Genome-Wide Association Study Singles Out SCD and LEPR as the Two Main Loci Influencing Intramuscular Fat Content and Fatty Acid Composition in Duroc Pigs

[EN] Intramuscular fat (IMF) content and fatty acid composition affect the organoleptic quality and nutritional value of pork. A genome-wide association study was performed on 138 Duroc pigs genotyped with a 60k SNP chip to detect biologically relevant genomic variants influencing fat content and composition. Despite the limited sample size, the genome-wide association study was powerful enough to detect the association between fatty acid composition and a known haplotypic variant in SCD (SSC14) and to reveal an association of IMF and fatty acid composition in the LEPR region (SSC6). The association of LEPR was later validated with an independent set of 853 pigs using a candidate quantitative trait nucleotide. The SCD gene is responsible for the biosynthesis of oleic acid (C18:1) from stearic acid. This locus affected the stearic to oleic desaturation index (C18:1/C18:0), C18: 1, and saturated (SFA) and monounsaturated (MUFA) fatty acids content. These effects were consistently detected in gluteus medius, longissimus dorsi, and subcutaneous fat. The association of LEPR with fatty acid composition was detected only in muscle and was, at least in part, a consequence of its effect on IMF content, with increased IMF resulting in more SFA, less polyunsaturated fatty acids (PUFA), and greater SFA/PUFA ratio. Marker substitution effects estimated with a subset of 65 animals were used to predict the genomic estimated breeding values of 70 animals born 7 years later. Although predictions with the whole SNP chip information were in relatively high correlation with observed SFA, MUFA, and C18: 1/C18: 0 (0.48-0.60), IMF content and composition were in general better predicted by using only SNPs at the SCD and LEPR loci, in which case the correlation between predicted and observed values was in the range of 0.36 to 0.54 for all traits. Results indicate that markers in the SCD and LEPR genes can be useful to select for optimum fatty acid profiles of pork.This research was funded by the Spanish Ministry of Economy and Competitiveness (MINECO; grants AGL2012-33529 and AGL2015-65846-R).Ros-Freixedes, R.; Gol, S.; Pena, R.; Tor, M.; Ibañez Escriche, N.; Dekkers, J.; Estany, J. (2016). Genome-Wide Association Study Singles Out SCD and LEPR as the Two Main Loci Influencing Intramuscular Fat Content and Fatty Acid Composition in Duroc Pigs. PLoS ONE. 11(3). https://doi.org/10.1371/journal.pone.0152496S113Cameron, N. ., Enser, M., Nute, G. ., Whittington, F. ., Penman, J. ., Fisken, A. ., … Wood, J. . (2000). Genotype with nutrition interaction on fatty acid composition of intramuscular fat and the relationship with flavour of pig meat. Meat Science, 55(2), 187-195. doi:10.1016/s0309-1740(99)00142-4Christophersen, O. A., & Haug, A. (2011). Animal products, diseases and drugs: a plea for better integration between agricultural sciences, human nutrition and human pharmacology. Lipids in Health and Disease, 10(1), 16. doi:10.1186/1476-511x-10-16Ntawubizi, M., Colman, E., Janssens, S., Raes, K., Buys, N., & De Smet, S. (2010). Genetic parameters for intramuscular fatty acid composition and metabolism in pigs1. Journal of Animal Science, 88(4), 1286-1294. doi:10.2527/jas.2009-2355Ros-Freixedes, R., Reixach, J., Tor, M., & Estany, J. (2012). Expected genetic response for oleic acid content in pork1. Journal of Animal Science, 90(12), 4230-4238. doi:10.2527/jas.2011-5063Clop, A., Ovilo, C., Perez-Enciso, M., Cercos, A., Tomas, A., Fernandez, A., … Noguera, J. L. (2003). Detection of QTL affecting fatty acid composition in the pig. Mammalian Genome, 14(9), 650-656. doi:10.1007/s00335-002-2210-7Kim, Y., Kong, M., Nam, Y. J., & Lee, C. (2006). A Quantitative Trait Locus for Oleic Fatty Acid Content on Sus scrofa Chromosome 7. Journal of Heredity, 97(5), 535-537. doi:10.1093/jhered/esl026Sanchez, M.-P., Iannuccelli, N., Basso, B., Bidanel, J.-P., Billon, Y., Gandemer, G., … Le Roy, P. (2007). Identification of QTL with effects on intramuscular fat content and fatty acid composition in a Duroc × Large White cross. BMC Genetics, 8(1), 55. doi:10.1186/1471-2156-8-55Guo, T., Ren, J., Yang, K., Ma, J., Zhang, Z., & Huang, L. (2009). Quantitative trait loci for fatty acid composition in longissimus dorsi and abdominal fat: results from a White Duroc × Erhualian intercross F2population. Animal Genetics, 40(2), 185-191. doi:10.1111/j.1365-2052.2008.01819.xC.M. Dekkers, J. (2012). Application of Genomics Tools to Animal Breeding. Current Genomics, 13(3), 207-212. doi:10.2174/138920212800543057Uemoto, Y., Nakano, H., Kikuchi, T., Sato, S., Ishida, M., Shibata, T., … Suzuki, K. (2011). Fine mapping of porcine SSC14 QTL and SCD gene effects on fatty acid composition and melting point of fat in a Duroc purebred population. Animal Genetics, 43(2), 225-228. doi:10.1111/j.1365-2052.2011.02236.xUemoto, Y., Soma, Y., Sato, S., Ishida, M., Shibata, T., Kadowaki, H., … Suzuki, K. (2011). Genome-wide mapping for fatty acid composition and melting point of fat in a purebred Duroc pig population. Animal Genetics, 43(1), 27-34. doi:10.1111/j.1365-2052.2011.02218.xEstany, J., Ros-Freixedes, R., Tor, M., & Pena, R. N. (2014). A Functional Variant in the Stearoyl-CoA Desaturase Gene Promoter Enhances Fatty Acid Desaturation in Pork. PLoS ONE, 9(1), e86177. doi:10.1371/journal.pone.0086177Ramayo-Caldas, Y., Mercadé, A., Castelló, A., Yang, B., Rodríguez, C., Alves, E., … Folch, J. M. (2012). Genome-wide association study for intramuscular fatty acid composition in an Iberian × Landrace cross1. Journal of Animal Science, 90(9), 2883-2893. doi:10.2527/jas.2011-4900Muñoz, M., Rodríguez, M. C., Alves, E., Folch, J. M., Ibañez-Escriche, N., Silió, L., & Fernández, A. I. (2013). Genome-wide analysis of porcine backfat and intramuscular fat fatty acid composition using high-density genotyping and expression data. BMC Genomics, 14(1), 845. doi:10.1186/1471-2164-14-845Yang, B., Zhang, W., Zhang, Z., Fan, Y., Xie, X., Ai, H., … Ren, J. (2013). Genome-Wide Association Analyses for Fatty Acid Composition in Porcine Muscle and Abdominal Fat Tissues. PLoS ONE, 8(6), e65554. doi:10.1371/journal.pone.0065554Zhang, W., Zhang, J., Cui, L., Ma, J., Chen, C., Ai, H., … Yang, B. (2016). Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations. Genetics Selection Evolution, 48(1). doi:10.1186/s12711-016-0184-2Kim, E.-S., Ros-Freixedes, R., Pena, R. N., Baas, T. J., Estany, J., & Rothschild, M. F. (2015). Identification of signatures of selection for intramuscular fat and backfat thickness in two Duroc populations1. Journal of Animal Science, 93(7), 3292-3302. doi:10.2527/jas.2015-8879Bosch, L., Tor, M., Reixach, J., & Estany, J. (2009). Estimating intramuscular fat content and fatty acid composition in live and post-mortem samples in pigs. Meat Science, 82(4), 432-437. doi:10.1016/j.meatsci.2009.02.013AOAC. 1997. Supplement to AOAC Official Method 996.06: Fat (total, saturated, and monounsaturated) in foods hydrolytic extraction gas chromatographic method. Page 18 in Official Methods of Analysis (16th ed). Association of Official Analytical Chemists, Arlington, VA.ÓVILO, C., FERNÁNDEZ, A., NOGUERA, J. L., BARRAGÁN, C., LETÓN, R., RODRÍGUEZ, C., … TORO, M. (2005). Fine mapping of porcine chromosome 6 QTL and LEPR effects on body composition in multiple generations of an Iberian by Landrace intercross. Genetical Research, 85(1), 57-67. doi:10.1017/s0016672305007330Amills, M., Villalba, D., Tor, M., Mercad, A., Gallardo, D., Cabrera, B., … Estany, J. (2008). Plasma leptin levels in pigs with different leptin and leptin receptor genotypes. Journal of Animal Breeding and Genetics, 125(4), 228-233. doi:10.1111/j.1439-0388.2007.00715.xPurcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., … Sham, P. C. (2007). PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. The American Journal of Human Genetics, 81(3), 559-575. doi:10.1086/519795Bouwman, A. C., Janss, L. L., & Heuven, H. C. (2011). A Bayesian approach to detect QTL affecting a simulated binary and quantitative trait. BMC Proceedings, 5(S3). doi:10.1186/1753-6561-5-s3-s4Legarra, A., Croiseau, P., Sanchez, M., Teyssèdre, S., Sallé, G., Allais, S., … Elsen, J.-M. (2015). A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species. Genetics Selection Evolution, 47(1), 6. doi:10.1186/s12711-015-0087-7Kass, R. E., & Raftery, A. E. (1995). Bayes Factors. Journal of the American Statistical Association, 90(430), 773-795. doi:10.1080/01621459.1995.10476572Barrett, J. C., Fry, B., Maller, J., & Daly, M. J. (2004). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2), 263-265. doi:10.1093/bioinformatics/bth457Wolc, A., Arango, J., Settar, P., Fulton, J. E., O’Sullivan, N. P., Preisinger, R., … Dekkers, J. C. M. (2012). Genome-wide association analysis and genetic architecture of egg weight and egg uniformity in layer chickens. Animal Genetics, 43, 87-96. doi:10.1111/j.1365-2052.2012.02381.xChen, E. Y., Tan, C. M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G., … Ma’ayan, A. (2013). Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics, 14(1), 128. doi:10.1186/1471-2105-14-128Rabbit programme. 2012. Available from: http://www.dcam.upv.es/dcia/ablasco/Programas/THE%20PROGRAM%20Rabbit.pdfHu, Z.-L., Park, C. A., & Reecy, J. M. (2015). Developmental progress and current status of the Animal QTLdb. Nucleic Acids Research, 44(D1), D827-D833. doi:10.1093/nar/gkv1233Óvilo, C., Fernández, A., Fernández, A. I., Folch, J. M., Varona, L., Benítez, R., … Silió, L. (2010). Hypothalamic expression of porcine leptin receptor (LEPR), neuropeptide Y (NPY), and cocaine- and amphetamine-regulated transcript (CART) genes is influenced by LEPR genotype. Mammalian Genome, 21(11-12), 583-591. doi:10.1007/s00335-010-9307-1Muñoz, G., Alcázar, E., Fernández, A., Barragán, C., Carrasco, A., de Pedro, E., … Rodríguez, M. C. (2011). Effects of porcine MC4R and LEPR polymorphisms, gender and Duroc sire line on economic traits in Duroc×Iberian crossbred pigs. Meat Science, 88(1), 169-173. doi:10.1016/j.meatsci.2010.12.018Galve, A., Burgos, C., Silió, L., Varona, L., Rodríguez, C., Ovilo, C., & López-Buesa, P. (2012). The effects of leptin receptor (LEPR) and melanocortin-4 receptor (MC4R) polymorphisms on fat content, fat distribution and fat composition in a Duroc×Landrace/Large White cross. Livestock Science, 145(1-3), 145-152. doi:10.1016/j.livsci.2012.01.010UEMOTO, Y., KIKUCHI, T., NAKANO, H., SATO, S., SHIBATA, T., KADOWAKI, H., … SUZUKI, K. (2011). Effects of porcine leptin receptor gene polymorphisms on backfat thickness, fat area ratios by image analysis, and serum leptin concentrations in a Duroc purebred population. Animal Science Journal, 83(5), 375-385. doi:10.1111/j.1740-0929.2011.00963.xHirose, K., Ito, T., Fukawa, K., Arakawa, A., Mikawa, S., Hayashi, Y., & Tanaka, K. (2013). Evaluation of effects of multiple candidate genes (LEP,LEPR,MC4R,PIK3C3, andVRTN) on production traits in Duroc pigs. Animal Science Journal, 85(3), 198-206. doi:10.1111/asj.12134López-Buesa, P., Burgos, C., Galve, A., & Varona, L. (2013). Joint analysis of additive, dominant and first-order epistatic effects of four genes (IGF2,MC4R,PRKAG3andLEPR) with known effects on fat content and fat distribution in pigs. Animal Genetics, 45(1), 133-137. doi:10.1111/age.12091Mackowski, M., Szymoniak, K., Szydlowski, M., Kamyczek, M., Eckert, R., Rozycki, M., & Switonski, M. (2005). Missense mutations in exon 4 of the porcine LEPR gene encoding extracellular domain and their association with fatness traits. Animal Genetics, 36(2), 135-137. doi:10.1111/j.1365-2052.2005.01247.xLi, X., Kim, S.-W., Choi, J.-S., Lee, Y.-M., Lee, C.-K., Choi, B.-H., … Kim, K.-S. (2010). Investigation of porcine FABP3 and LEPR gene polymorphisms and mRNA expression for variation in intramuscular fat content. Molecular Biology Reports, 37(8), 3931-3939. doi:10.1007/s11033-010-0050-1Tyra, M., & Ropka-Molik, K. (2011). Effect of the FABP3 and LEPR gene polymorphisms and expression levels on intramuscular fat (IMF) content and fat cover degree in pigs. Livestock Science, 142(1-3), 114-120. doi:10.1016/j.livsci.2011.07.003Muraoka, O., Xu, B., Tsurumaki, T., Akira, S., Yamaguchi, T., & Higuchi, H. (2003). Leptin-induced transactivation of NPY gene promoter mediated by JAK1, JAK2 and STAT3 in the neural cell lines. Neurochemistry International, 42(7), 591-601. doi:10.1016/s0197-0186(02)00160-2Wood, J. D., Enser, M., Fisher, A. V., Nute, G. R., Sheard, P. R., Richardson, R. I., … Whittington, F. M. (2008). Fat deposition, fatty acid composition and meat quality: A review. Meat Science, 78(4), 343-358. doi:10.1016/j.meatsci.2007.07.019Clément, K., Vaisse, C., Lahlou, N., Cabrol, S., Pelloux, V., Cassuto, D., … Guy-Grand, B. (1998). A mutation in the human leptin receptor gene causes obesity and pituitary dysfunction. Nature, 392(6674), 398-401. doi:10.1038/32911Dubern, B., & Clement, K. (2012). Leptin and leptin receptor-related monogenic obesity. Biochimie, 94(10), 2111-2115. doi:10.1016/j.biochi.2012.05.010Lim, K.-S., Kim, J.-M., Lee, E.-A., Choe, J.-H., & Hong, K.-C. (2014). A Candidate Single Nucleotide Polymorphism in the 3′ Untranslated Region of Stearoyl-CoA Desaturase Gene for Fatness Quality and the Gene Expression in Berkshire Pigs. Asian-Australasian Journal of Animal Sciences, 28(2), 151-157. doi:10.5713/ajas.14.0529Saatchi, M., Garrick, D. J., Tait, R. G., Mayes, M. S., Drewnoski, M., Schoonmaker, J., … Reecy, J. M. (2013). Genome-wide association and prediction of direct genomic breeding values for composition of fatty acids in Angus beef cattlea. BMC Genomics, 14(1). doi:10.1186/1471-2164-14-730Chen, L., Ekine-Dzivenu, C., Vinsky, M., Basarab, J., Aalhus, J., Dugan, M. E. R., … Li, C. (2015). Genome-wide association and genomic prediction of breeding values for fatty acid composition in subcutaneous adipose and longissimus lumborum muscle of beef cattle. BMC Genetics, 16(1). doi:10.1186/s12863-015-0290-

Diversity in the Visible-NIR Absorption Band Characteristics of Lunar and Asteroidal Plagioclase

Studying the visible and near-infrared (VNIR) spectral properties of plagioclase has been challenging because of the difficulty in obtaining good plagioclase separates from pristine planetary materials such as meteorites and returned lunar samples. After an early study indicated that the 1.25 m band position of plagioclase spectrum might be correlated with the molar percentage of anorthite (An#) [1], there have been few studies which dealt with the band center behavior. In this study, the VNIR absorption band parameters of plagioclase samples have been derived using the modified Gaussian model (MGM) [2] following a pioneering study by [3]

Development of paints with infrared radiation reflective properties

AbstractLarge buildings situated in hot regions of the Globe need to be agreeable to their residents. Air conditioning is extensively used to make these buildings comfortable, with consequent energy consumption. Absorption of solar visible and infrared radiations are responsible for heating objects on the surface of the Earth, including houses and buildings. To avoid excessive energy consumption, it is possible to use coatings formulated with special pigments that are able to reflect the radiation in the near- infrared, NIR, spectrum. To evaluate this phenomenon an experimental study about the reflectivity of paints containing infrared-reflective pigments has been made. By irradiating with an IR source and by measuring the surface temperatures of the samples we evaluated: color according to ASTM D 2244-14, UV/VIS/NIR reflectance according to ASTM E 903-12 and thermal performance. Additionally, the spectral reflectance and the IR emittance were measured and the solar reflectance of the samples were calculated. The results showed that plates coated with paints containing IR-reflecting pigments displayed lower air temperature on the opposite side as compared to conventional coatings, indicating that they can be effective to reflect NIR and decrease the temperature of buildings when used in roofs and walls.</p

Post-traumatic stress disorder in children and adolescents one year after a super-cyclone in Orissa, India: exploring cross-cultural validity and vulnerability factors

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Genome-wide association study confirm major QTL for backfat fatty acid composition on SSC14 in Duroc pigs

Background: Fatty acid composition contributes importantly to meat quality and is essential to the nutritional value of the meat. Identification of genetic factors underlying levels of fatty acids can be used to breed for pigs with healthier meat. The aim of this study was to conduct genome-wide association studies (GWAS) to identify QTL regions affecting fatty acid composition in backfat from the pig breeds Duroc and Landrace. Results: Using data from the Axiom porcine 660 K array, we performed GWAS on 454 Duroc and 659 Landrace boars for fatty acid phenotypes measured by near-infrared spectroscopy (NIRS) technology (C16:0, C16:1n-7, C18:0, C18:1n-9, C18:2n-6, C18:3n-3, total saturated fatty acids, monounsaturated fatty acids and polyunsaturated fatty acids). Two QTL regions on SSC4 and SSC14 were identified in Duroc for the de novo synthesized fatty acids traits, whereas one QTL on SSC8 was detected in Landrace for C16:1n-7. The QTL region on SSC14 has been reported in previous studies and a putative causative mutation has been suggested in the promoter region of the SCD gene. Whole genome re-sequencing data was used for genotype imputation and to fine map the SSC14 QTL region in Norwegian Duroc. This effort confirms the location of the QTL on this chromosome as well as suggesting other putative candidate genes in the region. The most significant single nucleotide polymorphisms (SNPs) located on SSC14 explain between 55 and 76% of the genetic variance and between 27 and 54% of the phenotypic variance for the de novo synthesized fatty acid traits in Norwegian Duroc. For the QTL region on SSC8 in Landrace, the most significant SNP explained 19% of the genetic variance and 5% of the phenotypic variance for C16:1n-7. Conclusions: This study confirms a major QTL affecting fatty acid composition on SSC14 in Duroc, which can be used in genetic selection to increase the level of fatty acid desaturation. The SSC14 QTL was not segregating in the Landrace population, but another QTL on SSC8 affecting C16:1n-7 was identified and might be used to increase the level of desaturation in meat products from this breed

Migration Industries and the State: Guestwork Programs in East Asia

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