Multi-Thoracolumbar Variations and NR6A1 Gene Polymorphisms Potentially Associated with Body Size and Carcass Traits of Dezhou Donkey

Abstract

The number of thoracolumbar vertebrae is a quantitative trait positively correlated with the economic traits of livestock. More thoracolumbar vertebrae individuals could genetically be used to improve the livestock population, as more thoracolumbar vertebrae means a longer carcass, which could bring more meat production. Nuclear receptor subfamily 6 group A member 1 (NR6A1) is considered a strong candidate gene for effecting the number of vertebrae in livestock. The purposes of this study are as follows: (a) Analyzing the effect of TLN variation on body size and carcass traits of Dezhou donkey; (b) Studying the distribution of seven single nucleotide variants (SNVs) in NR6A1 gene of Dezhou donkey; (c) Exploring the relationship between latent SNVs and TLN, the body size and carcass traits. We examined the thoracic and lumbar vertebrae number and seven SNVs in NR6A1 gene of 455 Dezhou donkeys, and analyzed the relationships between them. Five types of thoracolumbar combinations (T17L5 (individual with 17 thoracic and five lumbar vertebrae) 2.4%, T18L5 75.8%, T19L5 1.1%, T17L6 11.9%, and T18L6 8.8%) of Dezhou donkeys were detected in this study. For one thoracolumbar vertebra added, the body length of Dezhou donkey increases by 3 cm and the carcass weight increases by 6 kg. Seven SNVs (g.18093100G > T, g.18094587G > T, g.18106043G > T, g.18108764G > T, g.18110615T > G, g.18112000C > T and g.18114954T > G) of the NR6A1 gene were found to have a significant association with the TLN, body size and carcass traits of Dezhou donkey (p < 0.05), respectively. For instance, g.18114954C > T is significantly associated with lumber vertebrae number, the total number of thoracolumbar, and carcass weight, and individuals with TT genotype had significantly larger value than CC genotype (p < 0.05). Using these 7SNVs, 16 different haplotypes were estimated. Compared to Hap3Hap3, individuals homozygous for Hap2Hap2 showed significantly longer length in one thoracic spine (STL), the total thoracic vertebrae and one thoracolumbar spine. Our study will not only extend the understanding of genetic variation in the NR6A1 gene of Dezhou donkey, but also provide useful information for marker assisted selection in donkey breeding program.

Association of HOXC8 Genetic Polymorphisms with Multi-Vertebral Number and Carcass Weight in Dezhou Donkey

“…The g.15179224C>T and g.15179674G>A sites may alter the binding of shear factor binding proteins to target sequences, leading to the appearance of phenotypic variants. Furthermore, the association of the HOXC8 gene with CW in Dezhou donkeys might be related to adipose differentiation and lipid deposition during livestock development and the regulation of LL and LN by the HOXC8 gene [ 18 , 44 , 45 ]. The correlation of the HOXC8 gene with LL and LN was possibly attributed to the differential expression of the HOXC8 gene during skeletal differentiation.…”

“…Based on our previous studies, it has been confirmed that gene single nucleotide polymorphisms do cause changes in body size, vertebrae number, and production performance in Dezhou donkeys. For example, the nuclear receptor subfamily 6 group A member 1 ( NR6A1 ) g.18114954C>T can significantly increase the number of lumbar vertebrae, the total number of thoracolumbar vertebrae, and carcass weight in Dezhou donkeys, which can be a candidate gene to explore the genetic mutation affecting vertebral development [ 18 ]. However, the research is not sufficient and more genes need to be examined to screen for more molecular markers to accelerate the selection process of new strains of Dezhou donkeys.…”

A Novel A > G Polymorphism in the Intron 1 of LCORL Gene Is Significantly Associated with Hide Weight and Body Size in Dezhou Donkey

“…Hide weight was weighted immediately after slaughter. Blood samples were collected from the jugular vein using EDTA blood collection tubes and immediately stored in a −20 °C refrigerator [ 17 ].…”

“…The 396 genomic DNA samples of Dezhou donkeys were extracted from whole blood with the M5 FlexGen Blood DNA kit (TIANGEN, Beijing, China) [ 17 ]. Then, DNA purity (OD 260 /OD 280 ) was detected using a spectrophotometer (B500, Metash, Shanghai, China) and the quantity of extracted genomic DNA was detected by 1% agarose gel [ 18 ].…”

“…The PCR amplification system consisted of 25 μL, including 12.5 μL PCR Mix (Mei5bio, Beijing, China), 8.5 μL ddH 2 O, 1 μL forward primer (Sangon Biotech, Shanghai, China), 1 μL reverse primer (Sangon Biotech, Shanghai, China) and 2 μL genomic DNA. The cycling parameters were as follows: 95 °C for 5 min, 30 cycles of denaturing at 95 °C for 30 s, annealing at 58 °C for 30 s and extension at 72 °C for 30 s, with a final extension at 72 °C for 10 min [ 17 ]. The PCR products were tested for specificity using 2% agarose gel, and those with specificity and correct fragment size were randomly screened 1 sample per genotype, and the samples were sent to BGI Genomics Co., Ltd. (Shenzhen, China) for Sanger sequencing.…”