Open AccessSelf‐Fertility in a Cultivated Diploid Potato Population Examined with the Infinium 8303 Potato Single‐Nucleotide Polymorphism Array
Author(s) -
Peterson Brenda A.,
Holt Sarah H.,
Laimbeer F. Parker E.,
Doulis Andreas G.,
Coombs Joseph,
Douches David S.,
Hardigan Michael A.,
Buell C. Robin,
Veilleux Richard E.
Publication year - 2016
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2016.01.0003
Subject(s) - biology , genetics , single nucleotide polymorphism , loss of heterozygosity , genotyping , population , ploidy , snp genotyping , inbreeding , genotype , allele , gene , demography , sociology
Within a population of F 1 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 F 1 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 F 1 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 S 3 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 S 3 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 F 1 generation were restricted to chromosome 12, whereas new genomic regions contributed to the ability of S 3 plants to set fruit after self‐pollination.