Academic journal article Genetics

Constructing Genetic Linkage Maps under a Tetrasomic Model

Academic journal article Genetics

Constructing Genetic Linkage Maps under a Tetrasomic Model

Article excerpt

ABSTRACT

An international consortium has launched the whole-genome sequencing of potato, the fourth most important food crop in the world. Construction of genetic linkage maps is an inevitable step for taking advantage of the genome projects for the development of novel cultivars in the autotetraploid crop species. However, linkage analysis in autopolyploids, the kernel of linkage map construction, is theoretically challenging and methodologically unavailable in the current literature. We present here a theoretical analysis and a statistical method for tetrasomic linkage analysis with dominant and/or codominant molecular markers. The analysis reveals some essential properties of the tetrasomic model. The method accounts properly for double reduction and incomplete information of marker phenotype in regard to the corresponding phenotype in estimating the coefficients of double reduction and recombination frequency and in testing their significance by using the marker phenotype data. Computer simulation was developed to validate the analysis and the method and a case study with 201 AFLP and SSR markers scored on 228 full-sib individuals of autotetraploid potato is used to illustrate the utility of the method in map construction in autotetraploid species.

POLYPLOIDY has played an important role in the evolution of eukaryotes, particularly flowering plants, and has implications for genetic improvement of many important agricultural crops such as alfalfa, potato, sugarcane, and cotton (GRANT 1971; LEWIS 1980; OTTO and WHITTON 2000). In the era of genomics, genetic linkage maps exist or are rapidly becoming available for most important diploid animal and plant species and provide the springboard for genome projects in these species. In sharp contrast, the corresponding study in autopolyploid species is still in its initial stages. As the theoretical kernel of genetic map construction, linkage analysis in this group of species has been a historical challenge since the years of pioneering quantitative geneticists such as HALDANE (1930), MATHER (1936), and FISHER (1947). This is largely due to the complexities of gene segregation and recombination during meiosis in such organisms, namely: (i) multiplex allele segregation; (ii) double reduction, a phenomenon in which sister chromatids enter in the same gamete and cause systematic segregation distortion and complex segregation pattern; and (iii) mixed bivalent and quadrivalent pairings among homologous chromosomes.

The current data sets available for linkage analyses in autotetraploids are DNA molecular polymorphisms that exhibit either dominant (e.g., AFLPs and RAPDs) or codominant (e.g., RFLPs and SSRs) segregation in a mapping population. In addition to the aforementioned complexities (i-iii), challenges in modeling these PCRbased genetic markers involve (iv) occurrence of null alleles due to experimental failure to identify the presence of some alleles and (v) one phenotype representing several genotypes. Linkage analyses of autopolyploids in the current literature have been based either on the use of single-dose (simplex) dominant markers (e.g., AFLPs and RAPDs) that segregate in a simple 1:1 ratio in mapping populations (Wu et al. 1992; MEYER et al. 1998; BROUWER and OSBORN 1999; BARCACCIA et al. 2003) or on assuming solely random bivalent pairing among homologous chromosomes (RiPOL et al. 1999; HACKETT et al. 2001; Luo et al. 2001; BRADSHAW et al. 2004; CAO et al. 2005). These have effectively avoided the analytical complexities but at the same time ignored some essential features of the problems.

Having considered these analytical complexities, we developed a statistical framework for genetic linkage analysis in autotetraploid species (Luo et al. 2004). The basis of the analysis is the theoretical model that relates the coefficients of double reduction at two loci with recombination frequency between them. A likelihoodbased approach was developed to estimate the model parameters and to test their significance. …

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