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The Plant Genome Abstract - Original Research

Self-Fertility in a Cultivated Diploid Potato Population Examined with the Infinium 8303 Potato Single-Nucleotide Polymorphism Array

 

This article in TPG

  1. Vol. 9 No. 3
    unlockOPEN ACCESS
     
    Received: Jan 11, 2016
    Accepted: May 10, 2016
    Published: August 18, 2016


    * Corresponding author(s): potato@vt.edu
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doi:10.3835/plantgenome2016.01.0003
  1. Brenda A. Petersona,
  2. Sarah H. Holta,
  3. F. Parker E. Laimbeera,
  4. Andreas G. Doulisb,
  5. Joseph Coombsc,
  6. David S. Douchesc,
  7. Michael A. Hardigand,
  8. C. Robin Buelld and
  9. Richard E. Veilleux *a
  1. a Dep. of Horticulture, Virginia Tech, 220 Ag Quad Lane, Blacksburg, VA 24061
    b Dep. of Horticulture, Virginia Tech, 220 Ag Quad Lane, Blacksburg, VA 24061 and Hellenic Agricultural Organization DEMETER (ex. NAGREF), Herakleion, Greece
    c Dep. of Crop and Soil Sciences, Michigan State Univ., East Lansing, MI 48824
    d Dep. of Plant Biology, Michigan State Univ., East Lansing, MI 48824
Core Ideas:
  • Self-fertility in diploid potato is independent of self-compatibility
  • SNP genotyping may be confounded by copy number variation
  • Genomic regions of a highly heterozygous species resist homozygosity during inbreeding

Abstract

Within a population of F1 hybrids between two genotypes (S. tuberosum L. Group Phureja DM 1-3 516 R44 [DM] and S. tuberosum L. Group Tuberosum RH89-039-16 [RH]) used in the potato genome sequencing project, we observed fruit set after self-pollination on many plants. Examination of pollen tube growth in self-fertile and self-unfruitful F1 plants after controlled self-pollinations revealed no difference in the ability of pollen tubes to reach the ovary. To identify genomic regions linked with self-fertility, we genotyped the F1 population using a genome-wide single-nucleotide polymorphism (SNP) array. Polymorphic and robust SNPs were analyzed to identify allelic states segregating with the self-fertile phenotype. All 88 highly significant SNPs occurred on chromosome 12. Seeds obtained after self-pollination of self-fertile individuals were used to advance the population for four generations. Genotyping 46 self-fruitful and 46 self-unfruitful S3 plants on the Infinium 8303 Potato SNP array revealed eight SNPs segregating with self-fertility on chromosomes 4, 9, 11, and 12. Three times more heterozygosity than expected was found in the S3 generation. Estimates of heterozygosity were influenced by copy number variation (CNV) in the potato genome leading to spurious heterozygous genotyping calls. Some spurious heterozygosity could be removed by application of a CNV filter developed from alignment of additional monoploid potato genomic sequence to the DM reference genome. The genes responsible for fruit set in self-fertile plants in the F1 generation were restricted to chromosome 12, whereas new genomic regions contributed to the ability of S3 plants to set fruit after self-pollination.

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