Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations

Chen, Minhui; Pan, Dunfei; Ren, Hongyan; Fu, Jinluan; Li, Junya; Su, Guosheng; Wang, Aiguo; Jiang, Li; Zhang, Qin; Liu, Jianfeng

doi:10.1186/s12711-016-0254-5

Cited by 43 publications

(33 citation statements)

References 52 publications

(78 reference statements)

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“…Only OAR6 harbored a large selected candidate region in both Latxa sheep populations, which constituted the major genomic difference with Sasi Ardi sheep. The absence of overlapping results between the different tests may be explained by their sensitivity to the different selection pressures [ 78 – 80 ]. Furthermore, a recent study that compared the performance of 11 different procedures for detecting selection signatures including Tajima’s D and F st reported low correlations [ 79 ].…”

Section: Discussionmentioning

confidence: 99%

Genomic selection signatures in sheep from the Western Pyrenees

et al. 2018

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BackgroundThe current large spectrum of sheep phenotypic diversity results from the combined product of sheep selection for different production traits such as wool, milk and meat, and its natural adaptation to new environments. In this study, we scanned the genome of 25 Sasi Ardi and 75 Latxa sheep from the Western Pyrenees for three types of regions under selection: (1) regions underlying local adaptation of Sasi Ardi semi-feral sheep, (2) regions related to a long traditional dairy selection pressure in Latxa sheep, and (3) regions experiencing the specific effect of the modern genetic improvement program established for the Latxa breed during the last three decades.ResultsThirty-two selected candidate regions including 147 annotated genes were detected by using three statistical parameters: pooled heterozygosity H, Tajima’s D, and Wright’s fixation index Fst. For Sasi Ardi sheep, chromosomes Ovis aries (OAR)4, 6, and 22 showed the strongest signals and harbored several candidate genes related to energy metabolism and morphology (BBS9, ELOVL3 and LDB1), immunity (NFKB2), and reproduction (H2AFZ). The major genomic difference between Sasi Ardi and Latxa sheep was on OAR6, which is known to affect milk production, with highly selected regions around the ABCG2, SPP1, LAP3, NCAPG, LCORL, and MEPE genes in Latxa sheep. The effect of the modern genetic improvement program on Latxa sheep was also evident on OAR15, on which several olfactory genes are located. We also detected several genes involved in reproduction such as ESR1 and ZNF366 that were affected by this selection program.ConclusionsNatural and artificial selection have shaped the genome of both Sasi Ardi and Latxa sheep. Our results suggest that Sasi Ardi traits related to energy metabolism, morphological, reproductive, and immunological features have been under positive selection to adapt this semi-feral sheep to its particular environment. The highly selected Latxa sheep for dairy production showed clear signatures of selection in genomic regions related to milk production. Furthermore, our data indicate that the selection criteria applied in the modern genetic improvement program affect immunity and reproduction traits.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0378-x) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genomic selection signatures in sheep from the Western Pyrenees

et al. 2018

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“…Protein-coding and RNA genes mapped within the candidate regions, based on the UMD3.1 bovine reference genome annotation, were processed using the functional annotation tool implemented in DAVID Bioinformatics resources 6.7 to determine the over-represented (enriched) functional terms (Huang da et al, 2009a,b). An enrichment score of 1.3, which is equivalent to the Fisher exact test P = 0.05, was used as a threshold to define the significantly enriched functional terms in comparison to the whole bovine reference genome background.…”

Section: Methodsmentioning

confidence: 99%

Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu

Bahbahani

Tijjani

Mukasa³

et al. 2017

Front. Genet.

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The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and ΔAF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them. A total of 142 functional variants, one novel, have been detected within these regions, in which 30 and 26 were classified as of zebu and African taurine origins, respectively. High density genome-wide SNP analysis of zebu × taurine admixed cattle populations from Uganda and Nigeria show that 25 of these regions are shared between KEASZ and Uganda cattle, and seven regions are shared across the KEASZ, Uganda, and Nigeria cattle. The identification of common candidate regions allows us to fine map 18 regions. These regions intersect with genes and QTL associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability.

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“…Studies showed that two or more approaches combined can minimize the biases and false positives, as in the case of dairy cattle (Rothammer et al ) and Debao pony (Liu et al ). In this study, we applied three analytical methods ( F ST , XP‐EHH and XP‐CLR) to identify candidate genes related to heat tolerance and disease resistance in DHH, and found that no gene was detected by above‐mentioned three methods, which is mainly attributed to the different characteristics of these methods (Chen et al ). Nonetheless, 15 of 28 common genes were associated with heat tolerance and disease resistance (Table and Table ) in our study.…”

Section: The Candidate Genes Are Associated With Heat Tolerance and Imentioning

confidence: 99%

Genome‐wide scan of selection signatures in Dehong humped cattle for heat tolerance and disease resistance

Chen

et al. 2019

Animal Genetics

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Summary Dehong humped cattle (DHH) is an indigenous zebu breed from southwestern China that possesses characteristics of heat tolerance and strong disease resistance and adapts well to the local tropical and subtropical climatic conditions. However, information on selection signatures of DHH is scarce. Herein, we compared the genomes of DHH and each of Diqing and Zhaotong cattle breeds using the population differentiation index (FST), cross‐population extended haplotype homozygosity (XP‐EHH) and cross‐population composite likelihood ratio (XP‐CLR) methods to explore the genomic signatures of heat tolerance and disease resistance in DHH. Several pathways and genes carried selection signatures, including thermal sweating (calcium signaling pathway), heat shock (HSF1) and oxidative stress response (PLCB1, PLCB4), coat color (RAB31), feed intake (ATP8A1, SHC3) and reproduction (TP63, MAP3K13, PTPN4, PPP3CC, ADAMTSL1, SS18L1, OSBPL2, TOX, RREB1, GRK2). These identified pathways and genes may contribute to heat tolerance in DHH. Simultaneously, we also identified LIPH, TP63 and CBFA2T3 genes under positive selection that were associated with immunity.

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Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations

Cited by 43 publications

References 52 publications

Genomic selection signatures in sheep from the Western Pyrenees

Genomic selection signatures in sheep from the Western Pyrenees

Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu

Genome‐wide scan of selection signatures in Dehong humped cattle for heat tolerance and disease resistance

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