Linkage Map of Lissotriton Newts Provides Insight into the Genetic Basis of Reproductive Isolation

Abstract Linkage maps are widely used to investigate structure, function, and evolution of genomes. In speciation research, maps facilitate the study of the genetic architecture of reproductive isolation by allowing identification of genomic regions underlying reduced fitness of hybrids. Here we present a linkage map for European newts of the Lissotriton vulgaris species complex, constructed using two families of F2 L. montandoni × L. vulgaris hybrids. The map consists of 1146 protein-coding genes on 12 linkage groups, equal to the haploid chromosome number, with a total length of 1484 cM (1.29 cM per marker). It is notably shorter than two other maps available for salamanders, but the differences in map length are consistent with cytogenetic estimates of the number of chiasmata per chromosomal arm. Thus, large salamander genomes do not necessarily translate into long linkage maps, as previously suggested. Consequently, salamanders are an excellent model to study evolutionary consequences of recombination rate variation in taxa with large genomes and a similar number of chromosomes. A complex pattern of transmission ratio distortion (TRD) was detected: TRD occurred mostly in one family, in one breeding season, and was clustered in two genomic segments. This is consistent with environment-dependent mortality of individuals carrying L. montandoni alleles in these two segments and suggests a role of TRD blocks in reproductive isolation. The reported linkage map will empower studies on the genomic architecture of divergence and interactions between the genomes of hybridizing newts.

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A Linkage Map of an F2 Hybrid Population of Antirrhinum majus and A. molle

Genetics ◽

10.1093/genetics/163.2.699 ◽

2003 ◽

Vol 163 (2) ◽

pp. 699-710 ◽

Cited By ~ 1

Author(s):

Zsuzsanna Schwarz-Sommer ◽

Eugenia de Andrade Silva ◽

Rita Berndtgen ◽

Wolf-Ekkehard Lönnig ◽

Andreas Müller ◽

...

Keyword(s):

Linkage Map ◽

Issr Markers ◽

Transmission Ratio Distortion ◽

Hybrid Population ◽

Linkage Groups ◽

Protein Coding ◽

F2 Population ◽

Molecular Linkage Map ◽

Marker Loci ◽

Ratio Distortion

Abstract To increase the utility of Antirrhinum for genetic and evolutionary studies, we constructed a molecular linkage map for an interspecific hybrid A. majus × A. molle. An F2 population (n = 92) was genotyped at a minimum of 243 individual loci. Although distorted transmission ratios were observed at marker loci throughout the genome, a mapping strategy based on a fixed framework of codominant markers allowed the loci to be placed into eight robust linkage groups consistent with the haploid chromosome number of Antirrhinum. The mapped loci included 164 protein-coding genes and a similar number of unknown sequences mapped as AFLP, RFLP, ISTR, and ISSR markers. Inclusion of sequences from mutant loci allowed provisional alignment of classical and molecular linkage groups. The total map length was 613 cM with an average interval of 2.5 cM, but most of the loci were aggregated into clusters reducing the effective distance between markers. Potential causes of transmission ratio distortion and its effects on map construction were investigated. This first molecular linkage map for Antirrhinum should facilitate further mapping of mutations, major QTL, and other coding sequences in this model genus.

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21 Unravelling Transmission Ratio Distortion Across the Genome of a Crossbreed Beef Cattle Population

Journal of Animal Science ◽

10.1093/jas/skab235.021 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 12-13

Author(s):

Daiane C Becker Scalez ◽

Samir Id-Lahoucine ◽

Pablo A S Fonseca ◽

Joaquim Casellas ◽

Angela Cánovas

Keyword(s):

Beef Cattle ◽

Bayes Factor ◽

Null Distribution ◽

Transmission Ratio Distortion ◽

Transmission Ratio ◽

Snp Analysis ◽

Cattle Population ◽

Empirical Null Distribution ◽

Ratio Distortion ◽

Genomic Regions

Abstract Transmission ratio distortion (TRD) is a process when one allele from either parent is preferentially transmitted to the offspring. The identification of genomic regions affected by TRD might help in the detection of lethal alleles or potential genes affecting reproduction. Here, we investigated TRD in crossbreed beef cattle population aiming to identify genomic regions showing altered deviations in segregation that could be affecting reproduction performance. A total of 237 genotyped animals were used including 46 sires, 80 dams, and 111 parent-offspring (trios). The predominant breeds of these animals were Angus (61.83%), Simmental (18.99%), Gelbvieh (6.12%), Charolais (3.65%), Hereford (2.46%) and Limousin (1.57%). After excluding SNPs with minor allele frequency lower than 0.05 and call-rate lower than 0.90, a total of 369,902 autosomal SNPs were retained for further analyses. The SNP-by-SNP analysis was performed within a Bayesian framework using TRDscanv.2.0 software, using 100,000 iterations, with 10,000 iterations being discarded as burn-in. As table 1 shows, 33 SNPs were identified with TRD, considering a Bayes Factor (BF)≥100 and the approximate empirical null distribution of TRD at 0.01% margin error. Among them, 26 SNPs were parent-unspecific and 7 SNPs were parent-specific TRD. For parent-specific TRD, 214 were identified for sire- and 162 for dam-TRD (BF≥100). Among them, 4 SNPs were detected with sire- and dam-TRD in opposite direction of preference of transmission. Preliminary functional and positional analysis was performed using the list of TRD regions with BF≥100 and the approximate empirical null distribution of TRD at 0.01% margin error. For sire-TRD, 14% of the identified QTL (n = 254) were related to non-return rate. For dam-TRD, 21 regions related to conception rate were found (1.5%) and 13 regions related to stillbirth (0.93%). Haplotype analysis is in progress to identify additional candidate regions and alleles with TRD to better understand this phenomenon in a crossbreed beef population.

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24 Unravelling Genomic Regions with Transmission Ratio Distortion: Identification of Candidate Lethal Alleles in Cattle.

Journal of Animal Science ◽

10.1093/jas/sky073.022 ◽

2018 ◽

Vol 96 (suppl_2) ◽

pp. 13-13

Author(s):

S Id-Lahoucine ◽

J Casellas ◽

P Fonseca ◽

F Miglior ◽

M Sargolzaei ◽

...

Keyword(s):

Transmission Ratio Distortion ◽

Transmission Ratio ◽

Ratio Distortion ◽

Genomic Regions

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Whole genome sequencing identifies allelic ratio distortion in sperm involving genes related to spermatogenesis in a swine model

DNA Research ◽

10.1093/dnares/dsaa019 ◽

2020 ◽

Vol 27 (5) ◽

Author(s):

Marta Gòdia ◽

Joaquim Casellas ◽

Aurora Ruiz-Herrera ◽

Joan E Rodríguez-Gil ◽

Anna Castelló ◽

...

Keyword(s):

Genetic Basis ◽

Transmission Ratio Distortion ◽

Swine Model ◽

Allelic Ratio ◽

Exact Test ◽

Allelic Differences ◽

Genomic Scale ◽

Ratio Distortion ◽

Genomic Regions ◽

Shed Light

Abstract Transmission Ratio Distortion (TRD), the uneven transmission of an allele from a parent to its offspring, can be caused by allelic differences affecting gametogenesis, fertilization or embryogenesis. However, TRD remains vaguely studied at a genomic scale. We sequenced the diploid and haploid genomes of three boars from leukocytes and spermatozoa at 50x to shed light into the genetic basis of spermatogenesis-caused Allelic Ratio Distortion (ARD). We first developed a Binomial model to identify ARD by simultaneously analysing all three males. This led to the identification of 55 ARD SNPs, most of which were animal-specific. We then evaluated ARD individually within each pig by a Fisher’s exact test and identified two shared genes (TOP3A and UNC5B) and four shared genomic regions harbouring distinct ARD SNPs in the three boars. The shared genomic regions contained candidate genes with functions related to spermatogenesis including AK7, ARID4B, BDKRB2, GSK3B, NID1, NSMCE1, PALB2, VRK1 and ZC3H13. Using the Fisher’s test, we also identified 378 genes containing variants with protein damaging potential in at least one boar, a high proportion of which, including FAM120B, TDRD15, JAM2 or AOX4 among others, are associated to spermatogenesis. Overall, our results show that sperm is subjected to ARD with variants associated to a wide variety of genes involved in different stages of spermatogenesis.

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47 Distortion of Mendelian segregation across Angus cattle genome reveal novel lethal haplotype affecting reproduction

Journal of Animal Science ◽

10.1093/jas/skaa278.009 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 5-5

Author(s):

Samir Id Lahoucine ◽

Joaquim Casellas ◽

Duc Lu ◽

Mehdi Sargolzaei ◽

Stephen P Miller ◽

...

Keyword(s):

Rapid Development ◽

Statistical Significance ◽

Transmission Ratio Distortion ◽

Daily Routine ◽

Genetic Determinants ◽

Mendelian Segregation ◽

Angus Cattle ◽

Current Availability ◽

Ratio Distortion ◽

Genomic Regions

Abstract The rapid development of DNA technologies, together with the adoption and daily routine use of commercial SNP arrays in livestock industries, provided a valuable resource of large and powerful data that can be explored for innovative applications for animal breeding purposes. Thus, the current availability of trios (i.e., sire-dam-offspring) of genotyped families enables the implementation of the transmission ratio distortion (TRD) approach to discover lethal alleles. Lethal alleles, which are crucial genetic determinants for reproduction, do not follow Mendelian principles but deviate from inheritance expectations, displaying signals of TRD. In this research, TRD was characterized using allelic (specific- and unspecific-parent TRD) and genotypic parameterizations (additive- and dominance-TRD) using both SNP- and haplotype-based methods. The analyses were performed using 258,140 Angus animals with 92,942 autosomal SNP genotypes, including 7,486 sires, 72,688 dams and 205,966 offspring. Across the whole genome, 852 regions displaying TRD were identified with different statistical significance. Among these findings, 19 haplotypes with recessive patterns (potential lethality for homozygote individuals) and 52 genomic regions with allelic patterns exhibiting complete or quasi-complete absence for homozygous individuals in addition to under-representation (potentially reduced viability) of heterozygous offspring were found. The average number of under-represented offspring (i.e., expected but not observed) across 52 allelic TRD regions ranged from 5,000 to 41,008. In contrast, the number of non-observed homozygous offspring for the 19 regions with recessive pattern ranges from 10 to 564. In addition, 64 and 20 genomic regions with TRD showed significant effects on the trait heifer pregnancy P < 0.05 and P < 0.01, respectively, reducing the progeny rate up to 15%. These novel findings in Angus present new candidate genomic regions putatively carrying lethal and semi-lethal alleles providing opportunities to reduce the rates of embryonic losses or death of offspring which could improve fertility and fitness in beef cattle populations.

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A European whitefish linkage map and its implications for understanding genome-wide synteny between salmonids following whole genome duplication

10.1101/310136 ◽

2018 ◽

Author(s):

Rishi De-Kayne ◽

Philine G.D. Feulner

Keyword(s):

Atlantic Salmon ◽

Linkage Map ◽

Genome Structure ◽

Model Organisms ◽

Rate Variation ◽

Linkage Maps ◽

Linkage Groups ◽

Sequencing Data ◽

Starting Point ◽

Selection Of Species

AbstractGenomic datasets continue to increase in size and ease of production for a wider selection of species including non-model organisms. For many of these species highly contiguous and well-annotated genomes are unavailable due to their prohibitive complexity and cost. As a result, a common starting point for genomic work in non-model species is the production of a linkage map, which involves the grouping and relative ordering of genetic markers along the genome. Dense linkage maps facilitate the analysis of genomic data in a variety of ways, from broad scale observations regarding genome structure e.g. chromosome number and type or sex-related structural differences, to fine scale patterns e.g. recombination rate variation and co-localisation of differentiated regions. Here we present both a sex-averaged and sex-specific linkage maps for Coregonus sp. “Albock” containing 5395 single nucleotide polymorphism (SNP) loci across 40 linkage groups to facilitate future investigation into the genomic basis of whitefish adaptation and speciation. The map was produced using restriction-site associated digestion (RAD) sequencing data from two wild-caught parents and 156 F1 offspring in Lep-MAP3. We discuss the differences between our sex-avagerated and sex-specific maps and identify synteny between C. sp. “Albock” linkage groups and the Atlantic salmon (Salmo salar) genome. Our synteny analysis confirms that many patterns of homology observed between Atlantic salmon and Oncorhynchus and Salvelinus species are also shared by members of the Coregoninae subfamily.

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A genetic linkage map of Silene vulgaris based on AFLP markers

Genome ◽

10.1139/g05-114 ◽

2006 ◽

Vol 49 (4) ◽

pp. 320-327 ◽

Cited By ~ 21

Author(s):

Martin Bratteler ◽

Christian Lexer ◽

Alex Widmer

Keyword(s):

Linkage Map ◽

Genetic Linkage ◽

Genetic Linkage Map ◽

Genome Mapping ◽

Mapping Population ◽

Segregation Ratio ◽

Aflp Markers ◽

Transmission Ratio Distortion ◽

Silene Vulgaris ◽

Ratio Distortion

A genetic linkage map of an intraspecific cross between 2 Silene vulgaris s.l. ecotypes is presented. Three-hundred AFLP markers from 2 different restriction enzyme combinations were used to genotype an F2 mapping population. Maternal and paternal pure-coupling phase maps with 114 and 186 markers on 12 and 13 linkage groups, respectively, were constructed. Total map length of the paternal and maternal maps are 547 and 446 Kosambi cM, respectively. Nearly half of the markers (49%) exhibited significant transmission ratio distortion. Genome coverage and potential causes of the observed segregation ratio distortions are discussed. The maps represent a first step towards the identification of quantitative trait loci associated with habitat adaptation in the non-model species Silene vulgaris.Key words: AFLP, genome mapping, segregation distortion, Silene vulgaris.

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