Association of taurine with ovarian follicular steroids and postpartum anestrus condition in Murrah buffaloes.

Taurine is an abundant intracellular beta-amino acid majorly synthesized in the liver and transported through plasma. In mammals, taurine was reported to be involved in various physiological functions, including the enhancement of testosterone levels, the major estradiol precursor. Therefore, we hypothesize that taurine levels are associated with ovarian follicular steroids as well as with a reproductive problem called postpartum anestrus (PPA) in dairy buffaloes. To understand the taurine levels and its possible role in buffalo ovarian follicles, a correlation was established among taurine, estradiol, and testosterone levels in the ovarian follicular fluid. For this purpose, buffalo ovaries were obtained from the slaughterhouse, and follicular fluid samples were collected from small (<4 mm), medium (4-8 mm) and large (>8 mm) follicles. Taurine and steroid levels in the follicular fluid were analyzed by TLC and ELISA, respectively. Taurine and testosterone levels were significantly (P < 0.05) higher in the follicular fluid of small and medium follicles than large follicles, whereas the estradiol levels were significantly (P < 0.001) higher in the large follicles. Thus, taurine showed a positive correlation (r = 0.75) with testosterone and a negative correlation (r = -0.77) with estradiol in buffalo follicular fluid, indicating its possible role in testosterone function during follicular development. Interestingly, significantly (P < 0.001) lower plasma taurine levels in PPA (n = 50) than normal cyclic (n = 50) buffaloes represented its association with PPA. Therefore, our present study recommends the need for future nutrition studies on taurine supplementation to PPA buffaloes.

Identification of species-specific novel transcripts in pig reproductive tissues using RNA-seq.

Although structural properties of the porcine reproductive system are shared by many placental mammals, some combination of these properties is unique to pigs. To explore whether genomic elements specific to pigs could potentially underlie this uniqueness, we made the first step to identify novel transcripts in two representative pig reproductive tissues by the technique of massively parallel sequencing. To automate the whole process, we built a computational pipeline, which can also be easily extended for similar studies in other species. In total, 5516 and 9061 novel transcripts were found, and 159 and 252 novel transcripts appear to be specific to pigs for the placenta and testis respectively. Furthermore, these novel transcripts were found to be enriched in quantitative trait loci (QTL) regions for reproduction traits in pigs. We validated eight of these novel transcripts by quantitative real-time PCR. With respect to their genomic organization and their functional relationship to reproduction, these transcripts need to be further validated and explored in various pig breeds to better comprehend the relevant aspects of pig physiology that contribute to reproductive performance.

Relationship between gilt behavior and meat quality using principal component analysis.

Pig on-farm behavior has important repercussions on pig welfare and performance, but generally its relationship with meat quality is not well understood. We used principal component analysis to determine the relationship between meat quality traits, feeding patterns, scale activity, and number of conflict-avoidance interactions. The first principal component indicated that gilts with greater daily feed intake stayed longer in the feeder and their meat had increased intramuscular fat (IMF), was lighter in color, and, in the second principal component, had better juiciness, tenderness, chewiness, and flavor. Meat from gilts with lower scale activity scores appeared to have more IMF but greater drip losses (DL). The third principal component suggested that dominant gilts could gain priority access to the feeder, eating more and growing fatter. In conclusion, except for the slight associations with IMF and DL, gilt scale activity and conflict-avoidance behaviors were not good indicators of final meat quality attributes.

In a shake of a lamb's tail: using genomics to unravel a cause of chondrodysplasia in Texel sheep.

Chondrodysplasia in Texel sheep is a recessively inherited disorder characterized by dwarfism and angular deformities of the forelimbs. A genome-wide association study using the Illumina OvineSNP50 BeadChip on 15 sheep diagnosed as affected and eight carriers descended from three affected rams was conducted to uncover the genetic cause. A homozygous region of 25 consecutive single nucleotide polymorphism (SNP) loci was identified in all affected sheep, covering a region of 1 Mbp on ovine chromosome 4. Seven positional candidate genes - including the solute carrier family 13 (sodium/sulphate symporters), member 1 (SLC13A1) - were identified and used to search for new SNPs for fine mapping of the causal locus. The SLC13A1 gene, encoding a sodium/sulphate transporter, was the primary candidate gene attributable to similar phenotypes observed in the Slc13a1 knockout mouse model. We discovered a 1-bp deletion of T (g.25513delT) at the 107 bp position of exon 3 in the SLC13A1 gene. Genotyping by direct sequencing and restriction fragment length polymorphism analysis for this mutation showed that all 15 affected sheep were g.25513delT/g.25513delT; the eight carriers were g.25513delT/T and 54 normal controls were T/T. The mutation g.25513delT shifts the open reading frame of SLC13A1 to introduce a stop codon and truncate C-terminal amino acids. It was concluded that the g.25513delT mutation in the SLC13A1 gene was responsible for the chondrodysplasia seen in these Texel sheep. This knowledge can be used to identify carriers with the defective g.[25513delT] allele to avoid at-risk matings to improve animal welfare and decrease economic losses.

A missense mutation in AGTPBP1 was identified in sheep with a lower motor neuron disease.

A type of lower motor neuron (LMN) disease inherited as autosomal recessive in Romney sheep was characterized with normal appearance at birth, but with progressive weakness and tetraparesis after the first week of life. Here, we carried out genome-wide homozygosity mapping using Illumina Ovine SNP50 BeadChips on lambs descended from one carrier ram, including 19 sheep diagnosed as affected and 11 of their parents that were therefore known carriers. A homozygous region of 136 consecutive single-nucleotide polymorphism (SNP) loci on chromosome 2 was common to all affected sheep and it was the basis for searching for the positional candidate genes. Other homozygous regions shared by all affected sheep spanned eight or fewer SNP loci. The 136-SNP region contained the sheep ATP/GTP-binding protein 1 (AGTPBP1) gene. Mutations in this gene have been shown to be related to Purkinje cell degeneration (pcd) phenotypes including ataxia in mice. One missense mutation c.2909G>C on exon 21 of AGTPBP1 was discovered, which induces an Arg to Pro substitution (p.Arg970Pro) at amino-acid 970, a conserved residue for the catalytic activity of AGTPBP1. Genotyping of this mutation showed 100% concordant rate with the recessive pattern of inheritance in affected, carrier, phenotypically normal and unrelated normal individuals. This is the first report showing a mutant AGTPBP1 is associated with a LMN disease in a large mammal animal model. Our finding raises the possibility of human patients with the same etiology caused by this gene or other genes in the same pathway of neuronal development.

A whole-genome association study for pig reproductive traits.

A whole-genome association study was performed for reproductive traits in commercial sows using the PorcineSNP60 BeadChip and Bayesian statistical methods. The traits included total number born (TNB), number born alive (NBA), number of stillborn (SB), number of mummified foetuses at birth (MUM) and gestation length (GL) in each of the first three parities. We report the associations of informative QTL and the genes within the QTL for each reproductive trait in different parities. These results provide evidence of gene effects having temporal impacts on reproductive traits in different parities. Many QTL identified in this study are new for pig reproductive traits. Around 48% of total genes located in the identified QTL regions were predicted to be involved in placental functions. The genomic regions containing genes important for foetal developmental (e.g. MEF2C) and uterine functions (e.g. PLSCR4) were associated with TNB and NBA in the first two parities. Similarly, QTL in other foetal developmental (e.g. HNRNPD and AHR) and placental (e.g. RELL1 and CD96) genes were associated with SB and MUM in different parities. The QTL with genes related to utero-placental blood flow (e.g. VEGFA) and hematopoiesis (e.g. MAFB) were associated with GL differences among sows in this population. Pathway analyses using genes within QTL identified some modest underlying biological pathways, which are interesting candidates (e.g. the nucleotide metabolism pathway for SB) for pig reproductive traits in different parities. Further validation studies on large populations are warranted to improve our understanding of the complex genetic architecture for pig reproductive traits.

Whole-genome association analyses for lifetime reproductive traits in the pig.

Profits for commercial pork producers vary in part because of sow productivity or sow productive life (SPL) and replacement costs. During the last decade, culling rates of sows have increased to more than 50% in the United States. Both SPL and culling rates are influenced by genetic and nongenetic factors. A whole-genome association study was conducted for pig lifetime reproductive traits, including lifetime total number born (LTNB), lifetime number born alive (LNBA), removal parity, and the ratio between lifetime nonproductive days and herd life. The proportion of phenotypic variance explained by markers was 0.15 for LTNB and LNBA, 0.12 for removal parity, and 0.06 for the ratio between lifetime nonproductive days and herd life. Several informative QTL regions (e.g., 14 QTL regions for LTNB) and genes within the regions (e.g., SLC22A18 on SSC2 for LTNB) were associated with lifetime reproductive traits in this study. Genes associated with LTNB and LNBA were similar, reflecting the high genetic correlation (0.99 ± 0.003) between these traits. Functional annotation revealed that many genes at the associated regions are expressed in reproductive tissues. For instance, the SLC22A18 gene on SSC2 associated with LTNB has been shown to be expressed in the placenta of mice. Many of the QTL regions showing associations coincided with previously identified QTL for fat deposition. This reinforces the role of fat regulation for lifetime reproductive traits. Overall, this whole-genome association study provides a list of genomic locations and markers associated with pig lifetime reproductive traits that could be considered for SPL in future studies.

A gene-based SNP linkage map for pacific white shrimp, Litopenaeus vannamei.

Pacific white shrimp (Litopenaeus vannamei) are of particular economic importance to the global shrimp aquaculture industry. However, limited genomics information is available for the penaeid species. We utilized the limited public information available, mainly single nucleotide polymorphisms (SNPs) and expressed sequence tags, to discover markers for the construction of the first SNP genetic map for Pacific white shrimp. In total, 1344 putative SNPs were discovered, and out of 825 SNPs genotyped, 418 SNP markers from 347 contigs were mapped onto 45 sex-averaged linkage groups, with approximate coverage of 2071 and 2130 cm for the female and male maps, respectively. The average-squared correlation coefficient (r(2)), a measure of linkage disequilibrium, for markers located more than 50 cm apart on the same linkage group, was 0.15. Levels of r(2) increased with decreasing inter-marker distance from approximately 80 cm, and increased more rapidly from approximately 30 cm. A QTL for shrimp gender was mapped on linkage group 13. Comparative mapping to model organisms, Daphnia pulex and Drosophila melanogaster, revealed extensive rearrangement of genome architecture for L. vannamei, and that L. vannamei was more related to Daphnia pulex. This SNP genetic map lays the foundation for future shrimp genomics studies, especially the identification of genetic markers or regions for economically important traits.

The role of gene discovery, QTL analyses and gene expression in reproductive traits in the pig.

The reproductive performance of the sow is one of the key factors affecting production profitability of the pig industry. Reproductive traits are in general, lowly heritable, and with reliable markers, they can be used to enhance current selection procedures for improvement of these traits. To find potential markers, large scale quantitative trait loci (QTL) and candidate gene studies have been conducted for reproductive traits. The present review discusses QTL and candidate gene discovery, large scale SNP association studies, gene expression profiling and discovery of miRNA regulation of pig reproductive tissues. Many QTL have been found for reproduction traits and a limited number of useful genes (e.g.: ESR1, PRLR, FSHB, EPOR and RBP4) have been found to have significant associations with reproductive traits. Expression studies with reproductive tissues have revealed differential expression within a few gene networks which need further mapping and association analyses to select prospective gene markers. The near completion of the pig genome sequence and the development of high density SNP chips will allow for large scale SNP association studies for pig reproductive traits in the future. Collection of appropriate phenotypes in large numbers and in broad populations representative of the swine industry are required if such genomic studies will ultimately be successful.

The MMP2 gene may be associated with longissimus dorsi muscle area in the pig (Sus scrofa).

The matrix metalloproteinase-2 gene (MMP2) was found to be associated with hip structure in pigs. Recently three quantitative trait loci (QTLs) for loin muscle area were found on chromosome 6, to which MMP2 was mapped. In the present study, association analyses were conducted in two pig populations for a single-nucleotide polymorphism (SNP) c.-1959C>G present at a putative promoter region of the MMP2 gene. The association results showed that the animals with the C allele have a significantly larger loin muscle area than that of the animals with the G allele (P < 0.05). To confirm the present results, further functional studies and an additional causative SNP discovery in pigs with various genetic backgrounds are necessary.

Identification of genetic markers associated with fatness and leg weakness traits in the pig.

Pigs have undergone long-term selection in commercial conditions for improved rate and efficiency of lean gain. Interestingly, it has been observed in both experimental and field conditions that leg weakness has increased over time, concurrent with the selection for improved rate of lean gain, while fatter animals tend to have better leg action, and foot and leg (FL) structure. The exact molecular mechanisms or individual genes responsible for this apparent genetic correlation between fatness and leg weakness and other physical adaptability traits have been less well reported. Based on our recent studies involving candidate genes and leg weakness traits, the present investigation has identified 30 SNPs from 26 genes that were found to be associated with 10th rib backfat in a sow population consisting of 2066 animals. The specific alleles associated with increased backfat tended to be associated with better overall leg action, as shown for the genes including MTHFR, WNT2, APOE, BMP8, GNRHR and OXTR, while inconsistent associations with the single FL structure trait and backfat were observed for other genes. This study suggests that in some cases there may be a common genetic mechanism or linked genes regulating fatness and leg weakness. Such relationships are clearly complex, and the utilization of genetic markers associated with both traits should be treated cautiously.

Detailed characterization of the porcine MC4R gene in relation to fatness and growth.

In contrast to the human MC4R gene, where multiple variants have been described, several of which are associated with appetite and obesity, few MC4R variants have been reported in the pig. The most interesting polymorphism reported to date in the pig is p.Asp298Asn, which is significantly associated with variation in growth and fatness traits in most breeds and crosses. However, some reports have seemingly failed to confirm this association. The discrepancy of p.Asp298Asn associations in some pig populations suggested that further discovery of SNPs in MC4R would be useful. Utilizing the recently released pig genome sequence information, we obtained the whole MC4R genome sequence and detected five additional SNPs, a variable (CA)(n) repeat and a C indel in the ISU Berkshire x Yorkshire pig resource family. Linkage disequilibrium (LD) analysis revealed that the additional five SNPs were not in strong LD with p.Asp298Asn, but single marker association analysis indicated that they were significantly (P < 0.05) associated with fatness measures and very highly significantly (P < 0.0001) associated with average daily gain on test (ADGTEST). Three major haplotypes were identified and the subsequent association analyses suggested that the two non-synonymous SNPs had different effects, e.g. p.Arg236His influenced back fat and growth on test while p.Asp298Asn was primarily associated with variation in growth rate in this population. An interaction effect between these two SNPs was found for ADGTEST, which may partly explain some of the previous discrepancies reported for MC4R in different pig populations. Examination of the p.Arg236His polymorphism in populations where the effect of p.Asp298Asn is limited is warranted.

SNP detection and comparative linkage mapping of 66 bone-related genes in the pig.

Osteoporosis is a multigenic complex disorder. Though the mouse and rat are used as experimental models for human osteoporosis, the pig bone remodeling cycle is histologically more similar to human than the rat or mouse. Moreover, livestock genomics have many advantages over model organisms and human studies for complex trait dissection. Hence, in the present work 66 bone-related genes were newly genetically mapped on pig chromosomes. Comparative chromosomal patterns of bone-related genes in the pig, human, mouse and rat provide clues that the chromosomal organization of bone-related genes in pigs is more similar to human than that of the mouse and rat. Therefore, the pig can be considered as one of the better models for studying the molecular genetics of bone-related disorders.

SNP discovery in genes affecting leg health traits in pigs.

Sow reproductive life is influenced by lameness issues. It has been reported that up to 44 percent of sows have locomotive problems. To date, few genome scans or association studies have been conducted to look at genes controlling lameness and other gait traits. In addition to health problems associated with leg and bone disorders, the pig has been suggested to be a good model for human bone disorders. Hence, the present study examined 134 porcine genes affecting skeletal development, mineral metabolism and other candidate genes for single nucleotide polymorphism (SNP) discovery. Atotal of over 370 SNPs have been identified to date and are being mapped. These SNPs are also being investigated for their associations with gait and locomotion problems in approximately 2,000 commercial pigs scored for various leg and locomotion traits. The association analysis of 22 genes revealed that the genes CALCR, HDBP CALCA, MTHFR, OXTR, IHH, ANKH, LRCH1 and OPN were significantly associated with leg and body conformation traits which affect the health and productivity of pigs.