scholarly journals Genome-wide analysis reveals signatures of selection for gait traits in Yili horse

2018 ◽  
Author(s):  
Ling-Ling Liu ◽  
Chao Fang ◽  
Jun Meng ◽  
Johann Detilleux ◽  
Wu-Jun Liu ◽  
...  
Keyword(s):  
Breeding Programs ◽  
Genotyping Array ◽  
Genome Wide ◽  
Locomotory Behavior ◽  
Genome Array ◽  
Signatures Of Selection ◽  
Selection For ◽  
The Moment ◽  
Genomic Regions ◽  
First Time

AbstractHigh quality gaits play an important role in many breeding programs, but the genes of gait were limited at the moment. Here, we present an analysis of genomic selection signatures in 53 individuals from two breeds, using genotype data from the Affymetrix Equine 670K SNP genotyping array. The 11 selection regions of Yili horse were identified using an FST statistic and XP-EHH calculated in 200-kb windows across the genome. In total, 50 genes could be found in the 11 regions, and two candidate genes related to locomotory behavior (CLN6, FZD4). The genome of Yili horse and Russian horse were shaped by natural and artificial selection. Our results suggest that gait trait of Yili horse may related to two genes. This is the first time when whole genome array data is utilized to study genomic regions affecting gait in Yili horse breed.

scholarly journals Signatures of selection in the genome of Swedish warmblood horses selected for sport performance

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Michela Ablondi ◽  
Åsa Viklund ◽  
Gabriella Lindgren ◽  
Susanne Eriksson ◽  
Sofia Mikko
Keyword(s):  
Complex Traits ◽  
Sport Performance ◽  
Functional Studies ◽  
Snp Data ◽  
Genome Wide ◽  
A Genome ◽  
Physical Abilities ◽  
Signatures Of Selection ◽  
Selection For ◽  
Genomic Regions

Abstract Background A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits. Results The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85% of the genotyped SWB individuals. Such ROH were located on ECA4, ECA6, ECA7, ECA10 and ECA17. Long ROH were instead distributed evenly across the genome of Exmoor ponies in 77% of the chromosomes. Two population differentiation tests (FST and XP-EHH) revealed signatures of selection on ECA1, ECA4, and ECA6 in SWB horses. Conclusions Genes related to behaviour, physical abilities and fertility, appear to be targets of selection in the SWB breed. This study provides a genome-wide map of selection signatures in SWB horses, and ground for further functional studies to unravel the biological mechanisms behind complex traits in horses.

scholarly journals Genetics of Germination and Seedling Traits under Drought Stress in a MAGIC Population of Maize

Plants ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1786
Author(s):  
Soumeya Rida ◽  
Oula Maafi ◽  
Ana López-Malvar ◽  
Pedro Revilla ◽  
Meriem Riache ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Genome Wide Association Study ◽  
Genetic Regulation ◽  
Breeding Programs ◽  
Seedling Traits ◽  
Genome Wide ◽  
A Genome ◽  
Positive Correlations ◽  
Genomic Regions ◽  
Magic Population

Drought is one of the most detrimental abiotic stresses hampering seed germination, development, and productivity. Maize is more sensitive to drought than other cereals, especially at seedling stage. Our objective was to study genetic regulation of drought tolerance at germination and during seedling growth in maize. We evaluated 420 RIL with their parents from a multi-parent advanced generation inter-cross (MAGIC) population with PEG-induced drought at germination and seedling establishment. A genome-wide association study (GWAS) was carried out to identify genomic regions associated with drought tolerance. GWAS identified 28 and 16 SNPs significantly associated with germination and seedling traits under stress and well-watered conditions, respectively. Among the SNPs detected, two SNPs had significant associations with several traits with high positive correlations, suggesting a pleiotropic genetic control. Other SNPs were located in regions that harbored major QTLs in previous studies, and co-located with QTLs for cold tolerance previously published for this MAGIC population. The genomic regions comprised several candidate genes related to stresses and plant development. These included numerous drought-responsive genes and transcription factors implicated in germination, seedling traits, and drought tolerance. The current analyses provide information and tools for subsequent studies and breeding programs for improving drought tolerance.

scholarly journals AnnoGen: annotating genome-wide pragmatic features

2020 ◽  
Vol 36 (9) ◽  
pp. 2899-2901
Author(s):  
Quanhu Sheng ◽  
Hui Yu ◽  
Olufunmilola Oyebamiji ◽  
Jiandong Wang ◽  
Danqian Chen ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Reference Genome ◽  
Bioinformatics Analysis ◽  
Sequence Information ◽  
Genomic Features ◽  
Single Base ◽  
Annotation Data ◽  
Genome Wide ◽  
Genomic Regions ◽  
First Time

Abstract Motivation Genome annotation is an important step for all in-depth bioinformatics analysis. It is imperative to augment quantity and diversity of genome-wide annotation data for the latest reference genome to promote its adoption by ongoing and future impactful studies. Results We developed a python toolkit AnnoGen, which at the first time, allows the annotation of three pragmatic genomic features for the GRCh38 genome in enormous base-wise quantities. The three features are chemical binding Energy, sequence information Entropy and Homology Score. The Homology Score is an exceptional feature that captures the genome-wide homology through single-base-offset tiling windows of 100 continual nucleotide bases. AnnoGen is capable of annotating the proprietary pragmatic features for variable user-interested genomic regions and optionally comparing two parallel sets of genomic regions. AnnoGen is characterized with simple utility modes and succinct HTML report of informative statistical tables and plots. Availability and implementation https://github.com/shengqh/annogen.

scholarly journals Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 524 ◽  
Author(s):  
Sangang He ◽  
Jiang Di ◽  
Bing Han ◽  
Lei Chen ◽  
Mingjun Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Average Length ◽  
Inbreeding Coefficient ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Genotyping Array ◽  
Genome Region ◽  
Genome Wide ◽  
Genomic Regions ◽  
Genome Wide Scan

In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.

scholarly journals Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions

BMC Genomics ◽  
2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Zhaohua Liu ◽  
Zhibin Ji ◽  
Guizhi Wang ◽  
Tianle Chao ◽  
Lei Hou ◽  
...  
Keyword(s):  
Domestic Sheep ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Signatures Of Selection ◽  
Selection For

scholarly journals Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions

2021 ◽  
Vol 12 ◽  
Author(s):  
Pedro H. F. Freitas ◽  
Yachun Wang ◽  
Ping Yan ◽  
Hinayah R. Oliveira ◽  
Flavio S. Schenkel ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Thermal Tolerance ◽  
Climatic Conditions ◽  
Biological Processes ◽  
Biological Mechanisms ◽  
Cattle Breeds ◽  
Signatures Of Selection ◽  
Selection For ◽  
Genomic Regions

Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (FST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.

scholarly journals Detection of selection signatures in farmed coho salmon (Oncorhynchus kisutch) using dense genome-wide information

2020 ◽  
Author(s):  
M.E. López ◽  
M.I. Cádiz ◽  
E.B. Rondeau ◽  
B.F. Koop ◽  
J.M. Yáñez
Keyword(s):  
Disease Resistance ◽  
Coho Salmon ◽  
Phenotypic Diversity ◽  
Oncorhynchus Kisutch ◽  
Culture Conditions ◽  
Selection Signatures ◽  
Breeding Programs ◽  
Genome Wide ◽  
Genetic Mechanisms ◽  
Signatures Of Selection

AbstractAnimal domestication and artificial selection give rise to gradual changes at the genomic level in populations. Subsequent footprints of selection known as selection signatures or selective sweeps have been traced in the genomes of many animal livestock species by exploiting variations in linkage disequilibrium patterns and/or reduction of genetic diversity.Domestication of most aquatic species is recent in comparison with land animals, and salmonids are one of the most important fish species in aquaculture. Coho salmon (Oncorhynchus kisutch), cultivated primarily in Chile, has been subject to breeding programs to improve growth, disease resistance traits, and flesh color. This study aimed to identify selection signatures that may be involved in adaptation to culture conditions and traits of productive interest. To do so, individuals of two domestic populations cultured in Chile were genotyped with 200 thousand SNPs, and analyses were conducted using iHS, XP-EHH and CLR. Several signatures of selection on different chromosomal regions were detected across both populations. Some of the identified regions under selection contained genes such anapc2, alad, chp2 and myn that have been previously associated with body weight in Atlantic salmon or sec24d and robo1 that have been associated with disease resistance to Piscirickettsia salmonis in coho salmon. Findings in our study can contribute to an integrated genome-wide map of selection signatures, to help identify the genetic mechanisms of phenotypic diversity in coho salmon.

scholarly journals Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
M. Yaro ◽  
K. A. Munyard ◽  
E. Morgan ◽  
R. J. N. Allcock ◽  
M. J. Stear ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Reference Genome ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Multiple Regions ◽  
Signatures Of Selection ◽  
Selection For ◽  
Animal Trypanosomiasis ◽  
Genomic Regions ◽  
Production Losses

Abstract Background The Djallonke sheep is well adapted to harsh environmental conditions, and is relatively resistant to Haemonchosis and resilient to animal trypanosomiasis. The larger Sahelian sheep, which cohabit the same region, is less well adapted to these disease challenges. Haemonchosis and Trypanosomiasis collectively cost the worldwide animal industry billions of dollars in production losses annually. Results Here, we separately sequenced and then pooled according to breed the genomes from five unrelated individuals from each of the Djallonke and Sahelian sheep breeds (sourced from Ghana), at greater than 22-fold combined coverage for each breed. A total of approximately 404 million (97%) and 343 million (97%) sequence reads from the Djallonke and Sahelian breeds respectively, were successfully mapped to the sheep reference genome Oar v3.1. We identified approximately 11.1 million and 10.9 million single nucleotide polymorphisms (SNPs) in the Djallonke and Sahelian breeds, with approximately 15 and 16% respectively of these not previously reported in sheep. Multiple regions of reduced heterozygosity were also found; 70 co-localised within genomic regions harbouring genes that mediate disease resistance, immune response and adaptation in sheep or cattle. Thirty- three of the regions of reduced heterozygosity co-localised with previously reported genes for resistance to haemonchosis and trypanosomiasis. Conclusions Our analyses suggest that these regions of reduced heterozygosity may be signatures of selection for these economically important diseases.

Sign in / Sign up

Export Citation Format

Share Document