Bovine HOXA11 Gene Identified from RNA-Seq: mRNA Profile Analysis and Genetic Variation Detection Using ME Method and Their Associations with Carcass Traits

The Homeobox A11 (HOXA11) gene regulates limb skeletal development and muscle growth, thus, it was selected as a candidate gene for bovine carcass traits. In this study, we analyzed the mRNA expression level of HOXA11 in various tissues and cells, and determined the genetic variations in the HOXA11 gene, which might be used as molecular markers for cattle breeding. The mRNA expression profiles of HOXA11 in bovine different tissues showed that HOXA11 was highly expressed in both fat and muscle. The gene expression trend of HOXA11 in myoblasts and adipocytes indicated that HOXA11 might be involved in the differentiation of bovine myoblasts and adipocytes. The data in the Ensembl database showed that there are two putative insertion/deletion (InDel) polymorphisms in the bovine HOXA11 gene. The insertion site (rs515880802) was located in the upstream region (NC_037331.1: g. 68853364-68853365) and named as P1-Ins-4-bp, and the deletion site (rs517582703) was located in the intronic region (NC_037331.1: g. 68859510-68859517) and named as P2-Del-8-bp. These polymorphisms within the HOXA11 gene were identified and genotyped by PCR amplification, agarose gel electrophoresis and DNA sequencing in the 640 Shandong Black Cattle Genetic Resource (SDBCGR) population. Moreover, the mutation frequency was very low after detection, so the mathematical expectation (ME) method was used for detection. Statistical analysis demonstrated that P1-Ins-4-bp was significantly correlated with the beef shoulder (p = 0.012) and tongue root (p = 0.004). Meanwhile, P2-Del-8-bp displayed a significant correlation with the back tendon (p = 0.008), money tendon (p = 2.84 × 10^-4), thick flank (p = 0.034), beef shin (p = 9.09 × 10^-7), triangle thick flank (p = 0.04), triangle flank (p = 1.00 × 10^-6), rump (p = 0.018) and small tenderloin (p = 0.043) in the female SDBCGR population. In summary, these outcomes may provide a new perspective for accelerating the molecular breeding of cattle through marker-assisted selection (MAS) strategies.

Molecular Characterization, Expression Profile, and A 21-bp Indel within the ASB9 Gene and Its Associations with Chicken Production Traits

A growing number of studies have shown that members of the ankyrin repeat and suppressors of cytokine signaling (SOCS) box-containing protein (ASB) family are extensively involved in biological processes such as cell growth, tissue development, insulin signaling, ubiquitination, protein degradation, and skeletal muscle membrane protein formation, while the specific biological role of ankyrin-repeat and SOCS box protein 9 (ASB9) remains unclear. In this study, a 21 bp indel in the intron of ASB9 was identified for the first time in 2641 individuals from 11 different breeds and an F₂ resource population, and differences were observed among individuals with different genotypes (II, ID, and DD). An association study of a cross-designed F₂ resource population revealed that the 21-bp indel was significantly related to growth and carcass traits. The significantly associated growth traits were body weight (BW) at 4, 6, 8, 10, and 12 weeks of age; sternal length (SL) at 4, 8, and 12 weeks of age; body slope length (BSL) at 4, 8, and 12 weeks of age; shank girth (SG) at 4 and 12 weeks of age; tibia length (TL) at 12 weeks of age; and pelvic width (PW) at 4 weeks of age (p < 0.05). This indel was also significantly correlated with carcass traits including semievisceration weight (SEW), evisceration weight (EW), claw weight (CLW), breast muscle weight (BMW), leg weight (LeW), leg muscle weight (LMW), claw rate (CLR), and shedding weight (ShW) (p < 0.05). In commercial broilers, the II genotype was the dominant genotype and underwent extensive selection. Interestingly, the ASB9 gene was expressed at significantly higher levels in the leg muscles of Arbor Acres broilers than those of Lushi chickens, while the opposite was true for the breast muscles. In summary, the 21-bp indel in the ASB9 gene significantly influenced the expression of the ASB9 gene in muscle tissue and was associated with multiple growth and carcass traits in the F₂ resource population. These findings suggested that the 21-bp indel within the ASB9 gene could be used in marker-assisted selection breeding for traits related to chicken growth.

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.

Rapid detection of InDel within the KDM3B gene in five sheep breeds using the mathematical expectation (ME) method

Lysine demethylase 3B (KDM3B), a candidate gene associated with bone formation and growth, and differentiation of osteoblast, might affect the animal growth traits. Herein, the insertion/deletion (InDel) of the KDM3B gene was quickly detected in 882 sheep from five breeds using the mathematical expectation (ME) method. The results showed that there were two genotypes of 7-bp variation in KDM3B, including II (insertion/insertion) and ID (insertion/deletion), and the frequency of two genotypes varied among the five sheep breeds. Association analysis results demonstrated that the 7-bp indel was significantly associated with chest depth of LFT sheep (P = 0.012), and body weight (P = 0.006), body height (P = 0.030), chest depth (P = 0.043), chest circumference (P = 0.016), abdominal width (P = 0.035) and height at hip cross (P = 0.022) in LXBH sheep. Moreover, II genotype was the predominant genotype with excellent consistency in sheep growth traits (P < 0.05). Collectively, the above results suggest that this locus can be used as an effective molecular marker to improve the sheep growth traits and provide a scientific basis for the development of sheep breeding.

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).

Novel InDel variations of the Cry2 gene are associated with litter size in Australian White sheep

Cryptochrome 2 (Cry2) gene regulates circadian rhythm and affects reproduction and pregnancy. Therefore, this study aimed to explore polymorphisms of the Cry2 gene and their associations with litter size at different parity in Australian White (AuW) ewes. Five putative insertion or deletion mutations within the Cry2 gene were selected to study their association with litter size. Two novel deletion mutations were identified in intronic region of Cry2 gene and were genotyped by agarose gel electrophoresis and DNA sequencing. The polymorphism information content (PIC) indicated that both mutations were low polymorphism in tested groups. Statistical analysis revealed that the P1-Del-6-bp was significantly correlated with litter size at third parity (P = 0.010), in which individuals with insertion/deletion (ID) genotype had larger litter size than insertion/insertion (II) genotype (P < 0.05). Whereas, the P2-Del-6-bp was significantly correlated with litter size at first parity (P = 0.036), in which individuals with insertion/insertion (II) genotype had larger litter size than insertion/deletion (ID) genotype (P < 0.05). Collectively, these findings may provide new insights to expedite molecular breeding in sheep through marker-assisted selection strategies (MAS).

Novel InDels of GHR, GHRH, GHRHR and Their Association with Growth Traits in Seven Chinese Sheep Breeds

The GH growth axis plays an important role in the growth and development of animals and runs through the whole life of animals. Many studies have shown that molecular mutations in key genes of the GH axis will affect the growth and development of animals. The purpose of this study was to explore the distribution characteristics of InDels of GHR, GHRH, and GHRHR in seven Chinese sheep populations, and to further explore the relationship between InDels and sheep growth traits. GHR showed high variation in Chinese sheep, and GHR-53 showed the highest minimum allele frequency (MAF). There was only one InDel mutation site in both GHRH and GHRHR. The genotype frequencies of Hu sheep (HS), Tong sheep (TS), and Lanzhou fat-tail sheep (LFTS) were quite different from other breeds. The association between GHR, GHRH, and GHRHR InDels and body size traits in seven varieties were analyzed. The results showed that there was no significant relationship between GHRH and body size traits in the seven sheep populations. There was a positive association between GHR-21 and hip height of LFSH (p < 0.05). GHR-43 reduced body height and chest depth of Small tail han sheep (STHS) and hip width of TS. GHR-44 significantly affected the body weight of HS, the body height of STHS and the head depth of TS. GHR-53 significantly reduced cannon girth of HS, chest of STHS and forehead width of TS. GHRHR-2 significantly reduced the body weight of LFHS. To sum up, this study revealed the effects of GHR, GHRH, and GHRHR InDels on sheep phenotypic traits, which indicated their potential application prospects in the genetic improvement of mutton sheep.

A 17-bp InDel (rs668420586) within goat CHCHD7 gene located in growth-related QTL affecting body measurement traits

The Coiled-Coil-Helix-Coiled-Coil-Helix Domain Containing 7 (CHCHD7) gene was located in a growth-related major QTL that participated in the process of bone cells metabolism in animals by regulating mitochondrial copper homeostasis and cytochrome C oxidase assembly. Therefore, we speculated that CHCHD7 gene might be involved in animal growth and body size. Herein, we discovered a 17-bp insertion/deletion (indel) within the goat CHCHD7 gene. Then, we detected this variation in Shaanbei White Cashmere (SBWC, n = 1055) goats and Inner Mongolia White Cashmere (IMWC, n = 743) goats (Alathai type) using the mathematical expectation (ME) method. We then analyzed the correlation between these genotypes and goat body measurement traits. The results showed that the minor allelic frequency (MAF) was 0.011 in SBWC, and 0.048 in IMWC. In SBWC and IMWC, the reaction time by ME method was reduced by 36.78% and 27.59%, respectively, compared to the traditional method of screening samples one by one. Moreover, in SBWC goats, the 17-bp indel was significantly associated with body measurement traits (e.g. body height, and body length) in adults. In IMWC goats, the 17-bp indel was correlated with body measurement traits (e.g. body height) in weaners. In SBWC and IMWC goat populations, the body measurement traits of the individuals homozygous for 17-bp indel were higher than those in heterozygous individuals, except for the case of cannon circumference in IMWC weaners. These findings showed that the 17-bp insertion mutation within the goat CHCHD7 gene significantly affected body morphometric traits, and could provide a basis for marker-assisted selection (MAS) breeding of cashmere goats.

Novel indel variations of the sheep FecB gene and their effects on litter size

Various studies had shown that the FecB gene (also known as BMPRIB, BMPR1B or ALK-6) was the major gene influencing sheep litter size, for which its SNPs' variations were reportedly linked. Yet, surprisingly, there was no published information on the insertion/deletion (indel) variation of this gene. Herein, using a population of Chinese Australian White sheep (n = 932), we identified five novel indels in the different introns of the FecB gene. Among them, the 12-bp indel was distinguished as a splicing region variation that was completely linked to the 17-bp indel. Analysis of variance revealed that only the 10-bp indel was significantly associated with sheep litter size (P = 0.010), for which the deletion/deletion (DD) genotype was the harmful one for fecundity. Nevertheless, the combined genotypes of these five indels were significantly (P = 0.033) correlated with the litter size. These findings would provide fresh insight into developing a sounder basis to accelerate molecular breeding in sheep via DNA markers in a marker-assisted selection strategy.

A Deletion Downstream of the CHCHD7 Gene Is Associated with Growth Traits in Sheep

Simple Summary

The genes CHCHD7 and PLAG1 are located on the same growth-related major quantitative trait locus of sheep. PLAG1 affects sheep growth, but no corresponding studies have been conducted on CHCHD7. However, polymorphisms in the CHCHD7 gene are associated with carcass weight and muscle formation in cattle, body height in cattle and humans, and weaning weight in Duroc pigs. In this study, the mathematical expectation method was used to analyze an 8-bp deletion mutation located downstream of the CHCHD7 gene in 2350 individuals from seven sheep breeds. The associations between wild-type and deletion genotypes and growth traits in Tan sheep were also analyzed. The 8-bp deletion locus was significantly associated with body length (p = 0.032), chest depth (p = 0.015), and chest width (p = 0.047) of Tan sheep. Additionally, wild-type genotype carriers were more numerous than those heterozygous for the deletion genotype. Thus, the genotyped 8-bp deletion downstream of the CHCHD7 gene may be associated with growth and development traits in sheep.

Abstract

In sheep, the coiled-coil-helix-coiled-coil-helix domain containing 7 (CHCHD7) gene and the pleiomorphic adenoma gene 1 (PLAG1) are on the same growth-related major quantitative trait locus, positioned head-to-head approximately 420 bp apart on chromosome 9. PLAG1 affects sheep growth, but the effects of CHCHD7 have not been determined. In this study, an 8-bp deletion downstream of CHCHD7 was analyzed in 2350 sheep from seven breeds. The associations between the deletion and growth traits of Tan sheep were also determined. Both genotypes (homozygous wild-type and heterozygous) for the 8-bp deletion were found in Tan (TS), Luxi Blackhead (LXBH), Small-Tail Han (STHS), and Lanzhou Fat-Tail (LFTS) sheep. However, there were no polymorphic sites for the mutation in Hu (HS), Sartuul (SS), and Australian White (AUW) sheep. In TS, LXBH, STHS, and LFTS sheep, the deletion genotype was less frequent than the wild-type genotype, and the allele frequencies of the deletion variant were 0.007 (TS), 0.011 (LBXH), 0.008 (STHS), and 0.010 (LFTS). The 8-bp deletion was significantly associated with body length (p = 0.032), chest depth (p = 0.015), and chest width (p = 0.047) in Tan sheep. Thus, the 8-bp deletion downstream of the CHCHD7 gene might be associated with growth and development traits of sheep.

Exploring insertions and deletions (indels) of MSRB3 gene and their association with growth traits in four Chinese indigenous cattle breeds

Methionine sulfoxide reductase B3 (MSRB3) is instrumental in ossification and fat deposition, which regulate the growth and development of cattle directly. The purpose of this study was aimed to explore insertions and deletions (indels) in MSRB3 gene and investigate their association with growth traits in four indigenous cattle breeds (Luxi cattle, Qinchuan cattle, Nanyang cattle, and Jiaxian Red cattle). Four indels were identified by sequencing with DNA pool. Association analysis showed that three of them were associated with growth traits (P<0.05). For P1, the DD (deletion and deletion) genotype was significantly associated with body length of Nanyang cattle; for P6, II (insertion and insertion) and/or DD genotypes were significantly associated with enhanced growth traits of Qinchuan cattle; for P7, II genotype was significantly associated with hucklebone width of Luxi cattle. Our results demonstrated that the polymorphisms in bovine MSRB3 gene were significantly associated with growth traits, which could be candidate loci for marker-assisted selection (MAS) in cattle breeding.

Detection of Insertions/Deletions Within SIRT1, SIRT2 and SIRT3 Genes and Their Associations with Body Measurement Traits in Cattle

Growth traits are complex quantitative traits controlled by numerous candidate genes, and they can be well-evaluated using body measurement traits. As the members of the nicotinamide adenine dinucleotide-dependent family of histone deacetylases, class I sirtuin genes (including SIRT1, SIRT2 and SIRT3) play crucial roles in regulating lipid metabolism, cellular growth and metabolism, suggesting that they are potential candidate genes affecting body measurement traits in animals. Hence, the objective of this work aimed to detect novel insertions/deletions (indels) of SIRT1, SIRT2 and SIRT3 genes in 955 cattle belonging to five breeds, as well as to evaluate their effects on body measurement traits. Herein, the novel 12-bp indel of SIRT1 gene, the 7-bp indel of SIRT2 gene and the 26-bp indel of SIRT3 gene were firstly reported, respectively. The association analysis indicated that the indels within SIRT1 and SIRT2 genes were significantly associated with body measurement traits such as body weight, chest circumference, height at hip cross, hip width, body height, etc. (P < 0.05 or P < 0.01). Therefore, based on these findings, the two novel indel variants within bovine SIRT1 and SIRT2 genes could be considered as potential molecular markers for growth traits in cattle selection practices and breeding.

Identification of a novel 12-bp insertion/deletion (indel) of iPS-related Oct4 gene and its association with reproductive traits in male piglets

As a key factor of cellular reprogramming, Oct4 is one of vital transcription factors for induced pluripotent stem cells (iPSCs). Loss of its function or deletion causes apoptosis in primordial germ cells (PGCs), which affect reproductive traits in mammals. In this study, a novel 12-bp insertion/deletion (indel) polymorphism (NC_010449:g.2759-2760insGGTTTTTGTCTA) within the Oct4 gene was identified in 442 pigs of Large White (LW) and Landrace (LD) breeds, showing three genotypes designated as II, ID, and DD. The frequencies of allele "I" in LW and LD pigs were 0.587 and 0.648, respectively. The male piglets with homozygous II or DD genotypes of Oct4 gene exhibited better reproductive traits than those with heterozygous ID genotype. Moreover, there were two significant associations between this 12-bp indel polymorphism and testis long circumference (TLC) (P=0.005) and testis short girth (TSG) (P=0.003) as well as 15-day testis weight (TW) (P=0.013) in the LW male piglets. These findings suggest that the 12-bp indel polymorphism of the Oct4 gene might be a potential DNA marker for selecting preferred individuals in relation to reproductive traits in pig marker-assisted selection (MAS) breeding, which could contribute to the breeding and genetics in male piglets.

The 10 bp duplication insertion/deletion in the promoter region within paired box 7 gene is associated with growth traits in cattle

Abstract. Paired box 7 (Pax7) gene, a member of the paired box gene family, plays a critical role in animal growth and muscle development, especially in cell proliferation and self-renewal. The aim of this study was to detect the 10 base pair (bp) duplication insertion/deletion (indel) in the promoter region within the bovine Pax7 gene as well as its association with growth traits. Herein, a total of 718 individuals from five Chinese cattle breeds were sampled and detected. The 10 bp duplication indel was found in these cattle breeds and there were three genotypes: II (insertion/insertion), ID (insertion/deletion), and DD (deletion/deletion). Moreover, this indel was significantly associated with the body weight in Xianan cattle (P = 0.006), the body height in Jinjiang cattle (P = 0.046), and the hip width in Pi'nan cattle (P = 0.020). Consistently, the individuals with II genotype showed better phenotypic traits than those with the other genotypes in these five breeds. These findings suggest that the 10 bp duplication indel within the bovine Pax7 gene could be considered as an effective DNA molecular marker that provides valuable theoretical basis for marker-assisted selection (MAS) in beef cattle in the future.

Exploration of the exonic variations of the iPSC-related <i>Nanog</i> gene and their effects on phenotypic traits in cattle

Abstract. Nanog is an important pluripotent transcription regulator transforming somatic cells to induced pluripotent stem cells (iPSCs), and its overexpression leads to a high expression of the growth and differentiation factor 3 (GDF3), which affects animal growth traits. Therefore, the aim of this study was to explore the genetic variations within the Nanog gene and their effects on phenotypic traits in cattle. Six novel exonic single nucleotide polymorphisms (SNPs) were found in six cattle breeds. Seven haplotypes were analyzed: TCAACC (0.260), TCAATA (0.039), TCATCC (0.019), TCGACC (0.506), TCGATA (0.137), TCGTCC (0.036), and CTGATA (0.003). There were strong linkage disequilibriums of SNP1 and SNP2 in Jiaxian cattle as well as of SNP5 and SNP6 in both Jiaxian cattle and Nanyang cattle. Moreover, SNP3, SNP4, and SNP5 were associated with phenotypes. The individuals with GG genotype at the SNP3 locus or AA genotype at the SNP4 locus showed better body slanting length and chest circumference or body height and hucklebone width in Nanyang cattle. The superiority of the SNP5-C allele regarding body height and cannon circumference was observed in Jiaxian cattle. The combination of SNP3 and SNP4 (GG–AA) had positive effects on body height, body slanting length, and chest circumference. These findings may indicate that Nanog, as a regulator of bovine growth traits, could be a candidate gene for marker-assisted selection (MAS) in breeding and genetics in cattle.