Association of polymorphisms in NR6A1, PLAG1 and VRTN with the number of vertebrae in Chinese Tongcheng × Large White crossbred pigs

Whole-genome sequencing reveals genomic diversity and selection signatures in Xia'nan cattle

BACKGROUND

The crossbreeding of specialized beef cattle breeds with Chinese indigenous cattle is a common method of genetic improvement. Xia'nan cattle, a crossbreed of Charolais and Nanyang cattle, is China's first specialized beef cattle breed with independent intellectual property rights. After more than two decades of selective breeding, Xia'nan cattle exhibit a robust physique, good environmental adaptability, good tolerance to coarse feed, and high meat production rates. This study analyzed the population genetic structure, genetic diversity, and genomic variations of Xia'nan cattle using whole-genome sequencing data from 30 Xia'nan cattle and 178 published cattle genomic data.

RESULT

The ancestry estimating composition analysis showed that the ancestry proportions for Xia'nan cattle were mainly Charolais with a small amount of Nanyang cattle. Through the genetic diversity studies (nucleotide diversity and linkage disequilibrium decay), we found that the genomic diversity of Xia'nan cattle is higher than that of specialized beef cattle breeds in Europe but lower than that of Chinese native cattle. Then, we used four methods to detect genome candidate regions influencing the excellent traits of Xia'nan cattle. Among the detected results, 42 genes (θπ and CLR) and 131 genes (FST and XP-EHH) were detected by two different detection strategies. In addition, we found a region in BTA8 with strong selection signals. Finally, we conducted functional annotation on the detected genes and found that these genes may influence body development (NR6A1), meat quality traits (MCCC1), growth traits (WSCD1, TMEM68, MFN1, NCKAP5), and immunity (IL11RA, CNTFR, CCL27, SLAMF1, SLAMF7, NAA35, and GOLM1).

CONCLUSION

We elucidated the genomic features and population structure of Xia'nan cattle and detected some selection signals in genomic regions potentially associated with crucial economic traits in Xia'nan cattle. This research provided a basis for further breeding improvements in Xia'nan cattle and served as a reference for genetic enhancements in other crossbreed cattle.

Genomic background of biotypes related to growth, carcass and meat quality traits in Duroc pigs based on principal component analysis

As the swine industry continues to explore pork quality traits alongside growth, feed efficiency and carcass leanness traits, it becomes imperative to understand their underlying genetic relationships. Due to this increase in the number of desirable traits, animal breeders must also consider methods to efficiently perform direct genetic changes for each trait and evaluate alternative selection indexes with different sets of phenotypic measurements. Principal component analysis (PCA) and genome-wide association studies (GWAS) can be combined to understand the genetic architecture and biological mechanisms by defining biological types (biotypes) that relate these valuable traits. Therefore, the main objectives of this study were to: (1) estimate genomic-based genetic parameters; (2) define animal biotypes utilizing PCA; and (3) utilize GWAS to link the biotypes to candidate genes and quantitative trait loci (QTL). The phenotypic dataset included 2583 phenotypic records from female Duroc pigs from a terminal sire line. The pedigree file contained 193,764 animals and the genotype file included 21,309 animals with 35,651 single nucleotide polymorphisms (SNPs). Eight principal components (PCs), accounting for a total of 99.7% of the population variation, were defined for three growth, eight conventional carcass, 10 pork quality and 18 novel carcass traits. The eight biotypes defined from the PCs were found to be related to growth rate, maturity, meat quality and body structure, which were then related to candidate genes. Of the 175 candidate genes found, six of them [LDHA (SSC1), PIK3C3 (SSC6), PRKAG3 (SSC15), VRTN (SSC7), DLST (SSC7) and PAPPA (SSC1)] related to four PCs were found to be associated with previously defined QTL, linking the biotypes with biological processes involved with muscle growth, fat deposition, glycogen levels and skeletal development. Further functional analyses helped to make connections between biotypes, relating them through common KEGG pathways and gene ontology (GO) terms. These findings contribute to a better understanding of the genetic relationships between growth, carcass and meat quality traits in Duroc pigs, enabling breeders to better understand the biological mechanisms underlying the phenotypic expression of these traits.

Genome-wide association study using a single-step approach for teat number in Duroc, Landrace and Yorkshire pigs in Korea

We investigated the genetic basis of teat number in sows, which is an important factor in their reproductive performance. We collected genotyping data from 20 353 pigs of three breeds (Duroc, Landrace and Yorkshire) using the Porcine SNP60K Bead Chip, and analyzed phenotypic data from 240 603 pigs. The heritability values of total teat number were 0.33 ± 0.02, 0.51 ± 0.01 and 0.50 ± 0.01 in Duroc, Landrace and Yorkshire pigs, respectively. A genome-wide association study was used to identify significant chromosomal regions associated with teat number in SSC7 and SSC9 in Duroc pig, SSC3, SSC7 and SSC18 in Landrace pig, and SSC7, SSC8 and SSC10 in Yorkshire pig. Among the markers, MARC0038565, located between the vertnin (VRTN) and synapse differentiation-inducing 1-like (SYNDIG1L) genes, showed the strongest association in the Duroc pig and was significant in all breeds. In Landrace and Yorkshire pigs, the most significant markers were located within the apoptosis resistant E3 ubiquitin protein ligase 1 (AREL1) and latent transforming growth factor beta-binding protein 2 (LTBP2) genes in SSC7, respectively. VRTN is a candidate gene regulating the teat number. Most markers were located in SSC7, indicating their significance in determining teat number and their potential as valuable genomic selection targets for improving this trait. Extensive linkage disequilibrium blocks were identified in SSC7, supporting their use in genomic selection strategies. Our study provides valuable insights into the genetic architecture of teat numbers in pigs, and helps identify candidate genes and genomic regions that may contribute to this economically important trait.

Goat Pleomorphic Adenoma Gene 1 (PLAG1): mRNA Expression, CNV Detection and Associations with Growth Traits

The pleomorphic adenoma gene 1 (PLAG1) gene, as the major gene responsible for growth, plays a vital role in myogenesis. Meanwhile, the relationship between copy number variation (CNV) of this gene and growth traits in goats remains unclear. Therefore, this study investigated four aspects: bioinformatics analysis, mRNA expression (n = 6), CNV detection (n = 224), and association analysis. The findings indicated that the gene had a large number of conserved motifs, and the gene expression level was higher in fetal goats than in adult goats. Three CNV loci were selected from the database, among which CNV1 was located in the bidirectional promoter region and was associated with goat growth traits. CNV analysis showed that CNV2 and CNV3 of the PLAG1 gene were associated with growth traits such as body weight, heart girth, height at hip cross, and hip width (p < 0.05), with CNV1 loss genotype being the superior genotype, and CNV2 and CNV3 median and gain genotypes of being superior genotypes. This finding further confirms that the PLAG1 gene is the dominant gene for growth traits, which will serve as theoretical guidance for goat breeding.

PLAG1 g.8795C>T Mutation Regulates Early Body Weight in Hu Sheep by Weakening miR-139 Binding

Sheep birth and weaning weights indicate their growth and survival. Thus, identifying molecular genetic markers for early body weight is important in sheep breeding. Pleomorphic adenoma gene 1 (PLAG1) is important for regulating birth weight and body length in mammals; however, its relationship with sheep body weight remains unknown. Here, the 3'-untranslated region (3'-UTR) of the Hu sheep PLAG1 gene was cloned, single nucleotide polymorphisms (SNPs) were screened, genotype-early body weight relationships were analyzed, and the possible molecular mechanism was explored. PLAG1 3'-UTR sequences with five forms of base sequences plus poly(A) tails were detected in Hu sheep and the g.8795C>T mutation was identified. Luciferase reporter assay indicated that the g.8795C>T mutation influenced PLAG1 post-transcriptional activity. miRBase prediction showed that the g.8795C>T mutation was located in the miR-139 seed sequence binding region, and miR-139 overexpression significantly decreased both PLAG1-CC and PLAG1-TT activities. Moreover, the luciferase activity of PLAG1-CC was significantly lower than that of the PLAG1-TT, but miR-139 inhibition substantially increased both PLAG1-CC and PLAG1-TT luciferase activities, suggesting that PLAG1 is the target gene of miR-139. Thus, the g.8795C>T mutation upregulates PLAG1 expression by weakening its binding with miR-139, promoting PLAG1 expression, and increasing Hu sheep birth and weaning weights.

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

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.

A further survey of the quantitative trait loci affecting swine body size and carcass traits in five related pig populations

Breeding for good meat quality performance while maintaining large body size and desirable carcass traits has been the major challenge for modern swine selective breeding. To address this goal, in the present work we studied five related populations produced by two commercial breeds (Berkshire and Duroc) and two Chinese breeds (Licha black pig and Lulai black pig). A single-trait GWAS performed on 20 body size and carcass traits using a self-developed China Chip-1 porcine SNP50K BeadChip identified 11 genome-wide significant QTL on nine chromosomes and 22 suggestive QTL on 15 chromosomes. For the 11 genome-wide significant QTL, eight were detected in at least two populations, and the rest were population-specific and only mapped in Shanxia black pig. Most of the genome-wide significant QTL were pleiotropic; for example, the QTL around 75.65 Mb on SSC4 was associated with four traits at genome-wide significance level. After screening the genes within 50 kb of the top SNP for each genome-wide significant QTL, NR6A1 and VRTN were chosen as candidate genes for vertebrae number; PLAG1 and BMP2 were identified as candidate genes for body size; and MC4R was the strong candidate gene for body weight. The four genes have been reported as candidates for thoracic vertebrae number, lumbar vertebrae number, carcass length and body weight respectively in previous studies. The effects of VRTN on thoracic vertebrae number, carcass length and body length have been verified in Shanxia black pig. Therefore, the VRTN genotype could be used in gene-assisted selection, and this could accelerate genetic improvement of body size and carcass traits in Shanxia black pig.

Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies

Simple Summary

Number of teats is very important for lactating sows. We conducted genome-wide association studies (GWAS) and estimated the genetic parameters for traits related to teat number. Results showed that there were nine and 22 SNPs exceeding genome-wide significance and suggestive significance levels, respectively. Eighteen genes annotated near them were concentrated on chromosomes 7 and 10. Among them, three new candidate genes were located on the genomic regions around the significant SNPs. Our findings provide new insight into investigating the complex genetic mechanism of traits related to teat number in pigs.

Abstract

The number of teats is related to the nursing ability of sows. In the present study, we conducted genome-wide association studies (GWAS) for traits related to teat number in Duroc pig population. Two mixed models, one for counted and another for binary phenotypic traits, were employed to analyze seven traits: the right (RTN), left (LTN), and total (TTN) teat numbers; maximum teat number on a side (MAX); left minus right side teat number (LR); the absolute value of LR (ALR); and the presence of symmetry between left and right teat numbers (SLR). We identified 11, 1, 4, 13, and 9 significant SNPs associated with traits RTN, LTN, MAX, TTN, and SLR, respectively. One significant SNP (MARC0038565) was found to be simultaneous associated with RTN, LTN, MAX and TTN. Two annotated genes (VRTN and SYNDIG1L) were located in genomic region around this SNP. Three significant SNPs were shown to be associated with TTN, RTN and MAX traits. Seven significant SNPs were simultaneously detected in two traits of TTN and RTN. Other two SNPs were only identified in TTN. These 13 SNPs were clustered in the genomic region between 96.10—98.09 Mb on chromosome 7. Moreover, nine significant SNPs were shown to be significantly associated with SLR. In total, four and 22 SNPs surpassed genome-wide significance and suggestive significance levels, respectively. Among candidate genes annotated, eight genes have documented association with the teat number relevant traits. Out of them, DPF3 genes on Sus scrofa chromosome (SSC) 7 and the NRP1 gene on SSC 10 were new candidate genes identified in this study. Our findings demonstrate the genetic mechanism of teat number relevant traits and provide a reference to further improve reproductive performances in practical pig breeding programs.

Positive selection signatures in Anqing six-end-white pig population based on reduced-representation genome sequencing data

Anqing six-end-white (AQ) pig performs well on resistance to coarse fodder and disease, reproduction and meat quality, offering high potential for exploitation. Environmental conditions and strict selections from local farmers have cultivated the AQ pig to be an outstanding and unique local pig breed. Thus we aim to detect genetic positive selection signatures within the AQ pig population to explore underlying genetic mechanisms. A relative extended haplotype homozygosity (REHH) test was performed in the population of 79 AQ pigs to seek evidence demonstrating that selective actions have left an imprint on the whole genome. In total, 430 500 REHH tests were performed on 53 067 core regions with average REHH tests of 8.11, average lengths of 11.50 kb and an overall length of 610.38 Mb which accounted for 26.94% of the whole genome. Finally, a total of 1819 core haplotypes (P < 0.01) and 586 candidate genes were obtained. These genes were mainly related to meat quality (MYOG, SNX19), resistance to disease (CRISPLD2, CD14) and reproduction traits (ERBB2, NRP2). A panel of genes within the 30 top significant REHH tests was mainly categorized to traits of meat quality and disease resistance. Among 13 KEGG pathways, MAPK, GnRH and Oxytocin signaling pathways, associated with the biological processes of crucial economic traits, were noteworthy. The excellent characteristics of the AQ pig benefited from the combination of natural and human factors. We provide a sketch map that shows the distribution of selection footprints on the whole genome of AQ pig and found potential genes for future studies.

NR6A1 Allelic Frequencies as an Index for both Miniaturizing and Increasing Pig Body Size

BACKGROUND/AIM

The number of vertebrae in swine varies from 19 to 23 and is associated with body size. Nuclear receptor subfamily 6 group A member 1 (NR6A1) is considered a strong candidate for affecting the number of vertebrae in swine. Wild boars, which uniformly have 19 vertebrae, have the wild type allele while multi-vertebrae European commercial pigs have the mutated allele. Our aim was to confirm the factor of the miniaturization.

MATERIALS AND METHODS

We examined vertebrae number and NR6A1 polymorphism in the Microminipig and three domestic breeds that vary in body size.

RESULTS

The Microminipig had 19 or less vertebrae and a wild type NR6A1 genotype. Three domestic breeds had more than 21 vertebrae while the largest vertebrae number was observed in multi-vertebrae-fixed Large White. Heterozygous genotypes were observed in the middle-sized indigenous pig while homozygous NR6A1 mutations were observed in European commercial breeds.

CONCLUSION

NR6A1 could be a useful index for both miniaturizing and increasing pig body size.

Genome-Wide Association Analysis Identified BMPR1A as a Novel Candidate Gene Affecting the Number of Thoracic Vertebrae in a Large White × Minzhu Intercross Pig Population

Simple Summary

The number of thoracic vertebrae (NTV) and number of vertebrae (NV) varies among pig breeds with a high correlation of about 0.8. It is important to discover variants associated with the NTV by considering the effect of the NV in pig. The results suggest that regulation variants on SSC7 might play crucial roles in the NTV and the FOS on SSC7 should be further studied as a critical candidate gene. In addition, BMPR1A was identified as a novel candidate gene affecting the NTV in pigs.

Abstract

The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies on a fixed NV have mainly considered the absolute numbers of thoracic vertebrae instead of vertebral segmentation. Therefore, this study aimed to discover variants associated with the NTV by considering the effect of the NV in pigs. The NTV and NV of 542 F2 individuals from a Large White × Minzhu pig crossbreed were recorded. All animals were genotyped for VRTN g.19034 A > C, LTBP2 c.4481A > C, and 37 missense or splice variants previously reported in a 951-kb interval on SSC7 and 147 single nucleotide polymorphisms (SNPs) on SSC14. To identify NTV-associated SNPs, we firstly performed a genome-wide association study (GWAS) using the Q + K (population structure + kinship matrix) model in TASSEL. With the NV as a covariate, the obtained data were used to identify the SNPs with the most significant genome-wide association with the NTV by performing a GWAS on a PorcineSNP60K Genotyping BeadChip. Finally, a conditional GWAS was performed by fixing this SNP. The GWAS showed that 31 SNPs on SSC7 have significant genome-wide associations with the NTV. No missense or splice variants were found to be associated with the NTV significantly. A linkage disequilibrium analysis suggested the existence of quantitative trait loci (QTL) in a 479-Kb region on SSC7, which contained a critical candidate gene FOS for the NTV in pigs. Subsequently, a conditional GWAS was performed by fixing M1GA0010658, the most significant of these SNPs. Two SNPs in BMPR1A were found to have significant genome-wide associations and a significant dominant effect. The leading SNP, S14_87859370, accounted for 3.86% of the phenotypic variance. Our study uncovered that regulation variants in FOS on SSC7 and in BMPR1A on SSC14 might play important roles in controlling the NTV, and thus these genetic factors may be harnessed for increasing the NTV in pigs.

Polymorphism of VRTN Gene g.20311_20312ins291 Was Associated with the Number of Ribs, Carcass Diagonal Length and Cannon Bone Circumference in Suhuai Pigs

Simple Summary

An increase in the number of ribs (RIB) could improve carcass length (CL) and body size. Cannon bone circumference (CBC) is a pivotal body size trait, and a large CBC could enhance the capacity to bear excessive body weight, vigorous exercise, and resistance to injuries. Several researchers showed that the vertnin (VRTN) gene g.20311_20312ins291 (NC_010449.5 7: g.20311_20312ins291) is an important variant that is related to RIB and CL of Western pigs. However, it is unknown whether this variant could affect the CBC of pigs. Our study showed that this variant was significantly associated with RIB, carcass diagonal length (CDL), and CBC in Suhuai pigs; therefore, it could be used as a potential molecular marker for improving RIB, CDL, and CBC in this breed.

Abstract

The vertnin (VRTN) gene g.20311_20312ins291 was reported as an important variant related to the number of ribs (RIB), and the ins/ins genotype was advantageous for improving RIB of Western pigs. The purpose of this study was to determine whether the VRTN gene g.20311_20312ins291 influences RIB, carcass traits, and body size traits, including cannon bone circumference (CBC) in Chinese Suhuai pigs. We found that the VRTN gene g.20311_20312ins291 was polymorphic in Suhuai fattening pigs and gilts. The polymorphism of g.20311_20312ins291 was significantly associated with RIB and CDL in Suhuai fattening pigs (p < 0.01), whereas this variant had no influence on carcass weight (CWT). There was a tendency of association between this variant and carcass straight length (CSL) in Suhuai fattening pigs (p = 0.06). The polymorphism of g.20311_20312ins291 was also significantly associated with CBC in Suhuai gilts (p = 0.04). Furthermore, CBC was positively genetically correlated with body length (0.22, p < 0.01) and body weight (0.15, p < 0.01). Our results indicated that the VRTN gene g.20311_20312ins291 could be used as a potential marker for improving RIB, CDL, and CBC in Suhuai pigs.

GWAS on Imputed Whole-Genome Resequencing From Genotyping-by-Sequencing Data for Farrowing Interval of Different Parities in Pigs

The whole-genome sequencing (WGS) data can potentially discover all genetic variants. Studies have shown the power of WGS for genome-wide association study (GWAS) lies in the ability to identify quantitative trait loci and nucleotides (QTNs). However, the resequencing of thousands of target individuals is expensive. Genotype imputation is a powerful approach for WGS and to identify causal mutations. This study aimed to evaluate the imputation accuracy from genotyping-by-sequencing (GBS) to WGS in two pig breeds using a resequencing reference population and to detect single-nucleotide polymorphisms (SNPs) and candidate genes for farrowing interval (FI) of different parities using the data before and after imputation for GWAS. Six hundred target pigs, 300 Landrace and 300 Large White pigs, were genotyped by GBS, and 60 reference pigs, 20 Landrace and 40 Large White pigs, were sequenced by whole-genome resequencing. Imputation for pigs was conducted using Beagle software. The average imputation accuracy (allelic R ²) from GBS to WGS was 0.42 for Landrace pigs and 0.45 for Large White pigs. For Landrace pigs (Large White pigs), 4,514,934 (5,533,290) SNPs had an accuracy >0.3, resulting an average accuracy of 0.73 (0.72), and 2,093,778 (2,468,645) SNPs had an accuracy >0.8, resulting an average accuracy of 0.94 (0.93). Association studies with data before and after imputation were performed for FI of different parities in two populations. Before imputation, 18 and 128 significant SNPs were detected for FI in Landrace and Large White pigs, respectively. After imputation, 125 and 27 significant SNPs were identified for dataset with an accuracy >0.3 and 0.8 in Large White pigs, and 113 and 18 SNPs were found among imputed sequence variants. Among these significant SNPs, six top SNPs were detected in both GBS data and imputed WGS data, namely, SSC2: 136127645, SSC5: 103426443, SSC6: 27811226, SSC10: 3609429, SSC14: 15199253, and SSC15: 150297519. Overall, many candidate genes could be involved in FI of different parities in pigs. Although imputation from GBS to WGS data resulted in a low imputation accuracy, association analyses with imputed WGS data were optimized to detect QTNs for complex trait. The obtained results provide new insight into genotype imputation, genetic architecture, and candidate genes for FI of different parities in Landrace and Large White pigs.

A Novel 13 bp Deletion within the NR6A1 Gene Is Significantly Associated with Growth Traits in Donkeys

Simple Summary

The detection of genes potentially associated with economic traits and identification of effective variants can provide a basis for molecular marker-assisted selection of livestock. NR6A1 is a member of the nuclear receptor family and is an important candidate gene related to body size traits. Previous studies showed that NR6A1 gene was associated with body size traits in pigs and other livestock, however, it has not yet been observed in donkeys. In the current study, a 13 bp deletion in NR6A1 gene was firstly identified in donkeys. Analysis showed that this deletion had significant associations with body size traits.

Abstract

Nuclear receptor subfamily 6, group A, member 1 (NR6A1), as an important member of the nuclear receptor family, plays an important role in regulating growth, metabolism, and differentiation of embryonic stem cells. For this reason, the NR6A1 gene is considered to be a promising candidate for economic traits and was found to be associated with body size traits in many livestock. However, no studies have been conducted on NR6A1 in donkeys so far. Thus, in this research, we focused on donkeys and identified a 13 bp deletion in intron-1 of the NR6A1 gene among 408 individuals from Guanzhong and Dezhou donkeys using polyacrylamide gel electrophoresis. Three genotypes were identified, namely II, ID, and DD. The association analysis indicated that the body lengths and body heights5f genotype II individuals were significantly different to those of genotype ID in Dezhou donkeys. Conclusively, the 13 bp deletion was associated with growth traits in both Guanzhong donkeys and Dezhou donkeys, indicating that the NR6A1 gene could be a possible candidate gene in marker-assisted selection for donkey breeding programs.