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Research Paper

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

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Pages 42-53 | Received 25 Sep 2017, Accepted 10 Nov 2017, Published online: 02 Feb 2018
 

ABSTRACT

Prion protein (PRNP) gene is well known for affecting mammal transmissible spongiform encephalopathies (TSE), and is also reported to regulate phenotypic traits (e.g. growth traits) in healthy ruminants. To identify the insertion/deletion (indel) variations of the PRNP gene and evaluate their effects on growth traits, 768 healthy individuals from five sheep breeds located in China and Mongolia were identified and analyzed. Herein, four novel indel polymorphisms, namely, Intron-1-insertion-7bp (I1-7bp), Intron-2-insertion-15bp (I2-15bp), Intron-2-insertion-19bp (I2-19bp), and 3′ UTR-insertion-7bp (3′ UTR-7bp), were found in the sheep PRNP gene. In five analyzed breeds, the minor allelic frequencies (MAF) of the above indels were in the range of 0.008 to 0.986 (I1-7bp), 0.113 to 0.336 (I2-15bp), 0.281 to 0.510 (I2-19bp), and 0.040 to 0.238 (3′ UTR-7bp). Additionally, there were 15 haplotypes and the haplotype ‘II2-15bp-D3’UTR-7bp-DI2-19bp-DI1-7bp’ had the highest frequency, which varied from 0.464 to 0.629 in five breeds. Moreover, association analysis revealed that all novel indel polymorphisms were significantly associated with 13 different growth traits (P < 0.05). Particularly, the influences of I2-15bp on chest width (P = 0.001) in Small Tail Han sheep (ewe), 3′ UTR-7bp on chest circumference (P = 0.003) in Hu sheep, and I2-19bp on tail length (P = 0.001) in Tong sheep, were highly significant (P < 0.01). These findings may be a further step toward the detection of indel-based typing within and across sheep breeds, and of promising target loci for accelerating the progress of marker-assisted selection in sheep breeding.

Disclosure of potential conflicts of interest

The authors certify that there is no conflict of interest with any financial organization regarding the material discussed in the manuscript.

Financial disclosure statements

The study was funded by the National Natural Science Foundation of China (No.31660642), Natural Science Foundation of Gansu Province (No.1610RJZA103), and Central Special Funds for Basic Research in Universities Operating Expenses of “An Excellent and Three Special” Discipline Construction (No.31920170170). We greatly thanked the staffs of TS Elite Reservation Farm (Baishui county, Shannxi Province), Ruilin Sci-Tech Culture and Breeding Limit Company (Yongjing county, Gansu Province), Shanshan Agriculture and Animal Husbandry Sci-tech Company (Mengjin county, Henan Province), and Zhawkhan Tsum Sureg Farm, (Tsagann Khairkhan Sum, Zhawkhan Province, Mongolia) for collecting samples.

Abbreviations

BBH=

body back height

BH=

body height

BL=

body length

BLI=

body length index

BW=

body weight

CaC=

cannon circumference

CaCI=

cannon circumference index

ChC=

chest circumference

ChCI=

chest circumference index

ChW=

chest width

ChWI=

chest width index

DD=

deletion/deletion

He=

heterozygosity

HL=

head length

Ho=

homozygosity

HS=

Hu sheep

HWE=

Hardy-Weinberg equilibrium

ID=

insertion/deletion

II=

insertion/insertion

indel=

insertion/deletion

I1-7 bp=

Intron-1-insertion-7 bp

I2-15 bp=

Intron-2-insertion-15 bp

I2-19 bp=

Intron-2-insertion-19 bp

LFTS=

Lanzhou Fat-Tail sheep

MAS=

application of marker assisted selection

ME=

mathematical expectation

ORF=

open reading frame

PCR=

polymerase chain reaction

PIC=

Polymorphism information content

PRND=

prion-related doppel gene

PRNP,=

Prion protein gene

PrPc=

prion protein

SH=

sacral height

SNPs=

single nucleotide polymorphisms

SS=

Sartuul sheep

STHS=

Small Tail Han sheep

TL=

tail length

TS=

Tong sheep

TSE=

transmissible spongiform encephalopathies

WL=

wool length.

3′ UTR=

3′ untranslated region

3′ UTR-7 bp=

3′ UTR-insertion-7 bp

Additional information

Funding

National Natural Science Foundation of China (NSFC) (No.31660642). Central Special Funds for Basic Research in Universities Operating Expenses of An Excellent and Three Special Discipline Construction (No.31920170170). Natural Science Foundation of Gansu Province (No.1610RJZA103).

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