Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits
The cultivated potato (Solanum tuberosum) has a complex genetic structure due to its autotetraploidy and vegetative propagation which leads to accumulation of mutations and a highly heterozygous genome. A high degree of heterozygosity has been considered to be the main driver of fitness and agronomi...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2018-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2018.00944/full |
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| author | Norma C. Manrique-Carpintero Joseph J. Coombs Gina M. Pham F. Parker E. Laimbeer Guilherme T. Braz Jiming Jiang Jiming Jiang Richard E. Veilleux C. Robin Buell C. Robin Buell David S. Douches |
| author_facet | Norma C. Manrique-Carpintero Joseph J. Coombs Gina M. Pham F. Parker E. Laimbeer Guilherme T. Braz Jiming Jiang Jiming Jiang Richard E. Veilleux C. Robin Buell C. Robin Buell David S. Douches |
| author_sort | Norma C. Manrique-Carpintero |
| collection | DOAJ |
| description | The cultivated potato (Solanum tuberosum) has a complex genetic structure due to its autotetraploidy and vegetative propagation which leads to accumulation of mutations and a highly heterozygous genome. A high degree of heterozygosity has been considered to be the main driver of fitness and agronomic trait performance in potato improvement efforts, which is negatively impacted by genetic load. To understand the genetic landscape of cultivated potato, we constructed a gynogenic dihaploid (2n = 2x = 24) population from cv. Superior, prior to development of a high-density genetic map containing 12,753 single nucleotide polymorphisms (SNPs). Common quantitative trait loci (QTL) were identified for tuber traits, vigor and height on chromosomes 2, 4, 7, and 10, while specific QTL for number of inflorescences per plant, and tuber shape were present on chromosomes 4, 6, 10, and 11. Simplex rather than duplex loci were mainly associated with traits. In general, the Q allele (main effect) detected in one or two homologous chromosomes was associated with lower mean trait values suggesting the importance of dosage allelic effects, and the presence of up to two undesired alleles in the QTL region. Loss of heterozygosity has been associated with a lower rate of fitness, yet no correlation between the percent heterozygosity and increased fitness or agronomic performance was observed. Based upon linkage phase, we reconstructed the four homologous chromosome haplotypes of cv. Superior. revealing heterogeneity throughout the genome yet nearly duplicate haplotypes occurring among the homologs of particular chromosomes. These results suggest that the potentially deleterious mutations associated with genetic load in tetraploid potato could be mitigated by multiple loci which is consistent with the theory that epistasis complicates the identification of associations between markers and phenotypic performance. |
| first_indexed | 2024-12-10T07:28:16Z |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-10T07:28:16Z |
| publishDate | 2018-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-2d6cc9cfaac24666955b9c5b3c7a55f62022-12-22T01:57:38ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-07-01910.3389/fpls.2018.00944374402Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic TraitsNorma C. Manrique-Carpintero0Joseph J. Coombs1Gina M. Pham2F. Parker E. Laimbeer3Guilherme T. Braz4Jiming Jiang5Jiming Jiang6Richard E. Veilleux7C. Robin Buell8C. Robin Buell9David S. Douches10Potato Breeding and Genetics Program, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United StatesPotato Breeding and Genetics Program, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United StatesDepartment of Plant Biology, Michigan State University, East Lansing, MI, United StatesDepartment of Horticulture, Virginia Tech, Blacksburg, VA, United StatesDepartment of Plant Biology, Michigan State University, East Lansing, MI, United StatesDepartment of Plant Biology, Michigan State University, East Lansing, MI, United StatesDepartment of Horticulture, Michigan State University, East Lansing, MI, United StatesDepartment of Horticulture, Virginia Tech, Blacksburg, VA, United StatesDepartment of Plant Biology, Michigan State University, East Lansing, MI, United StatesPlant Resilience Institute, Michigan State University, East Lansing, MI, United StatesPotato Breeding and Genetics Program, Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United StatesThe cultivated potato (Solanum tuberosum) has a complex genetic structure due to its autotetraploidy and vegetative propagation which leads to accumulation of mutations and a highly heterozygous genome. A high degree of heterozygosity has been considered to be the main driver of fitness and agronomic trait performance in potato improvement efforts, which is negatively impacted by genetic load. To understand the genetic landscape of cultivated potato, we constructed a gynogenic dihaploid (2n = 2x = 24) population from cv. Superior, prior to development of a high-density genetic map containing 12,753 single nucleotide polymorphisms (SNPs). Common quantitative trait loci (QTL) were identified for tuber traits, vigor and height on chromosomes 2, 4, 7, and 10, while specific QTL for number of inflorescences per plant, and tuber shape were present on chromosomes 4, 6, 10, and 11. Simplex rather than duplex loci were mainly associated with traits. In general, the Q allele (main effect) detected in one or two homologous chromosomes was associated with lower mean trait values suggesting the importance of dosage allelic effects, and the presence of up to two undesired alleles in the QTL region. Loss of heterozygosity has been associated with a lower rate of fitness, yet no correlation between the percent heterozygosity and increased fitness or agronomic performance was observed. Based upon linkage phase, we reconstructed the four homologous chromosome haplotypes of cv. Superior. revealing heterogeneity throughout the genome yet nearly duplicate haplotypes occurring among the homologs of particular chromosomes. These results suggest that the potentially deleterious mutations associated with genetic load in tetraploid potato could be mitigated by multiple loci which is consistent with the theory that epistasis complicates the identification of associations between markers and phenotypic performance.https://www.frontiersin.org/article/10.3389/fpls.2018.00944/fullhaplotypedihaploidgenetic loadcomplex traitslinkage map |
| spellingShingle | Norma C. Manrique-Carpintero Joseph J. Coombs Gina M. Pham F. Parker E. Laimbeer Guilherme T. Braz Jiming Jiang Jiming Jiang Richard E. Veilleux C. Robin Buell C. Robin Buell David S. Douches Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits Frontiers in Plant Science haplotype dihaploid genetic load complex traits linkage map |
| title | Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits |
| title_full | Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits |
| title_fullStr | Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits |
| title_full_unstemmed | Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits |
| title_short | Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits |
| title_sort | genome reduction in tetraploid potato reveals genetic load haplotype variation and loci associated with agronomic traits |
| topic | haplotype dihaploid genetic load complex traits linkage map |
| url | https://www.frontiersin.org/article/10.3389/fpls.2018.00944/full |
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