A Bivalent Polyploid Model for Mapping Quantitative Trait Loci in Outcrossing Tetraploids

Abstract

Two major aspects have made the genetic and genomic study of polyploids extremely difficult. First, increased allelic or nonallelic combinations due to multiple alleles result in complex gene actions and interactions for quantitative trait loci (QTL) in polyploids. Second, meiotic configurations in polyploids undergo a complex biological process including either bivalent or multivalent formation, or both. For bivalent polyploids, different degrees of preferential chromosome pairings may occur during meiosis. In this article, we develop a maximum-likelihood-based model for mapping QTL in tetraploids by considering the quantitative inheritance and meiotic mechanism of bivalent polyploids. This bivalent polyploid model is implemented with the EM algorithm to simultaneously estimate QTL position, QTL effects, and QTL-marker linkage phases by incorporating the impact of a cytological parameter determining bivalent chromosome pairings (the preferential pairing factor). Simulation studies are performed to investigate the performance and robustness of our statistical method for parameter estimation. The implication and extension of the bivalent polyploid model are discussed. Considering the availability of marker and phenotype plant breeding (Zeven 1979; Bever and Felber 1992; data in a variety of polyploid species ranging from tetra-

Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models

“…Despite advances in genetic studies in autotetraploids, (Mather 1936; Fisher 1943, 1947; Hackett et al 2001; Luo et al 2004, 2006; Wu et al 2004; Leach et al 2010; Li et al 2010; Hackett et al 2013; Xu et al 2013; Rehmsmeier 2013; Zheng et al 2016), there is still a shortage of statistical methods to address organisms with higher ploidy levels, such as sweet potato (Kriegner et al 2003; Arizio et al 2014; Shirasawa et al 2017), sugarcane (Wang et al 2010; Garcia et al 2013), some ornamental flowers and forage crops (reviewed in (Soltis et al 2014b)). In this work, we denote as high-level autopolyploids those autopolyploid organisms with ploidy level greater than four.…”

Sugarcane: Breeding Methods and Genetic Mapping

“…It is important to mention that, for sugarcane (an autopolyploid species), proposals have been made for genetic mapping that consider polyploidy (da Silva, 1993;da Silva et al, 1995;da Silva and Sorrells, 1996;Ripol et al, 1999;Doerge and Craig, 2000;Wu et al, 2001;Luo et al, 2001;Luo et al, 2004;Wu et al, 2004;Cao et al, 2005), although the approach used in most practical situations corresponds to the application of mapping similarly to what occurs in the diploid species. This approach is based on the use of markers that segregate at 1:1 and 3:1 ratios.…”

Linkage analysis and haplotype phasing in experimental autopolyploid populations with high ploidy level using hidden Markov models

“…Despite all advances in genetic studies in autotetraploids 18 [13,14,20,21,27,30,32,34,61,64,65], there is still a shortage of statistical methods to 19 address organisms with higher ploidy levels, such as sweet potato [1,24,47], 20 sugarcane [16,59], some ornamental flowers and forage crops (reviewed in [50]). In this 21 work, we denote as high-level autopolyploids those autopolyploid organisms with ploidy 22 level greater than four.…”