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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 |