Between- and within-breed variations of spine characteristics in sheep

Whole-Genome Resequencing of Ujimqin Sheep Identifies Genes Associated with Vertebral Number

The number of vertebrae is a crucial economic trait that can significantly impact the carcass length and meat production in animals. However, our understanding of the quantitative trait loci (QTLs) and candidate genes associated with the vertebral number in sheep (Ovis aries) remains limited. To identify these candidate genes and QTLs, we collected 73 Ujimqin sheep with increased numbers of vertebrae (T13L7, T14L6, and T14L7) and 23 sheep with normal numbers of vertebrae (T13L6). Through high-throughput genome resequencing, we obtained a total of 24,130,801 effective single-nucleotide polymorphisms (SNPs). By conducting a selective-sweep analysis, we discovered that the most significantly selective region was located on chromosome 7. Within this region, we identified several genes, including VRTN, SYNDIG1L, LTBP2, and ABCD4, known to regulate the spinal development and morphology. Further, a genome-wide association study (GWAS) performed on sheep with increased and normal vertebral numbers confirmed that ABCD4 is a candidate gene for determining the number of vertebrae in sheep. Additionally, the most significant SNP on chromosome 7 was identified as a candidate QTL. Moreover, we detected two missense mutations in the ABCD4 gene; one of these mutations (Chr7: 89393414, C > T) at position 22 leads to the conversion of arginine (Arg) to glutamine (Gln), which is expected to negatively affect the protein's function. Notably, a transcriptome expression profile in mouse embryonic development revealed that ABCD4 is highly expressed during the critical period of vertebral formation (4.5-7.5 days). Our study highlights ABCD4 as a potential major gene influencing the number of vertebrae in Ujimqin sheep, with promising prospects for future genome-assisted breeding improvements in sheep.

Advancements in Genetic Marker Exploration for Livestock Vertebral Traits with a Focus on China

In livestock breeding, the number of vertebrae has gained significant attention due to its impact on carcass quality and quantity. Variations in vertebral traits have been observed across different animal species and breeds, with a strong correlation to growth and meat production. Furthermore, vertebral traits are classified as quantitative characteristics. Molecular marker techniques, such as marker-assisted selection (MAS), have emerged as efficient tools to identify genetic markers associated with vertebral traits. In the current review, we highlight some key potential genes and their polymorphisms that play pivotal roles in controlling vertebral traits (development, length, and number) in various livestock species, including pigs, donkeys, and sheep. Specific genetic variants within these genes have been linked to vertebral development, number, and length, offering valuable insights into the genetic mechanisms governing vertebral traits. This knowledge has significant implications for selective breeding strategies to enhance structural characteristics and meat quantity and quality in livestock, ultimately improving the efficiency and quality of the animal husbandry industry.

Identification of LTBP2 gene polymorphisms and their association with thoracolumbar vertebrae number, body size, and carcass traits in Dezhou donkeys

The number of thoracolumbar vertebrae in Dezhou donkeys varies from 22 to 24 and is associated with body size and carcass traits. In mammals, the latent transforming growth factor beta binding protein 2 (LTBP2) has been found to have some functions in the development of thoracolumbar vertebrae. The relationship between LTBP2 and TLN (the number of thoracolumbar vertebrae) of Dezhou donkeys is yet to be reported. The purposes of this study are as follows: 1) to quantify the effect of thoracolumbar vertebrae number variation of Dezhou donkeys on body size and carcass trait; 2) to study the distribution of single nucleotide variants (SNVs) in the LTBP2 gene of Dezhou donkeys; and 3) to explore whether these SNVs can be used as candidate sites to study the mechanism of Dezhou donkey muti-thoracolumbar vertebrae development. The TLN, body size, and carcass traits of 392 individuals from a Dezhou donkey breed were recorded. All animals were sequenced for LTBP2 using GBTS liquid chip and 16 SNVs were used for further analysis. We then analyzed the relationship between these SNVs with TLN, body size, and carcass traits. The results showed that: 1) c.5547 + 860 C > T, c.5251 + 281 A > C, c.3769 + 40 C > T, and c.2782 + 3975 A > G were complete genetic linkages and significantly associated with thoracic vertebrae number (TN) (p < 0.05) (wild-type homozygotes had more TN than heterozygotes); 2) c.1381 + 768 T > G and c.1381 + 763 G > T were significantly associated with lumber vertebrae number (LN) (p < 0.05); 3) c.1003 + 704 C > T, c.1003 + 651 C > T, c.1003 + 626 A > G, and c.812 + 22526 T > G were significantly associated with chest circumference (CHC), front carcass weight (CWF), after carcass weight (CWA), and carcass weight (CW) (p < 0.05) (wild-type homozygotes were larger than other genotypes in CHC, CWF, CWA, and CW); and 4) the effect of variation is not consistent in c.565 + 11921 A > G, c.565 + 6840 A > G, c.565 + 3453 C > T, and c.494 + 5808 C > T. These results provide useful information that the polymorphism of LTBP2 is significantly associated with TLN, body size, and carcass traits in Dezhou donkeys, which can serve as a molecule marker to improve donkey production performance.

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.

Regulation of posterior Hox genes by sex steroids explains vertebral variation in inbred mouse strains

A series of elegant embryo transfer experiments in the 1950s demonstrated that the uterine environment could alter vertebral patterning in inbred mouse strains. In the intervening decades, attention has tended to focus on the technical achievements involved and neglected the underlying biological question: how can genetically homogenous individuals have a heterogenous number of vertebrae? Here I revisit these experiments and, with the benefit of knowledge of the molecular-level processes of vertebral patterning gained over the intervening decades, suggest a novel hypothesis for homeotic transformation of the last lumbar vertebra to the adjacent sacral type through regulation of Hox genes by sex steroids. Hox genes are involved in both axial patterning and development of male and female reproductive systems and have been shown to be sensitive to sex steroids in vitro and in vivo. Regulation of these genes by sex steroids and resulting alterations to vertebral patterning may hint at a deep evolutionary link between the ribless lumbar region of mammals and the switch from egg-laying to embryo implantation. An appreciation of the impact of sex steroids on Hox genes may explain some puzzling aspects of human disease, and highlights the spine as a neglected target for in utero exposure to endocrine disruptors.

Whole-genome resequencing to investigate the determinants of the multi-lumbar vertebrae trait in sheep

Multi-lumbar vertebrae trait is a beneficial mutation that can significantly improve livestock meat production. However, the genetic basis of the multi-lumbar vertebrae in sheep is still unclear. Here, we analysed the number of lumbar vertebrae of Duolang sheep and found three different traits of lumbar vertebrae number. Compared with the normal sheep, the length and weight of animal carcass from the multi-lumbar vertebrae sheep increased by 2.21 cm and 0.78 kg, respectively. We performed high-throughput genome resequencing on multi-lumbar vertebrae (n = 18) and normal (n = 11) Duolang sheep and obtained a total of more than 528.87 GB data. We found that the most significantly selective region were located in the 49.68-49.74 MB of chromosome 4 by selective-sweep analysis. We annotated this region and found that it contains SFRP4 which is known to regulate bone development. We further used the PCR-SSCP technology to detect the single nucleotide polymorphism (SNP) of the putative candidate SFRP4 and found that the two SNPs (rs600370085:C > T and rs415133338: A > G) of this gene were significantly associated with the multi-lumbar vertebrae of Duolang sheep. Our study indicates that the SFRP4 may be a potential major gene that affects the number of lumbar vertebrae in Duolang sheep, and has the potential to be utilized for sheep breeding in the future.

Expression analysis and single-nucleotide polymorphisms of SYNDIG1L and UNC13C genes associated with thoracic vertebral numbers in sheep (Ovis aries)

The objective of the current study was to analyze expression levels of synapse differentiation inducing 1-like (SYNDIG1L) and unc-13 homolog C (UNC13C) genes in different tissues, while single-nucleotide polymorphisms (SNPs) of two genes were associated with multiple thoracic vertebrae traits in both Small-tailed Han sheep (STH) and Sunite sheep (SNT). The expression levels of SYNDIG1L and UNC13C were analyzed in the brain, cerebellum, heart, liver, spleen, lung, kidney, adrenal gland, uterine horn, longissimus muscle, and abdominal adipose tissues of two sheep breeds with different thoracic vertebral number (TVN) sheep (T13 groups and T14 groups) by real-time quantitative polymerase chain reaction (RT-qPCR). Meanwhile, the polymorphisms of UNC13C gene g.52919279C>T and SYNDIG1L gene g.82573325C>A in T14 and T13 were genotyped by the Sequenom MassARRAY^® SNP assay, and association analysis was performed with the TVN. The results demonstrated that UNC13C gene was extensively expressed in 11 tissues. The expression of UNC13C gene in longissimus muscle of T14 groups of STH was significantly higher than that of T13 groups (P<0.05). SYNDIG1L gene was overexpressed in brain and cerebellum tissues, and the expression level of UNC13C gene in the brain and cerebellum of T13 groups in SNT was significantly higher than that of T14 groups (P<0.01). Association analysis showed that SNPs found in the UNC13C gene had no significant effects on TVN for both two genes. The polymorphism of SYNDIG1L g.82573325C>A was significantly correlated with the TVN in both STH (P<0.05) and SNT (P<0.01). Taken together, the SYNDIG1L gene was related to thoracic vertebral development, and this variation may be potentially used as a molecular marker to select the multiple thoracic vertebrae in sheep.

Whole-Genome Resequencing Reveals Loci Associated With Thoracic Vertebrae Number in Sheep

The number of vertebrae, especially thoracic vertebrae, is an important economic trait that may influence carcass length and meat production in animals. However, the genetic basis of vertebrae number in sheep is still poorly understood. To detect the candidate genes, 400 increased number of thoracic vertebrae (T14L6) and 200 normal (T13L6) Kazakh sheep were collected. We generated and sequenced 60 pools of genomic DNA (each pool prepared by mixing genomic DNA from 10 sheep with the same thoracic traits), with an average depth of coverage of 25.65×. We identified a total of 42,075,402 SNPs and 11 putatively selected genomic regions, including the VRTN gene and the HoxA gene family that regulate vertebral development. The most prominent areas of selective elimination were located in a region of chromosome 7, including VRTN, which regulates spinal development and morphology. Further investigation indicated that the expression level of the VRTN gene during fetal development was significantly higher in sheep with more thoracic vertebrae than in those with a normal number of thoracic vertebrae. A genome-wide comparison between sheep with increased and normal numbers of thoracic vertebrae showed that the VRTN gene is the major selection locus for the number of thoracic vertebrae in sheep and has the potential to be utilized in sheep breeding in the future.

Expression profiles of MicroRNAs from multiple lumbar spine in sheep

The formation of the spine is a critical stage of mammalian development. The increase of the number of individual axons affects its performance, especially in meat production. To understand the role of miRNAs in sheep vertebrae development, the purpose of this article is to screen candidate microRNAs (miRNAs) associated with sheep spine development. MicroRNAs (miRNAs) are a rich family of small regulatory RNAs that negatively regulate gene expression at the post-transcriptional level. In this study, we used high-throughput sequencing techniques to analyze the microRNAs (miRNAs) expression profiles of L6 (6 lumbar vertebrae) and L7 (7 lumbar vertebrae) in sheep. A total number of 223 miRNAs were detected in the two libraries, and a total of 150 and 148 conserved miRNAs were obtained in L6 and L7, respectively. A total of 5 miRNAs expression differences in L6 compared to L7 (P < 0.05). Of the five obviously differently expressed miRNAs, four miRNAs were down-regulated in the L6 of sheep, and one was up-regulated. In order to further explore the functions of these miRNAs, we predicted the target genes of these differently expressed miRNAs, and obtained 1298 target genes. At the same time, NDRG2 gene, targeted by novel miR-391, which possible plays an important role in the development of the spine. Linkage-integration analysis method was used to construct the interaction network of spinal-associated miRNA and its hypothesized target. In summary, this study provides valuable resources for the transcriptome of multiple vertebral traits in sheep.

Advances in Sheep and Goat Meat Products Research

The main goal of this chapter was to review the state of the art in the recent advances in sheep and goat meat products research. Research and innovation have been playing an important role in sheep and goat meat production and meat processing as well as food safety. Special emphasis will be placed on the imaging and spectroscopic methods for predicting body composition, carcass and meat quality. The physicochemical and sensory quality as well as food safety will be referenced to the new sheep and goat meat products. Finally, the future trends in sheep and goat meat products research will be pointed out.

Whole-genome resequencing of Ujumqin sheep to investigate the determinants of the multi-vertebral trait

The Ujumqin sheep is one of the most profitable breeds in China, with unique multi-vertebral characteristics. We performed high-throughput genome resequencing of five multi-vertebral and three non-multi-vertebral sheep in an Ujumqin population. We identified the genomic regions that correlated with the germplasm characteristics to establish the cause of the "multi-vertebral" phenotype in this breed. Sequencing generated a total of 314 952 000 000 bp of raw data. The alignment rate of all the samples was between 98.53% and 99.11%, and the mean depth of coverage relative to the reference genome was between 11.58× and 14.92×. After comparing the differences between the two groups, we identified 21 homozygous single nucleotide polymorphisms (SNPs) in the mutant exons of 14 genes. Nineteen loci of 10 genes contained nonsynonymous mutations, while two loci contained synonymous mutations. Resequencing revealed homozygous mutations comprised of 44 indels located within exons of 19 genes. These indels included 37 frameshift mutations, 6 non-frameshift mutations, and 1 stopgain single nucleotide variation (SNV). Finally, comparisons of genotypic variations revealed 17 genes with homozygous mutations in their coding regions, 5 of which have previously been associated with vertebral development and the remaining 12 genes were newly identified in this study.

Effects of vertebral number variations on carcass traits and genotyping of Vertnin candidate gene in Kazakh sheep

Objective

The vertebral number is associated with body length and carcass traits, which represents an economically important trait in farm animals. The variation of vertebral number has been observed in a few mammalian species. However, the variation of vertebral number and quantitative trait loci in sheep breeds have not been well addressed.

Methods

In our investigation, the information including gender, age, carcass weight, carcass length and the number of thoracic and lumbar vertebrae from 624 China Kazakh sheep was collected. The effect of vertebral number variation on carcass weight and carcass length was estimated by general linear model. Further, the polymorphic sites of Vertnin (VRTN) gene were identified by sequencing, and the association of the genotype and vertebral number variation was analyzed by the one-way analysis of variance model.

Results

The variation of thoracolumbar vertebrae number in Kazakh sheep (18 to 20) was smaller than that in Texel sheep (17 to 21). The individuals with 19 thoracolumbar vertebrae (T13L6) were dominant in Kazakh sheep (79.2%). The association study showed that the numbers of thoracolumbar vertebrae were positively correlated with the carcass length and carcass weight, statistically significant with carcass length. To investigate the association of thoracolumbar vertebrae number with VRTN gene, we genotyped the VRTN gene. A total of 9 polymorphic sites were detected and only a single nucleotide polymorphism (SNP) (rs426367238) was suggested to associate with thoracic vertebral number statistically.

Conclusion

The variation of thoracolumbar vertebrae number positively associated with the carcass length and carcass weight, especially with the carcass length. VRTN gene polymorphism of the SNP (rs426367238) with significant effect on thoracic vertebral number could be as a candidate marker to further evaluate its role in influence of thoracolumbar vertebral number.

Non-invasive methods for the determination of body and carcass composition in livestock: dual-energy X-ray absorptiometry, computed tomography, magnetic resonance imaging and ultrasound: invited review

The ability to accurately measure body or carcass composition is important for performance testing, grading and finally selection or payment of meat-producing animals. Advances especially in non-invasive techniques are mainly based on the development of electronic and computer-driven methods in order to provide objective phenotypic data. The preference for a specific technique depends on the target animal species or carcass, combined with technical and practical aspects such as accuracy, reliability, cost, portability, speed, ease of use, safety and for in vivo measurements the need for fixation or sedation. The techniques rely on specific device-driven signals, which interact with tissues in the body or carcass at the atomic or molecular level, resulting in secondary or attenuated signals detected by the instruments and analyzed quantitatively. The electromagnetic signal produced by the instrument may originate from mechanical energy such as sound waves (ultrasound - US), 'photon' radiation (X-ray-computed tomography - CT, dual-energy X-ray absorptiometry - DXA) or radio frequency waves (magnetic resonance imaging - MRI). The signals detected by the corresponding instruments are processed to measure, for example, tissue depths, areas, volumes or distributions of fat, muscle (water, protein) and partly bone or bone mineral. Among the above techniques, CT is the most accurate one followed by MRI and DXA, whereas US can be used for all sizes of farm animal species even under field conditions. CT, MRI and US can provide volume data, whereas only DXA delivers immediate whole-body composition results without (2D) image manipulation. A combination of simple US and more expensive CT, MRI or DXA might be applied for farm animal selection programs in a stepwise approach.

Effect of the Texel muscling QTL (TM-QTL) on spine characteristics in purebred Texel lambs

Previous work showed that the Texel muscling QTL (TM-QTL) results in pronounced hypertrophy in the loin muscle, with the largest phenotypic effects observed in lambs inheriting a single copy of the allele from the sire. As the loin runs parallel to the spinal vertebrae, and the development of muscle and bone are closely linked, the primary aim of this study was to investigate if there were any subsequent associations between TM-QTL inheritance and underlying spine characteristics (vertebrae number, VN; spine region length, SPL; average length of individual vertebrae, VL) of the thoracic, lumbar, and thoracolumbar spine regions. Spine characteristics were measured from X-ray computed tomography (CT) scans for 142 purebred Texel lambs which had been previously genotyped. Least-squares means were significantly different between genotype groups for lumbar and thoracic VN and lumbar SPL. Similarly for these traits, contrasts were shown to be significant for particular modes of gene action but overall were inconclusive. In general, the results showed little evidence that spine trait phenotypes were associated with differences in loin muscling associated with the different TM-QTL genotypes.