Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps

In most sexual, diploid eukaryotes, at least one crossover occurs between each pair of homologous chromosomes during meiosis, presumably in order to ensure proper segregation. Well-known exceptions to this rule are species in which one sex does not recombine and specific chromosomes lacking crossover. We review other possible exceptions, including species with chromosome maps of less than 50 cM in one or both sexes. We discuss the idea that low recombination rates may favour sex–asex transitions, or, alternatively may be a consequence of it. We then show that a yet undescribed species of brine shrimp Artemia from Kazakhstan ( A . sp. Kazakhstan), the closest known relative of the asexual Artemia parthenogenetica , has one of the shortest genetic linkage maps known. Based on a family of 42 individuals and 589 RAD markers, we find that many linkage groups are considerably shorter than 50 cM, suggesting either no obligate crossover or crossovers concentrated at terminal positions with little effect on recombination. We contrast these findings with the published map of the more distantly related sexual congener, A. franciscana , and conclude that the study of recombination in non-model systems is important to understand the evolutionary causes and consequences of recombination. This article is part of the themed issue ‘Evolutionary causes and consequences of recombination rate variation in sexual organisms’.

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Construction of Genetic Linkage Maps From a Hybrid Family of Large Yellow Croaker (Larimichthys crocea)

Frontiers in Genetics ◽

10.3389/fgene.2021.792666 ◽

2022 ◽

Vol 12 ◽

Author(s):

Xinxiu Yu ◽

Rajesh Joshi ◽

Hans Magnus Gjøen ◽

Zhenming Lv ◽

Matthew Kent

Keyword(s):

Recombination Rate ◽

Genetic Linkage ◽

Genetic Maps ◽

Large Yellow Croaker ◽

Linkage Maps ◽

Nucleotide Polymorphisms ◽

Larimichthys Crocea ◽

Association Analyses ◽

Total Length ◽

Genetic Linkage Maps

Consensus and sex-specific genetic linkage maps for large yellow croaker (Larimichthys crocea) were constructed using samples from an F1 family produced by crossing a Daiqu female and a Mindong male. A total of 20,147 single nucleotide polymorphisms (SNPs) by restriction site associated DNA sequencing were assigned to 24 linkage groups (LGs). The total length of the consensus map was 1757.4 centimorgan (cM) with an average marker interval of 0.09 cM. The total length of female and male linkage map was 1533.1 cM and 1279.2 cM, respectively. The average female-to-male map length ratio was 1.2 ± 0.23. Collapsed markers in the genetic maps were re-ordered according to their relative positions in the ASM435267v1 genome assembly to produce integrated genetic linkage maps with 9885 SNPs distributed across the 24 LGs. The recombination pattern of most LGs showed sigmoidal patterns of recombination, with higher recombination in the middle and suppressed recombination at both ends, which corresponds with the presence of sub-telocentric and acrocentric chromosomes in the species. The average recombination rate in the integrated female and male maps was respectively 3.55 cM/Mb and 3.05 cM/Mb. In most LGs, higher recombination rates were found in the integrated female map, compared to the male map, except in LG12, LG16, LG21, LG22, and LG24. Recombination rate profiles within each LG differed between the male and the female, with distinct regions indicating potential recombination hotspots. Separate quantitative trait loci (QTL) and association analyses for growth related traits in 6 months fish were performed, however, no significant QTL was detected. The study indicates that there may be genetic differences between the two strains, which may have implications for the application of DNA-information in the further breeding schemes.

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The recombination landscape in wild house mice inferred using population genomic data

10.1101/112094 ◽

2017 ◽

Author(s):

Tom R. Booker ◽

Rob W. Ness ◽

Peter D. Keightley

Keyword(s):

House Mouse ◽

Recombination Rate ◽

Inbred Lines ◽

House Mice ◽

Rate Variation ◽

Recombination Hotspots ◽

Population Genomic ◽

Wild House Mice ◽

Recombination Rate Variation ◽

Broad Scale

AbstractCharacterizing variation in the rate of recombination across the genome is important for understanding many evolutionary processes. The landscape of recombination has been studied previously in the house mouse, Mus musculus, and it is known that the different subspecies exhibit different suites of recombination hotspots. However, it is not established whether broad-scale variation in the rate of recombination is conserved between the subspecies. In this study, we construct a fine-scale recombination map for the Eastern house mouse subspecies, M. m. castaneus, using 10 individuals sampled from its ancestral range. After inferring phase, we use LDhelmet to construct recombination maps for each autosome. We find that the spatial distribution of recombination rate is strongly positively between our castaneus map and a map constructed using inbred lines of mice derived predominantly from M. m. domesticus. We also find that levels of genetic diversity in M. m. castaneus are positively correlated with the rate of recombination, consistent with pervasive natural selection acting in the genome. Our study suggests that recombination rate variation is conserved at broad scales between M. musculus subspecies.

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Faculty Opinions recommendation of The fine-scale structure of recombination rate variation in the human genome.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1018661.213437 ◽

2004 ◽

Author(s):

Mary Carrington

Keyword(s):

Human Genome ◽

Recombination Rate ◽

Scale Structure ◽

Rate Variation ◽

Fine Scale ◽

Recombination Rate Variation

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Faculty Opinions recommendation of The fine-scale structure of recombination rate variation in the human genome.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1018661.211505 ◽

2004 ◽

Author(s):

Jonathan Pritchard

Keyword(s):

Human Genome ◽

Recombination Rate ◽

Scale Structure ◽

Rate Variation ◽

Fine Scale ◽

Recombination Rate Variation

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Construction of genetic linkage maps of silver birch based on AFLP markers

Hereditas (Beijing) ◽

10.3724/sp.j.1005.2009.00213 ◽

2009 ◽

Vol 31 (2) ◽

pp. 213-218 ◽

Cited By ~ 1

Author(s):

Fu-Ling GAO ◽

Ting-Bo JIANG

Keyword(s):

Genetic Linkage ◽

Silver Birch ◽

Aflp Markers ◽

Linkage Maps ◽

Genetic Linkage Maps

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VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽

10.1093/aobpla/plaa064 ◽

2020 ◽

Vol 12 (6) ◽

Author(s):

Morad M Mokhtar ◽

Ebtissam H A Hussein ◽

Salah El-Din S El-Assal ◽

Mohamed A M Atia

Keyword(s):

Vicia Faba ◽

Faba Bean ◽

Expressed Sequence Tags ◽

Genetic Linkage ◽

Genetic Maps ◽

Linkage Maps ◽

Microrna Target ◽

Genetic Linkage Maps ◽

Expressed Sequence ◽

Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

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Integrating Genetic Linkage Maps With Pachytene Chromosome Structure in Maize

Genetics ◽

10.1093/genetics/166.4.1923 ◽

2004 ◽

Vol 166 (4) ◽

pp. 1923-1933 ◽

Cited By ~ 8

Author(s):

Lorinda K Anderson ◽

Naser Salameh ◽

Hank W Bass ◽

Lisa C Harper ◽

W Z Cande ◽

...

Keyword(s):

Genetic Linkage ◽

Chromosome Structure ◽

Single Copy ◽

Chromosome 9 ◽

Linkage Maps ◽

Cytogenetic Map ◽

Recombination Nodules ◽

Novel Approach ◽

Genetic Linkage Maps ◽

High Degree

Abstract Genetic linkage maps reveal the order of markers based on the frequency of recombination between markers during meiosis. Because the rate of recombination varies along chromosomes, it has been difficult to relate linkage maps to chromosome structure. Here we use cytological maps of crossing over based on recombination nodules (RNs) to predict the physical position of genetic markers on each of the 10 chromosomes of maize. This is possible because (1) all 10 maize chromosomes can be individually identified from spreads of synaptonemal complexes, (2) each RN corresponds to one crossover, and (3) the frequency of RNs on defined chromosomal segments can be converted to centimorgan values. We tested our predictions for chromosome 9 using seven genetically mapped, single-copy markers that were independently mapped on pachytene chromosomes using in situ hybridization. The correlation between predicted and observed locations was very strong (r2 = 0.996), indicating a virtual 1:1 correspondence. Thus, this new, high-resolution, cytogenetic map enables one to predict the chromosomal location of any genetically mapped marker in maize with a high degree of accuracy. This novel approach can be applied to other organisms as well.

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