Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis

Ewe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes’ genome to identify genes affecting pregnancy outcomes and lamb growth after parturition in Iranian Baluchi sheep. Three maternal composite traits at birth and weaning were considered. The traits were progeny birth weight, litter mean weight at birth, total litter weight at birth, progeny weaning weight, litter mean weight at weaning, and total litter weight at weaning. GWASs were performed on original phenotypes as well as on estimated breeding values. The significant SNPs associated with composite traits at birth were located within or near genes RDX, FDX1, ARHGAP20, ZC3H12C, THBS1, and EPG5. Identified genes and pathways have functions related to pregnancy, such as autophagy in the placenta, progesterone production by the placenta, placental formation, calcium ion transport, and maternal immune response. For composite traits at weaning, genes (NR2C1, VEZT, HSD17B4, RSU1, CUBN, VIM, PRLR, and FTH1) and pathways affecting feed intake and food conservation, development of mammary glands cytoskeleton structure, and production of milk components like fatty acids, proteins, and vitamin B-12, were identified. The results show that calcium ion transport during pregnancy and feeding lambs by milk after parturition can have the greatest impact on weight gain as compared to other effects of maternal origin.

A Combined Morphological and Molecular Evolutionary Analysis of Karst-Environment Adaptation for the Genus Urophysa (Ranunculaceae)

The karst environment is characterized by low soil water content, periodic water deficiency, and poor nutrient availability, which provides an ideal natural laboratory for studying the adaptive evolution of its inhabitants. However, how species adapt to such a special karst environment remains poorly understood. Here, transcriptome sequences of two Urophysa species (Urophysa rockii and Urophysa henryi), which are Chinese endemics with karst-specific distribution, and allied species in Semiaquilegia and Aquilegia (living in non-karst habitat) were collected. Single-copy genes (SCGs) were extracted to perform the phylogenetic analysis using concatenation and coalescent methods. Positively selected genes (PSGs) and clusters of paralogous genes (Mul_genes) were detected and subsequently used to conduct gene function annotation. We filtered 2,271 SCGs and the coalescent analysis revealed that 1,930 SCGs shared the same tree topology, which was consistent with the topology detected from the concatenated tree. Total of 335 PSGs and 243 Mul_genes were detected, and many were enriched in stress and stimulus resistance, transmembrane transport, cellular ion homeostasis, calcium ion transport, calcium signaling regulation, and water retention. Both molecular and morphological evidences indicated that Urophysa species evolved complex strategies for adapting to hostile karst environments. Our findings will contribute to a new understanding of genetic and phenotypic adaptive mechanisms of karst adaptation in plants.

Comparative Transcriptome Profiling of Ovary Tissue between Black Muscovy Duck and White Muscovy Duck with High- and Low-Egg Production

The egg-laying rate is an important indicator for evaluating fertility of poultry. In order to better understand the laying mechanism of Muscovy ducks, gene expression profiles and pathways of ovarian tissues in high- and low-laying black (BH and BL) and white Muscovy ducks (WH and WL) during the peak production period were performed by using RNA-seq. The total number of reads produced for each ovarian sample ranged from 44,344,070 to 47,963,328. A total of 113, 619 and 87 differentially expressed genes (DEGs) were identified in BH-vs-WH, BL-vs-BH and BL-vs-WL, respectively. Among them, 54, 356 and 49 genes were up regulated and 59, 263 and 38 genes were down regulated. In addition, there were only 10 up-regulated genes in WL-vs-WH. In the comparison of DEGs in black and white Muscovy ducks, two co-expressed DEG genes were detected between BH-vs-WH and BL-vs-WL and seven DEGs were co-expressed between BL-vs-BH and WL-vs-WH. The RNA-Seq data were confirmed to be reliable by qPCR. Numerous DEGs known to be involved in ovarian development were identified, including TGFβ2, NGFR, CEBPD, CPEB2, POSTN, SMOC1, FGF18, EFNA5 and SDC4. Gene Ontology (GO) annotations indicated that DEGs related to ovarian development were mainly enriched in biological processes of “circadian sleep/wake cycle process,” “negative regulation of transforming growth factor-β secretion,” “positive regulation of calcium ion transport” in BH-vs-WH and “cell surface receptor signaling pathway,” “Notch signaling pathway” and “calcium ion transport” in BL-vs-BH. Besides, “steroid biosynthetic process,” “granulosa cell development” and “egg coat formation” were mainly enriched in BL-vs-WL and “reproduction,” “MAPK cascade” and “mitotic cell cycle” were mainly enriched in WL-vs-WH. KEGG pathway analysis showed that the PI3K-Akt signaling pathway and ovarian steroidogenesis were the most enriched in Muscovy duck ovary transcriptome data. This work highlights potential genes and pathways that may affect ovarian development in Muscovy duck.

MODELING AND SIMULATION OF SKELETAL MUSCLE BASED ON METABOLISM PHYSIOLOGY

Skeletal muscle energy metabolism plays a very important role in controlling movement of the whole body and has important theoretical guidance for making exercise training plans and losing weight. In this paper, we developed a mathematical model of skeletal muscle excitation–contraction pathway based on the energy metabolism that links excitation to contraction to explore the effects of different metabolic energy systems on calcium ion changes and the force during skeletal muscle contraction. In this paper, a membrane potential model, a calcium cycle model, a cross-bridge dynamics model and an energy metabolism model were established. Finally, the physiological phenomenon of calcium ion transport and calcium ion concentration change of the sarcoplasm was simulated. The results show that the phosphagen system has the fastest metabolic rate and the phosphagen system has the largest impact on the explosive power of skeletal muscle exercise. The specific characteristics of the three metabolic energy systems supporting skeletal muscle movement in vivo were also analyzed in detail.

Shared loci of telomere length with brain morphology, and pleiotropy in transcriptomic and epigenomic profiles of brain

Premature shortening of telomere length is observed in neuropsychiatric disorders. We tested genetic colocalization of seven and nine leukocyte telomere length (LTL) loci in two ancestry groups, European (EUR) and East-Asian (EAS), respectively (total n=60,601) with brain morphology measures for 101 region-of-interests (ROI) (n=21,821). The posterior probability (>90%) was observed for fourth ventricle, gray matter and cerebellar vermal lobules I-IV volumes. We found regulatory genes (p ≤ 2.47 x10-6) by integrating transcriptomic (EAS=4;EUR=5) and methylation data (EUR=17; EAS=4) of brain tissues using Summary-based Mendelian Randomization (SMR). The LTL SNP associations were tested for brain-based chromatin profiles using H-MAGMA (EUR=50; EAS=97; p<= 1.02 x10-6). Pathway enrichment of tissue-specific genes highlighted calcium ion transport (fetal brain) and G2/M cell cycle transition (adult brain). This study provides evidence that previously reported LTL associations with neuropsychiatric disorders could be related to a shared genetic relationship between LTL and brain structural and regulatory traits.

RNA-Seq analysis of compatible and incompatible styles of Pyrus species at the beginning of pollination

In Rosaceae, incompatible pollen can penetrate into the style during the gametophytic self-incompatibility response. It is therefore considered a stylar event rather than a stigmatic event. In this study, we explored the differences in gene expression between compatibility and incompatibility in the early stage of pollination. The self-compatible pear variety “Jinzhuili” is a naturally occurring bud mutant from “Yali”, a leading Chinese native cultivar exhibiting typical gametophytic self-incompatibility. We collected the styles of ‘Yali’ and ‘Jinzhuili’ at 0.5 and 2 h after self-pollination and then performed high-throughput sequencing. According to the pathway enrichment analysis of the differentially expressed genes, “plant-pathogen interaction” was the most represented pathway. Quantitative PCR was used to validate these differential genes. The expression levels of genes related to pollen growth and disease inhibition, such as LRR (LEUCINE-RICH REPEAT EXTENSIN), resistance, and defensin, differed significantly between compatible and incompatible pollination. Interestingly, at 0.5 h, most of these genes were upregulated in the compatible pollination system compared with the incompatible pollination system. Calcium ion transport, which requires ATPase, also demonstrated upregulated expression. In summary, the self-incompatibility reaction was initiated when the pollen came into contact with the stigma.

Assessment of the Potential Role ofStreptomycesin Cave Moonmilk Formation

Moonmilk is a karstic speleothem mainly composed of fine calcium carbonate crystals (CaCO3) with different textures ranging from pasty to hard, in which the contribution of biotic rock-building processes is presumed to involve indigenous microorganisms. The real bacterial input in the genesis of moonmilk is difficult to assess leading to controversial hypotheses explaining the origins and the mechanisms (biotic versus abiotic) involved. In this work we undertook a comprehensive approach in order to assess the potential role of filamentous bacteria, particularly a collection of moonmilk-originatingStreptomyces, in the genesis of this speleothem. Scanning electron microscopy (SEM) confirmed that indigenous filamentous bacteria could indeed participate in moonmilk development by serving as nucleation sites for CaCO3deposition. The metabolic activities involved in CaCO3transformation were furthermore assessedin vitroamong the collection of moonmilkStreptomyces, which revealed that peptides/amino acids ammonification, and to a lesser extend ureolysis, could be privileged metabolic pathways participating in carbonate precipitation by increasing the pH of the bacterial environment. Additionally,in silicosearch for the genes involved in biomineralization processes including ureolysis, dissimilatory nitrate reduction to ammonia, active calcium ion transport, and reversible hydration of CO2allowed to identify genetic predispositions for carbonate precipitation inStreptomyces. Finally, their biomineralization abilities were confirmed by environmental SEM, which allowed to visualize the formation of abundant mineral deposits under laboratory conditions. Overall, our study provides novel evidences that filamentous Actinobacteria could be key protagonists in the genesis of moonmilk through a wide spectrum of biomineralization processes.