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Luo Z. Mapping quantitative trait loci in autotetraploids under a genuine tetrasomic model. THE NEW PHYTOLOGIST 2024; 242:21-22. [PMID: 38359878 DOI: 10.1111/nph.19597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Affiliation(s)
- Zewei Luo
- Institute of Biostatistics, School of Life Sciences, Fudan University, Shanghai, 200433, China
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2
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da Costa Lima Moraes A, Mollinari M, Ferreira RCU, Aono A, de Castro Lara LA, Pessoa-Filho M, Barrios SCL, Garcia AAF, do Valle CB, de Souza AP, Vigna BBZ. Advances in genomic characterization of Urochloa humidicola: exploring polyploid inheritance and apomixis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:238. [PMID: 37919432 DOI: 10.1007/s00122-023-04485-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 10/11/2023] [Indexed: 11/04/2023]
Abstract
KEY MESSAGE We present the highest-density genetic map for the hexaploid Urochloa humidicola. SNP markers expose genetic organization, reproduction, and species origin, aiding polyploid and tropical forage research. Tropical forage grasses are an important food source for animal feeding, with Urochloa humidicola, also known as Koronivia grass, being one of the main pasture grasses for poorly drained soils in the tropics. However, genetic and genomic resources for this species are lacking due to its genomic complexity, including high heterozygosity, evidence of segmental allopolyploidy, and reproduction by apomixis. These complexities hinder the application of marker-assisted selection (MAS) in breeding programs. Here, we developed the highest-density linkage map currently available for the hexaploid tropical forage grass U. humidicola. This map was constructed using a biparental F1 population generated from a cross between the female parent H031 (CIAT 26146), the only known sexual genotype for the species, and the apomictic male parent H016 (BRS cv. Tupi). The linkage analysis included 4873 single nucleotide polymorphism (SNP) markers with allele dosage information. It allowed mapping of the ASGR locus and apospory phenotype to linkage group 3, in a region syntenic with chromosome 3 of Urochloa ruziziensis and chromosome 1 of Setaria italica. We also identified hexaploid haplotypes for all individuals, assessed the meiotic configuration, and estimated the level of preferential pairing in parents during the meiotic process, which revealed the autopolyploid origin of sexual H031 in contrast to apomictic H016, which presented allopolyploid behavior in preferential pairing analysis. These results provide new information regarding the genetic organization, mode of reproduction, and allopolyploid origin of U. humidicola, potential SNPs markers associated with apomixis for MAS and resources for research on polyploids and tropical forage grasses.
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Affiliation(s)
- Aline da Costa Lima Moraes
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Marcelo Mollinari
- Department of Horticultural Science, Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | | | - Alexandre Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | | | | | | | | | | | - Anete Pereira de Souza
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
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Chen J, Leach L, Yang J, Zhang F, Tao Q, Dang Z, Chen Y, Luo Z. A tetrasomic inheritance model and likelihood-based method for mapping quantitative trait loci in autotetraploid species. THE NEW PHYTOLOGIST 2021; 230:387-398. [PMID: 31913501 PMCID: PMC7984458 DOI: 10.1111/nph.16413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
Dissecting the genetic architecture of quantitative traits in autotetraploid species is a methodologically challenging task, but a pivotally important goal for breeding globally important food crops, including potato and blueberry, and ornamental species such as rose. Mapping quantitative trait loci (QTLs) is now a routine practice in diploid species but is far less advanced in autotetraploids, largely due to a lack of analytical methods that account for the complexities of tetrasomic inheritance. We present a novel likelihood-based method for QTL mapping in outbred segregating populations of autotetraploid species. The method accounts properly for sophisticated features of gene segregation and recombination in an autotetraploid meiosis. It may model and analyse molecular marker data with or without allele dosage information, such as that from microarray or sequencing experiments. The method developed outperforms existing bivalent-based methods, which may fail to model and analyse the full spectrum of experimental data, in the statistical power of QTL detection, and accuracy of QTL location, as demonstrated by an intensive simulation study and analysis of data sets collected from a segregating population of potato (Solanum tuberosum). The study enables QTL mapping analysis to be conducted in autotetraploid species under a rigorous tetrasomic inheritance model.
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Affiliation(s)
- Jing Chen
- School of BiosciencesThe University of BirminghamBirminghamB15 2TTUK
| | - Lindsey Leach
- School of BiosciencesThe University of BirminghamBirminghamB15 2TTUK
| | - Jixuan Yang
- Institute of BiostatisticsFudan UniversityShanghai200433China
| | - Fengjun Zhang
- Institute of BiostatisticsFudan UniversityShanghai200433China
- Qinghai Academy of Agricultural and Forestry SciencesXiningQinghai810016China
| | - Qin Tao
- Institute of BiostatisticsFudan UniversityShanghai200433China
| | - Zhenyu Dang
- Institute of BiostatisticsFudan UniversityShanghai200433China
| | - Yue Chen
- Institute of BiostatisticsFudan UniversityShanghai200433China
| | - Zewei Luo
- School of BiosciencesThe University of BirminghamBirminghamB15 2TTUK
- Institute of BiostatisticsFudan UniversityShanghai200433China
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Mollinari M, Olukolu BA, Pereira GDS, Khan A, Gemenet D, Yencho GC, Zeng ZB. Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping. G3 (BETHESDA, MD.) 2020; 10:281-292. [PMID: 31732504 PMCID: PMC6945028 DOI: 10.1534/g3.119.400620] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/12/2019] [Indexed: 12/18/2022]
Abstract
The hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and plays a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly developed software, MAPpoly. The resulting genetic map revealed 96.5% collinearity between I. batatas and its diploid relative I. trifida We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%), were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato.
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Affiliation(s)
- Marcelo Mollinari
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina,
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Bode A Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee
| | - Guilherme da S Pereira
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, New York, and
| | - Dorcus Gemenet
- International Potato Center, ILRI Campus, Nairobi, Kenya
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Zhao-Bang Zeng
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
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5
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Mollinari M, Olukolu BA, Pereira GDS, Khan A, Gemenet D, Yencho GC, Zeng ZB. Unraveling the Hexaploid Sweetpotato Inheritance Using Ultra-Dense Multilocus Mapping. G3 (BETHESDA, MD.) 2020. [PMID: 31732504 DOI: 10.25387/g3.10255844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
The hexaploid sweetpotato (Ipomoea batatas (L.) Lam., 2n = 6x = 90) is an important staple food crop worldwide and plays a vital role in alleviating famine in developing countries. Due to its high ploidy level, genetic studies in sweetpotato lag behind major diploid crops significantly. We built an ultra-dense multilocus integrated genetic map and characterized the inheritance system in a sweetpotato full-sib family using our newly developed software, MAPpoly. The resulting genetic map revealed 96.5% collinearity between I. batatas and its diploid relative I. trifida We computed the genotypic probabilities across the whole genome for all individuals in the mapping population and inferred their complete hexaploid haplotypes. We provide evidence that most of the meiotic configurations (73.3%) were resolved in bivalents, although a small portion of multivalent signatures (15.7%), among other inconclusive configurations (11.0%), were also observed. Except for low levels of preferential pairing in linkage group 2, we observed a hexasomic inheritance mechanism in all linkage groups. We propose that the hexasomic-bivalent inheritance promotes stability to the allelic transmission in sweetpotato.
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Affiliation(s)
- Marcelo Mollinari
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina,
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Bode A Olukolu
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, Tennessee
| | - Guilherme da S Pereira
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Awais Khan
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, New York, and
| | - Dorcus Gemenet
- International Potato Center, ILRI Campus, Nairobi, Kenya
| | - G Craig Yencho
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
| | - Zhao-Bang Zeng
- Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina
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6
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Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3-GENES GENOMES GENETICS 2019; 9:3297-3314. [PMID: 31405891 PMCID: PMC6778803 DOI: 10.1534/g3.119.400378] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Modern SNP genotyping technologies allow measurement of the relative abundance of different alleles for a given locus and consequently estimation of their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels for a set of SNP markers using hidden Markov models. Our method uses efficient two-point procedures to reduce the search space for the best linkage phase configuration and reestimate the final parameters by maximizing the likelihood of the Markov chain. To evaluate the method, and demonstrate its properties, we rely on simulations of autotetraploid, autohexaploid and autooctaploid populations and on a real tetraploid potato data set. The results show the reliability of our approach, including situations with complex linkage phase scenarios in hexaploid and octaploid populations.
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7
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Mollinari M, Garcia AAF. Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models. G3 (BETHESDA, MD.) 2019. [PMID: 31405891 DOI: 10.1101/415232v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Modern SNP genotyping technologies allow measurement of the relative abundance of different alleles for a given locus and consequently estimation of their allele dosage, opening a new road for genetic studies in autopolyploids. Despite advances in genetic linkage analysis in autotetraploids, there is a lack of statistical models to perform linkage analysis in organisms with higher ploidy levels. In this paper, we present a statistical method to estimate recombination fractions and infer linkage phases in full-sib populations of autopolyploid species with even ploidy levels for a set of SNP markers using hidden Markov models. Our method uses efficient two-point procedures to reduce the search space for the best linkage phase configuration and reestimate the final parameters by maximizing the likelihood of the Markov chain. To evaluate the method, and demonstrate its properties, we rely on simulations of autotetraploid, autohexaploid and autooctaploid populations and on a real tetraploid potato data set. The results show the reliability of our approach, including situations with complex linkage phase scenarios in hexaploid and octaploid populations.
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Affiliation(s)
- Marcelo Mollinari
- Department of Horticultural Science, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, and
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8
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Chen J, Zhang F, Wang L, Leach L, Luo Z. Orthogonal contrast based models for quantitative genetic analysis in autotetraploid species. THE NEW PHYTOLOGIST 2018; 220:332-346. [PMID: 29987874 DOI: 10.1111/nph.15284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/18/2018] [Indexed: 06/08/2023]
Abstract
Dissecting the genetic architecture of quantitative traits is a crucial goal for efficient breeding of polyploid plants, including autotetraploid crop species, such as potato and coffee, and ornamentals such as rose. To meet this goal, a quantitative genetic model is needed to link the genetic effects of genes or genotypes at quantitative trait loci (QTL) to the phenotype of quantitative traits. We present a statistically tractable quantitative genetic model for autotetraploids based on orthogonal contrast comparisons in the general linear model. The new methods are suitable for autotetraploid species with any population genetic structure and take full account of the essential features of autotetrasomic inheritance. The statistical properties of the new methods are explored and compared to an alternative method in the literature by simulation studies. We have shown how these methods can be applied for quantitative genetic analysis in autotetraploids by analysing trait phenotype data from an autotetraploid potato segregating population. Using trait segregation analysis, we showed that both highly heritable traits of flowering time and plant height were under the control of major QTL. The orthogonal model directly dissects genetic variance into independent components and gives consistent estimates of genetic effects provided that tetrasomic gene segregation is considered.
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Affiliation(s)
- Jing Chen
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Fengjun Zhang
- Institute of Biostatistics and Genetics, Fudan University, Shanghai, 200433, China
| | - Lin Wang
- Institute of Biostatistics and Genetics, Fudan University, Shanghai, 200433, China
| | - Lindsey Leach
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Zewei Luo
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Biostatistics and Genetics, Fudan University, Shanghai, 200433, China
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9
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Bourke PM, Voorrips RE, Kranenburg T, Jansen J, Visser RGF, Maliepaard C. Integrating haplotype-specific linkage maps in tetraploid species using SNP markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2211-2226. [PMID: 27561740 PMCID: PMC5069339 DOI: 10.1007/s00122-016-2768-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/12/2016] [Indexed: 05/24/2023]
Abstract
Linkage mapping can help unravel the complexities of polyploid genomes. Here, we integrate haplotype-specific linkage maps in autotetraploid potato and explore the possibilities for mapping in other polyploid species. High-density linkage mapping in autopolyploid species has become possible in recent years given the increasing number of molecular markers now available through modern genotyping platforms. Such maps along with larger experimental populations are needed before we can obtain sufficient accuracy to make marker-trait association studies useful in practice. Here, we describe a method to create genetic linkage maps for an autotetraploid species with large numbers of markers and apply it to an F1 population of tetraploid potato (Solanum tuberosum L.) of 235 individuals genotyped using a 20K SNP array. SNP intensity values were converted to allele dosages after which we calculated pairwise maximum likelihood estimates of recombination frequencies between all marker segregation types under the assumption of random bivalent pairing. These estimates were used in the clustering of markers into linkage groups and their subsequent ordering into 96 homologue maps. The homologue maps were integrated per chromosome, resulting in a total map length of 1061 cM from 6910 markers covering all 12 potato chromosomes. We examined the questions of marker phasing and binning and propose optimal strategies for both. We also investigated the effect of quadrivalent formation and preferential pairing on recombination frequency estimation and marker phasing, which is of great relevance not only for potato but also for genetic studies in other tetraploid species for which the meiotic pairing behaviour is less well understood.
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Affiliation(s)
- Peter M Bourke
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, P.O. Box 386, 6708 PB, Wageningen, The Netherlands
| | - Roeland E Voorrips
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, P.O. Box 386, 6708 PB, Wageningen, The Netherlands
| | - Twan Kranenburg
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, P.O. Box 386, 6708 PB, Wageningen, The Netherlands
| | - Johannes Jansen
- Biometris, Wageningen University and Research Centre, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Richard G F Visser
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, P.O. Box 386, 6708 PB, Wageningen, The Netherlands
| | - Chris Maliepaard
- Wageningen UR Plant Breeding, Wageningen University and Research Centre, Droevendaalsesteeg 1, P.O. Box 386, 6708 PB, Wageningen, The Netherlands.
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Vigna BBZ, Santos JCS, Jungmann L, do Valle CB, Mollinari M, Pastina MM, Pagliarini MS, Garcia AAF, Souza AP. Evidence of Allopolyploidy in Urochloa humidicola Based on Cytological Analysis and Genetic Linkage Mapping. PLoS One 2016; 11:e0153764. [PMID: 27104622 PMCID: PMC4841517 DOI: 10.1371/journal.pone.0153764] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/04/2016] [Indexed: 01/30/2023] Open
Abstract
The African species Urochloa humidicola (Rendle) Morrone & Zuloaga (syn. Brachiaria humidicola (Rendle) Schweick.) is an important perennial forage grass found throughout the tropics. This species is polyploid, ranging from tetra to nonaploid, and apomictic, which makes genetic studies challenging; therefore, the number of currently available genetic resources is limited. The genomic architecture and evolution of U. humidicola and the molecular markers linked to apomixis were investigated in a full-sib F1 population obtained by crossing the sexual accession H031 and the apomictic cultivar U. humidicola cv. BRS Tupi, both of which are hexaploid. A simple sequence repeat (SSR)-based linkage map was constructed for the species from 102 polymorphic and specific SSR markers based on simplex and double-simplex markers. The map consisted of 49 linkage groups (LGs) and had a total length of 1702.82 cM, with 89 microsatellite loci and an average map density of 10.6 cM. Eight homology groups (HGs) were formed, comprising 22 LGs, and the other LGs remained ungrouped. The locus that controls apospory (apo-locus) was mapped in LG02 and was located 19.4 cM from the locus Bh027.c.D2. In the cytological analyses of some hybrids, bi- to hexavalents at diakinesis were observed, as well as two nucleoli in some meiocytes, smaller chromosomes with preferential allocation within the first metaphase plate and asynchronous chromosome migration to the poles during anaphase. The linkage map and the meiocyte analyses confirm previous reports of hybridization and suggest an allopolyploid origin of the hexaploid U. humidicola. This is the first linkage map of an Urochloa species, and it will be useful for future quantitative trait locus (QTL) analysis after saturation of the map and for genome assembly and evolutionary studies in Urochloa spp. Moreover, the results of the apomixis mapping are consistent with previous reports and confirm the need for additional studies to search for a co-segregating marker.
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Affiliation(s)
- Bianca B. Z. Vigna
- University of Campinas (UNICAMP), Center of Molecular Biology and Genetic Engineering (CBMEG), CP 6010, CEP 13083–970, Campinas, SP, Brazil
- Embrapa Pecuária Sudeste, CP 399, CEP 13560–970, São Carlos, SP, Brazil
| | - Jean C. S. Santos
- University of Campinas (UNICAMP), Center of Molecular Biology and Genetic Engineering (CBMEG), CP 6010, CEP 13083–970, Campinas, SP, Brazil
| | - Leticia Jungmann
- Embrapa Gado de Corte, Av. Radio Maia, 830, CEP 79106–550, Campo Grande, MS, Brazil
| | - Cacilda B. do Valle
- Embrapa Gado de Corte, Av. Radio Maia, 830, CEP 79106–550, Campo Grande, MS, Brazil
| | - Marcelo Mollinari
- University of São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Department of Genetics, CP 83, CEP 13400–970, Piracicaba, SP, Brazil
| | - Maria M. Pastina
- Embrapa Milho e Sorgo, Rod. MG 424, Km 65, CEP 35701–970, Sete Lagoas, MG, Brazil
| | - Maria Suely Pagliarini
- University of Maringá (UEM), Department of Genetics and Cell Biology, Av. Colombo, 5790, Zona 7, CEP 87020–900, Maringá, PR, Brazil
| | - Antonio A. F. Garcia
- University of São Paulo, Escola Superior de Agricultura Luiz de Queiroz, Department of Genetics, CP 83, CEP 13400–970, Piracicaba, SP, Brazil
| | - Anete P. Souza
- University of Campinas (UNICAMP), Center of Molecular Biology and Genetic Engineering (CBMEG), CP 6010, CEP 13083–970, Campinas, SP, Brazil
- University of Campinas (UNICAMP), Biology Institute, Department of Plant Biology, CP6109, CEP 13083–970, Campinas, SP, Brazil
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11
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Probabilistic Multilocus Haplotype Reconstruction in Outcrossing Tetraploids. Genetics 2016; 203:119-31. [PMID: 26920758 DOI: 10.1534/genetics.115.185579] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/22/2016] [Indexed: 01/29/2023] Open
Abstract
For both plant (e.g., potato) and animal (e.g., salmon) species, unveiling the genetic architecture of complex traits is key to the genetic improvement of polyploids in agriculture. F1 progenies of a biparental cross are often used for quantitative trait loci (QTL) mapping in outcrossing polyploids, where haplotype reconstruction by identifying the parental origins of marker alleles is necessary. In this paper, we build a novel and integrated statistical framework for multilocus haplotype reconstruction in a full-sib tetraploid family from biallelic marker dosage data collected from single-nucleotide polymorphism (SNP) arrays or next-generation sequencing technology given a genetic linkage map. Compared to diploids, in tetraploids, additional complexity needs to be addressed, including double reduction and possible preferential pairing of chromosomes. We divide haplotype reconstruction into two stages: parental linkage phasing for reconstructing the most probable parental haplotypes and ancestral inference for probabilistically reconstructing the offspring haplotypes conditional on the reconstructed parental haplotypes. The simulation studies and the application to real data from potato show that the parental linkage phasing is robust to, and that the subsequent ancestral inference is accurate for, complex chromosome pairing behaviors during meiosis, various marker segregation types, erroneous genetic maps except for long-range disturbances of marker ordering, various amounts of offspring dosage errors (up to ∼20%), and various fractions of missing data in parents and offspring dosages.
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Mollinari M, Serang O. Quantitative SNP genotyping of polyploids with MassARRAY and other platforms. Methods Mol Biol 2015; 1245:215-41. [PMID: 25373761 DOI: 10.1007/978-1-4939-1966-6_17] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Accurate genotyping is essential for building genetic maps and performing genome assembly of polyploid species. Recent high-throughput techniques, such as Illumina GoldenGate™ and Sequenom iPLEX MassARRAY®, have made it possible to accurately estimate the relative abundances of different alleles even when the ploidy of the population is unknown. Here we describe the experimental methods for collecting these relative allele intensities and then demonstrate the practical concerns for inferring genotypes using Bayesian inference via the software package SuperMASSA.
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Garcia AAF, Mollinari M, Marconi TG, Serang OR, Silva RR, Vieira MLC, Vicentini R, Costa EA, Mancini MC, Garcia MOS, Pastina MM, Gazaffi R, Martins ERF, Dahmer N, Sforça DA, Silva CBC, Bundock P, Henry RJ, Souza GM, van Sluys MA, Landell MGA, Carneiro MS, Vincentz MAG, Pinto LR, Vencovsky R, Souza AP. SNP genotyping allows an in-depth characterisation of the genome of sugarcane and other complex autopolyploids. Sci Rep 2013; 3:3399. [PMID: 24292365 PMCID: PMC3844970 DOI: 10.1038/srep03399] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 11/15/2013] [Indexed: 12/12/2022] Open
Abstract
Many plant species of great economic value (e.g., potato, wheat, cotton, and sugarcane) are polyploids. Despite the essential roles of autopolyploid plants in human activities, our genetic understanding of these species is still poor. Recent progress in instrumentation and biochemical manipulation has led to the accumulation of an incredible amount of genomic data. In this study, we demonstrate for the first time a successful genetic analysis in a highly polyploid genome (sugarcane) by the quantitative analysis of single-nucleotide polymorphism (SNP) allelic dosage and the application of a new data analysis framework. This study provides a better understanding of autopolyploid genomic structure and is a sound basis for genetic studies. The proposed methods can be employed to analyse the genome of any autopolyploid and will permit the future development of high-quality genetic maps to assist in the assembly of reference genome sequences for polyploid species.
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Affiliation(s)
- Antonio A F Garcia
- 1] Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz" Universidade de São Paulo, Brazil [2]
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Li J, Das K, Liu J, Fu G, Li Y, Tobias C, Wu R. Statistical models for genetic mapping in polyploids: challenges and opportunities. Methods Mol Biol 2012; 871:245-261. [PMID: 22565841 DOI: 10.1007/978-1-61779-785-9_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Statistical methods for genetic mapping have well been developed for diploid species but are lagging in the more complex polyploids. The genetic mapping of polyploids, where genome number is higher than two, is complicated by uncertainty about the genotype-phenotype correspondence, inconsistent meiotic mechanisms, heterozygous genome structures, and increased allelic (action) and nonallelic (interaction) combinations. According to their meiotic configurations, polyploids can be classified as bivalent polyploids, in which only two chromosomes pair during meiosis at a time, and multivalent polyploids, where multiple chromosomes pair simultaneously. For some polyploids, these two types of pairing occur at the same time, leading to a mixed category. This chapter reviews several challenges due to the complexities of linkage analysis in polyploids and describes statistical models and algorithms that have been developed for linkage mapping based on their distinct meiotic characteristics. We discuss several issues that should be addressed to better understand the genome structure and organization of polyploids and the genetic architecture of complex traits for this unique group of plants.
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Affiliation(s)
- Jiahan Li
- Department of Statistics and Center for Statistical Genetics, Pennsylvania State University, Hershey, PA 17033, USA
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Gar O, Sargent DJ, Tsai CJ, Pleban T, Shalev G, Byrne DH, Zamir D. An autotetraploid linkage map of rose (Rosa hybrida) validated using the strawberry (Fragaria vesca) genome sequence. PLoS One 2011; 6:e20463. [PMID: 21647382 PMCID: PMC3103584 DOI: 10.1371/journal.pone.0020463] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 04/24/2011] [Indexed: 01/21/2023] Open
Abstract
Polyploidy is a pivotal process in plant evolution as it increase gene redundancy and morphological intricacy but due to the complexity of polysomic inheritance we have only few genetic maps of autopolyploid organisms. A robust mapping framework is particularly important in polyploid crop species, rose included (2n = 4x = 28), where the objective is to study multiallelic interactions that control traits of value for plant breeding. From a cross between the garden, peach red and fragrant cultivar Fragrant Cloud (FC) and a cut-rose yellow cultivar Golden Gate (GG), we generated an autotetraploid GGFC mapping population consisting of 132 individuals. For the map we used 128 sequence-based markers, 141 AFLP, 86 SSR and three morphological markers. Seven linkage groups were resolved for FC (Total 632 cM) and GG (616 cM) which were validated by markers that segregated in both parents as well as the diploid integrated consensus map.The release of the Fragaria vesca genome, which also belongs to the Rosoideae, allowed us to place 70 rose sequenced markers on the seven strawberry pseudo-chromosomes. Synteny between Rosa and Fragaria was high with an estimated four major translocations and six inversions required to place the 17 non-collinear markers in the same order. Based on a verified linear order of the rose markers, we could further partition each of the parents into its four homologous groups, thus providing an essential framework to aid the sequencing of an autotetraploid genome.
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Affiliation(s)
- Oron Gar
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | | | - Ching-Jung Tsai
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Tzili Pleban
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Gil Shalev
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - David H. Byrne
- Department of Horticultural Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Dani Zamir
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- * E-mail:
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