Genome-wide association study and inbreeding depression on body size traits in Qira black sheep (Ovis aries).

Qira black sheep is a famous indigenous sheep breed in China. The objectives of this study are to identify candidate genes related to body size, and to estimate the level of inbreeding depression on body size based on runs of homozygosity in Qira black sheep. Here, 188 adult Qira black sheep were genotyped with a high density (630 K) SNP chip and genome-wide association study for body weight and body size traits (including withers height, body slanting length, tail length, chest girth, chest width, and chest depth) were performed using an additive linear model. In consequence, 12 genome- and chromosome-wide significant SNPs and, accordingly, six candidate genes involved in muscle differentiation, metabolism and cell processes were identified. Of them, ZNF704 (zinc finger protein 704) was identified for body weight; AK2 (adenylate kinase 2) and PARK2 (parkin RBR E3 ubiquitin protein ligase) for tail length; MOCOS (molybdenum cofactor sulfurase) and ELP2 (elongator acetyltransferase complex subunit 2) for chest width; and MFAP1 (microfibril associated protein 1) for chest girth. Additionally, inbreeding depressions on body size were observed in the current herd. These results will provide insightful understandings into the genetic mechanisms of adult body size, and into the conservation and utilization of Qira black sheep.

Identification of genes associated with litter size combining genomic approaches in Luzhong mutton sheep.

Litter size is one of the most important reproductive traits of sheep, which has pronounced effects on the profit of husbandry enterprises and enthusiasm of breeders. Despite the importance of litter size, the underlying genetic mechanisms have not been entirely elucidated. Therefore, based on a high-density SNP chip, genome-wide comparative analysis was performed between two groups with different fecundity to reveal candidate genes linked to litter size via detection of homozygosity and selection signatures in Luzhong mutton sheep. Consequently, nine promising genes were identified from six runs of homozygosity islands, and functionally linked to reproduction (ACTL7A, ACTL7B, and ELP1), embryonic development (KLF5 and PIBF1), and cell cycle (DACH1, BORA, DIS3, and MZT1). A total of 128 genes were observed under selection, of which HECW1 and HTR1E were related to total lambs born, GABRG3, LRP1B, and MACROD2 to teat number, and AGBL1 to reproductive seasonality. Additionally, the presence of inbreeding depression implies the urgency of reasonable mating system to increase litter size in the present herd. These findings provide a comprehensive insight to the genetic makeup of litter size, and also contribute to implementation of marker-assisted selection in sheep.

Combined approaches to reveal genes associated with litter size in Yunshang black goats.

Intensive artificial selection has been imposed in Yunshang black goats, the first black specialist mutton goat breed in China, with a breeding object of improving reproductive performance, which has contributed to reshaping of the genome including the characterization of SNP, ROH and haplotype. However, variation in reproductive ability exists in the present population. A WGS was implemented in two subpopulations (polytocous group, PG, and monotocous group, MG) with evident differences of litter size. Following the mapping to reference genome, and SNP calling and pruning, three approaches - GWAS, ROH analysis and detection of signatures of selection - were employed to unveil candidate genes responsible for litter size. Consequently, 12 candidate genes containing OSBPL8 with the minimum P-value were uncovered by GWAS. Differences were observed in the pattern of ROH between two subpopulations that shared similar low inbreeding coefficients. Two ROH hotspots and 12 corresponding genes emerged from ROH pool association analysis. Based on the nSL statistic, 15 and 61 promising genes were disclosed under selection for MG and PG respectively. Of them, some promising genes participate in ovarian function (PPP2R5C, CDC25A, ESR1, RPS26 and SERPINBs), seasonal reproduction (DIO3, BTG1 and CRYM) and metabolism (OSBPL8, SLC39A5 and SERPINBs). Our study pinpointed some novel promising genes influencing litter size, provided a comprehensive insight into genetic makeup of litter size and might facilitate selective breeding in goats.

Genome-wide association study of body weight and conformation traits in neonatal sheep.

Sheep, an important source of meat, dairy products and wool, play an essential part in the global agricultural economy. Body weight and body conformation are key traits in the sheep industry; however, their underlying genetic mechanisms are poorly understood. In this study, a GWAS was implemented to identify promising genes possibly linked to birth weight (BW) and body conformation traits in neonatal sheep, using a high-throughput chip (630 K). After quality control, 277 individuals and 518 203 variants were analyzed using gemma software in a mixed linear model. A total of 48 genome-wide suggestive SNPs were obtained, of which four were associated with BW, four with withers height (WH), 11 with body length (BL) and 29 with chest girth (CG). In total, 39 genes associated with BW and body conformation traits were identified by aligning to the sheep genome (Ovis aries_v4.0), and most of them were involved in the cell cycle and body development. Promising candidate genes found included the following: FOS like 2 or AP-1 transcription factor subunit (FOSL2) for BW; potassium voltage-gated channel subfamily D member 2 (KCND2) for WH; transmembrane protein 117 (TMEM117), transforming growth factor beta induced (TGFBI), and leukocyte cell-derived chemotaxin 2 (LECT2) for BL; and trafficking kinesin protein 1 (TRAK1) and LOC101102529 for CG. These results provide cues for similar studies aiming at uncovering the genetic mechanisms underlying body development, and marker-assisted selection programs focusing on BW and body conformation traits in sheep.

Differential expression of Toll-like receptors in goat dominant and nondominant follicles.

The mechanism of dominant follicle selection is unclear because of its physiological complexity. However, some studies have reported that the immune system plays an important role in reproductive physiology. The objective of the current study was to investigate the differential expression of Toll-like receptors (TLRs) in the dominant (DFs) and nondominant follicles (NFs), and to determine the correlation between the expression of TLRs and the related genes, such as WNT4 and FOXL2. In this comparative study, the expression levels of TLRs, WNT4, and FOXL2 genes of DFs and NFs were obtained from three Dazu black goats were estimated using the real-time PCR. Our results showed no significant difference in the expression of seven TLRs (excluding TLR2, TLR5, and TLR8), WNT4, and FOXL2 between the DFs and NFs. In addition, the mRNA expression levels of WNT4 significantly correlated with the relative expression of TLR6 (r = 0.949739, P < 0.01); however, no significant expression of the TLR genes was found to be associated with FOXL2 mRNA expression. Our results support the fact that TLRs are not involved in the process of dominant follicle selection; however, TLR6 might play a role in the development of follicles by interacting with WNT4.

Characterization and analysis of differentially expressed microRNAs in hircine ovaries during the follicular and luteal phases.

Ovarian activity, which is mainly controlled by follicle-stimulating hormone and luteinizing hormone, is vital to successful reproduction and maintaining reproductive efficiency in livestock. To determine if the regulation of follicular-luteal transition occurs at the post-transcriptional level in hircine ovaries, the expression patterns of small RNAs in the ovarian tissues of Anhui white goats in the follicular and luteal phases were analyzed using Solexa sequencing. In total, 1039 miRNAs were co-expressed in the two libraries, and 278 and 469 miRNAs were specifically expressed in the hircine ovaries during the follicular and luteal phases, respectively. A total of 43 potential novel miRNAs were predicted in the two libraries. GO annotation and KEGG pathway analysis were applied to analyze the target genes of all miRNAs predicted in the two libraries. The highly and differentially expressed miRNAs included miR-26-5p, miR-145-5p, miR-145, miR-145a-5p, miR-125a-5p, miR-320d, and miR-320c, which may participate in follicular-luteal transition. Five co-expressed miRNAs, of which 2 were differentially expressed between the two libraries, were randomly selected to validate the expression pattern using RT-PCR, and the results were consistent with the Solexa sequencing data. Our present results help to clarify the roles of miRNAs in the regulation of follicular-luteal transition in goat ovaries, which may further enhance the reproductive efficiency of commercially important animals in the future.

A SNP in the 3'-UTR of HSF1 in dairy cattle affects binding of target bta-miR-484.

The heat shock transcription factor 1 gene (HSF1) plays a key role in the heat stress response. We previously found a single nucleotide polymorphism (SNP) in the 3'-untranslated region (g.4693G>T) of HSF1 that was related to thermo tolerance in Chinese Holstein cattle through association analysis. However, it is not known whether other SNPs also affect thermo tolerance.In this study a novel SNP, g.1451G>T, was identified by DNA sequencing and genotyped using creating restriction site-polymerase chain reaction methodology. The g.1451G>T polymorphic site met Hardy-Weinberg equilibrium (P > 0.05). Association analysis demonstrated that this SNP had no effect on thermo tolerance traits in Holstein cattle. Findings of the study compared to the analysis of g.4693 G>T further indicated that g.4693 G>T may play an important role in thermo tolerance, although the mechanism is not clear. RNA hybrid and Targetscan prediction showed that the minimum free energy hybridization of bta-miR-484 with HSF1 3'-UTR was -31.9 kcal/mol and g.4693 G>T was in the seed sequence of bovine HSF1 that binds to bta-miR-484. Analysis by Luciferase assay indicated that HSF1 expression was directly targeted by bta-miR-484 in HEK 293T cells, and the Rluc/luc ratio of wildtype (GG) was lower than that of the mutant (TT) (P < 0.05). These results suggest that g.4693 G>T affects binding of HSF1 to bta-miR-484.

Subtraction suppressive hybridisation analysis of differentially expressed genes associated with puberty in the goat hypothalamus.

The cost of developing replacement nanny goats could be reduced by decreasing the age at puberty because this way nanny goats could be brought into production at an earlier age. The aim of the present study was to screen genes related to puberty to investigate the molecular mechanisms of puberty. Subtracted cDNA libraries were constructed for hypothalami from juvenile (Group A), pubertal (Group B) and age-matched control pubertal (Group E) Jining grey (JG) and Liaoning cashmere (LC) goats using suppression subtractive hybridisation (SSH). Differentially expressed genes were analysed by bioinformatics methods. There were 203 expressed sequence tags (ESTs) in the subtracted cDNA libraries that were differentially expressed between JG and LC goats at the juvenile stage, 226 that were differentially expressed at puberty and 183 that were differentially expressed in the age-matched control group. The differentially expressed ESTs in each subtracted cDNA library were classified as known gene, known EST and unknown EST according to sequence homology in the GenBank non-redundant (NR) and EST database. According to gene function analysis in the COG (Cluster of Orthologous Groups) database, the known genes were grouped into 10 subdivisions in Group A, into seven subdivisions in Group E and into nine subdivisions in Group B under three categories: cellular processes and signalling, information storage and processing, and metabolism. Pathway analysis in the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database of known genes revealed that the three pathways that most differentially expressed genes were involved in were metabolic pathways, Parkinson's disease and oxidative phosphorylation. Protein interaction analysis of the high homology genes revealed the most dominant network to be structure of ribosome/protein translation, oxidative phosphorylation and carbohydrate metabolism. The results reveal that the onset of puberty is a complex event involving multiple genes in multiple biological processes. The differentially expressed genes include genes related to both neuroendocrine and energy metabolism.

Expression profiles of differentially expressed genes affecting fecundity in goat ovarian tissues.

Although RNA-Seq is an effective method for identifying and exploring novel functional genes in mammals, it has rarely been applied to study fertility-related genes in the goat. In this study, RNA-Seq was used to screen the estrus ovaries of uniparous and multiparous Anhui white goats (AWGs). In total, 15,890 genes were identified and 2201 of these were found to be differentially expressed between the genetic libraries from uniparous and multiparous goats. Compared to the uniparous library, 1583 genes were up-regulated and 618 genes were down-regulated in the multiparous library. The FER1L4 gene showed the level of highest up-regulation in the multiparous library, while SRD5A2 expression showed the greatest down-regulation. In order to determine the functions of FER1L4 and SRD5A2 in goats, the expression profiles of the two genes in different tissues from AWGs and Boer goats at diestrus were analyzed by quantitative PCR. FER1L4 and SRD5A2 showed tissue specific expression patterns and were highly expressed in ovaries from both AWGs and Boer goats. FER1L4 was more highly expressed in ovaries from multiparous than uniparous AWGs. In contrast, SRD5A2 was expressed at a lower level in multiparous AWGs. These results indicated that FER1L4 and SRD5A2 may be associated with the high fecundity of AWGs.

Polymorphism of the melatonin receptor genes and its relationship with seasonal reproduction in the Gulin Ma goat breed.

Melatonin is thought to be the main molecule that transmits the signal of seasonal change to the neuroendocrine system in seasonal breeding species. Melatonin exerts its effects through specific melatonin receptors, MTNR1A and MTNR1B. In the present study, six native goat breeds in China and one introduced goat breed were analysed to investigate the relationship between the genetic polymorphism of receptor genes and seasonal reproduction. Sequencing results showed that there were five polymorphic mutations in the MTNR1A gene and two in the MTNR1B gene. In the MTNR1A gene, genotypes AA, AB and BB for 424C>T and genotypes CC, CD and DD for 589C>A were observed in these goat breeds. In all six native goat breeds, only genotype AA was detected. In the MTNR1B gene, genotypes EE, EF and FF for 1179G>A and genotypes GG, GH and HH for 1529A>G were detected. However, in Gulin Ma goats, the genotypes EE and HH were not found. Moreover, the base of G at position 1179 and A at position 1529 were linked (By Arlequin ver 3.1, Zoological Institute, Berne, Switzerland, http://cmpg.unibe.ch/software/arlequin3,D' = 0.7496, r(2)  = 0.4421, χ(2)  = 489.8679, p = 0.000). Among these mutations, no amino acid change was found in MTNR1A, while both of the mutations in MTNR1B gene caused amino acid changes of R222H and S339G, respectively. The structural analysis showed that the R222H mutation occurred in the first amino acid residue of the third cytoplasmic loop, and the S339G mutation was located in the carboxyl terminus of the protein. In terms of seasonal breeding, all the genotypes we detected showed a similar kidding frequency distribution trend with a higher frequency in May-August than in January-April and in September-December. This suggests that the relationship between the polymorphisms in the MTNR1A and MTNR1B genes and seasonal breeding could not be established.

Analysis on DNA sequence of TSHB gene and its association with reproductive seasonality in goats.

Thyroid stimulating hormone beta chain (TSHB) is mainly expressed in pituitary and its expression is closely related to photoperiodic control of seasonal reproduction in animals. In the present study, ten primer pairs have been used to clone the DNA sequence and to detect genetic mutations of goat TSHB gene. Two DNA fragments of goat TSHB gene were obtained, which were 2,614 and 1,031 bp in length, respectively. They comprised about 2.5 kb 5' regulatory region, all of the three exons and two introns. Goat TSHB gene has a coding region of 417 bp, encoding 138 amino acids which was predicted to be a secretory protein with a signal peptide of 16 amino acids. The sequence of TSHB gene is highly conserved among mammals. In addition, five mutations (C53A, 3 bp Indel at the 287-289 locus, 34 bp Indel at the 584-617 locus, A1819C and E2_72TA) were found in goat TSHB gene and they were shown to be in strong linkage disequilibrium. Interestingly, the genotype distributions for both single locus and haplotype have shown to be significant different between seasonal and nonseasonal goat breeds. And haplotype H2 and diplotype H2/H4 may be related to year-round estrus. We preliminarily presumed that the five closely linked mutations of goat TSHB gene may be part of the causal sources for the diversities of reproductive seasonality in goats. Our study may provide a possible efficient genetic way to decrease seasonality in goats.

Analysis on DNA sequence of goat RFRP gene and its possible association with average daily sunshine duration.

Goat RFRP gene was cloned and its mutations were detected in thirteen goat breeds whose reproductive seasonality and litter size were different. Then sequence characteristics were analyzed and association analyses were performed to reveal the relationships between mutations of RFRP gene and average daily sunshine duration, reproductive seasonality as well as litter size in goats. A 4,862 bp DNA fragment of goat RFRP gene was obtained and the complete CDS of 591 bp encodes 196 amino acids, having high homology with that of other mammals. The protein was predicted to be a secreted protein with a signal peptide of 21 amino acids. Moreover, two mutations (A712G, T1493C) in 5' regulatory region and one mutation (A3438T) in exon 2 were detected. The test of genotype distribution in six selective goat breeds showed that there was no uniform significant association between the three polymorphisms and seasonal reproduction. The association just existed in some goat breeds for each locus. Interestingly, however, there was a strong positive correlation (r = 0.830, P = 0.003) between the G allele frequency of the A712G locus and average daily sunshine duration in ten local goat breeds, suggesting that RFRP gene has undergone a selective pressure in sunshine duration and may have indirect relationship with reproductive seasonality in goats. Additionally, no significant difference was found in litter size between genotypes in prolific Jining Grey goats.

Polymorphism of insulin-like growth factor 1 gene and its association with litter size in Small Tail Han sheep.

The insulin-like growth factor 1 (IGF1) gene was studied as a candidate gene for high prolificacy in sheep. Polymorphisms of 5' regulatory region and all four exons of IGF1 gene were detected in Small Tail Han (n = 277), Hu (n = 58), Texel (n = 48) and Dorset (n = 46) sheep by PCR-RFLP and PCR-SSCP analysis. A microsatellite polymorphic site and a restriction fragment length polymorphism were shown in the 5' regulatory region of IGF1 gene. The ewes with genotype 123/123 bp had 0.81 (P < 0.05) or 1.03 (P < 0.01) lambs more than those with genotype 125/125 bp or 125/127 bp, the ewes with genotype 123/125 bp had 0.46 (P < 0.05) or 0.68 (P < 0.01) lambs more than those with genotype 125/125 bp or 125/127 bp. In addition, there were two mutations (C1511G and A1513G) in 5' regulatory region of IGF1 gene. The ewes with genotype BB or AB had 0.96 (P < 0.05) or 0.38 (P < 0.05) lambs more than those with genotype AA, but there were no significant differences between BB and AB genotypes (P > 0.05) in Small Tail Han sheep. These results preliminarily indicated that these polymorphisms of IGF1 gene could be used in molecular marker-assisted selection for sheep breeding programs.

Polymorphism of 5' regulatory region of ovine FSHR gene and its association with litter size in Small Tail Han sheep.

Single nucleotide polymorphisms of 5' regulatory region of follicle-stimulating hormone receptor (FSHR) gene were detected in two high prolificacy sheep breeds (Small Tail Han and Hu sheep) and two low prolificacy sheep breeds (Corriedale and Chinese Merino sheep) by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). The results indicated that there were three genotypes (AA, AB and BB) detected by primer 1 in Hu sheep while only one genotype (AA) in other three sheep breeds, and frequencies of AA, AB and BB genotypes in Hu sheep were 0.700, 0.225 and 0.075, respectively. There were three genotypes (EE, EF and EG) detected by primer 3 in Small Tail Han sheep while only EE genotype occurred in other three sheep breeds, and frequencies of EE, EF and EG genotypes in Small Tail Han sheep were 0.775, 0.200 and 0.025, respectively. No polymorphism was detected in four sheep breeds by primer 2 and primer 4. The sequencing results showed that there were two nucleotide mutations (g. -681T>C and g. -629C>T) in genotype BB compared with AA for primer 1. As for primer 3, two mutations (g. -197G>A and g. -98T>C) in genotype EF compared with EE and two mutations (g. -200G>A and g. -197G>A) in genotype EG compared with EE. The heterozygous ewes with EG or EF had 0.89 (P < 0.05) or 0.42 (P < 0.05) lambs more than homozygous ewes (EE genotype) in Small Tail Han sheep, respectively, while there was no significant difference on litter size between EG and EF ewes.

Predictive potential of microsatellite markers on heterosis of fecundity in crossbred sheep.

Small Tail Han (STH) sheep is a famous Chinese local breed and has perfect prolificacy performance, but it is inferior to imported mutton sheep breeds on meat production. In this study, six imported male sheep populations (White Suffolk, Black Suffolk, Texel, Dorper, South African Mutton Merino and East Friesian) were crossbred with STH female sheep respectively. The heterosis values of litter size, average daily gain (ADG) and feed conversion ratio (FCR) of crossbred sheep were analyzed for seeking the optimal cross. Meanwhile 28 microsatellite markers were used to measure the genetic distance between imported populations and STH population. Regression between the genetic distance and heterosis was analyzed for evaluating potential of microsatellite on predicting heterosis. Results showed a significant positive linear correlation (r = 0.892, P < 0.05) between heterosis of litter size and genetic distance D (A) of six crosses. This implied that these microsatellite markers had moderate potential to forecast heterosis of litter size in sheep. Results of this study also indicated that South African Mutton Merino and East Friesian sheep would be the optimal sire breeds for the litter size and might bring the greatest economic benefit in six imported populations; Suffolk sheep could be prior consideration as sire breeds when breeding objective focused on ADG. Finally these results provided valuable information for Chinese sheep industry.

Polymorphisms of STAT5A gene and their association with milk production traits in Holstein cows.

The STAT5A gene was studied as a candidate gene for five milk production traits (milk yield at 305 days, protein percentage, fat percentage, lactose percentage and dry matter percentage) in Holstein cows. According to the sequence of bovine STAT5A gene, two pairs of primers (P1 and P2) were designed to detect polymorphisms of STAT5A gene in 401 Holstein cows by PCR-RFLP and PCR-SSCP. The results showed that the products amplified by primers P1 and P2 displayed polymorphisms. For P1, three genotypes (AA, AG, and GG) were detected, and the frequency of AA/AG/GG was 0.252/0.486/0.262, respectively. Sequence analysis revealed a single nucleotide substitution A-G at 14217 bp (GenBank NC_007317) of bovine STAT5A gene while compared GG genotype with AA genotype. The differences of the least squares means for the four milk production traits (milk yield at 305 days, fat percentage, lactose percentage and dry matter percentage) between AA, AG and GG were not significant (P > 0.05). Least squares mean of protein percentage for AG or GG was significantly higher than that for AA (P < 0.05); the difference of the least squares mean for protein percentage was not significant between AG and GG (P > 0.05). For P2, three genotypes (CC, CT, and TT) were detected in Holstein cows, and the frequency of CC/CT/TT was 0.751/0.234/0.015, respectively. Sequencing revealed an insertion CCT at 17266 (NC_007317) of bovine STAT5A gene while compared CC genotype with TT genotype. The differences of the least squares means for the three milk production traits (protein percentage, lactose percentage and dry matter percentage) between CC, CT and TT were not significant (P > 0.05). Least squares mean of milk yield at 305 days for TT or CT was significantly higher than that for CC (P < 0.05); the difference of the least squares mean for milk yield at 305 days was not significant between TT and CT (P > 0.05). Least squares mean of fat percentage for CC or CT was significantly higher than that for TT (P < 0.05); the difference of the least squares mean for fat percentage was not significant between CC and CT (P > 0.05). The results preliminarily indicated that allele G of A14217G polymorphic site of STAT5A gene is a potential DNA marker for improving protein percentage in dairy cattle, 17266indelCCT polymorphic site of STAT5A gene is a potential DNA marker for improving milk yield at 305 days and fat percentage in dairy cattle.

Polymorphism of exon 2 of BoLA-DRB3 gene and its relationship with somatic cell score in Beijing Holstein cows.

In the present study, the exon 2 and 3' end sequence of intron 1 of BoLA-DRB3 gene of 211 Beijing Holstein cows was amplified and a uniform fragment of 284 bp was obtained. The genetic polymorphism was investigated by PCR-RFLP using two restriction endonucleases HaeIII and BstYI. Seven genotypes were detected by digesting the PCR products with HaeIII. The frequency of AA, AB, AC, AD, BB, BC and BF genotypes was 0.4638, 0.0193, 0.0193, 0.3478, 0.0290, 0.0386 and 0.0822, respectively. Three genotypes were found by digesting the PCR products with BstYI. The frequency of AA, AB and BB genotypes was 0.0569, 0.2844 and 0.6587, respectively. The relationship between the polymorphisms in exon 2 of BoLA-DRB3 gene and somatic cell score (SCS) in Beijing Holstein cows was analyzed by least squares linear model. No significant difference was detected among least squares means of SCS for seven HaeIII-RFLP genotypes (P > 0.05). As for BstYI-RFLP analysis, least squares mean of SCS for AA was significantly lower than that for AB (P < 0.05) or BB (P < 0.05), and no significant difference was detected between AB and BB genotypes (P > 0.05). BstYI AA was the most favorable genotype and BstYI BB was the most unfavorable genotype for mastitis resistance. The information found in the present study is very important for improving mastitis resistance in dairy cattle by marker assisted selection.

Polymorphisms of caprine POU1F1 gene and their association with litter size in Jining Grey goats.

Seven pairs of primers were designed to amplify 5' promoter region, six exons and partial introns and to detect the polymorphisms of POU1F1 gene in five goat breeds with different prolificacy. The results showed that six mutations were identified in caprine POU1F1 gene including C256T in exon 3, C53T and T123G in intron 3, and G682T (A228S), T723G and C837T in exon 6. The former four mutations were novel SNPs in goat POU1F1 gene. The 53 and 123 loci were in complete linkage disequilibrium in five caprine breeds. Regarding the 256 locus, the Jining Grey goat does with genotype CT had 0.66 kids more than those with genotype CC (P < 0.05), while does with genotype GT had 0.63 (P < 0.05) kids more than those with genotype GG at the 682 locus. The present study preliminarily showed an association between allele T at the 256 and 682 loci of POU1F1 gene and high litter size in Jining Grey goats. Totally 16 haplotypes and 50 genotypes were identified at the above six loci in POU1F1 gene of five goat breeds. Three common haplotypes (hap2, hap3 and hap4) were identified in five goat breeds joined. Four specific haplotypes (hap7, hap9, hap11 and hap13) were detected in Jining Grey goats. The predominant haplotype was hap1 (35.29% and 48.25%) in both Jining Grey and Guizhou White goats, while hap4 (50%) in Boer goats, and hap2 (42.86% and 38.75%) in both Wendeng Dairy and Liaoning Cashmere goats. The most frequent genotypes at six loci in the above five goat breeds were hap1/hap2 (14.38%) and hap1/hap4 (14.38%), hap1/hap2 (38.60%), hap4/hap4 (40.91%), hap2/hap4 (26.53%), hap2/hap5 (20.00%), respectively. The Jining Grey goat does with nine genotypes analyzed of POU1F1 gene showed no obvious difference in litter size.

Polymorphism of GDF9 gene and its association with litter size in goats.

Growth differentiation factor 9 (GDF9) was studied as a candidate gene for high prolificacy in goats. The polymorphism of exon 1 and flanking of GDF9 gene was detected by PCR-SSCP in five goat breeds with different prolificacy. Three genotypes (AA, AB and BB) were detected in goat breeds joined and two silent mutations (c.183A>C and c.336C>T) were identified in comparison genotype AA with genotype BB. Heterozygous genotype AB and wild type BB were detected in all five goat breeds and homozygous genotype AA was only detected in Jining Grey goats. The frequencies of genotypes AA, AB and BB were 0.18, 0.42 and 0.40 in Jining Grey goats, respectively. The genotype distribution was different (P < 0.01) between high prolificacy breed (Jining Grey goat) and low prolificacy breeds (Boer, Wendeng Dairy, Liaoning Cashmere and Beijing native goats). The Jining Grey goat does with genotype AA and AB had 0.72 (P < 0.01) and 0.56 (P < 0.01) kids more than those with genotype BB, respectively. The does with genotype AA had 0.16 (P > 0.05) kids more than those with genotype AB. These indicated that the allele A may have certain correlation with prolificacy in Jining Grey goats.

Polymorphisms of the cocaine-amphetamine-regulated transcript (CART) gene and their association with reproductive traits in Chinese goats.

Polymorphisms of the CART gene were investigated by PCR-single-strand conformation polymorphism analysis in 540 samples from 10 goat breeds. Ten novel single-nucleotide polymorphisms as well as three microsatellites were detected; a mutation, 77T → C, led to an amino acid change (Leu → Ser). Associations between polymorphic loci and reproductive traits were analyzed in Chuandong White, Guizhou White and Gulin Ma breeds. Mutation at position 524 had no significant effect on litter size in these three goat breeds. The polymorphism 539C → A differed significantly among the three breeds (P < 0.05); C(7)T(8)/C(9)T(8) at 939 was associated with larger litter size (P < 0.05) than genotypes C(7)T(8)/C(7)T(8) and C(7)T(8)/C(8)T(8). No significant association of birth weight was found with gene variation (524C → T, 539C → A and 939 CnTn). These findings could be valuable for marker-assisted selection for goat breeding.