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 A Scan for Linkage Disequilibrium Across the Human Genome

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1711-1722 ◽  
Author(s):  
Gavin A Huttley ◽  
Michael W Smith ◽  
Mary Carrington ◽  
Stephen J O’Brien
Keyword(s):  
Linkage Disequilibrium ◽  
Human Genome ◽  
Pedigree Analysis ◽  
Exact Test ◽  
Genomic Scale ◽  
Genomic Regions ◽  
Formal Test ◽  
Scale Data ◽  
Short Tandem ◽  
Tandem Repeat Polymorphism

Abstract Linkage disequilibrium (LD), the tendency for alleles of linked loci to co-occur nonrandomly on chromosomal haplotypes, is an increasingly useful phenomenon for (1) revealing historic perturbation of populations including founder effects, admixture, or incomplete selective sweeps; (2) estimating elapsed time since such events based on time-dependent decay of LD; and (3) disease and phenotype mapping, particularly for traits not amenable to traditional pedigree analysis. Because few descriptions of LD for most regions of the human genome exist, we searched the human genome for the amount and extent of LD among 5048 autosomal short tandem repeat polymorphism (STRP) loci ascertained as specific haplotypes in the European CEPH mapping families. Evidence is presented indicating that ∼4% of STRP loci separated by <4.0 cM are in LD. The fraction of locus pairs within these intervals that display small Fisher’s exact test (FET) probabilities is directly proportional to the inverse of recombination distance between them (1/cM). The distribution of LD is nonuniform on a chromosomal scale and in a marker density-independent fashion, with chromosomes 2, 15, and 18 being significantly different from the genome average. Furthermore, a stepwise (locus-by-locus) 5-cM sliding-window analysis across 22 autosomes revealed nine genomic regions (2.2-6.4 cM), where the frequency of small FET probabilities among loci was greater than or equal to that presented by the HLA on chromosome 6, a region known to have extensive LD. Although the spatial heterogeneity of LD we detect in Europeans is consistent with the operation of natural selection, absence of a formal test for such genomic scale data prevents eliminating neutral processes as the evolutionary origin of the LD.

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.

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

2017 ◽  
Vol 7 (7) ◽  
pp. 2115-2124 ◽  
Author(s):  
Marta Niedzicka ◽  
Katarzyna Dudek ◽  
Anna Fijarczyk ◽  
Piotr Zieliński ◽  
Wiesław Babik
Keyword(s):  
Reproductive Isolation ◽  
Linkage Map ◽  
Transmission Ratio Distortion ◽  
Rate Variation ◽  
Linkage Maps ◽  
Protein Coding ◽  
Lissotriton Vulgaris ◽  
Ratio Distortion ◽  
Genomic Regions ◽  
Evolutionary Consequences

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.

scholarly journals A structural gene (Tcp-1) within the mouse t complex is separable from effects on tail length and lethality but may be associated with effects on spermatogenesis

1981 ◽  
Vol 38 (2) ◽  
pp. 115-123 ◽  
Author(s):  
Lee M. Silver
Keyword(s):  
Genetic Basis ◽  
Genetic Factors ◽  
Tail Length ◽  
Transmission Ratio Distortion ◽  
Transmission Ratio ◽  
Cell Protein ◽  
Wild Type ◽  
T Complex ◽  
Interaction Factor ◽  
Ratio Distortion

SUMMARYThe Tcp-1 gene is located within the t complex and codes for a major testicular cell protein called p63/6.9. All wild-type chromosomes carry the Tcp-1b allele which codes for a basic form of this protein, while all complete t haplotypes carry the Tcp-1a allele which codes for an acidic form of this protein. It is not clear whether the Tcp-1 gene is associated with phenotypic effects of t haplotypes on embryogenesis and/or spermatogenesis, since the genetic basis for these effects is extremely complex. The elegant analysis of Lyon & Mason (1977) has allowed the identification and separation of a family of genetic factors which interact to produce the observed phenotypes associated with various combinations of t haplotypes. The data summarized in this report indicate that the Tcp-1a locus is separable from all of the identified t haplotype factors except for one; a complete correlation has been obtained between Tcp-1a and a proximal t haplotype factor which is involved in effects on transmission ratio distortion. Two other novel points emerge from this analysis. First, it appears that the tail interaction factor and the proximal sperm factors represent distinct genetic loci. Second, the accumulated data lead to the proposal that the TOrl chromosome carries a short segment of t haplotype chromatin containing Tcp-1a and proximal sperm factors involved in transmission ratio distortion and sterility.

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

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.

scholarly journals Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa

2021 ◽  
Vol 22 (7) ◽  
pp. 3477
Author(s):  
Julia Zaborowska ◽  
Bartosz Łabiszak ◽  
Annika Perry ◽  
Stephen Cavers ◽  
Witold Wachowiak
Keyword(s):  
Population Structure ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Redox Homeostasis ◽  
Snp Markers ◽  
Regulation Of Transcription ◽  
Single Nucleotide ◽  
Homeostasis Regulation ◽  
Genomic Regions ◽  
Mountain Plants

Mountain plants, challenged by vegetation time contractions and dynamic changes in environmental conditions, developed adaptations that help them to balance their growth, reproduction, survival, and regeneration. However, knowledge regarding the genetic basis of species adaptation to higher altitudes remain scarce for most plant species. Here, we attempted to identify such corresponding genomic regions of high evolutionary importance in two closely related European pines, Pinus mugo and P. uncinata, contrasting them with a reference lowland relative—P. sylvestris. We genotyped 438 samples at thousands of single nucleotide polymorphism (SNP) markers, tested their genetic differentiation and population structure followed by outlier detection and gene ontology annotations. Markers clearly differentiated the species and uncovered patterns of population structure in two of them. In P. uncinata three Pyrenean sites were grouped together, while two outlying populations constituted a separate cluster. In P. sylvestris, Spanish population appeared distinct from the remaining four European sites. Between mountain pines and the reference species, 35 candidate genes for altitude-dependent selection were identified, including such encoding proteins responsible for photosynthesis, photorespiration and cell redox homeostasis, regulation of transcription, and mRNA processing. In comparison between two mountain pines, 75 outlier SNPs were found in proteins involved mainly in the gene expression and metabolism.

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