Determining paternity in polyploids: Hexaploid simulation studies

Abstract

The breeding of new sweetpotato varieties is a highly inefficient process, confounded by incompatibility, poor fertility, open-pollination and hexaploidy. Upwards of 12-20 lines are combined in open pollinated nurseries based on horticulturally important characteristics. After several years of selection most progeny can be traced back to just 3 or 4 maternal lines. A method that would identify the paternal parent of superior progeny would enable breeders to combine parents that exhibit superior combining ability in more efficient, smaller nurseries. The objective of this work is to explore by means of computer simulation the application of genealogy reconstruction techniques on hexaploid individuals based on co-dominant marker data. The progeny obtained from each female parent is categorically assigned to each male with non-zero exclusion probability based on its paternity likelihood. Computer simulations show that even with polysomic segregation types, it is possible to discriminate between putative parents with few errors or mis-assignments. The number of loci scored for a 10 parent population should not be less than 20 in the case of 3 alleles per locus, and no more than 10 loci for a five allele model. An increment in the number of alleles or loci increases the discriminatory power with the number of alleles yielding a far more important effect than the number of loci. This study also demonstrates the feasibility of using simulations to determine the minimum requirements, i.e. number of loci to be genotyped, for unambiguous parentage allocation in polyploids.