Two missense mutations in exon 9 of caprinePRLRgene were associated with litter size

Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-white goat prolificacya

In this study, we evaluated the copy number variation in the genomes of two groups of Beichuan-white goat populations with large differences in litter size by FST method, and identified 1739 genes and 485 missense mutations in the genes subject to positive selection. Through functional enrichment, ITGAV, LRP4, CDH23, TPRN, RYR2 and CELSR1 genes, involved in embryonic morphogenesis, were essential for litter size trait, which received intensive attention. In addition, some mutation sites of these genes have been proposed (ITGAV: c.38C > T; TPRN: c.133A > T, c.1192A > G, c.1250A > C; CELSR1: c.7640T > C), whose allele frequencies were significantly changed in the high fecundity goat group. Besides, we found that new mutations at these sites altered the hydrophilicity and 3D structure of the protein. Candidate genes related to litter size in this study and their missense mutation sites were identified. These candidate genes are helpful to understand the genetic mechanism of fecundity in Beichuan white goat, and have important significance for future goat breeding.

Association between the cashmere production performance, milk production performance, and body size traits and polymorphism of COL6A5 and LOC102181374 genes in Liaoning cashmere goats

The purpose of this study was to analyze the relationship between COL6A5 (collagen type VI alpha 5 chain) and LOC102181374 (alcohol dehydrogenase 1) genes and the production performance of Liaoning cashmere goats by single nucleotide polymorphism (SNP). We have searched for SNP loci of COL6A5 and LOC102181374 genes through sequence alignment and PCR experiments, and have used SPSS and SHEsis software to analyze production data. We obtained five SNP loci in total, including three SNP loci (G50985A, G51140T, G51175A) in COL6A5 gene and two SNP loci (A10067G, T10108C) in LOC102181374 gene. The genotypes G50985A (AG), G51140T (GT), G51175A (AA), A10067G (AA), and T10108C (CC) of these loci have certain advantages in improving the production performance of Liaoning cashmere goats. The haplotype combinations that can improve production performance in COL6A5 gene were H1H5:AGGGAG, H4H4:GGGGAA, and H4H4:GGGGAA. H3H3:GGCC and H2H4:AGTT were the dominant combinations in LOC102181374 gene. At G51175A and A10067G loci, we found that H1H2:AAAG and H1H3:AGAA have dominant effects. These results may provide some support for the molecular breeding of production traits in Liaoning cashmere goats.

Allele mining in prolactin receptor gene and its association with some economic traits in Egyptian goat breeds

The objectives of the current study were to identify polymorphism in the prolactin receptor (PRLR) gene among three Egyptian goat breeds (Zaraibi, Damascus, and Barki) and to investigate the association between PRLR genotype, parity, season of kidding, and litter size factors with milk yield and reproductive traits of Zaraibi goats. One hundred and ninety blood samples were collected for DNA extraction, with 110 from Zaraibi, 40 from Barki, and 40 from Damascus breeds. Three genotypes, CC, CT and TT, for the prolactin receptor gene were identified in the 190 DNA samples using restriction fragment length polymorphism and were confirmed by direct sequencing technique. Milk yield during suckling and lactation periods in addition to age at first conception, gestation length, and litter size were determined in 110 Zaraibi goats. The Zaraibi goats recorded the highest heterozygosity (0.495) and the effective number of alleles (1.972). The g.62130C > T SNP showed a significant association (p < 0.01) with suckling, lactation, and total milk yield of Zaraibi goats with the highest values recorded at the third parity. Age at the first conception and gestation length traits were significantly influenced by the kidding season (p < 0.05) with younger age in autumn and shorter length in spring seasons. Milk yield during the suckling period was significantly (p < 0.01) higher in the case of triplets' litter size. The current study showed that litter size and parity played an important role in the amount of Zaraibi goats' milk yield. The g.62130C > T SNP of the PRLR gene may be a useful marker for assisted selection programs to improve goat milk yield during suckling and lactation periods with the heterozygous genotype CT recording the highest values.

Genome-wide association study reveals novel candidate genes for litter size in Markhoz goats

Introduction

The Markhoz goat is the only breed that can produce high-quality fiber called mohair in Iran; however, the size of its population has faced a dramatic decline during the last decades, mainly due to the reluctance of farmers to rear Markhoz goats caused by a reduction in goat production income. Litter size at birth (LSB) and weaning (LSW) are two economically important reproductive traits for local goat breeders and have the potential of increasing the population growth rate. The present study was aimed to identify possible genomic regions that are associated with LSB and LSW in Markhoz goats using a genome-wide association study (GWAS).

Methods

To this end, 136 Markhoz goats with record(s) of kidding were selected for GWAS using the Illumina Caprine 50K bead chip. The individual breeding values (BV) of available LSB and LSW records estimated under an animal mixed model were used as the dependent variable in the GWAS, thereby incorporating repeated categorical variables of litter size.

Results

Four SNPs on chromosomes 2, 20 and 21 were identified to be significantly associated (FDR p < 0.05) with LSB after multiple testing correction under a Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model. Least-square analysis was performed to investigate the effects of detected genotypes on LSB. Ultimately, the GWAS results introduced six candidate genes, including GABRA5, AKAP13, SV2B, PPP1R1C, SSFA2 and TRNAS-GCU in a 100 kb adjacent region of the identified SNPs. Previous studies proposed functional roles of GABRA5 and AKAP13 genes in reproductive processes; however, the role of other candidate genes in reproduction is not clear.

Conclusion

These findings warrant further investigation for use in marker-assisted selection programs in Markhoz goats.

Association of PRLR, IGF1, and LEP genes polymorphism with milk production and litter size in Egyptian Zaraibi goat

Studying variation in genes responsible for physiological characters is important to enhance goat productive and reproductive efficiency. This study aimed to detect specific nucleotide polymorphisms in prolactin receptor (PRLR), insulin-like growth factor (IGF1), and leptin (LEP) genes and their correlation with milk production (MP) and litter size (LS) traits in Zaraibi goat. PCR-SSCP products of different patterns of each gene were sequenced and aligned to reveal two mutations (T > C) and (G > A) in 3′UTR of PRLR gene and registered on NCBI with accession numbers OM418863 for TT and OM418864 for CT, while (G > A) variation was registered as OM418861 for GG and OM418862 for AG in exon 10. TT, CT, AG, and GG genotypes were distributed in the studied animals with frequencies 0.43, 0.57, 0.65, and 0.35, respectively. While alleles C, T, A, and G frequencies were 0.28, 0.72, 0.32, and 0.68, respectively. CT and AG genotypes associated significantly (P < 0.05) with higher MP and LS, respectively. By studying the haplotypes of PRLR, C-A and T-A were associated with the highest and the lowest level of MP, respectively. For LS, T-A and C-G showed significant correlation with the highest and the lowest rate, respectively. Regarding IGF1 gene, two polymorphisms were detected; T74C at exon 4 which registered on NCBI as OM418860, and combined mutations as ins. G470, A531G, and T534C (PP genotype) at 5′ flanking region that registered as OM418859. For LEP, only one polymorphism was found in intron 2 (G281A) which submitted to NCBI as OM418855. All detected polymorphisms have shown to be involved in regulating the MP or LS as reproductive traits in goat.

Long noncoding RNA and mRNA profiling of hypothalamic-pituitary-mammary gland axis in lactating sows under heat stress

Heat stress (HS) seriously affects sow lactation performance and Long non-coding RNAs (lncRNAs) play vital roles in the regulation of transcription and post transcription. However, the mechanism of lncRNAs expression affecting lactation performance on the hypothalamus-pituitary-mammary axis of sows is still unclear. In this study, we performed RNA sequencing and bioinformatics analysis of the hypothalamus, pituitary, and mammary gland tissues of lactating sows under HS and thermal comfort. In total, the analysis identified 658, 6021, and 6745 differently expressed (DE) mRNAs, 26, 126, and 169 DE lncRNAs between comparison groups in the hypothalamus, pituitary, and mammary glands, respectively. The hormone genes and most DE mRNAs encoding heat shock protein were differently expressed in the HS group. In addition, 2, 60, and 86 pairs of DE lncRNAs and mRNAs correlation were observed in those tissues, respectively. Some lncRNAs may be involved in the regulation of lactation performance in the HS sows.

Two indel variants of prolactin receptor (PRLR) gene are associated with growth traits in goat

Prolactin receptor (PRLR) gene plays a crucial role in the milk production, reproduction and the growth of mammals. To fully characterize the structure of the mutation and to further study the function of the goat PRLR gene, two insertion/deletion (indel) loci (12 bp; 16-bp; 5-bp) were detected in 1038 Shaanbei white cashmere (SBWC) goats. Associated analysis revealed that the 16-bp indel mutation was significantly associated the body length, body height, chest depth (CD), body length index (BLI), heart girth index and cannon circumference index (CCI) (p < 0.05). The polymorphism of 5-bp indel was significantly associated with CD, heart girth, CCI and BLI (p < 0.05). Overall, individuals with genotype DD showed better phenotypic traits than individuals with other genotypes at the two loci of PRLR gene in SBWC goat. These findings suggested that the two novel indels within the caprine PRLR gene could be considered as effective DNA molecular markers and could provide a valuable theoretical basis for the application of marker-assisted selection in the goat industry.

Remarkable genetic diversity detected at river buffalo prolactin receptor (PRLR) gene and association studies with milk fatty acid composition

Prolactin is an anterior pituitary peptide hormone involved in many different endocrine activities and is essential for reproductive performance. This action is mediated by its receptor, the prolactin receptor, encoded by the PRLR gene. In this study, we sequenced and characterized the Mediterranean river buffalo PRLR gene (from exon 3 to 10), and we found remarkable genetic diversity. In particular, we found 24 intronic polymorphisms and 13 exonic SNPs, seven of which were non-synonymous. Furthermore, the polymorphisms identified in the 3'-UTR were investigated to establish their possible influence on microRNA binding sites. Considering all the amino acid changes and the observed allelic combinations, it is possible to deduce at least six different translations of the buffalo prolactin receptor and, consequently, the presence at the PRLR gene of at least six alleles. Furthermore, we identified a deletion of a CACTACC heptamer between nucleotides 1102 and 1103 of exon 10 (3'-UTR), and we developed an allele-specific PCR to identify the carriers of this genetic marker. Finally, the SNP g.11188A>G, detected in exon 10 and responsible for the amino acid replacement p.His328Arg, was genotyped in 308 Italian Mediterranean river buffaloes, and an association study with milk fat traits was carried out. The statistical analysis showed a tendency that approached significance for the AA genotype with higher contents of odd branched-chain fatty acids. Thus, our results suggest that the PRLR gene is a good candidate for gene association studies with qualitative traits related to buffalo milk production.

Study on LOC426217 as a candidate gene for beak deformity in chicken

Background

The beak deformity (crossed beaks) was found in some indigenous chickens of China, such as Beijing-You (BJY), Qingyuan Partridge, and Huxu Chickens. Birds with deformed beaks have reduced feed intake and drinking, impeded growth rate, and poor production performance. Beak deformity reduces the economy of poultry industry and affects animal welfare as well. The genetic basis of this malformation remains incompletely understood. LOC426217, also named claw keratin-like, was the most up-regulated gene in the deformed beaks from a previous digital gene expression (DGE) analysis and was selected as an important candidate gene for further analysis.

Results

In the present study, quantitative real-time PCR (qRT-PCR) was firstly performed to determine the expression pattern of LOC426217 gene in deformed and normal beaks to verify the DGE results. Tissue-specific expression profile of this gene in 14 tissues was also determined using qRT-PCR. The LOC426217 was amplified from the genomic DNA of 171 deformed and 164 normal beaks, and sequenced to detect the single nucleotide polymorphisms (SNPs). The results showed that LOC426217 was significantly high-expressed in the deformed beaks, which was in good agreement with the DGE results. This gene was specifically high-expressed in beaks than other tissues. Eight SNPs were detected in LOC426217: -62G > T, 24 T > C, 36G > C, 192A > T, 204C > T, 222 T > C, 285G > T, and 363 T > C. Genotype frequency of G-62 T, T24C, G36C, T222C, and T363C loci was significant different between deformed and normal beaks. Haplotype analysis revealed one block with SNPs T24C and G36C, and one block with SNPs A192T, C204T, T222C, and G285T in normal birds, while the block with SNPs G36C and A192T in deformed ones.

Conclusions

It was concluded from these results that the over-expression of LOC426217 in the beak maybe related to the malformation. The polymorphisms of LOC426217 gene were associated with the beak deformity trait where the SNPs of G-62 T, T24C, G36C, T222C, and T363C loci maybe used as markers. The specific haplotype block in deformed birds may be a potential linkage marker for this trait.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0353-x) contains supplementary material, which is available to authorized users.