Abstract
Whole genome duplication (WGD) is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW) to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents (Triticum turgidum; 2n = 4x = 28, AABB subgenomes) with the progenitor species Aegilops tauschii (syn Ae. squarrosa, T. tauschii; 2n = 2x = 14, DD subgenome). The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy, which will facilitate the effective utilization of wheat wild relatives in breeding.
Highlights
Polyploidization, whole genome duplication (WGD), is a natural process in which a single genome can be duplicated to form autopolyploids with more than two homologs for each chromosome, or multiple genomes are duplicated following hybridization between two or more species to form allopolyploids with multiple pairs of homologs derived from different ancestral genomes, termed homoeologs
Synthetic hexaploid wheat (SHW) germplasm is a proven source of genetic diversity to improve yield (Gororo et al, 2002; Dreccer et al, 2007; Ogbonnaya et al, 2007, 2013), soil-borne pathogen (Mulki et al, 2013), insect (El-Bouhssini et al, 2013; Joukhadar et al, 2013), and fungal disease resistance (Zegeye et al, 2014; Jighly et al, 2016), as well as boron (Emebiri and Ogbonnaya, 2015) and salinity tolerance (Dreccer et al, 2004; Ogbonnaya et al, 2008a). It remains uncertain how the three subgenomes (A, B, and D) of bread wheat contribute to observed phenotypes or whether the wild Aegilops parent makes a considerable contribution to the additive genetic variance for different traits especially when crossed with an improved or elite durum wheat parent
It is worth noting that these values should be less than the actual heritabilities as they depend on the genotyped SNPs only (Manolio et al, 2009)
Summary
Polyploidization, whole genome duplication (WGD), is a natural process in which a single genome can be duplicated to form autopolyploids with more than two homologs for each chromosome, or multiple genomes are duplicated following hybridization between two or more species to form allopolyploids with multiple pairs of homologs derived from different ancestral genomes, termed homoeologs. SHW germplasm is a proven source of genetic diversity to improve yield (Gororo et al, 2002; Dreccer et al, 2007; Ogbonnaya et al, 2007, 2013), soil-borne pathogen (Mulki et al, 2013), insect (El-Bouhssini et al, 2013; Joukhadar et al, 2013), and fungal disease resistance (Zegeye et al, 2014; Jighly et al, 2016), as well as boron (Emebiri and Ogbonnaya, 2015) and salinity tolerance (Dreccer et al, 2004; Ogbonnaya et al, 2008a) It remains uncertain how the three subgenomes (A, B, and D) of bread wheat contribute to observed phenotypes or whether the wild Aegilops parent makes a considerable contribution to the additive genetic variance for different traits especially when crossed with an improved or elite durum wheat parent. This can be investigated by partitioning the total additive trait variance into different chromosomes in a SHW population
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