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In this study lean meat water-holding capacity (WHC) of a Duroc × Pietrain (DuPi) resource population with corresponding genotypes and transcriptomes was investigated using genetical genomics. WHC was characterized by drip loss measured in M. longissimus dorsi. The 60K Illumina SNP chips identified genotypes of 169 F DuPi animals. Whole-genome transcriptomes of muscle samples were available for 132 F animals using the Affymetrix 24K GeneChip® Porcine Genome Array. Performing genome-wide association studies of transcriptional profiles, which are correlated with phenotypes, allows elucidation of cis- and trans-regulation. Expression levels of 1,228 genes were significantly correlated with drip loss and were further analyzed for enrichment of functional annotation groups as defined by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways. A hypergeometric gene set enrichment test was performed and revealed glycolysis/glyconeogenesis, pentose phosphate pathway, and pyruvate metabolism as the most promising pathways. For 267 selected transcripts, expression quantitative trait loci (eQTL) analysis was performed and revealed a total of 1,541 significant associations. Because of positional accordance of the gene underlying transcript and the eQTL location, it was possible to identify eight eQTL that can be assumed to be cis-regulated. Comparing the results of gene set enrichment and the eQTL detection tests, molecular networks and potential candidate genes, which seemed to play key roles in the expression of WHC, were detected. The α- 1- microglobulin/bikunin precursor ( AMBP) gene was assumed to be cis-regulated and was part of the glycolysis pathway. This approach supports the identification of trait-associated SNPs and the further biological understanding of complex traits. [ABSTRACT FROM AUTHOR]

While numerous Fabaceae seeds are a good nutritional source of high-quality protein, the use of some species is hampered by toxic effects caused by exposure to metabolites that accumulate in the seeds. One such species is the faba or broad bean (Vicia faba L.), which accumulates vicine and convicine. These two glycoalkaloids cause favism, the breakdown of red blood cells in persons with a glucose-6-phosphate dehydrogenase deficiency. Because this is the most common enzyme deficiency worldwide, faba bean breeding efforts have focused on developing cultivars with low levels of these alkaloids. Consequently, quantification methods have been developed; however, they quantify vicine and convicine only and not the derivatives of these compounds that potentially generate the same bio-active molecules. Based on the recognition of previously unknown (con)vicine-containing compounds, we screened the fragmentation spectra of LC-MS/MS data from five faba bean cultivars using the characteristic fragments generated by (con)vicine. This resulted in the recognition of more than a hundred derivatives, of which 89 were tentatively identified. (Con)vicine was mainly derivatized through the addition of sugars, hydroxycinnamic acids, and dicarboxylic acids, with a group of compounds composed of two (con)vicine residues linked by dicarboxyl fatty acids. In general, the abundance profiles of the different derivatives in the five cultivars mimicked that of vicine and convicine, but some showed a derivative-specific profile. The description of the (con)vicine diversity will impact the interpretation of future studies on the biosynthesis of (con)vicine, and the content in potentially bio-active alkaloids in faba beans may be higher than that represented by the quantification of vicine and convicine alone. [ABSTRACT FROM AUTHOR]

The aim of this study was to integrate multi omics data to characterize underlying functional pathways and candidate genes for drip loss in pigs. The consideration of different omics levels allows elucidating the black box of phenotype expression. Metabolite and protein profiling was applied in Musculus longissimus dorsi samples of 97 Duroc × Pietrain pigs. In total, 126 and 35 annotated metabolites and proteins were quantified, respectively. In addition, all animals were genotyped with the porcine 60 k Illumina beadchip. An enrichment analysis resulted in 10 pathways, amongst others, sphingolipid metabolism and glycolysis/gluconeogenesis, with significant influence on drip loss. Drip loss and 22 metabolic components were analyzed as intermediate phenotypes within a genome-wide association study (GWAS). We detected significantly associated genetic markers and candidate genes for drip loss and for most of the metabolic components. On chromosome 18, a region with promising candidate genes was identified based on SNPs associated with drip loss, the protein "phosphoglycerate mutase 2" and the metabolite glycine. We hypothesize that association studies based on intermediate phenotypes are able to provide comprehensive insights in the genetic variation of genes directly involved in the metabolism of performance traits. In this way, the analyses contribute to identify reliable candidate genes. [ABSTRACT FROM AUTHOR]

The aim of the study was to investigate single nucleotide polymorphisms (SNPs) and expression of SOX-6 to support its candidacy for growth, carcass, and meat quality traits in pigs. The first SNP, rs81358375, was associated with pH 45 min post mortem in loin (pH1 L ), the thickness of backfat and side fat, and carcass length in Pietrain (Pi) population, and related with backfat thickness and daily gain in Duroc × Pietrain F 2 (DuPi) population. The other SNP, rs321666676, was associated with meat colour in Pi population. In DuPi population, the protein, not mRNA, level of SOX-6 in high pH1 L pigs was significantly less abundant compared with low pH1 L pigs, where microRNAs targeting SOX-6 were also differently regulated. This paper shows that SOX-6 could be a potential candidate gene for porcine growth, carcass, and meat quality traits based on genetic association and gene expression. [ABSTRACT FROM AUTHOR]

Grain legumes are important crops required for protein-rich animal fodder. The aim of this study was to (i) examine the suitability of grain legume cropping systems for cultivation as protein-rich fodder, (ii) compare the performance of winter and spring types of faba beans and peas, as well as to compare the performance of peas sown in pure stand and in mixture with cereals, and (iii) determine the impact of previous legume crop on succeeding wheat under less favorable soil conditions in organic agriculture. In a field trial on a commercial farm in Luxembourg, eight grain legume cropping systems (as given under ii plus soybean and blue lupin) and a non-nitrogen fixing control crop (triticale) were cultivated followed by wheat in two consecutive seasons, employing a randomized complete block design with four replicates. All cropping systems except for winter pea in pure stand, were suitable for cultivation as protein-rich fodder even under less favourable soil conditions. Given sufficient soil moisture, faba beans constituted the best choice (protein yield: 961-1193 kg ha-1). Semi-leafless peas reached a significantly better yield when sown in pure stand (p ≤ 0.05; 3539-4154 kg ha-1) compared with the mixture (2920-3852 kg ha-1), whereas full-leaf types should be cultivated with a cereal partner. Winter vs. spring faba beans did not perform significantly different while for peas, the spring form performed best, likely again depending on leaf type rather than sowing time. The lower previous crop value of mono-cropped cereals (yield first experimental sequence: 2056 kg ha-1) compared with cereals in mixture with grain legumes was confirmed, with best performance of wheat succeeding spring pea in pure stand (first experimental sequence, yield: 3661 kg ha-1). Grain legumes in pure stand exhibited a higher previous crop value than winter triticale or grain legumes grown in mixture. In conclusion, grain legumes were promising candidates for generating protein-rich feedingstuffs, even under less favorable soil conditions in organic agriculture in Luxembourg. [ABSTRACT FROM AUTHOR]