Genome-wide association between single nucleotide polymorphisms with beef fatty acid profile in Nellore cattle using the single step procedure

Abstract

BackgroundSaturated fatty acids can be detrimental to human health and have received considerable attention in recent years. Several studies using taurine breeds showed the existence of genetic variability and thus the possibility of genetic improvement of the fatty acid profile in beef. This study identified the regions of the genome associated with saturated, mono- and polyunsaturated fatty acids, and n-6 to n-3 ratios in the Longissimus thoracis of Nellore finished in feedlot, using the single-step method.ResultsThe results showed that 115 windows explain more than 1 % of the additive genetic variance for the 22 studied fatty acids. Thirty-one genomic regions that explain more than 1 % of the additive genetic variance were observed for total saturated fatty acids, C12:0, C14:0, C16:0 and C18:0. Nineteen genomic regions, distributed in sixteen different chromosomes accounted for more than 1 % of the additive genetic variance for the monounsaturated fatty acids, such as the sum of monounsaturated fatty acids, C14:1 cis-9, C18:1 trans-11, C18:1 cis-9, and C18:1 trans-9. Forty genomic regions explained more than 1 % of the additive variance for the polyunsaturated fatty acids group, which are related to the total polyunsaturated fatty acids, C20:4 n-6, C18:2 cis-9 cis12 n-6, C18:3 n-3, C18:3 n-6, C22:6 n-3 and C20:3 n-6 cis-8 cis-11 cis-14. Twenty-one genomic regions accounted for more than 1 % of the genetic variance for the group of omega-3, omega-6 and the n-6:n-3 ratio.ConclusionsThe identification of such regions and the respective candidate genes, such as ELOVL5, ESSRG, PCYT1A and genes of the ABC group (ABC5, ABC6 and ABC10), should contribute to form a genetic basis of the fatty acid profile of Nellore (Bos indicus) beef, contributing to better selection of the traits associated with improving human health.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2511-y) contains supplementary material, which is available to authorized users.

Gene expression profile of intramuscular muscle in Nellore cattle with extreme values of fatty acid

“…The authors reported some regions near to DEG identified in this study. In this regard, the ACSM3 and ACSM1 genes were differentially expressed for ω3 acids and were located in a region (BTA25, 12 Mb) which explained more than 1 % of the additive variance genetic for ω3, as reported by [52]. Those authors also reported QTL detected by GWAS in the same region that the TNXB (tenascin XB) and PPARD (peroxisome proliferator-activated receptor delta) genes were differentially expressed in this study.…”

“…In a recent GWAS study, [52] used a population with 963 Nellore bulls, which contained 48 animals used in this study, and identified several genomic regions which explained more than 1 % of the additive genetic variance for beef FAs composition. The authors reported some regions near to DEG identified in this study.…”

Genome wide association study and genomic prediction for fatty acid composition in Chinese Simmental beef cattle using high density SNP array

“…Previous genome-wide association studies have been conducted for fatty acid composition in multiple cattle breeds, including Angus, Japanese Black, Nellore and other crossbreds [8, 30, 32, 35, 36]. To our knowledge, this study is the first attempt to investigate molecular mechanism underling fatty acid composition using high density SNP array and evaluate the accuracy of genomic predictions in Chinese Simmental cattle population.…”

“…Despite the fact that single-SNP based GWAS methods have been widely used in many studies, these methods may not be powerful for studying the complex traits with low or moderate heritability. Due to the polygenic characteristics of fatty acid composition in cattle, GWAS using the Bayesian methods have enabled to identify many associated loci that have missed by the single-SNP regression approach [33, 35, 36]. BayesB has been widely used for GWAS of complex trait in farm animals [39–42].…”

“…However, many studies were conducted in populations with relatively low density SNP arrays. Despite recent GWAS for fatty acid composition have been investigated using the high density BovineHD (770 K) SNP array, those studies were mostly limited in Nellore cattle [35, 36]. On the other hand, extensive attention has been paid to investigate the accuracies of genomic prediction using multiple methods in different populations [32, 33].…”