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Amundson KR, Ordoñez B, Santayana M, Nganga ML, Henry IM, Bonierbale M, Khan A, Tan EH, Comai L. Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability. THE PLANT CELL 2021; 33:2149-2163. [PMID: 33792719 PMCID: PMC8364225 DOI: 10.1093/plcell/koab100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/26/2021] [Indexed: 05/03/2023]
Abstract
In cultivated tetraploid potato (Solanum tuberosum), reduction to diploidy (dihaploidy) allows for hybridization to diploids and introgression breeding and may facilitate the production of inbreds. Pollination with haploid inducers (HIs) yields maternal dihaploids, as well as triploid and tetraploid hybrids. Dihaploids may result from parthenogenesis, entailing the development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and the loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of HI DNA in some dihaploids. We characterized the genomes of 919 putative dihaploids and 134 hybrids produced by pollinating tetraploid clones with three HIs: IVP35, IVP101, and PL-4. Whole-chromosome or segmental aneuploidy was observed in 76 dihaploids, with karyotypes ranging from 2n = 2x - 1 = 23 to 2n = 2x + 3 = 27. Of the additional chromosomes in 74 aneuploids, 66 were from the non-inducer parent and 8 from the inducer parent. Overall, we detected full or partial chromosomes from the HI parent in 0.87% of the dihaploids, irrespective of parental genotypes. Chromosomal breaks commonly affected the paternal genome in the dihaploid and tetraploid progeny, but not in the triploid progeny, correlating instability to sperm ploidy and to haploid induction. The residual HI DNA discovered in the progeny is consistent with genome elimination as the mechanism of haploid induction.
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Affiliation(s)
- Kirk R. Amundson
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
| | - Benny Ordoñez
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
- International Potato Center (CIP), Lima 15024, Peru
- Integrative Genetics and Genomics Graduate Group, University of California, Davis, California 95616
| | | | - Mwaura Livingstone Nganga
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
| | - Isabelle M. Henry
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
| | - Merideth Bonierbale
- International Potato Center (CIP), Lima 15024, Peru
- Duquesa Business Centre, Malaga 29692, Spain
| | - Awais Khan
- International Potato Center (CIP), Lima 15024, Peru
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Geneva, New York 14456
| | - Ek Han Tan
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - Luca Comai
- Plant Biology Graduate Group and Genome Center, University of California, Davis, Davis, California 95616
- Author for correspondence:
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Amundson KR, Ordoñez B, Santayana M, Tan EH, Henry IM, Mihovilovich E, Bonierbale M, Comai L. Genomic Outcomes of Haploid Induction Crosses in Potato ( Solanum tuberosum L.). Genetics 2020; 214:369-380. [PMID: 31871130 PMCID: PMC7017018 DOI: 10.1534/genetics.119.302843] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/09/2019] [Indexed: 01/12/2023] Open
Abstract
The challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination with S. tuberosum Andigenum Group (formerly S. phureja) cultivars. The mechanism underlying haploid formation of these crosses is unclear, and questions regarding the frequency of paternal DNA transmission remain. Previous reports have described aneuploid and euploid progeny that, in some cases, displayed genetic markers from the haploid inducer (HI). Here, we surveyed a population of 167 presumed dihaploids for large-scale structural variation that would underlie chromosomal addition from the HI, and for small-scale introgression of genetic markers. In 19 progeny, we detected 10 of the 12 possible trisomies and, in all cases, demonstrated the noninducer parent origin of the additional chromosome. Deep sequencing indicated that occasional, short-tract signals appearing to be of HI origin were better explained as technical artifacts. Leveraging recurring copy number variation patterns, we documented subchromosomal dosage variation indicating segregation of polymorphic maternal haplotypes. Collectively, 52% of the assayed chromosomal loci were classified as dosage variable. Our findings help elucidate the genomic consequences of potato haploid induction and suggest that most potato dihaploids will be free of residual pollinator DNA.
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Affiliation(s)
- Kirk R Amundson
- Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Benny Ordoñez
- Plant Biology and Genome Center, University of California, Davis, California 95616
- International Potato Center (CIP), Lima 12, Peru
| | | | - Ek Han Tan
- Plant Biology and Genome Center, University of California, Davis, California 95616
- School of Biology and Ecology, University of Maine, Orono, Maine 04469
| | - Isabelle M Henry
- Plant Biology and Genome Center, University of California, Davis, California 95616
| | | | | | - Luca Comai
- Plant Biology and Genome Center, University of California, Davis, California 95616
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Bartkiewicz A, Chilla F, Terefe-Ayana D, Lübeck J, Strahwald J, Tacke E, Hofferbert HR, Flath K, Linde M, Debener T. Improved genetic resolution for linkage mapping of resistance to potato wart in monoparental dihaploids with potential diagnostic value in tetraploid potato varieties. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2555-2566. [PMID: 30159644 PMCID: PMC6244520 DOI: 10.1007/s00122-018-3172-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/27/2018] [Indexed: 05/21/2023]
Abstract
KEY MESSAGE We achieved improved mapping resolution of the major wart resistance locus Xla-TNL containing also Sen1 in a dihaploid population using SNP data and developed additional markers with diagnostic value in tetraploid varieties. We analyzed a segregating monoparental dihaploid potato population comprising 215 genotypes derived from a tetraploid variety that is highly resistant to Synchytrium endobioticum pathotypes 18 and 6. The clear bimodal segregation for both pathotypes indicated that a major dominant resistance factor in a simplex allele configuration was present in the tetraploid donor genotype. Compared to that in previous analyses of the same tetraploid donor in conventional crosses with susceptible tetraploid genotypes, a segregation pattern with a reduced genetic complexity of resistance in dihaploids was observed here. Using the 12.8 k SolCAP SNP array, we mapped a resistance locus to the Xla-TNL region containing also Sen1 on potato chromosome 11. The improved mapping resolution provided by the monoparental dihaploids allowed for the localization of the genes responsible for the resistance to both pathotypes in an interval spanning less than 800 kbp on the reference genome. Furthermore, we identified eight molecular markers segregating without recombination to pathotype 18 and pathotype 6 resistance. Also, two developed markers display improved diagnostic properties in an independent panel of tetraploid varieties. Overall, our data provide the highest resolution mapping of wart resistance genes at the Xla-TNL locus thus far.
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Affiliation(s)
- Annette Bartkiewicz
- Institute of Plant Genetics, Department of Molecular Plant Breeding, Leibniz University Hannover, Hannover, Germany
- DHD-Consulting GmbH, Hildesheim, Germany
| | - Friederike Chilla
- Institute of Plant Genetics, Department of Molecular Plant Breeding, Leibniz University Hannover, Hannover, Germany
- Julius Kühn-Institut, Kleinmachnow, Germany
| | - Diro Terefe-Ayana
- Institute of Plant Genetics, Department of Molecular Plant Breeding, Leibniz University Hannover, Hannover, Germany
- Westhoff, Südlohn-Oeding, Germany
| | - Jens Lübeck
- SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany
| | | | - Eckhard Tacke
- Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany
| | | | | | - Marcus Linde
- Institute of Plant Genetics, Department of Molecular Plant Breeding, Leibniz University Hannover, Hannover, Germany
| | - Thomas Debener
- Institute of Plant Genetics, Department of Molecular Plant Breeding, Leibniz University Hannover, Hannover, Germany.
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