Functioning as a key regulator of circadian rhythms, the PER2 gene exerts a substantial impact on the reproductive traits of animals. However, the effect of the PER2 gene on ovarian development remains unclear. In order to examine the relationship between bovine reproductive trait and the PER2 gene, a total of 901 ovarian samples were collected, categorized into different oestrus cycles (proestrus, oestrus, post-oestrus, anoestrous), and subjected to analysis for two potential insertion/deletions (InDels) in the PER2 gene. Through agarose gel electrophoresis and DNA sequencing, two polymorphic deletion mutations (P2-D5-bp, P3-D13-bp) were identified. Furthermore, a significant association between mature follicle diameter and P2-D5-bp was found (P < 0.05). Additionally, several significant correlations with ovarian length, width, height, and white body diameter were found for P3-D13-bp (P < 0.05). These findings suggested that the bovine PER2 gene plays an important role in above-mentioned reproductive traits, offering new avenues for improving cow fertility through marker-assisted selection (MAS).

The Protein Phosphatase 6 Catalytic Subunit (PPP6C) is evolutionarily a conserved gene in eukaryotes known to play a significant role in mammalian reproduction. This study aimed to investigate expression patterns of PPP6C and explore its association with litter size in Shaanbei white cashmere (SBWC) goats. Initially, we determined the mRNA expression levels of PPP6C in both male and female goats across multiple tissues. The results showed that PPP6C mRNA was expressed in multiple tissues, with higher levels in the testis and fallopian tubes, suggesting its involvement in goat reproduction. Additionally, we identified a novel 19 bp InDel within the PPP6C gene in a population of 1030 SBWC goats, which exhibited polymorphism. Statistical analysis revealed a significant association between the19 bp InDel mutation and litter size (P < 0.05). Subsequent, bioinformatics analysis, including linkage disequilibrium (LD) block and selective scanning, highlighted the linkage tendency among most InDel loci did not stand out within B-8 block, there were still some InDel loci linked to the 19 bp within a relatively narrow region. Furthermore, comparative analysis with Bezoars, these selective signals all indicated that this gene was under higher selection pressure, implying that the 19 bp InDel locus within the PPP6C is potentially associated with domesticated traits, particularly in relation to litter size. The results of the present study suggest that the PPP6C is a vital candidate gene affecting prolificacy in goats, with implications for selective breeding programs for goat breeds.

In recent years, genome-wide association studies (GWAS) have uncovered that the HOXB13 gene is a key regulatory factor for the tail length trait of sheep. Further research has found that there is a functional 168 bp SINE element insertion upstream of the HOXB13 gene, which leads to the occurrence of long tails in sheep. However, the frequency of mutations in the 168 bp SINE element of the HOXB13 gene among different sheep breeds around the world and its relationship with growth traits are still unclear. This study used whole-genome sequencing (WGS) data, including 588 samples from 33 different sheep breeds around the world, to evaluate the frequency of HOXB13 gene mutations in different sheep breeds globally. At the same time, this study also selected 3392 sheep samples from six breeds. The genetic variation in the 168 bp InDel locus in the HOXB13 gene was determined through genotyping, and its association with the growth traits of Luxi black-headed sheep was analyzed. The research results indicate that the polymorphism of the 168 bp InDel locus is significantly correlated with the hip width of adult ewes in the Luxi black-headed sheep breed (p < 0.05) and that the hip width of adult ewes with the DD genotype is significantly larger than that of adult ewes with the ID genotype (p < 0.05). This study indicates that there is consistency between the research results on the sheep tail length trait and growth traits, which may contribute to the promotion of sheep breed improvement.

Osteogenesis is a complex multilevel process regulated by multiple genes. The GATA binding protein 4 (GATA4) gene has been extensively studied for its pivotal role in bone genesis and bone differentiation. However, its relationship with the growth traits of Shaanbei white cashmere (SBWC) and Guizhou black (GB) goats remains unclear. This work aims to investigate the potential influence of genetic mutations in the GATA4 gene on the growth traits goats. Thus, two Insertion/deletion (InDel) polymorphisms (8-bp-InDel and 9-bp-InDel) were screened and detected in a total of 1161 goats (including 980 SBWC goats and 181 GB goats) using PCR and agarose gel electrophoresis. The analyses revealed that there were two genotypes (ID and DD) for these two loci. In SBWC goats, 8-bp-InDel and 9-bp-InDel loci were significantly associated with heart girth (HG) and hip width (HW). Notably, individuals with DD genotype of 8-bp-InDel locus were superior while those with DD genotype of 9-bp-InDel locus were inferior. Correlation analyses of the four combined genotypes revealed significant associations with cannon circumference (CC), body height (BH), HG and HW. This work provides a foundation for the application of molecular marker-assisted selection (MAS) in goat breeding programs. Furthermore, the findings highlight the potential of the GATA4 gene and its genetic variations as valuable indicators for selecting goats with desirable growth traits.

OBJECTIVE: The Janus kinase/signal transducer and transporter activator (JAK/STAT) signaling pathway plays crucial roles in lipid metabolism, glucose metabolism and cell senescence, suggesting that they are potential candidate genes affecting growth traits in animals. The present study aimed to evaluate the association between InDels in the JAK/STAT pathway and growth traits of four Chinese sheep breeds, including Tong sheep, Hu sheep, Small-tailed Han sheep and Lanzhou fat-tailed sheep.
RESULTS: Seventy-six indel loci of 11 genes in JAK/STAT were detected, and three genotypes were selected at four loci by PCR amplification, electrophoresis and sequencing, including one locus in STAT3, one locus in STAT5A, and two loci in JAK1. The Correlation analysis indicated that there was no significant correlation between STAT3 and growth traits in four sheep breeds (P > 0.05); STAT5A was significantly associated with body height, rump width and tube circumference in Hu sheep and body length in Tong sheep (P < 0.05); JAK1 was significantly correlated with body height, body oblique length, cross height and tube circumference in Hu sheep (P < 0.05) and body oblique length, cross height and tube circumference in small-tailed Han sheep (P < 0.05).
CONCLUSIONS: Overall, our results indicated a potential association between the growth traits of sheep and the InDels of JAK1 and STAT5A.

In this study, the relationship between RORA 23bp indel genotype and allele frequency with twin pregnancy, fertility, live weight and milk yield in 106 female Akkaraman ewes raised in Elazığ province was investigated. In the study conducted in Elâzığ province, 10ml milk was collected from 106 Akkaraman sheep and DNA was extracted from these milk. In RORA 23bp indel genotype frequency, DD genotype was found more than ID and II genotypes and RORA 23bp indel ın allele frequency, the D allele was found to be higher than the I allele. In both the first and second parity, the twinning rate was found to be lower. In both the first and second parity, the twinning rate was higher in the DD genotype, and it was observed that this genotype promınated mıddle lıvestock weıght and mılk yıeld. According to the results of our study, mutations in the RORA gene, which is a gene affecting reproductive efficiency in sheep, do not have a positive effect on fertility and twinning rate in Akkaraman sheep. To sum, this study provided theoretical references for the comprehensively research of the function of RORA gene and the breeding of Akkaraman Sheep. The 23-bp indel variants can be considered as molecular markers for litter size of sheep for marker-assisted selection breeding.

General transcription factor IIA subunit 1 (GTF2A1) is required for transcriptional activation from most promoters in eukaryotic transcription. Previous whole-genome association analyses articles have predicted the effect of this gene on lambing in sheep. In the study, a total of nine insertion/deletion (indel) variants named L1 to L9 in the gene were selected to detect in 550 Australian White sheep (AuW) adult ewes. The polymorphisms were detected in four loci (L1, L2, L3 and L8locus) and the polymorphism information content (PIC) values were 0.270, 0.375, 0.372 and 0.314. Further, our study revealed that L1, L2 and L3 loci of GTF2A1 gene were significantly related to the first parity litter size and the polymorphism of L8 was significantly correlated with litter size in the second parity. In details, for the first parity, individuals with the II genotype of the L1 locus had higher little size than that with the ID genotype, individuals with the ID and DD genotype of the L2 locus had higher little size than that with the II genotype, and individuals with the DD genotype of the L3 locus had higher little size than that with the II genotype. All four loci do not follow to Hardy-Weinberg equilibrium, and have no linkage between them. In conclusion, the polymorphisms of GTF2A1 were confirmed and analysis results demonstrated that there are some relevance between difference genotypes and litter size, and these findings may provide new insights for accelerating sheep molecular breeding through molecular marker-assisted selection (MAS).

Platelet-derived growth factor D (PDGFD) is a member of the PDGF gene family, and it plays an important role in the regulation of adipocyte development in mammals. Furthermore, genome-wide association studies (GWAS) have previously identified it as a candidate gene associated with fleece fiber variation, body size, and the fat-tail phenotype in domestic Chinese sheep. In this study, a total of 1919 indigenous Chinese sheep were genotyped to examine the association between nucleotide sequence variations in PDGFD and body morphology. Our results detected both a 14 bp insertion in intron 2 and a 13 bp deletion in intron 4 of PDGFD. Moreover, these two InDel loci had low to moderate polymorphism. Notably, the 13 bp deletion mutation of PDGFD was found to significantly affect sheep body size. Yearling rams in the Luxi black-headed sheep (LXBH) containing a heterozygous genotype (insertion/deletion, ID) were found to have larger body length, chest depth, and body weight than those with wild genotypes. Furthermore, adult ewes in the Guiqian semi-fine wool sheep (GSFW) containing a homozygous mutation (deletion/deletion, DD) were found to have smaller chest width than their peers. Moreover, yearling ewes in this group with the same homozygous mutation were found to have lower body weight, chest width, and cannon circumference compared to those of other individuals. This study demonstrates that PDGFD InDel polymorphisms have the potential to be effective molecular markers to improve morphological traits in domestic Chinese sheep.

UNASSIGNED: The hippocampal abundant transcript 1 (HIAT1) gene, also known as major facilitator superfamily domain-containing 14A (MFSD14A), encodes for a transmembrane transporter protein and has been previously shown to be associated with milk production in buffalo and sheep breeds, as well as growth traits in chicken and goats. However, tissue level distribution of the ovine HIAT1 gene, as well as its effect on body morphometric traits in sheep, has yet to be studied.
UNASSIGNED: The HIAT1 mRNA expression profile of Lanzhou fat-tailed (LFT) sheep was determined by quantitative real-time PCR (qPCR). A total of 1498 sheep of three indigenous Chinese sheep breeds were PCR-genotyped for polymorphisms of HIAT1 gene. Student\'s t-test was used to observe the association between the genotype and sheep morphometric traits.
UNASSIGNED: HIAT1 was widely expressed in all examined tissues, and was particularly abundant in the testis of male LFT sheep. Additionally, a 9-bp insertion mutation (rs1089950828) located within the 5\'-upstream region of HIAT1 was investigated in Luxi black-headed (LXBH) sheep and Guiqian semi-fine wool (GSFW) sheep. The wildtype allele frequency \'D\' was found to be more prevalent than that of the mutant allele \'I\'. Furthermore, low genetic diversity was confirmed in all sampled sheep populations. Subsequent association analyses indicated an association between the 9-bp InDel mutation of interest and the morphometric traits of LXBH and GSFW sheep. Furthermore, yearling ewes with a heterozygous genotype (ID) demonstrated smaller body sizes, while yearling rams and adult ewes with the heterozygous genotype were found to have overall better growth performance.
UNASSIGNED: These findings imply that functional InDel polymorphism (rs1089950828) has the potential to be utilized for marker-assisted selection (MAS) of growth traits in domestic Chinese sheep populations.

OBJECTIVE: To investigate the genetic information of 57 autosomal InDel loci (A-InDels) included in AGCU InDel 60 fluorescence detection kit in the Beichuan Qiang population of Sichuan Province and evaluate its application value in forensic medicine.
METHODS: A total of 200 unrelated healthy individuals from Beichuan Qiang population of Sichuan Province were typing detected by AGCU InDel 60 fluorescence detection kit. Allele frequencies and population genetic parameters of the 57 A-InDels were statistically analyzed and compared with the available data of 26 populations.
RESULTS: After Bonferroni correction, there was no linkage disequilibrium between the 57 A-InDels, and all loci were in Hardy-Weinberg equilibrium. Except for rs66595817 and rs72085595, the minor allele frequencies of 55 A-InDels were above 0.3. PIC ranged from 0.298 3 to 0.375 0, CDP was 1-2.974 8×10-24, CPEduo was 0.999 062 660, and CPEtrio was 0.999 999 999. The calculation of the genetic distance showed that Beichuan Qiang population had the closest genetic distances with Beijing Han and South China Han populations, but far away from African populations.
CONCLUSIONS: The 57 A-InDels in AGCU InDel 60 fluorescence detection kit have a good genetic polymorphism in Beichuan Qiang population of Sichuan Province, which can be used as effective supplemental for individual identification and paternity identification in forensic medicine.
目的: 调查AGCU InDel 60荧光检测试剂盒中57个常染色体InDel（autosomal-InDel，A-InDel）位点在四川省北川羌族人群中的遗传学信息，并评估其法医学应用价值。方法: 采用AGCU InDel 60荧光检测试剂盒对北川200名羌族健康无关个体进行分型检测，统计分析57个A-InDel位点的等位基因频率和群体遗传学参数，并与已知的26个人群数据进行比较。结果: 经Bonferroni法校正，57个A-InDel位点之间不存在连锁不平衡现象，且所有位点均符合Hardy-Weinberg平衡。除rs66595817、rs72085595外，其他55个A-InDel位点的最小等位基因频率均大于0.3。PIC为0.298 3~0.375 0，CDP为1-2.974 8×10-24，CPEduo为0.999 062 660，CPEtrio为0.999 999 999。计算遗传距离发现，北川羌族人群与北京汉族和南方汉族人群遗传距离最近，与非洲人群遗传距离较远。结论: AGCU InDel 60荧光检测试剂盒所包含的57个A-InDel位点在四川省北川羌族人群中具有良好的遗传多态性，可作为法医学个体识别和亲权鉴定的有效补充。.