Universidade de Brasília UnB, DF, Brasília
- EMBRAPA Arroz e Feijão, CP 179, Goiânia GO 74001-970, Brazil
| | - Emlyn R Williams
- CSIRO Forestry and Forest Products, POBox E4008, Kingston ACT 2604, Australia
| | - Claudio Brondani
- EMBRAPA Recursos Genéticos e Biotecnologia, CP 02372, 70770-970 DF Brasilia, Brazil
- EMBRAPA Arroz e Feijão, CP 179, Goiânia GO 74001-970, Brazil
| | - Dario Grattapaglia
- EMBRAPA Recursos Genéticos e Biotecnologia, CP 02372, 70770-970 DF Brasilia, Brazil
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Catolica de Brasília, 70790-160 DF Brasilia, Brazil
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Goodwillie C, Ritland C, Ritland K. THE GENETIC BASIS OF FLORAL TRAITS ASSOCIATED WITH MATING SYSTEM EVOLUTION IN LEPTOSIPHON (POLEMONIACEAE): AN ANALYSIS OF QUANTITATIVE TRAIT LOCI. Evolution 2006. [DOI: 10.1554/05-471.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Poke FS, Vaillancourt RE, Potts BM, Reid JB. Genomic research in Eucalyptus. Genetica 2005; 125:79-101. [PMID: 16175457 DOI: 10.1007/s10709-005-5082-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Accepted: 04/05/2005] [Indexed: 11/25/2022]
Abstract
Eucalyptus L'Hérit. is a genus comprised of more than 700 species that is of vital importance ecologically to Australia and to the forestry industry world-wide, being grown in plantations for the production of solid wood products as well as pulp for paper. With the sequencing of the genomes of Arabidopsis thaliana and Oryza sativa and the recent completion of the first tree genome sequence, Populus trichocarpa, attention has turned to the current status of genomic research in Eucalyptus. For several eucalypt species, large segregating families have been established, high-resolution genetic maps constructed and large EST databases generated. Collaborative efforts have been initiated for the integration of diverse genomic projects and will provide the framework for future research including exploiting the sequence of the entire eucalypt genome which is currently being sequenced. This review summarises the current position of genomic research in Eucalyptus and discusses the direction of future research.
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Affiliation(s)
- Fiona S Poke
- Cooperative Research Centre for Sustainable Production Forestry and School of Plant Science, University of Tasmania, Churchill Avenue, Private Bag 55, Hobart, Tasmania 7001, Australia.
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Bouck A, Peeler R, Arnold ML, Wessler SR. Genetic mapping of species boundaries in Louisiana irises using IRRE retrotransposon display markers. Genetics 2005; 171:1289-303. [PMID: 16079236 PMCID: PMC1456832 DOI: 10.1534/genetics.105.044552] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2005] [Accepted: 07/20/2005] [Indexed: 01/25/2023] Open
Abstract
Genetic mapping studies provide insight into the pattern and extent of genetic incompatibilities affecting hybridization between closely related species. Genetic maps of two species of Louisiana Irises, Iris fulva and I. brevicaulis, were constructed from transposon-based molecular markers segregating in reciprocal backcross (BC1) interspecific hybrids and used to investigate genomic patterns of species barriers inhibiting introgression. Linkage mapping analyses indicated very little genetic incompatibility between I. fulva and I. brevicaulis in the form of map regions exhibiting transmission ratio distortion, and this was confirmed using a Bayesian multipoint mapping analysis. These results demonstrate the utility of transposon-based marker systems for genetic mapping studies of wild plant species and indicate that the genomes of I. fulva and I. brevicaulis are highly permeable to gene flow and introgression from one another via backcrossing.
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Affiliation(s)
- Amy Bouck
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA.
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36
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Martin NH, Bouck AC, Arnold ML. LOCI AFFECTING LONG-TERM HYBRID SURVIVORSHIP IN LOUISIANA IRISES: IMPLICATIONS FOR REPRODUCTIVE ISOLATION AND INTROGRESSION. Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb00922.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Hall MC, Willis JH. Transmission ratio distortion in intraspecific hybrids of Mimulus guttatus: implications for genomic divergence. Genetics 2005; 170:375-86. [PMID: 15781698 PMCID: PMC1449724 DOI: 10.1534/genetics.104.038653] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Accepted: 02/07/2005] [Indexed: 11/18/2022] Open
Abstract
We constructed a genetic linkage map between two divergent populations of Mimulus guttatus. We genotyped an F(2) mapping population (N = 539) at 154 AFLP, microsatellite, and gene-based markers. A framework map was constructed consisting of 112 marker loci on 14 linkage groups with a total map length of 1518 cM Kosambi. Nearly half of all markers (48%) exhibited significant transmission ratio distortion (alpha = 0.05). By using a Bayesian multipoint mapping method and visual inspection of significantly distorted markers, we detected 12 transmission ratio distorting loci (TRDL) throughout the genome. The high degree of segregation distortion detected in this intraspecific map indicates substantial genomic divergence that perhaps suggests genomic incompatibilities between these two populations. We compare the pattern of transmission ratio distortion in this map to an interspecific map constructed between M. guttatus and M. nasutus. A similar level of segregation distortion is detected in both maps. Collinear regions between maps are compared to determine if there are shared genetic patterns of non-Mendelian segregation distortion within and among Mimulus species.
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Affiliation(s)
- Megan C Hall
- Department of Biology, Duke University, Durham, North Carolina 27708, USA.
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38
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Martin NH, Bouck AC, Arnold ML. LOCI AFFECTING LONG-TERM HYBRID SURVIVORSHIP IN LOUISIANA IRISES: IMPLICATIONS FOR REPRODUCTIVE ISOLATION AND INTROGRESSION. Evolution 2005. [DOI: 10.1554/05-139.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Moyle LC, Graham EB. Genetics of hybrid incompatibility between Lycopersicon esculentum and L. hirsutum. Genetics 2004; 169:355-73. [PMID: 15466436 PMCID: PMC1448897 DOI: 10.1534/genetics.104.029546] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We examined the genetics of hybrid incompatibility between two closely related diploid hermaphroditic plant species. Using a set of near-isogenic lines (NILs) representing 85% of the genome of the wild species Lycopersicon hirsutum (Solanum habrochaites) in the genetic background of the cultivated tomato L. esculentum (S. lycopersicum), we found that hybrid pollen and seed infertility are each based on 5-11 QTL that individually reduce hybrid fitness by 36-90%. Seed infertility QTL act additively or recessively, consistent with findings in other systems where incompatibility loci have largely been recessive. Genetic lengths of introgressed chromosomal segments explain little of the variation for hybrid incompatibility among NILs, arguing against an infinitesimal model of hybrid incompatibility and reinforcing our inference of a limited number of discrete incompatibility factors between these species. In addition, male (pollen) and other (seed) incompatibility factors are roughly comparable in number. The latter two findings contrast strongly with data from Drosophila where hybrid incompatibility can be highly polygenic and complex, and male sterility evolves substantially faster than female sterility or hybrid inviability. The observed differences between Lycopersicon and Drosophila might be due to differences in sex determination system, reproductive and mating biology, and/or the prevalence of sexual interactions such as sexual selection.
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Affiliation(s)
- Leonie C Moyle
- Center for Population Biology, University of California, Davis, California 95616, USA.
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Myburg AA, Griffin AR, Sederoff RR, Whetten RW. Comparative genetic linkage maps of Eucalyptus grandis, Eucalyptus globulus and their F1 hybrid based on a double pseudo-backcross mapping approach. THEORETICAL AND APPLIED GENETICS 2003; 107:1028-42. [PMID: 12838392 DOI: 10.1007/s00122-003-1347-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2003] [Accepted: 05/12/2003] [Indexed: 05/22/2023]
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