Whole-genome sequences of 89 Chinese sheep suggest role of <i>RXFP2</i> in the development of unique horn phenotype as response to semi-feralization

Pan, Zhangyuan; Li, Shengdi; Liu, Qiuyue; Wang, Zhen; Zhou, Zhengkui; Di, Ran; Miao, Benpeng; Hu, Wenping; Wang, Xiangyu; Hu, Xiaoxiang; Xu, Ze; Wei, Dongkai; He, Xiaoyun; Yuan, Liyun; Guo, Xiaofei; Liang, Benmeng; Wang, Ruichao; Li, Xiaoyü; Cao, Xiaohan; Dong, Xinlong; Xia, Qing; H, Shi; Geng, Hao; Yang, Jean Yee Hwa; Luosang, Cuicheng; Zhao, Yaofeng; Jin, Mei; Zhang, Yingjie; Lv, Shenjin; Li, Fukuan; Ding, Guohui; Chu, Mingxing; Li, Yixue

doi:10.1093/gigascience/giy019

Cited by 93 publications

(96 citation statements)

References 56 publications

(62 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…More importantly, relaxin-like receptor 2 (RXFP2) gene was harbored in this genomic region. The ROH hotspot region also overlapped the selective signatures in RXFP2 across many sheep breeds [27,32,[45][46][47][48]. GWAS results demonstrated that RXFP2 region was associated with horn phenotype in sheep [49].…”

Section: Discussionmentioning

confidence: 80%

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

Jiang

Han

et al. 2020

Animals

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionmentioning

confidence: 80%

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

Jiang

Han

et al. 2020

Animals

View full text Add to dashboard Cite

show abstract

“…By contrast, in Southeast Asia, shattering in weedy rice is caused at least in part by adaptive introgression of wild alleles at sh4 [98]. Finally, in feral chickens and sheep [50,51], genome scans found only limited overlap between outlier loci (i.e., candidate 'feralization loci'), and genome regions that are known to have evolved under domestication. Altogether, these examples show that, at the genetic level, domestication-related changes are not predictably reversed by feralization.…”

Section: How Do Gene 3 Environment Relationships Influence Feralization?mentioning

confidence: 96%

“…Several methods are available for assessing how admixture affects fitness in feral populations, including: (i) direct measurements of growth, survival, reproduction, and health in hybrids; (ii) functional analyses of outlier loci detected in genome scans (e.g., [50,51]); and (iii) experimental tests of the effects of these loci in laboratory systems (e.g., [50]). In recipient wild populations of fish, these approaches often find outbreeding depression (e.g., [52,53]).…”

Section: Fitness Consequences Of Admixturementioning

confidence: 99%

Getting Back to Nature: Feralization in Animals and Plants

Gering

Incorvaia

Henriksen

et al. 2019

Trends in Ecology & Evolution

View full text Add to dashboard Cite

Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how 'domestication genes' act in wild settings, studying the brains and behaviors of feral animals, and comparative analyses of feral populations and taxa. This work offers feasible and exciting research opportunities with both theoretical and practical applications. Domestication Is Not a Dead EndDomesticated animals and plants comprise a rapidly growing proportion of life on our planet [1]. The vast ranges and abundance of these organisms show that domestication (see Glossary) can have remarkable evolutionary payoffs. At the same time, it can induce both plastic and genetic modifications that limit the capacity of an organism to thrive in nature (e.g., [2][3][4]). Despite this maladaptation, feralization of animals and plants has proven, sometimes to humans' great frustration, that domestication is not always a one-way process. The flow of domesticated organisms and their genes into noncaptive settings has important conservation implications; it also presents unique opportunities to characterize general and novel evolutionary processes of Anthropocene environments [5]. With these applications in mind, our review summarizes current knowledge regarding the process of feralization and provides a roadmap for further investigation into this tractable, exciting, and understudied research area.Feralization merits special consideration because its subjects are uniquely distinguished from other animals and plants. Biologists have long appreciated how domestication shapes wild organisms via both deliberate artificial selection by humans and unintended effects of anthropogenic propagation [6]. In recent decades, these effects have been elucidated by intensive studies bridging disparate fields (e.g., anthropology, plant and animal science, and organismal, behavioral, and developmental biology) [7][8][9]. By contrast, there has been relatively little research into the process of feralization. Here, progress is also hindered by long-held speculations and misconceptions. These include: (i) the idea that formerly domesticated populations are incapable of rapid adaptation, due to their genetic homogeneity or recent establishment [10]; (ii) the idea that captive propagation invariably reduces fitness outside of domesticated settings due to evolutionary tradeoffs and relaxed natural selection (e.g., [2,11]); and (iii) a belief that feralization predictably results in atavism (e.g., [12]). These ideas hav...

show abstract

“…We downloaded a total of 52 sheep whole-genome sequencing data including 20 fattailed sheep of two breeds from Xinjiang, China, 15 improved thin-tailed sheep of seven breeds from Europe and 17 wild Mouflon sheep (Ovis orientalis) from the Middle East (Additional file 1: Table S1) [43,44]. Selective sweeps between these thin-or fat-tailed sheep breeds and Mouflon sheep populations were scanned using a genome-wide sliding window strategy based on the SNPs with less than 10% missing data [45].…”

Section: Selective Sweeps Analysismentioning

confidence: 99%

Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

Shao¹,

He²,

Pan³

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: The thin-tailed sheep breeds from Europe and the fat-tailed sheep breeds from China exhibit distinct phenotypic differences in fat deposition and meat production traits. However, the molecular mechanisms underlying gene expression related to these phenotypic differences are not well understood. Allele-specific expression (ASE) refers to the significant imbalance of expression levels of two parental alleles. Characterization of such events in F1 hybrid offspring generated from these two groups of sheep breeds can minimize the external factors influencing gene expression and reveal the variants with a cis -regulatory effect on gene expression. The aim of the present study was to investigate the genetic factors that influence different fat-deposition and meat production traits between thin- and fat-tailed sheep.Results: Fifteen F1 hybrids were generated from crosses between Texel and Kazakh sheep as the representative phenotypes of thin- and fat-tailed breeds, respectively. Totally, 33 whole genomes from F1 individuals and their parents were sequenced with an average depth of ~17.21× coverage per sample. ASE analysis results from 70 RNA-seq samples of adipose and skeleton muscle tissues showed 128 ASE candidate genes were related to the function of fat deposition and meat production traits. A genome-wide scan of selective sweeps was also conducted between these two groups of sheep breeds in an effort to identify genomic regions related to fat deposition and meat production, respectively. We detected signatures of selection in ASE genes associated with fat deposition (e.g., PDGFD ) and meat production traits (e.g., LRCC2 ). Further analysis suggested that PDGFD and LRCC2 genes were speculated to be causative genes for fat deposition and meat production traits in sheep, respectively. Furthermore, AMPK signaling pathway was significantly enriched in ASE genes related to fatty acid biosynthesis in both adipose and skeleton muscle tissues, while PPAR signaling pathway was significantly enriched in ASE genes related to lipid metabolism in adipose tissue. Conclusions: Our finding illustrates that the expression of identified ASE genes could potentially lead to the differences in traits of fat deposition and meat production between thin- and fat-tailed sheep. Keywords: allele-specific expression, phenotypic difference, thin- and fat-tailed sheep, whole-genome sequencing, transcriptome

show abstract

Whole-genome sequences of 89 Chinese sheep suggest role of RXFP2 in the development of unique horn phenotype as response to semi-feralization

Cited by 93 publications

References 56 publications

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

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

Getting Back to Nature: Feralization in Animals and Plants

Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

Contact Info

Product

Resources

About