Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle

Kadri, Naveen Kumar; Harland, Chad; Faux, Pierre; Cambisano, Nadine; Karim, Latifa; Coppieters, Wouter; Fritz, Sébastien; Mullaart, E.; Baurain, Denis; Boichard, Didier; Spelman, Richard; Charlier, Carole; Georges, Michel; Druet, Tom

doi:10.1101/gr.204214.116

Cited by 77 publications

(142 citation statements)

References 63 publications

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“…Five of the genes that exhibit signatures of positive selection across the mammalian phylogeny have been associated with interindividual variation in recombination rate within species: RAD21L (Kong et al 2014), REC8 (Sandor et al 2012;Johnston et al 2016Johnston et al , 2018, MSH4 (Kong et al 2014;Ma et al 2015;Kadri et al 2016;Shen et al 2018), RNF212 (Kong et al 2008;Chowdhury et al 2009;Fledel-Alon et al 2011;Sandor et al 2012;Johnston et al 2016;Kadri et al 2016;Petit et al 2017), and TEX11 (Murdoch et al 2010). However, as a group, recombination genes previously associated with intraspecific variation in the genome-wide recombination rate evolve at similar rates to recombination genes lacking such an association.…”

Section: Discussionmentioning

confidence: 99%

“…Genome-wide association studies are beginning to reveal the genetic basis of variation in recombination rate within species. Individual recombination rates have been associated with variants in specific genes in populations of Drosophila melanogaster (Hunter et al 2016), humans (Kong et al 2008(Kong et al , 2014Chowdhury et al 2009;Fledel-Alon et al 2011), domesticated cattle (Sandor et al 2012;Ma et al 2015;Kadri et al 2016;Shen et al 2018), domesticated sheep (Petit et al 2017), Soay sheep (Johnston et al 2016), and red deer (Johnston et al 2018). Variants in several of these genes correlate with recombination rate in multiple species, including RNF212 (Kong et al 2008;Chowdhury et al 2009;Fledel-Alon et al 2011;Sandor et al 2012;Johnston et al 2016;Kadri et al 2016;Petit et al 2017), RNF212B (Johnston et al 2016(Johnston et al , 2018Kadri et al 2016), REC8 (Sandor et al 2012;Johnston et al 2016Johnston et al , 2018, HEI10/CCNB1IP1 (Kong et al 2014;Petit et al 2017), MSH4 (Kong et al 2014;Ma et al 2015;Kadri et al 2016;Shen et al 2018), CPLX1 (Kong et al 2014;Ma et al 2015;Johnston et al 2016;Shen et al 2018) and PRDM9 (Fledel-Alon et al 2011;Sandor et al 2012;…”

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confidence: 99%

“…First, the evolution of recombination rate has been measured along the mammalian phylogeny (Dumont and Payseur 2008;Segura et al 2013). Second, recombination rate variation has been associated with specific genes in mammalian populations (Kong et al 2008(Kong et al , 2014Chowdhury et al 2009;Sandor et al 2012;Ma et al 2015;Johnston et al 2016Johnston et al , 2018Kadri et al 2016;Petit et al 2017;Shen et al 2018). Third, laboratory mice have proven instrumental in the identification and functional characterization of recombination genes (de Vries et al 1999;Baudat et al 2000;Romanienko and Camerini-Otero 2000;Yang et al 2006;Ward et al 2007;Schramm et al 2011;Bisig et al 2012;Bolcun-Filas and Schimenti 2012;La Salle et al 2012;Kumar et al 2015;Finsterbusch et al 2016;Stanzione et al 2016).…”

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confidence: 99%

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Molecular evolution of the meiotic recombination pathway in mammals

Dapper

Payseur

2019

Evolution

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Meiotic recombination shapes evolution and helps to ensure proper chromosome segregation in most species that reproduce sexually. Recombination itself evolves, with species showing considerable divergence in the rate of crossing‐over. However, the genetic basis of this divergence is poorly understood. Recombination events are produced via a complicated, but increasingly well‐described, cellular pathway. We apply a phylogenetic comparative approach to a carefully selected panel of genes involved in the processes leading to crossovers—spanning double‐strand break formation, strand invasion, the crossover/non‐crossover decision, and resolution—to reconstruct the evolution of the recombination pathway in eutherian mammals and identify components of the pathway likely to contribute to divergence between species. Eleven recombination genes, predominantly involved in the stabilization of homologous pairing and the crossover/non‐crossover decision, show evidence of rapid evolution and positive selection across mammals. We highlight TEX11 and associated genes involved in the synaptonemal complex and the early stages of the crossover/non‐crossover decision as candidates for the evolution of recombination rate. Evolutionary comparisons to MLH1 count, a surrogate for the number of crossovers, reveal a positive correlation between genome‐wide recombination rate and the rate of evolution at TEX11 across the mammalian phylogeny. Our results illustrate the power of viewing the evolution of recombination from a pathway perspective.

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Molecular evolution of the meiotic recombination pathway in mammals

Dapper

Payseur

2019

Evolution

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“…The biochemical steps of CO formation that occur during this period include the following: i) extension of the initial nascent D-loop at the "leading" DSB end into a structure known as a "single end invasion" (SEI); ii) extension of the invaded strand by DNA synthesis; (iii) release of the second ("lagging") DSB end from its association with the donor homolog; iv) incorporation of that second end into the developing complex; v) additional steps as required to generate the dHJ; and vi) assembly of MLH1 complexes in preparation for dHJ resolution. [82] Since cytological focus patterns for these molecules correspond to the progression of events at the DNA level, detailed analysis of these patterns in both males and females could help to clarify the timing and nature of CMI. It is important to ensure that any rejected intermediate can undergo successful completion of a repair reaction to restore two intact DNA duplexes.…”

Section: When and How Does CMI Arise?mentioning

confidence: 99%

Crossover Interference, Crossover Maturation, and Human Aneuploidy

et al. 2019

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A striking feature of human female sexual reproduction is the high level of gametes that exhibit an aberrant number of chromosomes (aneuploidy). A high baseline observed in women of prime reproductive age is followed by a dramatic increase in older women. Proper chromosome segregation requires one or more DNA crossovers (COs) between homologous maternal and paternal chromosomes, in combination with cohesion between sister chromatid arms. In human females, CO designations occur normally, according to the dictates of CO interference, giving early CO-fated intermediates. However, ≈25% of these intermediates fail to mature to final CO products. This effect explains the high baseline of aneuploidy and is predicted to synergize with age-dependent cohesion loss to explain the maternal age effect. Here, modern advances in the understanding of crossing over and CO interference are reviewed, the implications of human female CO maturation inefficiency are further discussed, and areas of interest for future studies are suggested.

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“…Although the total number of COs that occur in a meiotic cell is known to differ between strains of mice, this is only beginning to be evaluated in livestock species [Sandor et al, 2012;Murdoch et al, 2010;Poissant et al, 2010;Vozdova et al, 2013;Fröhlich et al, 2015;Ma et al, 2015;Johnston et al, 2016;Kadri et al, 2016;Sebestova et al, 2016]. In this study, the numbers of COs were quantified and their locations on the SC characterized in males from different breeds of sheep.…”

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confidence: 99%

Meiotic Recombination Differences in Rams from Three Breeds of Sheep in the US

Davenport

McKay²,

Fahey

et al. 2018

Cytogenet Genome Res

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Meiotic recombination is an important contributor to genetic variation and ensures proper chromosome segregation during gametogenesis. Previous studies suggest that at least 1 crossover (CO) per chromosome arm is important to avoid mis-segregation. While the total number of COs per spermatocyte is known to differ in mice, this is only beginning to be evaluated in sheep. This study used a cytogenetic approach to quantify and compare the number of COs per spermatocyte in rams from 3 breeds of sheep: Suffolk, Icelandic, and Targhee. In total, 2,758 spermatocytes and over 170,000 COs were examined. Suffolk rams exhibited the lowest mean number of COs (61.1 ± 0.15) compared to Icelandic (63.5 ± 0.27) and Targhee (65.9 ± 0.26) rams. Significant differences in the number of COs per spermatocyte were observed between Suffolk, Icelandic, and Targhee breeds as well as within each breed. Additionally, the number and location of COs were characterized for homologous chromosomes in a subset of spermatocytes for each ram. A positive correlation was identified between the number of COs and the length of the homologous chromosome pair. Suffolk and Icelandic rams exhibited up to 7 COs per chromosome, while Targhee rams exhibited up to 9. Further, distinct CO location preferences on homologous chromosome pairs with 1, 2, 3, and 4 COs were observed in all 3 breeds. These data in sheep will aid in elucidating the mechanism of mammalian meiotic recombination, an important contributor to genetic diversity.

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Coding and noncoding variants in HFM1, MLH3, MSH4, MSH5, RNF212, and RNF212B affect recombination rate in cattle

Cited by 77 publications

References 63 publications

Molecular evolution of the meiotic recombination pathway in mammals

Molecular evolution of the meiotic recombination pathway in mammals

Crossover Interference, Crossover Maturation, and Human Aneuploidy

Meiotic Recombination Differences in Rams from Three Breeds of Sheep in the US

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