scholarly journals 352 Awardee Talk: Identification of novel haplotypes with recessive and allelic inheritance patterns affecting embryonic development processes, gestation losses and post-natal lethality in cattle

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 83-83
Author(s):  
Angela Canovas ◽  
Samir Id Lahoucine ◽  
Aroa Suarez-Vega ◽  
Pablo Augusto S Fonseca ◽  
Flavio Schenkel ◽  
...  
Keyword(s):  
Embryonic Development ◽  
Bayes Factor ◽  
Mendelian Inheritance ◽  
Transmission Ratio Distortion ◽  
Snp Analysis ◽  
Recessive Lethal ◽  
Sliding Windows ◽  
Scrotal Circumference ◽  
Development Processes ◽  
Genomic Regions

Abstract Genomic data allows the screening of homozygous haplotypes and recessive lethal alleles, which could affect reproductive performance in cattle and other species. Here, we propose an approach based on tracing the inheritance of alleles from heterozygous parents to offspring to identify significant departure from the expected Mendelian inheritance (Transmission Ratio Distortion – TRD). TRDscan software was used to identify genomic regions with TRD using 436,651 trios (sire-dam-offspring) of genotypes from Holstein dairy cattle. SNP-by-SNP analysis was performed using 132,990 SNPs. TRD haplotypes were identified using sliding windows of 2-,4-,7-,10- and 20-SNPs. In total, 109 SNPs and 495 haplotypes were identified with significant TRD (Bayes factor≥100). Interestingly, some of the identified TRD regions overlap with previously known regions with recessive lethal alleles (e.g., HH0, HH1, HH3, HH5). Novel genomic regions with significant TRD were also identified with annotated genes functionally clustered into specific phenotypes related to male and female infertility and postnatal lethality. Approximately 18% of previously identified quantitative trait loci mapped around the TRD regions were related with fertility traits (calving ease, scrotal circumference, fertility index, and non-return rate). Validation of the results was performed using ~13,000 of Holstein embryo genotypes, in trios. The results will be integrated with the TRD regions identified to fine mapping the contribution of the TRD for each embryonic stage and they may be helpful to precisely target genomic regions associated with fertility, embryonic development processes, gestation losses and post-natal lethality in cattle.

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

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.

scholarly journals Baseline and Innate Immune Response Characterization of a Zfp30 Knockout Mouse Strain

2020 ◽  
Author(s):  
Lucas T. Laudermilk ◽  
Adelaide Tovar ◽  
Alison K. Homstad ◽  
Joseph M. Thomas ◽  
Kathryn M. McFadden ◽  
...  
Keyword(s):  
Knockout Mouse ◽  
Essential Gene ◽  
Mendelian Inheritance ◽  
Neutrophil Recruitment ◽  
Innate Immune ◽  
Allergic Airway Disease ◽  
Transmission Ratio Distortion ◽  
Knockout Mouse Model ◽  
Heterochromatin Formation ◽  
A Genome

AbstractAirway neutrophilia is correlated with disease severity in a number of chronic and acute pulmonary diseases, and dysregulation of neutrophil chemotaxis can lead to host tissue damage. The gene Zfp30 was previously identified as a candidate regulator of neutrophil recruitment to the lungs and secretion of CXCL1, a potent neutrophil chemokine, in a genome-wide mapping study using the Collaborative Cross. ZFP30 is a putative transcriptional repressor with a KRAB domain capable of inducing heterochromatin formation. Using a CRISPR-mediated knockout mouse model, we investigated the role that Zfp30 plays in recruitment of neutrophils to the lung using models of allergic airway disease and acute lung injury. We found that the Zfp30 null allele did not affect CXCL1 secretion or neutrophil recruitment to the lungs in response to various innate immune stimuli. Intriguingly, despite the lack of neutrophil phenotype, we found there was a significant reduction in the proportion of live Zfp30 homozygous mutant mice produced from heterozygous matings. This deviation from the expected mendelian inheritance (i.e. transmission ratio distortion) implicates Zfp30 in fertility or embryonic development. Overall, our results indicate that Zfp30 is an essential gene but does not influence neutrophilic inflammation in this particular knockout model.

scholarly journals Sequencing of Supernumerary Chromosomes of Red Fox and Raccoon Dog Confirms a Non-Random Gene Acquisition by B Chromosomes

Genes ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 405 ◽  
Author(s):  
Alexey Makunin ◽  
Svetlana Romanenko ◽  
Violetta Beklemisheva ◽  
Polina Perelman ◽  
Anna Druzhkova ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Red Fox ◽  
B Chromosome ◽  
Mendelian Inheritance ◽  
B Chromosomes ◽  
Nyctereutes Procyonoides ◽  
Segmental Duplications ◽  
Raccoon Dog ◽  
Gene Acquisition ◽  
Genomic Regions

B chromosomes (Bs) represent a variable addition to the main karyotype in some lineages of animals and plants. Bs accumulate through non-Mendelian inheritance and become widespread in populations. Despite the presence of multiple genes, most Bs lack specific phenotypic effects, although their influence on host genome epigenetic status and gene expression are recorded. Previously, using sequencing of isolated Bs of ruminants and rodents, we demonstrated that Bs originate as segmental duplications of specific genomic regions, and subsequently experience pseudogenization and repeat accumulation. Here, we used a similar approach to characterize Bs of the red fox (Vulpes vulpes L.) and the Chinese raccoon dog (Nyctereutes procyonoides procyonoides Gray). We confirm the previous findings of the KIT gene on Bs of both species, but demostrate an independent origin of Bs in these species, with two reused regions. Comparison of gene ensembles in Bs of canids, ruminants, and rodents once again indicates enrichment with cell-cycle genes, development-related genes, and genes functioning in the neuron synapse. The presence of B-chromosomal copies of genes involved in cell-cycle regulation and tissue differentiation may indicate importance of these genes for B chromosome establishment.

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

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

scholarly journals csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows

2015 ◽  
Vol 44 (5) ◽  
pp. e45-e45 ◽  
Author(s):  
Aaron T.L. Lun ◽  
Gordon K. Smyth
Keyword(s):  
De Novo ◽  
Massively Parallel Sequencing ◽  
Real Data ◽  
Sequencing Data ◽  
Scientific Application ◽  
Sliding Windows ◽  
Treatment Conditions ◽  
Bioconductor Project ◽  
Differential Binding ◽  
Genomic Regions

Abstract Chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) is widely used to identify binding sites for a target protein in the genome. An important scientific application is to identify changes in protein binding between different treatment conditions, i.e. to detect differential binding. This can reveal potential mechanisms through which changes in binding may contribute to the treatment effect. The csaw package provides a framework for the de novo detection of differentially bound genomic regions. It uses a window-based strategy to summarize read counts across the genome. It exploits existing statistical software to test for significant differences in each window. Finally, it clusters windows into regions for output and controls the false discovery rate properly over all detected regions. The csaw package can handle arbitrarily complex experimental designs involving biological replicates. It can be applied to both transcription factor and histone mark datasets, and, more generally, to any type of sequencing data measuring genomic coverage. csaw performs favorably against existing methods for de novo DB analyses on both simulated and real data. csaw is implemented as a R software package and is freely available from the open-source Bioconductor project.

scholarly journals The evolutionary origin and domestication history of goldfish (Carassius auratus)

2020 ◽  
Vol 117 (47) ◽  
pp. 29775-29785
Author(s):  
Duo Chen ◽  
Qing Zhang ◽  
Weiqi Tang ◽  
Zhen Huang ◽  
Gang Wang ◽  
...  
Keyword(s):  
Mendelian Inheritance ◽  
Causal Gene ◽  
Anatomical Features ◽  
Goldfish Carassius Auratus ◽  
Comprehensive Collection ◽  
Hybridization Event ◽  
History Of ◽  
Tyrosine Protein Kinase ◽  
Genomic Regions ◽  
Tyrosine Protein Kinase Receptor

Goldfish have been subjected to over 1,000 y of intensive domestication and selective breeding. In this report, we describe a high-quality goldfish genome (2n = 100), anchoring 95.75% of contigs into 50 pseudochromosomes. Comparative genomics enabled us to disentangle the two subgenomes that resulted from an ancient hybridization event. Resequencing 185 representative goldfish variants and 16 wild crucian carp revealed the origin of goldfish and identified genomic regions that have been shaped by selective sweeps linked to its domestication. Our comprehensive collection of goldfish varieties enabled us to associate genetic variations with a number of well-known anatomical features, including features that distinguish traditional goldfish clades. Additionally, we identified a tyrosine-protein kinase receptor as a candidate causal gene for the first well-known case of Mendelian inheritance in goldfish—the transparent mutant. The goldfish genome and diversity data offer unique resources to make goldfish a promising model for functional genomics, as well as domestication.

Standard Deviations: The Biological Bases of Transmission Ratio Distortion

2019 ◽  
Vol 53 (1) ◽  
pp. 347-372 ◽  
Author(s):  
Lila Fishman ◽  
Mariah McIntosh
Keyword(s):  
Genetic Mapping ◽  
Mendelian Inheritance ◽  
Transmission Ratio Distortion ◽  
Transmission Ratio ◽  
Animal Reproduction ◽  
Selfish Genetic Elements ◽  
Genetic Mechanisms ◽  
Ratio Distortion ◽  
Experimental Approaches ◽  
Mapping Populations

The rule of Mendelian inheritance is remarkably robust, but deviations from the equal transmission of alternative alleles at a locus [a.k.a. transmission ratio distortion (TRD)] are also commonly observed in genetic mapping populations. Such TRD reveals locus-specific selection acting at some point between the diploid heterozygous parents and progeny genotyping and therefore can provide novel insight into otherwise-hidden genetic and evolutionary processes. Most of the classic selfish genetic elements were discovered through their biasing of transmission, but many unselfish evolutionary and developmental processes can also generate TRD. In this review, we describe methodologies for detecting TRD in mapping populations, detail the arenas and genetic interactions that shape TRD during plant and animal reproduction, and summarize patterns of TRD from across the genetic mapping literature. Finally, we point to new experimental approaches that can accelerate both detection of TRD and characterization of the underlying genetic mechanisms.

scholarly journals Maternal effect killing by a supergene controlling ant social organization

2020 ◽  
Vol 117 (29) ◽  
pp. 17130-17134
Author(s):  
Amaury Avril ◽  
Jessica Purcell ◽  
Sébastien Béniguel ◽  
Michel Chapuisat
Keyword(s):  
Social Organization ◽  
Maternal Effect ◽  
Evolutionary Dynamics ◽  
Mendelian Inheritance ◽  
Transmission Ratio Distortion ◽  
Gene Drive ◽  
Biological Organization ◽  
Evolutionary Mechanisms ◽  
Selfish Gene ◽  
Selfish Genetic Element

Supergenes underlie striking polymorphisms in nature, yet the evolutionary mechanisms by which they arise and persist remain enigmatic. These clusters of linked loci can spread in populations because they captured coadapted alleles or by selfishly distorting the laws of Mendelian inheritance. Here, we show that the supergene haplotype associated with multiple-queen colonies in Alpine silver ants is a maternal effect killer. All eggs from heterozygous queens failed to hatch when they did not inherit this haplotype. Hence, the haplotype specific to multiple-queen colonies is a selfish genetic element that enhances its own transmission by causing developmental arrest of progeny that do not carry it. At the population level, such transmission ratio distortion favors the spread of multiple-queen colonies, to the detriment of the alternative haplotype associated with single-queen colonies. Hence, selfish gene drive by one haplotype will impact the evolutionary dynamics of alternative forms of colony social organization. This killer hidden in a social supergene shows that large nonrecombining genomic regions are prone to cause multifarious effects across levels of biological organization.

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

DNA Research ◽  
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.

scholarly journals Genetic Analysis of Isoenzymes in Raspberry

1992 ◽  
Vol 117 (6) ◽  
pp. 996-999 ◽  
Author(s):  
Johanne C. Cousineau ◽  
Danielle J. Donnelly
Keyword(s):  
Linkage Group ◽  
Genetic Analysis ◽  
Isocitrate Dehydrogenase ◽  
Mendelian Inheritance ◽  
Rubus Idaeus ◽  
Lethal Gene ◽  
Expected Number ◽  
Recessive Lethal ◽  
Segregation Ratios ◽  
Aberrant Segregation

The inheritance of five isoenzymes was studied in red and purple raspberry F1 progenies (Rubus idaeus L. and Rubus × neglectus Peck). Isocitrate dehydrogenase (IDH; EC 1.1.1.42) was a dimeric enzyme present in the cytosol and coded for by one locus (Idh-1). Three of the four crosses analyzed at this locus had deviations from expected ratios, possibly caused by its linkage to a recessive lethal gene. Malate dehydrogenase (MDH; EC 1.1.1.37), phosphoglucoisomerase (PGI; EC 5.3.1.9), and triose phosphate isomerase (TPI; EC 5.3.1.1) were dimeric enzymes with two loci. Each of these three enzymes was present in an organelle and in the cytosol for locus 1 and 2, respectively. Phosphoglucomutase (PGM; EC 2.7.5.1) was monomeric with two loci, Pgm-1 and Pgm-2, located in an organelle and the cytosol, respectively. Each allele at Pgm-1 resulted in the formation of two bands. Although most progenies analyzed supported Mendelian inheritance of polymorphic loci (except for Idh-1), there was a higher than expected number of aberrant segregation ratios observed (18.4%). Analysis of 85 pairs of jointly segregating loci revealed a possible linkage group consisting of Mdh-2, Tpi-2, and Pgm-1.

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