Genetic effects of <i>PRNP</i> gene insertion/deletion (indel) on phenotypic traits in sheep

Li, Jie; Erdenee, Sarantsetseg; Zhang, Shaoli; Wei, Zhiyan; Zhang, Meng; Jin, Yunyun; Wu, Hui; Chen, Hong; Sun, Xiuzhu; Xu, Hongwei; Cai, Yong; Lan, Xianyong

doi:10.1080/19336896.2017.1405886

Cited by 34 publications

(16 citation statements)

References 52 publications

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“…The breed is now in peril of extinction because of human activity, climatic variation and destruction of its natural habitat (Li et al . , ). The fat tail, a valuable energy reserve characteristic of this breed, is considered an adaptive response to the harsh challenges of desert life and severe winters when pasture is scarce (Atti et al .…”

Section: Number Of Snps Identified From Three Sheep Breeds Using Rna‐mentioning

confidence: 99%

Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

Cai

et al. 2018

Animal Genetics

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The identification of genetic variations underlying desired phenotypes is one of the main challenges of current livestock genetic research. High-throughput transcriptome sequencing has been recognized as an efficient way to unravel the rich genetic variants across various species. The Lanzhou Fat-Tail sheep is an endangered sheep breed in China with a notable feature of an exaggerated fat tail that also independently occurs in other sheep breeds. However, the genetic mechanism underlying this particular trait has not been fully elucidated yet. In this study, we used RNA-seq on tissue samples (longissimus dorsi muscle, perinephric fat and tail fat) from three sheep breeds with either fat or thin tails and characterized the genetic variation in Lanzhou Fat-Tail sheep with the ultimate goal of identifying the causal genes and genetic networks responsible for the fat tail in this rare sheep breed. In total, 7 122 920 SNPs and 901 518 indels were detected in the nine individual sheep investigated, of which 606 952 SNPs (8.5%) and 77 633 indels (8.6%) overlapped with QTL associated with fat traits in sheep. Furthermore, we detected 26 613 specific SNPs in Lanzhou Fat-Tail sheep and 44 SNPs located in the same genomic position reported in another sheep breed with fat tails. Interestingly, 33 SNPs are selectively distributed on a chromosome 3 region (39.58-40.91 Mb) that was reported as a strong candidate genomic region for fat deposition in tails of sheep. Our research has also suggested that three genes (CREB1, WDR92 and ETAA1) may be associated with fat tail development. In summary, the resultant genetic variants data in this study provide a valuable resource for marker-assisted selection of the trait in Lanzhou Fat-Tail sheep populations.

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Section: Number Of Snps Identified From Three Sheep Breeds Using Rna‐mentioning

confidence: 99%

Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

Cai

et al. 2018

Animal Genetics

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“…Our previous work identified the significant relationship between ovine growth performance and polymorphisms in PRND [6] or PRNP [11]. Herein, polymorphisms of the homologous gene PRNT were also found be strongly correlated with sheep growth traits.…”

Section: Discussionmentioning

confidence: 82%

“…For insertion/deletion mutations of ovine PRNP, polymorphisms of intron-2-insertion-15 bp were significantly associated with chest width in Small Tail Han sheep (ewe). Additionally, correlations of 3 0 -UTR-insertion-7 bp on chest circumference in Hu sheep and intron-2-insertion-19 bp on tail length in Tong sheep were highly significant (P 0.001) [11]. However, to date, available data for East Asian sheep breeds and PRNT polymorphisms have been limited and no study has examined the effect of these polymorphisms on ovine phenotypic traits.…”

Section: Introductionmentioning

confidence: 99%

“…Moreover, previous work developed by our group [6] identified significant associations between novel 20 bp insertion/deletion (indel) polymorphisms in PRND with the cannon circumference index and trunk index in Chinese Hu sheep. Moreover, considering the linkage of PRND and its homologous gene, PRNP [7][8], our previous work also explored high rate of polymorphic mutations in PRNP and whether these were correlated with growth traits in Chinese cattle [9][10] or native sheep [11]. For insertion/deletion mutations of ovine PRNP, polymorphisms of intron-2-insertion-15 bp were significantly associated with chest width in Small Tail Han sheep (ewe).…”

Section: Introductionmentioning

confidence: 99%

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Nucleotide variants in prion-related protein (testis-specific) gene (PRNT) and effects on Chinese and Mongolian sheep phenotypes

Zhang

Erdenee

et al. 2018

Prion

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Studies of the ovine prion-related protein (testis-specific) gene (PRNT), including studies of genetic diversity, have highlighted its potential relationship to scrapie infection and economically important ovine traits. PRNT was previously reported to be highly polymorphic in Portuguese sheep. To characterize genetic polymorphisms in this gene in Asian sheep, a direct sequencing method was used to detect polymorphic loci in PRNT in 285 individual sheep from four Chinese and one Mongolian breeds. Seven SNP variants in PRNT were identified, including three novel variants (g.93G>A, g.162G>T, and g.190A>G) and four previously reported variants (g.17 C>T, g.112G>C, g.129C>T, and g.144A>G). In the five breeds that we analyzed, the mutation frequencies of g.190A>G in Lanzhou Fat-tail sheep (LFTS) and g.129C>T in the other four varieties were high (F>0.5). Moreover, thirteen different haplotypes that had a comparable distribution in the tested breeds were also identified; 'C-G-G-C-A-G-A' occurred at the highest frequency in the five sheep breeds. Additionally, we previously explored the significance of relationships between polymorphisms in PRNP or PRND and ovine growth performance. Here, we also performed correlation analysis in all tested loci. These loci polymorphisms were significantly associated with ten different growth traits (P<0.05), except for g.93G>A. Meanwhile, in contrast to a previous study, there was no significant association between the seven SNP loci analyzed and our previously reported sheep PRND or PRNP insertion/deletion mutations. Our findings may provide new insights into polymorphic variation in ovine PRNT, which may contribute to genetic improvements in economic traits that are important for sheep breeding.

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“…Distribution differences, for genotypic frequencies, between the mothers of a single kid and multiple kids were analyzed by χ 2 test (Li et al, 2018). The association of indel polymorphism with several traits was measured.…”

Section: Discussionmentioning

confidence: 99%

The novel 22 bp insertion mutation in a promoter region of the <i>PITX2</i> gene is associated with litter size and growth traits in goats

et al. 2018

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Abstract. The paired-like homeodomain 2 (PITX2) gene plays a critical role in regulating development, reproduction, and growth traits in ruminants. Hence, the objective of this study was to explore the polymorphisms of this gene and to evaluate their associations with quantitative traits. Herein, a novel insertion in the promoter region of the PITX2 gene was reported in Shaanbei white cashmere (SBWC) goats (n = 1012). The genotype distributions between mothers of single-kid and multi-kid groups within SBWC goats were significantly different (P < 0.01), implying that this indel mutation might affect the litter size. Furthermore, association analysis found that this indel mutation was significantly associated with litter size (P = 0.001). Individuals with genotype DD had a significantly smaller litter size than those with other genotypes (P < 0.01). Besides, this indel was significantly associated with the body length (P = 0.042) and the chest width (P = 0.031). Especially, the individuals with genotype DD had a significantly lower body length than those with genotype II (P < 0.05), which was consistent with the trend in litter size. These findings suggested that the new 22 bp indel mutation within the PITX2 gene is significantly associated with litter size and growth traits; this can be utilized as a functional molecular marker in goat breeding.

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Genetic effects of PRNP gene insertion/deletion (indel) on phenotypic traits in sheep

Cited by 34 publications

References 52 publications

Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

Nucleotide variants in prion-related protein (testis-specific) gene (PRNT) and effects on Chinese and Mongolian sheep phenotypes

The novel 22 bp insertion mutation in a promoter region of the <i>PITX2</i> gene is associated with litter size and growth traits in goats

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Genetic effects of PRNP gene insertion/deletion (indel) on phenotypic traits in sheep

Cited by 34 publications

References 52 publications

Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

Genetic variants in fat‐ and short‐tailed sheep from high‐throughput RNA‐sequencing data

Nucleotide variants in prion-related protein (testis-specific) gene (PRNT) and effects on Chinese and Mongolian sheep phenotypes

The novel 22 bp insertion mutation in a promoter region of the &lt;i&gt;PITX2&lt;/i&gt; gene is associated with litter size and growth traits in goats

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The novel 22 bp insertion mutation in a promoter region of the <i>PITX2</i> gene is associated with litter size and growth traits in goats