Assessment of Hard Red Spring Wheat Germplasm for Cold Temperature Germination Tolerance

When planted early in the season, hard red spring wheat (HRSW; Triticum aestivum L.) can help for both vegetative growth and yield providing maximum agronomic productivity. The north-central Great Plains growing region is considered best for developing varieties that germinate in sub-optimal temperatures. Within limited regions, spring wheat planting typically occurs between mid-April and late May, when soil temperatures are 8 °C to 14 °C. Early season planting may result in freezing stress, while late season planting can result in heat and drought stress. Our study tested the germination rate of hard red spring wheat (HRSW) over a range of low temperatures within a laboratory environment. Ten HRSW populations were selected and four replications of 100 randomly chosen seeds of each genotype were tested at a series of temperatures (5°C, 7°C, 9°C, 11°C, 13°C, and 15°C). The purpose of this study was to review information on cold temperature germination tolerances for the HRSW populations and develop a recommendation for early season planting of HRSW. As a result of this study, we found out that SD4011/BARLOW showed the highest germination rate at 5°C, whereas SD4330 was recorded as a highest germinating entry at the 5 °C to 15°C temperature range. The importance of this study is to help predict how cooler growing temperatures might affect planting dates and improve crop productivity in anticipation of climate warming which poses a significant threat to area farmers. According to USDA-NRCS, soil temperature data from the EROS Data center for SD five-year averages of soil temperatures showed that between first recorded 5°C and 11°C soil temperatures have approximately two weeks of differences. Planting may be completed up to two weeks earlier if a HRSW cultivar capable of germinating in cooler soils is used

Identification of expression quantitative trait loci (eQTL) and candidate genes associated with water holding capacity in porcine meat

Consumer assessment of meat quality is defined by the characteristics of sensory experience such as juiciness, muscle pH, water-holding capacity and colour. Water-holding capacity in terms of drip loss has a genetic as well as environmental component with low to medium heritability. The number of genes involved in the development of drip loss is unknown. The aim of this study was to identify the candidate genes and their transcriptional regulation responsible for the drip loss in pig meat. Twenty genes were selected for the candidate gene analysis and for their eQTL study. For the expression of genes quantitative real-time PCR and GenomeLab GeXP multi-plex were used in 300 DUPI animals. Multiple housekeeping genes were used for the accurate gene expression normalization. Analysis revealed expression of peroxisome proliferator activated receptor gamma, coactivator 1 alpha (PPARGC1) and alpha 1 microglobulin/bikunin (AMBP) genes were differentially regulated in animals with higher drip loss compared to lower drip loss. Moreover, expression of other genes showed significant association with different meat quality parameters. eQTL analysis showed that these genes are trans-regulated in DUPI population. By using different QTL models, on SSC2 vicinity of marker S0141 was detected as the most promising chromosomal region for drip loss supported by the literature as well. Ovelapping of detected eQTL with QTL in DUPI population and other pig populations showed promising chromosomal regions for further fine mapping and association studies.Identifizierung von expressions quantitativ trait Loci (eQTL) und Kandidatengenen für das Wasserhaltevermögen im SchweinefleischDie Beurteilung von Fleischqualität durch den Konsumenten ist definiert durch sensorische Merkmale, wie Saftigkeit, Muskel pH, Wasserhaltevermögen und Farbe. Das Wasserhaltevermögen in Bezug auf den Tropfsaftverlust hat sowohl eine genetische als auch eine ökologische Komponente mit geringer bis mittlerer Heritabilität. Die Anzahl der Gene die an dem Merkmal Tropfsaftverlust beteiligt sind, sind bislang noch unbekannt. Das Ziel dieser Studie war es, geeignete Kandidatengene, die für den Tropfsaftverlust im Schweinefleisch verantwortlich sind, zu identifizieren. Für die Kandidatengenanalyse und ihre eQTL Positionen wurden zwanzig Gene selektiert. Zur Erstellung der Expressionsprofile von 300 DUPI Tieren wurde einerseits eine quantitative Real-Time PCR verwendet, sowie das GenomeLab GeXP Multiplex Verfahren. Zur Normalisierung der Expression wurden mehrere Referenz Gene eingesetzt. Die Analyse zeigte das die Gene Peroxisome proliferator activated receptor gamma, coactivator 1 alpha (PPARGC1) und Alpha 1 microglobulin/bikunin (AMBP) in Vergleich zwischen hohem und niedrigem Tropfsaftverlust unterschiedlich exprimierten. Darüber, hinaus zeigte die Expression weiterer Gene signifikante Assoziationen mit verschiedenen Parametern der Fleischqualität. Die Analyse der eQTL erbrachte das diese Gene in der DUPI Population trans-reguliert waren. Durch die Verwendung verschiedener QTL Modelle wurde auf SSC2 in der Nähe des Markers S0141 eine vielversprechende chromosomale Region für Tropfsaftverlust entdeckt, dies konnte durch Fachliteratur bestätigt werden. Durch die Übereinstimmung entdeckter eQTL mit QTL in der DUPI Population und in anderen Schweine Populationen konnten weitere vielversprechende chromosomale Regionen für zukünftige Feinkartierungen und Assoziationsstudien a werden

Evaluation of suitable reference genes for gene expression studies in porcine alveolar macrophages in response to LPS and LTA

<p>Abstract</p> <p>Background</p> <p>To obtain reliable quantitative real-time PCR data, normalization relative to stable housekeeping genes (HKGs) is required. However, in practice, expression levels of 'typical' housekeeping genes have been found to vary between tissues and under different experimental conditions. To date, validation studies of reference genes in pigs are relatively rare and have never been performed in porcine alveolar macrophages (AMs). In this study, expression stability of putative housekeeping genes were identified in the porcine AMs in response to the stimulation with two pathogen-associated molecular patterns (PAMPs) lipopolysaccharide (LPS) and lipoteichoic acid (LTA). Three different algorithms (geNorm, Normfinder and BestKeeper) were applied to assess the stability of HKGs.</p> <p>Results</p> <p>The mRNA expression stability of nine commonly used reference genes (<it>B2M, BLM, GAPDH, HPRT1, PPIA, RPL4, SDHA, TBP </it>and <it>YWHAZ</it>) was determined by qRT-PCR in AMs that were stimulated by LPS and LTA <it>in vitro</it>. mRNA expression levels of all genes were found to be affected by the type of stimulation and duration of the stimulation (<it>P </it>< 0.0001). geNorm software revealed that <it>SDHA, B2M </it>and <it>RPL4 </it>showed a high expression stability in the irrespective to the stimulation group, while <it>SDHA, YWHAZ </it>and <it>RPL4 </it>showed high stability in non-stimulated control group. In all cases, <it>GAPDH </it>showed the least stability in geNorm. NormFinder revealed that <it>SDHA </it>was the most stable gene in all the groups. Moreover, geNorm software suggested that the geometric mean of the three most stable genes would be the suitable combination for accurate normalization of gene expression study.</p> <p>Conclusions</p> <p>There was discrepancy in the ranking order of reference genes obtained by different analysing algorithms. In conclusion, the geometric mean of the <it>SDHA, YWHAZ </it>and <it>RPL4 </it>seemed to be the most appropriate combination of HKGs for accurate normalization of gene expression data in porcine AMs without knowing the type of bacterial pathogenic status of the animals.</p

Detection of quantitative trait loci affecting serum cholesterol, LDL, HDL, and triglyceride in pigs

<p>Abstract</p> <p>Background</p> <p>Serum lipids are associated with many serious cardiovascular diseases and obesity problems. Many quantitative trait loci (QTL) have been reported in the pig mostly for performance traits but very few for the serum lipid traits. In contrast, remarkable numbers of QTL are mapped for serum lipids in humans and mice. Therefore, the objective of this research was to investigate the chromosomal regions influencing the serum level of the total cholesterol (CT), triglyceride (TG), high density protein cholesterol (HDL) and low density protein cholesterol (LDL) in pigs. For this purpose, a total of 330 animals from a Duroc × Pietrain F2 resource population were phenotyped for serum lipids using ELISA and were genotyped by using 122 microsatellite markers covering all porcine autosomes for QTL study in QTL Express. Blood sampling was performed at approximately 175 days before slaughter of the pig.</p> <p>Results</p> <p>Most of the traits were correlated with each other and were influenced by average daily gain, slaughter date and age. A total of 18 QTL including three QTL with imprinting effect were identified on 11 different porcine autosomes. Most of the QTL reached to 5% chromosome-wide (CW) level significance including a QTL at 5% experiment-wide (GW) and a QTL at 1% GW level significance. Of these QTL four were identified for both the CT and LDL and two QTL were identified for both the TG and LDL. Moreover, three chromosomal regions were detected for the HDL/LDL ratio in this study. One QTL for HDL on SSC2 and two QTL for TG on SSC11 and 17 were detected with imprinting effect. The highly significant QTL (1% GW) was detected for LDL at 82 cM on SSC1, whereas significant QTL (5% GW) was identified for HDL/LDL on SSC1 at 87 cM. Chromosomal regions with pleiotropic effects were detected for correlated traits on SSC1, 7 and 12. Most of the QTL identified for serum lipid traits correspond with the previously reported QTL for similar traits in other mammals. Two novel QTL on SSC16 for HDL and HDL/LDL ratio and an imprinted QTL on SSS17 for TG were detected in the pig for the first time.</p> <p>Conclusion</p> <p>The newly identified QTL are potentially involved in lipid metabolism. The results of this work shed new light on the genetic background of serum lipid concentrations and these findings will be helpful to identify candidate genes in these QTL regions related to lipid metabolism and serum lipid concentrations in pigs.</p

Molecular genetic analysis of boar taint

Boar taint is an unpleasant smell and taste of pork meat derived from some entire male pigs. The main causes of boar taint are the two compounds androstenone (5α-androst-16-en-3-one) and skatole (3-methylindole). It is crucial to understand the genetic mechanism of boar taint to select pigs for lower androstenone levels and thus reduce boar taint. The aim of this study was the identification of genes and pathways influencing boar taint and involved in androstenone and skatol metabolism. Therefore polymorphisms in relevant genes were identified and transcriptome analysis using Affymetrix-Chips and RNA-Seq in the two major organs involved in androstenone metabolism i.e the testis and the liver was performed. Differentially regulated genes in high androstenone testis and liver samples were involved in metabolic processes such as retinol metabolism, metabolism of xenobiotics by cytochrome P450 and fatty acid metabolism. Moreover, a number of genes encoding biosynthesis of steroids were highly expressed in high androstenone testis samples. Gene polymorphism analysis revealed potential mutations in HSP40, IGFBP1, CYP7A1 and FMO5 genes affecting androstenone levels. Further studies are required for verify the role of candidate genes to be used in genomic selection against boar taint in pig breeding programs. According to the results of association studies, FMO5, CYP21 and ESR1 turned out to be the most promising candidates for boar taint

Improvement of disease resistance in livestock: application of immunogenomics and CRISPR/Cas9 technology

Disease occurrence adversely affects livestock production and animal welfare, and havean impact on both human health and public perception of food-animals production. Combinedefforts from farmers, animal scientists, and veterinarians have been continuing to explore theeffective disease control approaches for the production of safe animal-originated food. Implementing the immunogenomics, along with genome editing technology, has been considering as the key approach for safe food-animal production through the improvement of the host genetic resistance. Next-generation sequencing, as a cutting-edge technique, enables the production of high throughput transcriptomic and genomic profiles resulted from host-pathogen interactions. Immunogenomics combine the transcriptomic and genomic data that links to host resistance to disease, and predict the potential candidate genes and their genomic locations. Genome editing, which involves insertion, deletion, or modification of one or more genes in the DNA sequence, is advancing rapidly and may be poised to become a commercial reality faster than it has thought. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) [CRISPR/Cas9] system has recently emerged as a powerful tool for genome editing in agricultural food production including livestock disease management. CRISPR/Cas9 mediated insertion of NRAMP1 gene for producing tuberculosis resistant cattle, and deletion of CD163 gene for producing porcine reproductive and respiratory syndrome (PRRS) resistant pigs are two groundbreaking applications of genome editing in livestock. In this review, we have highlighted the technological advances of livestock immunogenomics and the principles and scopes of application of CRISPR/Cas9-mediated targeted genome editing in animal breeding for disease resistance.Fil: Islam, Md Aminul. Tohoku University; Japón. Bangladesh Agricultural University; BangladeshFil: Sharmin, Aqter Rony. Bangladesh Agricultural University; BangladeshFil: Rahman, Mohammad Bozlur. Department of Livestock Services; BangladeshFil: Cinar, Mehmet Ulas. Erciyes University; Turquía. Washington State University; Estados UnidosFil: Villena, Julio Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina. Tohoku University; JapónFil: Uddin, Muhammad Jasim. Bangladesh Agricultural University; Bangladesh. University of Queensland; AustraliaFil: Kitazawa, Haruki. Tohoku University; Japó

Transcriptome profile of lung dendritic cells after in vitro porcine reproductive and respiratory syndrome virus (PRRSV) infection

The porcine reproductive and respiratory syndrome (PRRS) is an infectious disease that leads to high financial and production losses in the global swine industry. The pathogenesis of this disease is dependent on a multitude of factors, and its control remains problematic. The immune system generally defends against infectious diseases, especially dendritic cells (DCs), which play a crucial role in the activation of the immune response after viral infections. However, the understanding of the immune response and the genetic impact on the immune response to PRRS virus (PRRSV) remains incomplete. In light of this, we investigated the regulation of the host immune response to PRRSV in porcine lung DCs using RNA-sequencing (RNA-Seq). Lung DCs from two different pig breeds (Pietrain and Duroc) were collected before (0 hours) and during various periods of infection (3, 6, 9, 12, and 24 hours post infection (hpi)). RNA-Seq analysis revealed a total of 20,396 predicted porcine genes, which included breed-specific differentially expressed immune genes. Pietrain and Duroc infected lung DCs showed opposite gene expression courses during the first time points post infection. Duroc lung DCs reacted more strongly and distinctly than Pietrain lung DCs during these periods (3, 6, 9, 12 hpi). Additionally, cluster analysis revealed time-dependent co-expressed groups of genes that were involved in immune-relevant pathways. Key clusters and pathways were identified, which help to explain the biological and functional background of lung DCs post PRRSV infection and suggest IL-1β1 as an important candidate gene. RNA-Seq was also used to characterize the viral replication of PRRSV for each breed. PRRSV was able to infect and to replicate differently in lung DCs between the two mentioned breeds. These results could be useful in investigations on immunity traits in pig breeding and enhancing the health of pigs

Age-related changes in relative expression stability of commonly used housekeeping genes in selected porcine tissues

<p>Abstract</p> <p>Background</p> <p>Gene expression analysis using real-time RT-PCR (qRT-PCR) is increasingly important in biological research due to the high-throughput and accuracy of qRT-PCR. For accurate and reliable gene expression analysis, normalization of gene expression data against housekeeping genes or internal control genes is required. The stability of reference genes has a tremendous effect on the results of relative quantification of gene expression by qRT-PCR. The expression stability of reference genes could vary according to tissues, age of individuals and experimental conditions. In the pig however, very little information is available on the expression stability of reference genes. The aim of this research was therefore to develop a new set of reference genes which can be used for normalization of mRNA expression data of genes expressed in varieties of porcine tissues at different ages.</p> <p>Results</p> <p>The mRNA expression stability of nine commonly used reference genes (<it>B2M, BLM, GAPDH, HPRT1, PPIA, RPL4, SDHA, TBP </it>and <it>YWHAZ</it>) was determined in varieties of tissues collected from newborn, young and adult pigs. geNorm, NormFinder and BestKeeper software were used to rank the genes according to their stability. geNorm software revealed that <it>RPL4, PPIA </it>and <it>YWHAZ </it>showed high stability in newborn and adult pigs, while <it>B2M, YWHAZ </it>and <it>SDHA </it>showed high stability in young pigs. In all cases, <it>GAPDH </it>showed the least stability in geNorm. NormFinder revealed that <it>TBP </it>was the most stable gene in newborn and young pigs, while <it>PPIA </it>was most stable in adult pigs. Moreover, geNorm software suggested that the geometric mean of three most stable gene would be the suitable combination for accurate normalization of gene expression study.</p> <p>Conclusions</p> <p>Although, there was discrepancy in the ranking order of reference genes obtained by different analysing software methods, the geometric mean of the <it>RPL4, PPIA </it>and <it>YWHAZ </it>seems to be the most appropriate combination of housekeeping genes for accurate normalization of gene expression data in different porcine tissues at different ages.</p

Association of TMEM8B and SPAG8 with Mature Weight in Sheep

Signature of selection studies have identified many genomic regions with known functional importance and some without verified functional roles. Multiple studies have identified Transmembrane protein 8B (TMEM8B)rs426272889 as having been recently under extreme selection pressure in domesticated sheep, but no study has provided sheep phenotypic data clarifying a reason for extreme selection. We tested rs426272889 for production trait association in 770 U.S. Rambouillet, Targhee, Polypay, and Suffolk sheep. TMEM8Brs426272889 was associated with mature weight at 3 and 4 years (p &lt; 0.05). This suggested selection for sheep growth and body size might explain the historical extreme selection pressure in this genomic region. We also tested Sperm-associated antigen 8 (SPAG8) rs160159557 encoding a G493C substitution. While this variant was associated with mature weights at ages 3 and 4, it was not as strongly associated as TMEM8Brs426272889. Transmembrane protein 8B has little functional information except as an inhibitor of cancer cell proliferation. To our knowledge, this is the first study linking TMEM8B to whole organism growth and body size under standard conditions. Additional work will be necessary to identify the underlying functional variant(s). Once identified, such variants could be used to improve sheep production through selective breeding