Relationship between SNPs of POU1F1 Gene and Litter Size and Growth Traits in Shaanbei White Cashmere Goats

Genome-Wide DNA Methylation Analysis and Functional Validation of Litter Size Traits in Jining Grey Goats

DNA methylation (DNAm) is associated with the reproductive system. However, the genetic mechanism through which DNAm regulates gene expression and thus affects litter size in goats is unclear. Therefore, in the present work, genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues were comprehensively analyzed via WGBS, and RNA-Seq data were combined to identify candidate genes associated with litter size traits in the Jining Grey goat. Finally, BSP and RT-qPCR were used to verify the sequencing results of the key genes. Notably, the DNMT genes were downregulated at the expression level in the HP group. Both groups exhibited comparable levels of methylation. A total of 976 differentially methylated regions (DMRs) (973 DMRs for CG and 3 DMRs for CHG) and 310 differentially methylated genes (DMGs) were identified in this study. Through integration of WGBS and RNA-Seq data, we identified 59 differentially methylated and differentially expressed genes (DEGs) and ultimately screened 8 key DMGs (9 DMRS) associated with litter size traits in Jining Grey goats (SERPINB2: chr24_62258801_62259000, NDRG4: chr18_27599201_27599400, CFAP43: chr26_27046601_27046800, LRP1B. chr2_79720201_79720400, EPHA6: chr1_40088601_40088800, TTC29: chr17_59385801_59386000, PDE11A: chr2_117418601_117418800 and PGF: chr10_ 16913801_16914000 and chr10_16916401_16916600). In summary, our research comprehensively analyzed the genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues. The data findings suggest that DNAm in goat ovaries may play an important role in determining litter size.

Relationships between the mutations of the goat GATA binding protein 4 gene and growth traits

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.

Association between polymorphisms in NOBOX and litter size traits in Xiangsu pigs

The newborn ovary homeobox gene (NOBOX) regulates ovarian and early oocyte development, and thus plays an essential role in reproduction. In this study, the mRNA expression level and single nucleotide polymorphism (SNP) of NOBOX in various tissues of Xiangsu pigs were studied to explore the relationship between its polymorphism and litter size traits. Also, bioinformatics was used to evaluate the effects of missense substitutions on protein structure and function. The results revealed that NOBOX is preferentially expressed in the ovary. Six mutations were detected in the NOBOX sequence, including g.1624 T>C, g.1858 G>A, g.2770 G>A, g.2821 A>G, g.5659 A>G, and g.6025 T>A, of which g.1858 G>A was a missense mutation. However, only g.1858 G>A, g.5659 A>G, and g.6025 T>A were significantly associated with litter size traits (p < 0.05). Further prediction of the effect of the missense mutation g.1858 G>A on protein function revealed that p.V82M is a non-conservative mutation that significantly reduces protein stability and thus alters protein function. Overall, these findings suggest that NOBOX polymorphism is closely related to the litter size of Xiangsu pigs, which may provide new insights into pig breeding.

Genetic Characterization of Myf5 and POU1F1 Genes in Different Egyptian Local Rabbit Breeds and Their Association with Growth Traits

Genetic characterization and its association with quantitative traits in local breeds are important tools for the genetic improvement and sustainable management of animal genetic resources. Myogenic regulatory factor 5 (MYf5) and POU class 1 homeobox 1 (POU1F1) are candidate genes which play important roles in growth and development of mammals. The present study aims to detect the genetic diversity of the MYf5 and POU1F1 genes in four local Egyptian rabbit breeds and their association with growth traits, using PCR-restriction enzyme (PCR-RFLP), PCR-single-strand conformational polymorphism (PCR-SSCP), and direct sequencing techniques. The results showed that MYF5 exon 1 was observed with two genotypes in Baladi Black (BB), Gabali (GB) and New Zealand White (NZW) breeds while APRI-line (APRI) presented one genotype. The genetic diversity of Myf5 exon 2 between breeds showed two genotypes in APRI compared to three in NZW and four genotypes in BB and GB breeds. The genetic diversity of the POU1F1 gene (intron 5 and partial cds) in different rabbit breeds was two genotypes in NZW and three genotypes in BB, GB, and APRI breeds with different frequencies for each genotype. Based on the statistically significant difference between genes genotypes and growth weight, the results suggested that the genotypes of Myf5 exon 2 (1 and 2) of the BB breed, Myf5 exon 2 genotype 2 of the APRI breed, and genotype 1 of Myf5 exon 1 and genotype 1 of POU1F1 of the NZW breed compared to genotypes for each gene can be considered candidate molecular markers associated with the improvement of growth traits in these breeds.

Relationships between the Mini-InDel Variants within the Goat CFAP43 Gene and Body Traits

The cilia- and flagella-associated protein 43 (CFAP43) gene encodes a member of the cilia- and flagellum-associated protein family. Cilia on the cell surface influence intercellular signaling and are involved in biological processes such as osteogenesis and energy metabolism in animals. Previous studies have shown that insertion/deletion (InDel) variants in the CFAP43 gene affect litter size in Shaanbei white cashmere (SBWC) goats, and that litter size and body traits are correlated in this breed. Therefore, we hypothesized that there is a significant relationship between InDel variants within the CFAP43 gene and body traits in SBWC goats. Herein, we first investigated the association between three InDel variant loci (L-13, L-16, and L-19 loci) within CFAP43 and body traits in SBWC goats (n = 1827). Analyses revealed that the L-13, L-16, and L-19 loci were significantly associated with chest depth, four body traits, and three body traits, respectively. The results of this study are in good agreement with those previously reported and could provide useful molecular markers for the selection and breeding of goats for body traits.

The detection of mutation within goat cell division cycle 25 A and its effect on kidding number

Cell division cycle 25 A (CDC25A) accounts for an essential function on early folliculogenesis of female mammals, especially regulating the function of intra-ovarian, thus this gene is pinpointed as a candidate gene that influences the kidding number of goat. On this ground, the purpose of this study was to investigate whether the reported 20-nt nucleotide variants locus (rs639467625) of the CDC25A gene influences kidding number in Shaanbei white cashmere goat (SBWC). The χ²-test showed that there were more ID genotypes in mothers of multiple lambs than in mothers of single lambs. Interestingly, this indel locus was related to the first-born kidding number in the group of SBWC goats (p < 0.05). Similarly, the result of the t-test was consistent with the result of the χ²-test, showed the kidding number of ID genotype individuals was large than that of II individuals (p < 0.05). These findings proved that the different genotypes of CDC25A have impacts on goat kidding numbers. Thus, the results led us to speculate that the ID genotype of CDC25A was one of the main indel influencing goat kidding numbers. Simultaneously, this study was expected to provide useful DNA markers for superior individuals selection by marker-assisted selection (MAS) and make a contribution to goats breeding.

A 7-nt nucleotide sequence variant within the sheep KDM3B gene affects female reproduction traits

Lysine demethylase 3B (KDM3B) gene is a histone demethylase, demonstrating specific demethylation of the histone H3 lysine 9. It was detected as a sheep reproductive candidate gene by genome-wide scans, and related studies also showed its significance in female reproductive process. However, rare study researched its polymorphism. Herein, we hypothesized that the polymorphisms of KDM3B gene were associated with sheep reproduction traits. A 7-nt nucleotide sequence variant (rs1088697156) within KDM3B gene was identified in a total of 888 individuals, including the Australian White (AUW) sheep and Lanzhou Fat-tailed (LFT) sheep. II (insertion/insertion) and ID (insertion/deletion) genotypes of 7-nt variant were detected, which were at Hardy-Weinberg equilibrium (HWE) in detected breeds. Association analysis illustrated the 7-nt variant was significantly associated with the litter size, duration of pregnancy, live lamb number, live lamb rate, stillbirth number, stillbirth rate of average and different parity (P < 0.05) in AUW sheep. Moreover, 'ID' was the dominant genotype with excellent consistency in reproductive traits. It is instrumental to select individuals with ID genotype for improving the sheep reproduction traits. These findings suggest that the 7-nt variant within KDM3B gene can be used as a candidate marker of reproduction traits for sheep breeding improvement by marker-assisted selection.

Screen of small fragment mutations within the sheep thyroid stimulating hormone receptor gene associated with litter size

The thyroid stimulating hormone receptor (TSHR), a glycoprotein hormone receptor, plays an important role in metabolic regulation and photoperiod control in the time of reproduction in birds and mammals. Previous genome-wide association studies revealed that the TSHR gene was related to reproduction and its function was identified in female reproduction, but rare studies reported the polymorphism of TSHR gene. However, the molecular mutations of the TSHR gene in sheep have not been reported so far. Herein, we explored potential polymorphisms of the sheep TSHR gene, and a 29 bp nucleotide sequence variant (rs1089565492) was identified in the AUW sheep. There were three genotypes of the 29 bp variant locus detected which named 'II' 'DD' and 'ID' been identified. Association analysis results showed the 29 bp variant was significantly associated with the litter size of the AUW sheep (p < 0.05). This finding suggests that the 29 bp nucleotide sequence variant within TSHR gene could be a candidate marker of reproduction traits for sheep breeding improving through the marker-assisted selection (MAS).

Identification of polymorphic loci in the deiodinase 2 gene and their associations with head dimensions in geese

Objective

This study was conducted to clone and compare the molecular characteristics of the deiodinase 2 (DIO2) gene between Sichuan White geese and Landes geese, and to analyze the association between polymorphisms of the DIO2 gene and head dimensions in Tianfu meat geese.

Methods

The coding sequence of the DIO2 gene was cloned by polymerase chain reaction (PCR) and vector ligation and aligned by DNAMAN software. A total of 350 Tianfu meat geese were used to genotype the polymorphisms of the DIO2 gene and measure the head dimensions. Association analysis between the polymorphisms of the DIO2 gene and head dimensions was carried out.

Results

An 840-bp coding sequence of the DIO2 gene was obtained and comparison analysis identified four polymorphic loci between Sichuan White geese and Landes geese. Further analysis showed that the dominant alleles for the four polymorphic loci were G, G, A, and T and the frequency of the heterozygous genotype was higher than that of the homozygous genotype in Tianfu meat geese. Compared to that in the population of non-knob geese of Tianfu meat geese, the head dimensions in the population of knob geese were significantly higher except for nostril height. However, in the non-knob geese, beak width 1 (BW1), beak width 2 (BW2), nostril length (NL), cranial width 1 (CW1), and maxillary length (ML) had significant differences among different genotypes or haplotypes/diplotypes.

Conclusion

These results suggested that polymorphisms of the DIO2 gene could be considered molecular markers to select larger heads of geese in the population of non-knob geese.

Characterization of Chinese tongue sole (Cynoglossus semilaevis) 24-dehydrocholesterol reductase: Expression profile, epigenetic modification, and its knock-down effect

The sexual size dimorphism of the Chinese tongue sole (Cynoglossus semilaevis) has greatly obstructed its sustainable development; however, the underlying mechanism remains unclear. Based on C. semilaevis transcriptomic information, 24-dehydrocholesterol reductase (dhcr24) was identified in steroid biosynthesis, showing female-liver-biased expression. Dhcr24 has been reported to participate in various processes, such as cholesterol synthesis, oxidative stress response, neuroprotection, and cell survival. The present study assessed its role in the sexual size dimorphism in fish. First, detailed expression pattern analysis showed that dhcr24 mRNAs were extensively expressed in tissues and the highest levels were found in the liver and gonads of females. Analysis of the dhcr24 promoter region demonstrated different DNA methylation statuses in female, male, and pseudomale gonads with higher epigenetic modification in males. The confirmation of transcription activity of the dhcr24 promoter and putative transcription factors (e.g., ER, AR, SREBP, and POU1F1a) provides the foundation for studying its regulatory mechanism. Finally, dhcr24-siRNA mediated knock-down assay using C. semilaevis liver cells showed that steroid biosynthesis related genes (e.g., ebp, dhcr7, and sc5d), core component of PI3K/Akt pathway (e.g., pi3k), and igf1r exhibited different expression patterns. Further investigation on the interplay between steroid hormones, dhcr24, PI3K/Akt, and IGF-1 systems will be valuable to better understand the mechanism underlying the sexual size dimorphism in C. semilaevis.

Population validation of reproductive gene mutation loci and association with the litter size in Nubian goat

Litter size is an important component trait of doe reproduction. By improving it, production efficiency and economic benefits can be significantly provided. Genetic marker-assisted selection (MAS) based on proven molecular indicators could enhance the efficacy of goat selection, as well as litter size trait. Many molecular markers have been identified that they can be used to improve litter size in different goat breeds. However, the presence and value of these markers vary among goat breeds. In the present study, we used the reported loci on other breeds of goat as candidate loci to detect whether these loci appear in this Nubian goat population; then we proceed to genotype and detect surrounding loci (50 bp) by multiplex PCR and sequencing technology. As a result, 69 mutations (59 SNPs and 10 indels) were screened out from 23 candidate genes in Nubian goat population, 12 loci were significantly associated with the litter size of first-parity individuals; 5 loci were significantly associated with the litter size of second-parity individuals; 3 loci were significantly associated with the litter size of third-parity individuals. In addition, five loci were significantly associated with the average litter size. The additive effect value of KITLG: g.18047318 G>A in first parity, KITLG: g.18152042G>A in third parity, KISS-1: g.1341674 C>G in first parity, and GHR: g.32134187G>A in second parity exceed more than 0.40, and the preponderant alleles are G, C, A and G, respectively. Further, linkage disequilibrium analysis of 21 mutation loci shows that 3 haplotype blocks are formed, and the litter size of combination type AACC in KISS-1 gene and AAGG in KITLG gene are significantly lower than that of other combinations genotype in first parity (P<0.05). These findings can provide effective candidate DNA markers for selecting superior individuals in Nubian goat breeding.

Characterization of third exonic region of POU1F1 gene in the Osmanabadi breed of goat

The POU1F1 gene has been identified as one of the major gene for productivity, and its polymorphism is known to be associated with important production traits of various livestock. The present study was designed to investigate POU1F1 (exon-3) gene polymorphism and its association with body weight in Osmanabadi goat (n=217). The PCRSSCP and DNA sequencing revealed single ‘C’ > ‘T’ transition at nucleotide position 42 in the third exonic region (225 bp) POU1F1 gene of Osmanabadi goat. Genotyping revealed ‘TT’ and ‘CC’ genotypes with predominance of ‘C’ allele in the Osmanabadi goat population. Though no association between the said SNP and body weight was observed, these findings can be extended to find the genetic variability of POU1F1 gene associated with growth traits of various Indian goat breeds.

Exploration of Genetic Variants within the Goat A-Kinase Anchoring Protein 12 (AKAP12) Gene and Their Effects on Growth Traits

Simple Summary

AKAP12, the family of A-kinase anchoring proteins (AKAPs), plays an important role in the regulation of growth and development. There have been no corresponding studies of the effect of the AKAP12 gene on growth traits in goats. In our previous study, 7 bp (intron 3) and 13 bp (3′UTR) indels within the AKAP12 gene significantly influenced AKAP12 gene expression. This study expected to identify the association between these two genetic variations and growth-related traits in 1405 Shaanbei white cashmere (SBWC) goats. The P1–7 bp indel locus was significantly correlated with height at hip cross (HHC; p < 0.05) and the P2–13 bp indel locus was associated with body weight, body length, chest depth, chest width, hip width, chest circumference and cannon (bone) circumference in SBWC goats (p < 0.05). These results prove that the AKAP12 gene plays an important role in the growth and development of goats.

Abstract

The A-kinase anchoring protein 12 gene (AKAP12) is a scaffold protein, which can target multiple signal transduction effectors, can promote mitosis and cytokinesis and plays an important role in the regulation of growth and development. In our previous study, P1–7 bp (intron 3) and P2–13 bp (3′UTR) indels within the AKAP12 gene significantly influenced AKAP12 gene expression. Therefore, this study aimed to identify the association between these two genetic variations and growth-related traits in Shaanbei white cashmere goats (SBWC) (n = 1405). Herein, we identified two non-linkage insertions/deletions (indels). Notably, we found that the P1–7 bp indel mutation was related to the height at hip cross (HHC; p < 0.05) and the P2–13 bp indel was associated with body weight, body length, chest depth, chest width, hip width, chest circumference and cannon (bone) circumference in SBWC goats (p < 0.05). Overall, the two indels’ mutations of AKAP12 affected growth traits in goats. Compared to the P1–7 bp indel, the P2–13 bp indel is more suitable for the breeding of goat growth traits.

The InDel variants of sheep IGF2BP1 gene are associated with growth traits

Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) plays positive roles in the growth, proliferation of cells and early embryos development by binding mRNA targets. Recently, it had been shown that some polymorphic loci within IGF2BP1 gene were associated with growth traits in animals, especially in goats. Therefore, it has been hypothesized that some variants within IGF2BP1 gene may be also involved in growth traits of sheep. Nine insertion/deletion (InDel) mutations within IGF2BP1 were identified and three loci were polymorphic. Meanwhile, the association analyses between three InDels and growth traits were carried out in 745 sheep. The results showed that all InDels included 5 bp InDel in downstream region, 9 bp InDel in intron 4 and 15 bp InDel in intron 2 within IGF2BP1 were significantly associated with growth traits (p<.05). Furthermore, at 5 and 9 bp InDel loci, the individuals of heterozygous genotype (ID) had superior growing performance especially at body weight (BW). In all, three InDels were crucial variants correlated with growth traits and could be applied in marker-assisted selection (MAS) in sheep.

Deletion mutation within the goat PPP3CA gene identified by GWAS significantly affects litter size

The protein phosphatase 3 catalytic subunit α (PPP3CA) gene is a high reproduction traits candidate gene for goats as revealed by a genome-wide association study. The aim of this work was to explore the genetic variations of the goat PPP3CA as well as to evaluate the genetic effects on litter size. Three novel insertions/deletions (indels) within the goat PPP3CA were found and their minor allelic frequencies (MAF) were 0.105, 0.066, and 0.042, respectively. The results showed that only the 20bp indel polymorphism was significantly associated with litter size in Shaanbei white cashmere goats (P<0.05) and individuals with deletion/deletion (DD) genotypes demonstrated the junior phenotypes when compared with those with other genotypes. These findings suggested that the 20bp indel is a potential DNA marker for selecting superior individuals in marker-assisted selection for breeding concerning fecundity in goats.

Effect of indel variants within the sorting nexin 29 (SNX29) gene on growth traits of goats

The sorting nexin 29 gene (SNX29) is a well-known regulator of myocyte differentiation and proliferation. In this work, two indels (17-bp and 21-bp) were identified in the goat SNX29 gene, and their effects on the growth traits of 1,759 Shaanbei white cashmere (SBWC) goats were analyzed. Both indels had three genotypes [homozygote wild type (II), heterozygote (ID), and homozygote mutation (DD)] and displayed medium genetic diversity (0.25 < polymorphism information content (PIC) < 0.50) in the population. The 17-bp indel was significantly associated with chest width (p = 0.009), body weight (p = 0.021), and chest depth (p = 0.032), with the II genotype dominant. The 21-bp indel was significantly associated with chest width (p = 0.001), chest depth (p = 4.8E-5), heart girth (p = 0.007), and hip width (p = 0.002). Because the two indels were in the upstream (17-bp) and intron (21-bp) regions of the SNX29 gene, transcription factor binding sites were predicted. The IRF5 and MYC could bind with the 17-bp indel and 21-bp indel sequences, respectively. This study indicates that SNX29 is a promising candidate gene that can be used to improve meat production in goat breeding.

A novel 23 bp indel mutation in PRL gene is associated with growth traits in Luxi Blackhead sheep

Prolactin is a highly versatile pituitary hormone with multiple biological functions. PRL expression is regulated by POU1F1 and the prophet of POU1F1 (PROP1). The aim of this study was to investigate the indel variations in ovine PRL and the directly related (PROP1 and POU1F1) genes, and their associations with growth traits in Luxi Blackhead (LXBH) sheep. A monomorphism in PROP1 and POU1F1 genes, and one novel 23-bp insertion mutation in the PRL gene, were identified in LXBH sheep. The 23 bp insertion mutation within PRL gene was significantly associated with several body measurements (e.g., body weight, body height) in sheep of different ages (p < 0.05). Ram lambs (p = 0.036) of genotype insertion/insertion (II) had significantly higher body weights. Weaners (p = 0.018) of genotypes insertion/insertion (II) and insertion/deletion (ID) also had significantly higher body weights compared with male sheep of deletion/deletion (DD) genotype. Moreover, among ewe lambs, individuals of genotype insertion/insertion (II) had a higher paunch girth compared to those with other genotypes (p = 0.044). These findings indicate that a 23 bp indel variant of the ovine PRL gene is correlated with body measurements in LXBH sheep. The findings have potential utility for sheep breeding programs based on marker-assisted selection.

Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat

Litter size (LS), an important economic trait in livestock, is so complicate that involves many aspects of reproduction, the underlying mechanism of which particularly in goat has always been scanty. To uncover the genetic basis of LS, the genomic sequence of Jining Gray goat groups (one famous breed for high prolificacy in China) with LS 1, 2, and 3 for firstborn was analyzed, obtaining 563.67 Gb sequence data and a total of 31,864,651 high-quality single nucleotide polymorphisms loci were identified. Particularly, the increased heterozygosity in higher LS groups, and large continuous homozygous segments associated with lower LS group had been uncovered. Through an integrated analysis of three popular methods for detecting selective sweeps (Fst, nucleotide diversity, and Tajima’s D statistic), 111 selected regions and 42 genes associated with LS were scanned genome wide. The candidate genes with highest selective signatures included KIT, KCNH7, and KMT2E in LS2 and PAK1, PRKAA1, and SMAD9 in LS3 group, respectively. Meanwhile, functional terms of programmed cell death involved in cell development and regulation of insulin receptor signaling pathway were mostly enriched with 42 candidate genes, which also included reproduction related terms of steroid metabolic process and cellular response to hormone stimulus. In conclusion, our study identified novel candidate genes involving in regulation of LS in goat, which expand our understanding of genetic fundament of reproductive ability, and the novel insights regarding to LS would be potentially applied to improve reproductive performance.

Detection of rs665862918 (15-bp Indel) of the HIAT1 Gene and its Strong Genetic Effects on Growth Traits in Goats

Simple Summary

Growth traits are important in goats and can affect their body size and meat production. In this study, the hippocampus abundant transcript 1 (HIAT1) gene, which has been reported as a meat-associated trait in elite goat breeds and a dairy-associated trait in water buffalo, was chosen to detect its correlation with growth traits in goats. The results show that the rs665862918 polymorphism (a 15 bp insertion) in HIAT1 is associated with body length, chest width, chest depth, height at hip cross and heart girth in Shaanbei white cashmere goats (SBWC, n = 1013). Our results reveal that rs665862918 in HIAT1 is relevant to the growth traits of goats and could be used for marker-assisted selection (MAS) as a molecular marker in goat populations.

Abstract

The hippocampus abundant transcript 1 (HIAT1) gene, which was detected by the genome-wide identification of selective sweeps among elite goat breeds and water buffalo, is proposed to play an important role in meat characteristics. Four indels of the HIAT1 gene selected from the NCBI and Ensembl databases were detected via a pooling and sequencing strategy. A 15 bp insertion (rs665862918) in the first intron of HIAT1 was selected and classified on an electrophoresis platform in the Shaanbei white cashmere goat (SBWC) population. The correlation analysis revealed that rs665862918 is significantly highly associated with chest width (p = 1.57 × 10⁻⁵), chest depth (p = 8.85 × 10⁻⁵), heart girth (p = 1.05 × 10⁻⁷), body length (p = 0.022), and height at hip cross (p = 0.023) in the SBWC population (n = 1013). Further analysis revealed that individuals with a genotype insertion/insertion (II) of the rs665862918 locus exhibited better growth trait performance than individuals with an insertion/deletion (ID) or deletion/deletion (DD). These findings verify that HIAT1 affects the body size of goats and that rs665862918 could be a potential molecular marker for growth traits in goat breeding.

Screening of Deletion Variants within the Goat PRDM6 Gene and Its Effects on Growth Traits

Simple Summary

Genome-wide association studies found that the PR/SET Domain 6 (PRDM6) gene mutation was associated with bone development, bone density, and body mass index. This study found a 12 bp deletion variation within the PRDM6 gene in Shaanbei white cashmere goats in a large sample size (n = 1044). This variation polymorphism was associated with multiple goat growth traits in the yearling period, including heart girth (p = 0.027), cannon circumference (p = 0.008), chest depth (p = 2.10 × 10⁻⁵), chest width (p = 0.004), body height (p = 0.032), body length (p = 0.044), and hip-width (p = 0.014). The effects of the 12 bp variation were found to make no difference on adult goat growth traits. Taken together, these results demonstrate that the 12 bp deletion variant plays an important role in the early growth and development of goats and could be considered as a useful and effective molecular marker for goat breeding selection in the growth stage.

Abstract

By genome-wide association studies, the PRDM6 gene has been shown to affect multiple, apparently unrelated inherited traits, including bone density and body mass index. Therefore, it is considered a potentially pleiotropic gene. In this study, we identified a 12 bp deletion variant (NC_030814.1:rs651603667, g: 79985625-79985636delTTGACTGATCCA) within the PRDM6 gene in a large sample (SBWC goats; n = 1044). All goat samples were collected in Shaanxi province in July 2018. The frequency of the wt allele was higher than the frequency of the del allele, and this mutation polymorphism confirmed to be consistent with the Hardy–Weinberg equilibrium (p > 0.05). Further results showed that in a group of goats in the yearling period (18 months old, n = 567), this deletion variant of the PRDM6 gene was associated with heart girth (p = 0.027), cannon circumference (p = 0.008), chest depth (p = 2.10 × 10⁻⁵), chest width (p = 0.004), body height (p = 0.032), body length (p = 0.044) and hip-width (p = 0.014). For adult SBWC goats (36 months old, n = 477), the effects of the 12 bp variation on growth-related traits were found to make no difference. These findings show that the 12 bp deletion within the goat PRDM6 gene plays an important role in the early growth and development of goats. Using the 12 bp mutation, breeders can quickly and effectively select excellent individual goats at an early stage.

Myostatin (MSTN) Gene Indel Variation and Its Associations with Body Traits in Shaanbei White Cashmere Goat

Myostatin (MSTN) gene, also known as growth differentiation factor 8 (GDF8), is a member of the transforming growth factor-beta super-family and plays a negative role in muscle development. It acts as key points during pre- and post-natal life of amniotes that ultimately determine the overall muscle mass of animals. There are several studies that concentrate on the effect of a 5 bp insertion/deletion (indel) within the 5' untranslated region (5' UTR) of goat MSTN gene in goats. However, almost all sample sizes were below 150 individuals. Only in Boer goats, the sample sizes reached 482. Hence, whether the 5 bp indel was still associated with the growth traits of goats in large sample sizes which were more reliable is not clear. To find an effective and dependable DNA marker for goat rearing, we first enlarged the sample sizes (n = 1074, Shaanbei White Cashmere goat) which would enhance the robustness of the analysis and did the association analyses between the 5 bp indel and growth traits. Results uncovered that the 5 bp indel was significantly related to body height, height at hip cross, and chest width index (p < 0.05). In addition, individuals with DD genotype had a superior growing performance than those with the ID genotype. These findings suggested that the 5 bp indel in MSTN gene are significantly associated with growth traits and the specific genotype might be promising for maker-assisted selection (MAS) of goats.

An 11-bp Indel Polymorphism within the CSN1S1 Gene Is Associated with Milk Performance and Body Measurement Traits in Chinese Goats

The casein alpha s1 (CSN1S1) gene encodes α-s1 casein, one of the proteins constituting milk, which affects milk performance, as well as improving the absorption of calcium and bone development in mammals. A previous study found that an 11-bp insertion/deletion (indel) of this gene strongly affected litter size in goats. However, to our knowledge, the relationships between this polymorphism and the milk performance and body measurement traits of goats have not been reported. In this paper, the previously identified indel has been recognized in three Chinese goat breeds, namely the Guanzhong dairy goat (GZDG; n = 235), Shaanbei white cashmere goat (SBWC; n = 1092), and Hainan black goat (HNBG; n = 278), and the following three genotypes have been studied for all of the breeds: insertion/insertion (II), deletion/deletion (DD), and insertion/deletion (ID). The allele frequencies analyzed signified that the frequencies of the "D" allele were higher (47.8%-65.5%), similar to the previous report, which indicates that this polymorphism is genetically stable in different goat breeds. Further analysis showed that this indel was markedly associated with milk fat content, total solids content, solids-not-fat content, freezing point depression, and acidity in GZDG (p < 0.05), and also affected different body measurement traits in all three breeds (p < 0.05). The goats with II genotypes had superior milk performance, compared with the others; however, goats with DD genotypes had better body measurement sizes. Hence, it may be necessary to select goats with an II or DD genotype, based on the desired traits, while breeding. Our study provides information on the potential impact of the 11-bp indel polymorphism of the CSN1S1 gene for improving the milk performance and body measurement traits in goats.

Polymorphisms within the Boule Gene Detected by Tetra-Primer Amplification Refractory Mutation System PCR (T-ARMS-PCR) are Significantly Associated with Goat Litter Size

As a gene contributing to spermatogenesis, the Boule gene (also called Boll), whose mutations result in azoospermia and sterility of flies and mice, was conserved in reductional maturation divisions. However, in goats, the polymorphisms of Boule, especially with regard to their fundamental roles in female reproduction traits, are still unknown. Therefore, the aims of this study were to detect a potential mutation (rs661484476: g.7254T>C) located in intron 2 of the Boule gene by tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR) and to explore its potential association with the litter size of Shaanbei White-Cashmere goats (SBWGs). In this study, g.7254T>C was firstly detected. The TT genotype was the dominant genotype in the single-lamb group, and T was also the dominant allele in all tested groups. Additionally, the detected locus displayed moderate polymorphism with polymorphism information content (PIC) values among all studied goats ranging from 0.303 to 0.344. Notably, according to the χ² test, the distribution differences for the genotypic frequencies between the single- and multi-lamb groups was significant (p = 0.014). Furthermore, the polymorphisms of the goat Boule gene were significantly associated with the goat litter size in SBWGs (p < 0.05), which indicated that g.7254T>C could be a potential marker in the marker-assisted selection process for potential litter size in goats. These results also indicated that the Boule gene might exercise important functions in female goat reproduction, which provided new insight for female goat breeding and could accelerate the process of goat breeding.

Genome-wide selection signatures analysis of litter size in Dazu black goats using single-nucleotide polymorphism

Litter size is considered to be the most important index for estimating domestic animal productivity. The number of indigenous goats in China with higher litter sizes than those of commercial breeds in other countries may be helpful for accelerating genetic improvements in goat breeding. We performed a genome-wide selective sweep analysis of 31 Dazu black goats with extreme standard deviation in litter size within the third fetus to identify significant genomic regions and candidate genes through different analyses. The analysis identified a total of 33,917,703 variants, including 32,262,179 SNPs and 1,655,524 indels. In addition, two novel candidate genes (LRP1B and GLRB), which are related to litter size, were obtained with π, Tajima's D, πA/πB, and F _ST at the individual level with a 95% threshold for each parameter. These two genes were annotated in five GO terms (localization, binding, macromolecular complex, membrane part, and membrane) and two pathways (long-term depression and neuroactive ligand-receptor interaction pathway). Regarding the result of linkage disequilibrium (LD) analysis, in LRP1B and GRID2, the high-yield Dazu black goats exhibit significantly different LD patterns from low-yield goats. Litter size variability has low heritability and is related to multiple complex factors found in domestic animals. Obtaining a clear explanation and significant signal by genome-wide selective sweep analysis with a small sample size is difficult. However, we investigated some candidate genes, particularly LRP1B and GLRB, which may provide useful information for further research.

Correlation analysis of candidate gene SNP for high-yield in Liaoning cashmere goats with litter size and cashmere performance

This study was designed to identify the relationship of four genes (GDF9, BMPR-IB, FecB and ESR) polymorphisms in the 3'UTR region with litter size and cashmere performance of Liaoning cashmere goats (LCG, n = 1140). The ESR C463T and T575G loci of LCG were genotyped. The results of correlation analysis showed that five effective single nucleotide polymorphisms (SNPs) loci (C47T, C94T, C299T, C463T and T575G) were found in the four genes. The lambing number of CC and CT genotypic individuals at FecB C94T locus was significantly higher than that of TT genotypic individuals (45.7 and 46.8%, respectively); the lambing number of CC genotypic individuals at ESR C463T locus was significantly higher than that of CT, TT genotypic individuals (9 and 15%, respectively); There was a positive correlation between CC genotype at C463T locus and cashmere fineness. In this study, the relationship between FecB C94T and ESR C463T loci C alleles and lambing number in LCG was preliminarily revealed. These results further confirmed that FecB and ESR genes may be significantly correlated with high fecundity of LCG.