scholarly journals The LCORL Locus Is under Selection in Large-Sized Pakistani Goat Breeds

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 168
Author(s):  
Rashid Saif ◽  
Jan Henkel ◽  
Vidhya Jagannathan ◽  
Cord Drögemüller ◽  
Christine Flury ◽  
...  
Keyword(s):  
Mammalian Species ◽  
Causal Variant ◽  
Whole Genome Sequencing Data ◽  
Potential Candidate ◽  
Sequencing Data ◽  
Selection Signatures ◽  
Selection Signature ◽  
Replication Studies ◽  
Independent Replication ◽  
Selection For

Goat domestication and human selection for valued traits have formed diverse breeds with characteristic phenotypes. This process led to the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity—so-called “selection signatures”. We previously reported an analysis of selection signatures based on pooled whole-genome sequencing data of 20 goat breeds and bezoar goats. In the present study, we reanalyzed the data and focused on a subset of eight Pakistani goat breeds (Angora, Barbari, Beetal, Dera Din Panah, Kamori, Nachi, Pahari, Teddy). We identified 749 selection signatures based on reduced heterozygosity in these breeds. A search for signatures that are shared across large-sized goat breeds revealed that five medium-to-large-sized Pakistani goat breeds had a common selection signature on chromosome 6 in a region harboring the LCORL gene, which has been shown to modulate height or body size in several mammalian species. Fine-mapping of the region confirmed that all five goat breeds with the selection signature were nearly fixed for the same haplotype in a ~191 kb region spanning positions 37,747,447–37,938,449. From the pool sequencing data, we identified a frame-shifting single base insertion into an isoform-specific exon of LCORL as a potential candidate causal variant mediating the size-increasing effect. If this preliminary result can be confirmed in independent replication studies, genotyping of this variant might be used to improve breeding programs and the selection for stature in goats.

scholarly journals Pleistocene Mammal Population Fluctuation Patterns Inferred by Their Genomes

2018 ◽  
Author(s):  
Yulu Liu ◽  
Biao Liu ◽  
Xingxin Pan ◽  
Qiong Shi ◽  
Zhoujian Xiao ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Population Differentiation ◽  
Turning Point ◽  
Mammalian Species ◽  
Middle Pleistocene ◽  
Whole Genome Sequencing Data ◽  
Population Fluctuations ◽  
Sequencing Data ◽  
Wide Range ◽  
The Relationship

SummaryPaleoclimate fluctuations critically affect paleoecological systems and influence mammal populations, even resulting in population differentiation [1]. Historical effective population size (Ne) can reflect these influences [2, 3]. Dozens of recent studies have investigated the relationship between variations in Ne values of one or a small number of mammalian species, inferred from genomic data, and fluctuations in paleoclimate [4-7]. However, there lacks an integrated and comprehensive study on the relationship between the fluctuations in paleoclimate and variations in Ne values inferred from genome sequencing data of a wide range of mammals. To investigate patterns in mammalian Ne values during the the Pleistocene, we gathered whole genome sequencing data of 60 mammals from 35 species distributed across Afro-Eurasia and the Americas, then inferred their Ne curves using the Pairwise Sequentially Markovian Coalescent (PSMC) method; 30 mammalian Ne curves almost simultaneously started to contract at the turning point of the Middle Pleistocene Transition (MPT); then the population of seven mammals started to expand at the turning point of the Middle Brunhes Event (MBE), while the contraction of other mammals’ populations was prolonged to the later different time periods. Eight mammals experienced a severe population contraction around the Last Glaciation Maximum, as some aves did [8], while four potential ruminant beneficiaries showed an expanding population. Sus scrofa and Bos taurus experienced an internal population differentiation in the MPT. To conclude, the phenomenon that critical paleoclimate events facilitated contemporaneous animal population fluctuations in the paleoecological system is showed by our Ne curve analysis.

scholarly journals Identification and prioritisation of causal variants in human genetic disorders from exome or whole genome sequencing data

2017 ◽  
Author(s):  
Nagarajan Paramasivam ◽  
Martin Granzow ◽  
Christina Evers ◽  
Katrin Hinderhofer ◽  
Stefan Wiemann ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genetic Disorders ◽  
Causal Variant ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
Causal Variants ◽  
Small Set ◽  
Downstream Analysis ◽  
Human Genetic Disorders ◽  
Variant Identification

AbstractWith genome sequencing entering the clinics as diagnostic tool to study genetic disorders, there is an increasing need for bioinformatics solutions that enable precise causal variant identification in a timely manner.BackgroundWorkflows for the identification of candidate disease-causing variants perform usually the following tasks: i) identification of variants; ii) filtering of variants to remove polymorphisms and technical artifacts; and iii) prioritization of the remaining variants to provide a small set of candidates for further analysis.MethodsHere, we present a pipeline designed to identify variants and prioritize the variants and genes from trio sequencing or pedigree-based sequencing data into different tiers.ResultsWe show how this pipeline was applied in a study of patients with neurodevelopmental disorders of unknown cause, where it helped to identify the causal variants in more than 35% of the cases.ConclusionsClassification and prioritization of variants into different tiers helps to select a small set of variants for downstream analysis.

scholarly journals Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Irene M. Häfliger ◽  
Franz R. Seefried ◽  
Mirjam Spengeler ◽  
Cord Drögemüller
Keyword(s):  
Missense Variant ◽  
Whole Genome Sequencing Data ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Genome Wide ◽  
Early Embryonic Lethality ◽  
A Genome ◽  
Candidate Regions ◽  
Two Populations

Abstract Background This study was carried out on the two Braunvieh populations reared in Switzerland, the dairy Brown Swiss (BS) and the dual-purpose Original Braunvieh (OB). We performed a genome-wide analysis of array data of trios (sire, dam, and offspring) from the routine genomic selection to identify candidate regions showing missing homozygosity and phenotypic associations with five fertility, ten birth, and nine growth-related traits. In addition, genome-wide single SNP regression studies based on 114,890 single nucleotide polymorphisms (SNPs) for each of the two populations were performed. Furthermore, whole-genome sequencing data of 430 cattle including 70 putative haplotype carriers were mined to identify potential candidate variants that were validated by genotyping the current population using a custom array. Results Using a trio-based approach, we identified 38 haplotype regions for BS and five for OB that segregated at low to moderate frequencies. For the BS population, we confirmed two known haplotypes, BH1 and BH2. Twenty-four variants that potentially explained the missing homozygosity and associated traits were detected, in addition to the previously reported TUBD1:p.His210Arg variant associated with BH2. For example, for BS we identified a stop-gain variant (p.Arg57*) in the MRPL55 gene in the haplotype region on chromosome 7. This region is associated with the ‘interval between first and last insemination’ trait in our data, and the MRPL55 gene is known to be associated with early pregnancy loss in mice. In addition, we discuss candidate missense variants in the CPT1C, MARS2, and ACSL5 genes for haplotypes mapped in BS. In OB, we highlight a haplotype region on chromosome 19, which is potentially caused by a frameshift variant (p.Lys828fs) in the LIG3 gene, which is reported to be associated with early embryonic lethality in mice. Furthermore, we propose another potential causal missense variant in the TUBGCP5 gene for a haplotype mapped in OB. Conclusions We describe, for the first time, several haplotype regions that segregate at low to moderate frequencies and provide evidence of causality by trait associations in the two populations of Swiss Braunvieh. We propose a list of six protein-changing variants as potentially causing missing homozygosity. These variants need to be functionally validated and incorporated in the breeding program.

scholarly journals Genomic analysis reveals selection signatures of Yucatan miniature pig on its X chromosome during domestication

2019 ◽  
Author(s):  
Wei Zhang ◽  
Yuanlang Wang ◽  
Min Yang ◽  
Xudong Wu ◽  
Xiaodong Zhang ◽  
...  
Keyword(s):  
X Chromosome ◽  
Genetic Relationships ◽  
Genomic Analysis ◽  
Fixation Index ◽  
Sweat Glands ◽  
Whole Genome Sequencing Data ◽  
Miniature Pig ◽  
Sequencing Data ◽  
Selection Signatures ◽  
Long Time

AbstractYucatan miniature pig (YMP), a naturally small breed, has been domesticated in the hot and arid Yucatan Peninsula for a long time. However, its selection signatures on the X chromosome remain poorly understood. In this study, we focused on elucidating the selection signatures of YMP on the X chromosome during its domestication and breeding, using the whole-genome sequencing data. We performed population admixture analyses to determine its genetic relationships with other domesticated breeds and wild boars. Subsequently, we used two approaches, the fixation index (Fst) and π ratios, to identify the selection signatures with 100 kb windows sliding in 10 kb steps. As a result, we found that the ectodysplasin A (EDA) gene was related with hypoplasia or absence of hair and sweat glands. This could uncover the relative lack of odor in YMP and the presence of hypoplasia or absence of hair in pigs. Furthermore, we found several genes under selection in other animals. A bioinformatics analysis of the genes in selection regions showed that they were associated with growth, lipid metabolism, reproduction, and immune system. Our findings will lead to a better understanding of the unique genetic and phenotypic characteristics of YMP and offer a plausible method for their utilization as an animal model for hair and odor disease research.

scholarly journals The Sequencing-Based Mapping Method for Effectively Cloning Plant Mutated Genes

2021 ◽  
Vol 22 (12) ◽  
pp. 6224
Author(s):  
Li Yu ◽  
Yanshen Nie ◽  
Jinxia Jiao ◽  
Liufang Jian ◽  
Jie Zhao
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Low Cost ◽  
Causal Variant ◽  
Mapping Method ◽  
Small Population ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Plant Genes

A forward genetic approach is a powerful tool for identifying the genes underlying the phenotypes of interest. However, the conventional map-based cloning method is lengthy, requires a large mapping population and confirmation of many candidate genes in a broad genetic region to clone the causal variant. The whole-genome sequencing method clones the variants with a certain failure probability for multiple reasons, especially for heterozygotes, and could not be used to clone the mutation of epigenetic modifications. Here, we applied the highly complementary characteristics of these two methods and developed a sequencing-based mapping method (SBM) for identifying the location of plant variants effectively with a small population and low cost, which is very user-friendly for most popular laboratories. This method used the whole-genome sequencing data of two pooled populations to screen out enough markers. These markers were used to identify and narrow the candidate region by analyzing the marker-indexes and recombinants. Finally, the possible mutational sites were identified using the whole-genome sequencing data and verified in individual mutants. To elaborate the new method, we displayed the cloned processes in one Arabidopsis heterozygous mutant and two rice homozygous mutants. Thus, the sequencing-based mapping method could clone effectively different types of plant mutations and was a powerful tool for studying the functions of plant genes in the species with known genomic sequences.

scholarly journals Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes

2021 ◽  
Author(s):  
Eric S Tvedte ◽  
Mark Gasser ◽  
Benjamin C Sparklin ◽  
Jane Michalski ◽  
Carl E Hjelmen ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Hybrid Approach ◽  
Cost Effective ◽  
Fruit Fly ◽  
Drosophila Ananassae ◽  
Whole Genome Sequencing Data ◽  
Sequencing Data ◽  
E Coli ◽  
Hybrid Approaches ◽  
Long Read

Abstract The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.

scholarly journals A 127 kb truncating deletion of PGRMC1 is a novel cause of X-linked isolated paediatric cataract

2021 ◽  
Author(s):  
Johanna L. Jones ◽  
Mark A. Corbett ◽  
Elise Yeaman ◽  
Duran Zhao ◽  
Jozef Gecz ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Protein Interactions ◽  
Cholesterol Biosynthesis ◽  
Crystalline Lens ◽  
Whole Genome Sequencing Data ◽  
Mendelian Disease ◽  
Cataract Formation ◽  
Sequencing Data ◽  
Zebrafish Model ◽  
Paediatric Cataract

AbstractInherited paediatric cataract is a rare Mendelian disease that results in visual impairment or blindness due to a clouding of the eye’s crystalline lens. Here we report an Australian family with isolated paediatric cataract, which we had previously mapped to Xq24. Linkage at Xq24–25 (LOD = 2.53) was confirmed, and the region refined with a denser marker map. In addition, two autosomal regions with suggestive evidence of linkage were observed. A segregating 127 kb deletion (chrX:g.118373226_118500408del) in the Xq24–25 linkage region was identified from whole-genome sequencing data. This deletion completely removed a commonly deleted long non-coding RNA gene LOC101928336 and truncated the protein coding progesterone receptor membrane component 1 (PGRMC1) gene following exon 1. A literature search revealed a report of two unrelated males with non-syndromic intellectual disability, as well as congenital cataract, who had contiguous gene deletions that accounted for their intellectual disability but also disrupted the PGRMC1 gene. A morpholino-induced pgrmc1 knockdown in a zebrafish model produced significant cataract formation, supporting a role for PGRMC1 in lens development and cataract formation. We hypothesise that the loss of PGRMC1 causes cataract through disrupted PGRMC1-CYP51A1 protein–protein interactions and altered cholesterol biosynthesis. The cause of paediatric cataract in this family is the truncating deletion of PGRMC1, which we report as a novel cataract gene.

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