Detection and evaluation of selection signatures in sheep

Abstract: The recent development of genome-wide single nucleotide polymorphism (SNP) arrays made it possible to carry out several studies with different species. The selection process can increase or reduce allelic (or genic) frequencies at specific loci in the genome, besides dragging neighboring alleles in the chromosome. This way, genomic regions with increased frequencies of specific alleles are formed, caracterizing selection signatures or selective sweeps. The detection of these signatures is important to characterize genetic resources, as well as to identify genes or regions involved in the control and expression of important production and economic traits. Sheep are an important species for theses studies as they are dispersed worldwide and have great phenotypic diversity. Due to the large amounts of genomic data generated, specific statistical methods and softwares are necessary for the detection of selection signatures. Therefore, the objectives of this review are to address the main statistical methods and softwares currently used for the analysis of genomic data and the identification of selection signatures; to describe the results of recent works published on selection signatures in sheep; and to discuss some challenges and opportunities in this research field.

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Shared Ancestry and Signatures of Recent Selection in Gotland Sheep

Genes ◽

10.3390/genes12030433 ◽

2021 ◽

Vol 12 (3) ◽

pp. 433

Author(s):

Seyed Mohammad Ghoreishifar ◽

Christina Marie Rochus ◽

Sima Moghaddaszadeh-Ahrabi ◽

Pourya Davoudi ◽

Siavash Salek Ardestani ◽

...

Keyword(s):

Candidate Genes ◽

Growth Traits ◽

Significant Snps ◽

P Value ◽

Economic Traits ◽

Selection Signatures ◽

Shared Ancestry ◽

The Baltic ◽

Genomic Regions ◽

Recent Selection

Gotland sheep, a breed native to Gotland, Sweden (an island in the Baltic Sea), split from the Gute sheep breed approximately 100 years ago, and since, has probably been crossed with other breeds. This breed has recently gained popularity, due to its pelt quality. This study estimates the shared ancestors and identifies recent selection signatures in Gotland sheep using 600 K single nucleotide polymorphism (SNP) genotype data. Admixture analysis shows that the Gotland sheep is a distinct breed, but also has shared ancestral genomic components with Gute (~50%), Karakul (~30%), Romanov (~20%), and Fjällnäs (~10%) sheep breeds. Two complementary methods were applied to detect selection signatures: A Bayesian population differentiation FST and an integrated haplotype homozygosity score (iHS). Our results find that seven significant SNPs (q-value < 0.05) using the FST analysis and 55 significant SNPs (p-value < 0.0001) using the iHS analysis. Of the candidate genes that contain significant markers, or are in proximity to them, we identify several belongings to the keratin genes, RXFP2, ADCY1, ENOX1, USF2, COX7A1, ARHGAP28, CRYBB2, CAPNS1, FMO3, and GREB1. These genes are involved in wool quality, polled and horned phenotypes, fertility, twining rate, meat quality, and growth traits. In summary, our results provide shared founders of Gotland sheep and insight into genomic regions maintained under selection after the breed was formed. These results contribute to the detection of candidate genes and QTLs underlying economic traits in sheep.

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Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits

BMC Genomics ◽

10.1186/s12864-021-08042-x ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Dengying Liu ◽

Zhenliang Chen ◽

Wei Zhao ◽

Longyu Guo ◽

Hao Sun ◽

...

Keyword(s):

Candidate Genes ◽

Artificial Selection ◽

Sequence Data ◽

Holstein Cattle ◽

Cattle Population ◽

Economic Traits ◽

Selection Signatures ◽

Wide Range ◽

Candidate Regions ◽

Genomic Regions

Abstract Background Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures within the genome using genotyping by genome-reduced sequence data from 1092 cows. Results In total, 101 significant iHS genomic regions containing selection signatures encompassing a total of 256 candidate genes were detected. There were 27 significant |iHS| genomic regions with a mean |iHS| score > 2. The average number of ROH per individual was 42.15 ± 25.47, with an average size of 2.95 Mb. The length of 78 % of the detected ROH was within the range of 1–2 MB and 2–4 MB, and 99 % were shorter than 8 Mb. A total of 168 genes were detected in 18 ROH islands (top 1 %) across 16 autosomes, in which each SNP showed a percentage of occurrence > 30 %. There were 160 and 167 genes associated with the 52 candidate regions within health-related QTL intervals and 59 candidate regions within reproduction-related QTL intervals, respectively. Annotation of the regions harbouring clustered |iHS| signals and candidate regions for ROH revealed a panel of interesting candidate genes associated with adaptation and economic traits, such as IL22RA1, CALHM3, ITGA9, NDUFB3, RGS3, SOD2, SNRPA1, ST3GAL4, ALAD, EXOSC10, and MASP2. In a further step, a total of 1472 SNPs in 256 genes were matched with 352 cis-eQTLs in 21 tissues and 27 trans-eQTLs in 6 tissues. For SNPs located in candidate regions for ROH, a total of 108 cis-eQTLs in 13 tissues and 4 trans-eQTLs were found for 1092 SNPs. Eighty-one eGenes were significantly expressed in at least one tissue relevant to a trait (P value < 0.05) and matched the 256 genes detected by iHS. For the 168 significant genes detected by ROH, 47 gene-tissue pairs were significantly associated with at least one of the 37 traits. Conclusions We provide a comprehensive overview of selection signatures in Shanghai Holstein cattle genomes by combining iHS and ROH. Our study provides a list of genes associated with immunity, reproduction and adaptation. For functional annotation, the cGTEx resource was used to interpret SNP-trait associations. The results may facilitate the identification of genes relevant to important economic traits and can help us better understand the biological processes and mechanisms affected by strong ongoing natural or artificial selection in livestock populations.

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Unconventional Materials Processing Using Spark Plasma Sintering

Ceramics ◽

10.3390/ceramics4010003 ◽

2021 ◽

Vol 4 (1) ◽

pp. 20-40

Author(s):

Ambreen Nisar ◽

Cheng Zhang ◽

Benjamin Boesl ◽

Arvind Agarwal

Keyword(s):

Spark Plasma Sintering ◽

Real Life ◽

Functional Materials ◽

Research Field ◽

Advanced Materials ◽

Plasma Sintering ◽

Challenges And Opportunities ◽

Future Challenges ◽

Gas Quenching ◽

Spark Plasma

Spark plasma sintering (SPS) has gained recognition in the last 20 years for its rapid densification of hard-to-sinter conventional and advanced materials, including metals, ceramics, polymers, and composites. Herein, we describe the unconventional usages of the SPS technique developed in the field. The potential of various new modifications in the SPS technique, from pressureless to the integration of a novel gas quenching system to extrusion, has led to SPS’ evolution into a completely new manufacturing tool. The SPS technique’s modifications have broadened its usability from merely a densification tool to the fabrication of complex-shaped components, advanced functional materials, functionally gradient materials, interconnected materials, and porous filter materials for real-life applications. The broader application achieved by modification of the SPS technique can provide an alternative to conventional powder metallurgy methods as a scalable manufacturing process. The future challenges and opportunities in this emerging research field have also been identified and presented.

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Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin

Frontiers in Genetics ◽

10.3389/fgene.2021.657282 ◽

2021 ◽

Vol 12 ◽

Author(s):

Sèyi Fridaïus Ulrich Vanvanhossou ◽

Tong Yin ◽

Carsten Scheper ◽

Ruedi Fries ◽

Luc Hippolyte Dossa ◽

...

Keyword(s):

Production Systems ◽

Principal Component ◽

West African ◽

Economic Traits ◽

Selection Signatures ◽

Extended Haplotype ◽

Indigenous Cattle ◽

Environmental Pressures ◽

Inbreeding Coefficients ◽

Recent Selection

The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

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Effects of genomic and functional diversity on stand-level productivity and performance of non-native Arabidopsis

10.1101/2020.04.20.049593 ◽

2020 ◽

Author(s):

Kathryn G. Turner ◽

Claire M. Lorts ◽

Asnake T. Haile ◽

Jesse R. Lasky

Keyword(s):

Genetic Diversity ◽

Flowering Time ◽

Phenotypic Diversity ◽

A Priori ◽

Interference Competition ◽

Genomic Data ◽

Total Biomass ◽

High Resource ◽

And Performance ◽

Resource Conditions

AbstractBiodiversity can affect the properties of groups of organisms, such as ecosystem function and the persistence of colonizing populations. Genomic data offer a newly available window to diversity, complementary to other measures like taxonomic or phenotypic diversity. We tested whether native genetic diversity in field experimental stands of Arabidopsis thaliana affected their aboveground biomass and fecundity in their colonized range. We constructed some stands of genotypes that we a priori predicted would differ in performance or show overyielding. We found no relationship between genetic diversity and stand total biomass. However, increasing stand genetic diversity increased fecundity in high resource conditions. Polyculture (multiple genotype) stands consistently yielded less biomass than expected based on the yields of component genotypes in monoculture. This under-yielding was strongest in stands with late-flowering and high biomass genotypes, potentially due to interference competition by these genotypes. Using a new implementation of association mapping, we identified genetic loci whose diversity was associated with stand-level yield, revealing a major flowering time locus associated with under-yielding of polycultures. Our field experiment supports community ecology studies that find a range of diversity-function relationships. Nevertheless, our results suggest diversity in colonizing propagule pools can enhance population fitness. Furthermore, interference competition among genotypes differing in flowering time might limit the advantages of polyculture.

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Identification of Selection Signatures in Commercial Asian Rice Subspecies Deciphered Selection Footprints for Four Overrepresented Biological Processes

10.21203/rs.3.rs-121958/v1 ◽

2020 ◽

Author(s):

Siavash Salek Ardestani ◽

Mahmoud Amiri Roudbar ◽

Mohammad Hossein Banabazi ◽

Seyedeh Fatemeh Mousavi ◽

Madhav Bhatta ◽

...

Keyword(s):

Selection Pressure ◽

Rice Genome ◽

Fixation Index ◽

Biological Processes ◽

Selection Signatures ◽

Genomic Changes ◽

Asian Rice ◽

Genome Level ◽

Window Approach ◽

Genomic Regions

Abstract BackgroundSelective breeding pressures have led to gradual genomic changes in Asian commercial rice, which have shaped selection footprints on its genome level. Tracing genomic selection footprints might be illuminative for better understanding of recent selection breeding objectives, and how breeding strategies have formed the Asian commercial rice genome. ResultsIn this study, the genotypic information (HDRA 700K) of four Asian commercial rice subspecies including Indica (n=498), Aus (n=187), Temperate japonica (n=241), and Tropical japonica (n=361) were downloaded from Rice Diversity Project database (http://www.ricediversity.org) to detect selection signatures by employing the Z-transformed of fixation index and Tajima’s D test, based on a sliding window approach. Although we could not identify overrepresented genomic regions underlying selection pressure among all aforementioned Asian commercial rice subspecies, interestingly, our findings revealed four overrepresented biological processes underlying selection pressure including proteolysis (GO:0006508), phosphorylation (GO:0016310), protein catabolic process (GO:0030163), and transmembrane transport (GO:0055085) that might be associated with immunity, senescing leaves, transporting, and absorption of ions. ConclusionsThese results can provide knowledge on how breeding efforts shaped the Asian commercial rice subspecies genome, and which genomic regions of these subspecies have been targeted in recent decades.

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Genome-Wide Association Study and Selection Signatures Detect Genomic Regions Associated with Seed Yield and Oil Quality in Flax

International Journal of Molecular Sciences ◽

10.3390/ijms19082303 ◽

2018 ◽

Vol 19 (8) ◽

pp. 2303 ◽

Cited By ~ 18

Author(s):

Frank You ◽

Jin Xiao ◽

Pingchuan Li ◽

Zhen Yao ◽

Gaofeng Jia ◽

...

Keyword(s):

Association Study ◽

Seed Yield ◽

Phenotypic Variation ◽

Genome Wide Association Study ◽

Oil Quality ◽

Genome Wide Association ◽

Selection Signatures ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

A genome-wide association study (GWAS) was performed on a set of 260 lines which belong to three different bi-parental flax mapping populations. These lines were sequenced to an averaged genome coverage of 19× using the Illumina Hi-Seq platform. Phenotypic data for 11 seed yield and oil quality traits were collected in eight year/location environments. A total of 17,288 single nucleotide polymorphisms were identified, which explained more than 80% of the phenotypic variation for days to maturity (DTM), iodine value (IOD), palmitic (PAL), stearic, linoleic (LIO) and linolenic (LIN) acid contents. Twenty-three unique genomic regions associated with 33 quantitative trait loci (QTL) for the studied traits were detected, thereby validating four genomic regions previously identified. The 33 QTL explained 48–73% of the phenotypic variation for oil content, IOD, PAL, LIO and LIN but only 8–14% for plant height, DTM and seed yield. A genome-wide selective sweep scan for selection signatures detected 114 genomic regions that accounted for 7.82% of the flax pseudomolecule and overlapped with the 11 GWAS-detected genomic regions associated with 18 QTL for 11 traits. The results demonstrate the utility of GWAS combined with selection signatures for dissection of the genetic structure of traits and for pinpointing genomic regions for breeding improvement.

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The Timing and Direction of Introgression Under the Multispecies Network Coalescent

Genetics ◽

10.1534/genetics.118.301831 ◽

2019 ◽

Vol 211 (3) ◽

pp. 1059-1073 ◽

Cited By ~ 14

Author(s):

Mark S. Hibbins ◽

Matthew W. Hahn

Keyword(s):

Statistical Methods ◽

Biological Process ◽

Genomic Data ◽

Hybrid Speciation ◽

Saccharomyces Paradoxus ◽

Genomic Signatures ◽

Wild Yeast ◽

Other Information ◽

Homoploid Hybrid ◽

New Statistics

Introgression is a pervasive biological process, and many statistical methods have been developed to infer its presence from genomic data. However, many of the consequences and genomic signatures of introgression remain unexplored from a methodological standpoint. Here, we develop a model for the timing and direction of introgression based on the multispecies network coalescent, and from it suggest new approaches for testing introgression hypotheses. We suggest two new statistics, D1 and D2, which can be used in conjunction with other information to test hypotheses relating to the timing and direction of introgression, respectively. D1 may find use in evaluating cases of homoploid hybrid speciation (HHS), while D2 provides a four-taxon test for polarizing introgression. Although analytical expectations for our statistics require a number of assumptions to be met, we show how simulations can be used to test hypotheses about introgression when these assumptions are violated. We apply the D1 statistic to genomic data from the wild yeast Saccharomyces paradoxus—a proposed example of HHS—demonstrating its use as a test of this model. These methods provide new and powerful ways to address questions relating to the timing and direction of introgression.

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How to frame our behaviour in order to limit climate change?

European Journal of Public Health ◽

10.1093/eurpub/ckz185.400 ◽

2019 ◽

Vol 29 (Supplement_4) ◽

Author(s):

P Van Den Hazel

Keyword(s):

Public Health ◽

Climate Change ◽

General Population ◽

Environmental Psychology ◽

Environmental Values ◽

Research Field ◽

Behavioral Changes ◽

Economic Traits ◽

Self Image ◽

Major Domain

Abstract The climate is changing and speedy changes in society are needed to keep the damage within survival ranges. The aim is to keep the average raise of global temperature below 2 degrees Celsius. Changes in behavior of the overall population are needed to realize this aim. How can we get people to change? The research field of environmental psychology looks at framing issues to promote changes of behavior. More information helps to make people make decisions. Motivation is more important. Motivation is driven by our values and self-image. Four values are important for environmental behavior: hedonic, egoistic, altruistic and environmental values. Besides that culture, personal and timing issues play a role. The workshop explores the values in persons according to different examples. Can we influence the values to which we adhere? Socio-economic traits in people only explore a few percent in differences. Discussion: different strategies can be used with people with different dominant values. Public health is a major domain to support the local authorities to endorse the behavioral changes in the general population in order to limit the temperature increase.

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