A SNP Genetic Map for Pacific White Shrimp (Litopenaeus vannamei)

Pacific white shrimp are of particular economic importance to the global shrimp aquaculture industry. We utilized the limited public sequence information, mainly genetic markers called 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. 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

Short communication. SNP analyses of the 5HT1R and STAT genes in Pacific white shrimp, Litopenaeus vannamei

Shrimp aquaculture is one of the growing animal industries. Breeding stocks with high disease-resistance and growth rate are of particular interest to shrimp breeders. Association studies are useful to find genetic markers for marker assisted selection of animals. Using six Litopenaeus vannamei individuals from a sample population, four single nucleotide polymorphisms (SNPs) were found in the 5HT1R (5-hydroxytryptamine receptor1) gene and one SNP in the STAT (signal transducer and activator of transcription) gene. However, the SNP in the STAT gene was homozygous in a different population used for association analyses. The association analyses revealed that allele C of two SNPs, C109T and C395G in 5HT1R, tended to be associated with increased body weight. Further studies need to be conducted using a large and diverse population sample

Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

Background Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirement predicted from growth and maintenance. Pigs with low RFI have reduced feed costs without compromising their growth. Identification of genes or genetic markers associated with RFI will be useful for marker-assisted selection at an early age of animals with improved feed efficiency. Methodology/Principal findings Whole genome association studies (WGAS) for RFI, average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA) were performed on 1,400 pigs from the divergently selected ISU-RFI lines, using the Illumina PorcineSNP60 BeadChip. Various statistical methods were applied to find SNPs and genomic regions associated with the traits, including a Bayesian approach using GenSel software, and frequentist approaches such as allele frequency differences between lines, single SNP and haplotype analyses using PLINK software. Single SNP and haplotype analyses showed no significant associations (except for LMA) after genomic control and FDR. Bayesian analyses found at least 2 associations for each trait at a false positive probability of 0.5. At generation 8, the RFI selection lines mainly differed in allele frequencies for SNPs near (\u3c0.05 Mb) genes that regulate insulin release and leptin functions. The Bayesian approach identified associations of genomic regions containing insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI, of regions with energy homeostasis (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG, and of fat metabolism genes (e.g., ACOXL, AEBP1) with BF. Specifically, a very highly significantly associated QTL for LMA on SSC7 with skeletal myogenesis genes (e.g.,KLHL31) was identified for subsequent fine mapping. Conclusions/significance Important genomic regions associated with RFI related traits were identified for future validation studies prior to their incorporation in marker-assisted selection programs

Genome Wide Association Studies for Residual Feed Intake Traits in Pigs

Residual feed intake (RFI), a measure of feed efficiency, is the difference between observed feed intake and the expected feed requirements computed based ongrowth and maintenance of the pig. Efficient animals with low RFI can be selected at an early age with genetic markers. Hence, the present study in 1400 pigs used several statistical methods to find the associations between more than 50,000 genetic markers and RFI, and its related traits such as average daily feed intake (ADFI), average daily gain (ADG), back fat (BF) and loin muscle area (LMA). Associations were observed for a combination of genetic markers on chromosomal regions containing insulin release genes (e.g., GLP1R, CDKAL, SGMS1) with RFI and ADFI, energy balance (e.g., MC4R, PGM1, GPR81) and muscle growth related genes (e.g., TGFB1) with ADG, fat related genes (e.g., ACOXL, AEBP1) with BF and skeletal muscle development genes (e.g., KLHL31) with LMA. Overall, these studies identified important chromosomal regions for further scrutiny to consider them for selection of pigs for RFI and its related 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

Large-scale association study for structural soundness and leg locomotion traits in the pig

<p>Abstract</p> <p>Background</p> <p>Identification and culling of replacement gilts with poor skeletal conformation and feet and leg (FL) unsoundness is an approach used to reduce sow culling and mortality rates in breeding stock. Few candidate genes related to soundness traits have been identified in the pig.</p> <p>Methods</p> <p>In this study, 2066 commercial females were scored for 17 traits describing body conformation and FL structure, and were used for association analyses. Genotyping of 121 SNPs derived from 95 genes was implemented using Sequenom's MassARRAY system.</p> <p>Results</p> <p>Based on the association results from single trait and principal components using mixed linear model analyses and false discovery rate testing, it was observed that <it>APOE, BMP8, CALCR, COL1A2, COL9A1, DKFZ, FBN1 </it>and <it>VDBP </it>were very highly significantly (P < 0.001) associated with body conformation traits. The genes <it>ALOX5, BMP8</it>, <it>CALCR, OPG</it>, <it>OXTR </it>and <it>WNT16 </it>were very highly significantly (P < 0.001) associated with FL structures, and <it>APOE, CALCR, COL1A2, GNRHR, IHH</it>, <it>MTHFR </it>and <it>WNT16 </it>were highly significantly (P < 0.01) associated with overall leg action. Strong linkage disequilibrium between <it>CALCR </it>and <it>COL1A2 </it>on SSC9 was detected, and haplotype -ACGACC- was highly significantly (P < 0.01) associated with overall leg action and several important FL soundness traits.</p> <p>Conclusion</p> <p>The present findings provide a comprehensive list of candidate genes for further use in fine mapping and biological functional analyses.</p

Genome-Wide Association Study Identifies Loci for Body Composition and Structural Soundness Traits in Pigs

Background The recent completion of the swine genome sequencing project and development of a high density porcine SNP array has made genome-wide association (GWA) studies feasible in pigs. Methodology/Principal Findings Using Illumina\u27s PorcineSNP60 BeadChip, we performed a pilot GWA study in 820 commercial female pigs phenotyped for backfat, loin muscle area, body conformation in addition to feet and leg (FL) structural soundness traits. A total of 51,385 SNPs were jointly fitted using Bayesian techniques as random effects in a mixture model that assumed a known large proportion (99.5%) of SNPs had zero effect. SNP annotations were implemented through the Sus scrofa Build 9 available from pig Ensembl. We discovered a number of candidate chromosomal regions, and some of them corresponded to QTL regions previously reported. We not only have identified some well-known candidate genes for the traits of interest, such as MC4R (for backfat) and IGF2 (for loin muscle area), but also obtained novel promising genes, including CHCHD3 (for backfat), BMP2 (for loin muscle area, body size and several FL structure traits), and some HOXA family genes (for overall leg action). The candidate regions responsible for body conformation and FL structure soundness did not overlap greatly which implied that these traits were controlled by different genes. Functional clustering analyses classified the genes into categories related to bone and cartilage development, muscle growth and development or the insulin pathway suggesting the traits are regulated by common pathways or gene networks that exert roles at different spatial and temporal stages. Conclusions/Significance This study is one of the earliest GWA reports on important quantitative traits in pigs, and the findings will contribute to the further biological function analysis of the identified candidate genes and potential utilization of them in marker assisted selection

Genome-Wide Association Studies for Important Economic Traits in Domestic Animals Using High Density SNP Genotyping

New methods for genotyping large numbers of genetic markers have been developed, which are cheaper and faster than previous techniques. Iowa State University researchers helped to develop a tool known as the porcine 60K SNP chip that can genotype 64,232 genetic markers simultaneously in a single pig. Similar SNP chips are available for many other species, including sheep, chicken, cattle and dog. These new chips allow for trait association studies to be conducted using many more genetic markers spread across the genome (known as genome-wide association studies or GWASs). In our lab GWASs were performed for a variety of traits in pigs, sheep, and dogs. In pigs, a number of candidate genetic markers and chromosomal regions were associated with feed intake, average daily gain, body composition (such as 10th rib backfat and loin muscle area), feet and leg structure (such as overall leg action, front and rear leg pasterns), and reproductive traits. Other work in pigs involved looking for duplicated regions of the genome to identify genes that were duplicated, which could impact many traits in the pig. In sheep, chondrodysplasia (a condition in which the legs are malformed and other problems arise) was found to be associated with a group of consecutive markers on one chromosome. SNP chip research in dogs is ongoing to look for genes associated with cryptorchidism (retained testicles). These findings offer a promising list of genetic markers that can hopefully be used in the near future to improve animal production via lowered input costs and reduced incidence of disease