![]() A brief description of polysomic inheritance models can be found in the Supporting Information S1. Double reduction will result in gametes carrying identical-by-descent (IBD) alleles and increased homozygosity. For example, assume a tetraploid individual ABCD produces a gamete AA. Hereafter, we denote the allelic phenotype as a set of alleles and the genotype as a multiset of alleles, with the allelic phenotype being abbreviated as the ‘phenotype’.Ī peculiarity of polysomic inheritance is double-reduction, which occurs from a combination of three major events during meiosis: (a) the crossing-over between non-sister chromatids, (b) an appropriated pattern of disjunction, and (c) the subsequent migration of the chromosomal segments carrying a pair of sister chromatids to the same gamete (Darlington, 1929). However, due to varying amplification efficiency among alleles in PCR, the results of these methods are still unreliable. Some researchers have claimed that genotypes can be assigned from the band intensity (Esselink, Nybom, & Vosman, 2004) or allelic read depth (Voorrips, Gort, & Vosman, 2011) using such methods. Novel technologies such as genotyping-by-sequencing (GBS) also uses PCR and suffers from such problems. Therefore, the true genotype of individuals cannot be determined by electrophoresis and only the allelic phenotype is available for these markers. For example, for autotetraploids, the genotype AABB has the same electrophoresis band pattern as the genotype AAAB. In general, polyploid population genetics analyses present two major challenges: (a) genotyping ambiguities and (b) double-reduction.įor PCR-based markers, the dosage of alleles cannot be directly determined by electrophoresis. However, multivalent pairing can also occur in allopolyploids, resulting in a mixed inheritance pattern across loci in the genome, termed segmental allopolyploidy (Stebbins, 1950).īecause of differences in data formats and inheritance models, computer software designed for diploid organisms, such as genepop (Rousset, 2008) and arlequin (Excoffier & Lischer, 2010), cannot be used for autopolyploid species. Allopolyploids generally display disomic inheritance (Luo et al., 2006), because chromosomes from different species are not completely homologous. These are two extremes and many autopolyploid taxa represent intermediate stages (Butruille & Boiteux, 2000). In autopolyploids, both bivalents and multivalents can be formed during meiosis, resulting in disomic and polysomic inheritance, respectively. This paper mainly focuses on autopolyploids and allopolyploids that display polysomic inheritance. In allopolyploidy, chromosomes originate from two species in autopolyploidy, all chromosomes originate within a single species, often due to unreduced gametes. There are two distinct mechanisms of genome duplication that result in polyploidy: allopolyploidy and autopolyploidy. Due to their often important role in plant speciation, polyploids are regularly the subject of theoretical and experimental studies for evolutionary biology, molecular ecology and agriculture (Ling et al., 2018). Polyploidy has occurred in almost every ancestral plant lineage, and frequently occurs in extant species, especially in plants (Barker, Arrigo, Baniaga, Li, & Levin, 2016). Polyploids are cells or organisms having a genome with more than two sets of homologous chromosomes. polygene will thus facilitate molecular ecology research involving autopolyploids. polygene enables easy and convenient allelic phenotype- or genotype-based analysis for both autopolyploids and diploids.Comprehensive modes of genetic analyses are provided by polygene, which include genetic diversity analysis, tests for allelic phenotypic or genotypic distributions, linkage disequilibrium and genetic differentiation, genetic distance analysis, principal coordinates analysis, hierarchical clustering analysis, individual inbreeding coefficient estimation, individual heterozygosity index estimation, population assignment, pairwise relatedness estimation, parentage analysis, analysis of molecular variance and Bayesian clustering.Specifically, polygene obtains posterior probabilities for genotypes hidden within allelic phenotypes. ![]() To address these problems, we developed a new software package, polygene, which enables the estimation of genotypic frequencies for a number of polysomic inheritance models.When present, polyploidy presents problems for genetic data analysis, which are caused by both genotypic ambiguities and double-reduction. Polyploidy has appeared in almost every ancestral plant lineage, and in extant species, occurs frequently.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |