A Bayesian Approach for Discriminating Among Alternative Inheritance Hypotheses in Plant Polyploids: The Allotetraploid Origin of Genus Borderea (Dioscoreaceae)

Abstract

Polyploidy is a common phenomenon occurring in a vast number of land plants. Investigations of patterns of inheritance and the origins of plants (i.e., autopolyploidy vs. allopolyploidy) usually involve cytogenetic and molecular studies of chromosome pairing, chromosome mapping, and marker segregation analysis through experimental crosses and progeny tests. Such studies are missing for most wild species, for which artificial crosses are difficult, not feasible, or unaffordable. We report here a Bayesian method to discriminate between alternative inheritance patterns in the two extant, tetraploid species of the monocot genus Borderea (Dioscoreaceae), which does not involve progeny array tests. Our approach is based on the screening of a large number of SSR genotypes, which were obtained from successful amplifications of 17 microsatellite regions in individuals of both B. chouardii and B. pyrenaica. We tested for tetrasomic vs. disomic modes of inheritance, using the Bayes factor test. Assignment of genotypes under both alternatives could be unequivocally done for 14 and 11 of the 17 studied microsatellite regions in B. chouardii and B. pyrenaica, respectively, totaling 9502 analyzed genotypes. The comparison of posterior probabilities for the two competing hypotheses across the surveyed loci clearly favored a disomic inheritance pattern. Linkage tests indicated that none of the studied SSR loci were in linkage disequilibrium, thus representing independent samples of the Borderea genome. These results, along with previous allozyme data, support the allotetraploid origin of this paleoendemic genus and reveal the lowest reported chromosome base number for the family of the yams.

Polyploid origin, genetic diversity and population structure in the tetraploid sea lavender Limonium narbonense Miller (Plumbaginaceae) from eastern Spain

“…Some analytical methods have also implemented the modification of population genetic statistics to accommodate genomic attributes of polyploids and their different genetic behaviours (i.e. disomic inheritance in allopolyploids vs. polysomic inheritance and double reduction of autopolyploids) into different software packages (Ronfort et al 1998;Pritchard et al 2000;Thrall and Young 2000;Catalán et al 2006;Luo et al 2006;Markwith et al 2006;Tomiuk et al 2009;Clark and Jasieniuk 2011).…”

Eighteen SSR-primers for tetraploid Adansonia digitata and its relatives

“…Expanding to look also at offspring that had less than four alleles, polysomic inheritance was inferred for all loci except Ad09, Ad10, Ad12, and Ad13. More thorough testing will be possible once it has been established to what extent the allele peak area can be used to estimate the allelic configuration (e.g., Catalán et al 2006). It is suggested to test this by analysis of offspring from controlled test crosses between individuals with selected genotypes (e.g., Stift et al 2008).…”

Glacial survival, phylogeography, and a comparison of microsatellite evolution models for resolving population structure in two species of dwarf yams (Borderea, Dioscoreaceae) endemic to the central Pyrenees

“…Seventeen primer-pairs amplified trinucleotide (CTT) n microsatellite regions in both Borderea taxa (cf. Catalán et al 2006). The amplified products were run on an ABI310 automated sequencer (Applied Biosystems).…”

“…Genotypic data were obtained for those microsatellite loci that did not have overlapping alleles from the different parent genomes (Segarra-Moragues et al 2005Catalán et al 2006). This was done for 14 and 11 of the 17 assayed SSR primer-pairs in B. chouardii and B. pyrenaica, respectively.…”

“…from both putative parental genomes), thus providing genotypes at 18 and 14 SSR loci, respectively. These duplicated loci were analysed in the same way as for conventional diploids (see Catalán et al 2006 for further details).…”