Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley

Dreißig, Steven; Mascher, Martin; Heckmann, Stefan

doi:10.1093/molbev/msz141

Cited by 55 publications

(66 citation statements)

References 100 publications

(119 reference statements)

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“…Despite these limitations, the LD-based approach was successfully applied at the whole-genome level in many species including birds (Singhal et al 2015;Smeds et al 2016), yeast (Tsai et al 2010), Arabidopsis (Choi et al 2013), rice (Marand et al 2019), barley (Dreissig et al 2019) and bread wheat chromosome 3B (Darrier et al 2017). This latter study was limited to chromosome 3B as it was the only chromosome presenting a sufficiently high-standard reference sequence at that time (Choulet et al 2014;IWGSC 2014).…”

Section: Introductionmentioning

confidence: 99%

Evolution of recombination landscapes in diverging populations of bread wheat

Déserts

Bouchet

Sourdille

et al. 2021

Preprint

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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 heterogenous 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 significantly 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 SNP ascertainment and demography and suggests a relatively rapid evolution of factors determining the fine-scale localization of recombination in bread wheat.

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Section: Introductionmentioning

confidence: 99%

Evolution of recombination landscapes in diverging populations of bread wheat

Déserts

Bouchet

Sourdille

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Additionally, genetic divergence and structural variations are also influencing recombination rates (Ziolkowski et al ., 2015, 2017; Crown et al ., 2018; Rowan et al ., 2019). At the population level, recombination rates were shown to vary drastically depending on variations in meiotic genes or environmental conditions (Brand et al ., 2018; Dreissig et al ., 2019; Martin et al ., 2019; Samuk et al ., 2019; Schwarzkopf et al ., 2020).…”

Section: Introductionmentioning

confidence: 99%

Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley

et al. 2020

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Meiotic recombination rates vary considerably between species, populations and individuals. The genetic exchange between homologous chromosomes plays a major role in evolution by breaking linkage between advantageous and deleterious alleles in the case of introgressions. Identifying recombination rate modifiers is thus of both fundamental and practical interest to understand and utilize variation in meiotic recombination rates. We investigated recombination rate variation in a large intraspecific hybrid population (named HEB-25) derived from a cross between domesticated barley and 25 wild barley accessions. We observed quantitative variation in total crossover number with a maximum of a 1.4-fold difference between subpopulations and increased recombination rates across pericentromeric regions. The meiosis-specific a-kleisin cohesin subunit REC8 was identified as a candidate gene influencing crossover number and patterning. Furthermore, we quantified wild barley introgression patterns and revealed how local and genome-wide recombination rate variation shapes patterns of introgression. The identification of allelic variation in REC8 in combination with the observed changes in crossover patterning suggest a difference in how chromatin loops are tethered to the chromosome axis, resulting in reduced crossover suppression across pericentromeric regions. Local and genome-wide recombination rate variation is shaping patterns of introgressions and thereby directly influences the consequences of linkage drag.

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“…maps, including length and crossover frequency, may reflect variation in recombination rates 50,51 , which has been detected along chromosomes in many plant species 52,53 . Variation in the distribution of CO along chromosomes has been found to arise due to a range of factors, including the distribution of transposable elements, DNA methylation and histone marks, heterozygosity, domestication, environment, age, sex and pathogen infection [54][55][56][57][58] .…”

Section: Crossover Frequency and Recombination Varied Between Maps Dmentioning

confidence: 99%

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

Langdon

King

Baten

et al. 2020

Sci Rep

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the proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny. This allowed us to combine segregation data from overlapping subsets of >4,000 informative sequence-tagged markers to increase the effective coverage of the karyotype represented by the recombinant crossover events detected. All maps had 14 linkage groups, corresponding to the Macadamia haploid chromosome number, and enabled the anchoring and orientation of sequence scaffolds to construct a pseudo-chromosomal genome assembly for macadamia. Comparison of individual maps indicated a high level of congruence, with minor discrepancies satisfactorily resolved within the integrated maps. The combined set of maps significantly improved marker density and the proportion (70%) of the genome sequence assembly anchored. Overall, increasing our understanding of the genetic landscape and genome for this nut crop represents a substantial advance in macadamia genetics and genomics. The set of maps, large number of sequence-based markers and the reconstructed genome provide a toolkit to underpin future breeding that should help to extend the macadamia industry as well as provide resources for the long term conservation of natural populations in eastern Australia of this unique genus.

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Variation in Recombination Rate Is Shaped by Domestication and Environmental Conditions in Barley

Cited by 55 publications

References 100 publications

Evolution of recombination landscapes in diverging populations of bread wheat

Evolution of recombination landscapes in diverging populations of bread wheat

Natural variation in meiotic recombination rate shapes introgression patterns in intraspecific hybrids between wild and domesticated barley

Maximising recombination across macadamia populations to generate linkage maps for genome anchoring

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