Evolution of recombination landscapes in diverging populations of bread wheat

Abstract

Reciprocal exchanges of DNA (crossovers) that occur during meiosis are mandatory to ensure the production of fertile gametes in sexually reproducing species. They also contribute to shuffle parental alleles into new combinations thereby fuelling genetic variation and evolution. However, due to biological constraints, the recombination landscape is highly heterogeneous along the genome which limits the range of allelic combinations and the adaptability of populations. An approach to better understand the constraints on the recombination process is to study how it evolved in the past. In this work we tackled this question by constructing recombination profiles in four diverging bread wheat (Triticum aestivum L.) populations established from 371 landraces genotyped at 200,062 SNPs. We used linkage disequilibrium (LD) patterns to estimate in each population the past distribution of recombination along the genome and characterize its fine-scale heterogeneity. At the megabase scale, recombination rates derived from LD patterns were consistent with family-based estimates obtained from a population of 406 recombinant inbred lines. Among the four populations, recombination landscapes were positively correlated between each other and shared a statistically significant proportion of highly recombinant intervals. However, this comparison also highlighted that the similarity in recombination landscapes between populations was significantly decreasing with their genetic differentiation in most regions of the genome. This observation was found to be robust to SNPs ascertainment and demography and suggests a relatively rapid evolution of factors determining the fine-scale localization of recombination in bread wheat.

Resistance of the Wheat Cultivar ‘Renan’ to Septoria Leaf Blotch Explained by a Combination of Strain Specific and Strain Non-Specific QTL Mapped on an Ultra-Dense Genetic Map

“…The wheat population was genotyped on two different single nucleotide polymorphism(SNP) arrays, the Breedwheat Affymetrix Axiom 410K array [ 50 , 51 ] and the Illumina Infinium iSelect Wheat 90K array [ 52 ].…”

Broad-scale signatures of linked selection under divergent recombination landscapes and mating systems in natural populations of rye and barley

“…domestication events) would cause lower effective recombination rates caused by a reduction in the effective population size ( Ne ) (Torres et al 2020; Beissinger et al 2016). On the other hand, broad-scale LD-based estimates were shown to correlate well with per-generation meiotic recombination rates (cM/Mb) in plants estimated based on linkage maps (Choi et al 2013; Dreissig et al 2019; Marand et al 2019; Danguy des Déserts et al 2021; Fuentes et al 2021). Based on this, we focused on weedy and wild populations that did not undergo recent demographic changes such as domestication bottlenecks (Sun et al 2021; Badr et al 2000; Kilian et al 2006; Russell et al 2016).…”

“…Based on this, we focused on weedy and wild populations that did not undergo recent demographic changes such as domestication bottlenecks (Sun et al 2021; Badr et al 2000; Kilian et al 2006; Russell et al 2016). Recombination landscapes were shown to vary within and between plant and animal species, with rank correlations ranging from 0.4 to > 0.9 between populations within species (Bauer et al 2013; Dreissig et al 2019; Spence & Song 2019; Schreiber et al 2022; Danguy des Déserts et al 2021). In previous work, we characterized intraspecific recombination landscape variation among populations of rye, and found that the fraction of low-recombining regions varied from 24.2 % to 42.1 % between weedy and domesticated rye (Schreiber et al 2022).…”

Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection

“…Moreover, the high density of SNPs allowed us to observe a significant association of COs with genic features as well as a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals. A similar approach was adopted using the same SNP array to genotype 371 landraces representing four diverging populations (West Asia, East Asia, West Europe, and East Europe) [ 39 ]. Recombination landscapes of the four populations positively correlated between each other and significantly shared most recombinogenic intervals.…”