The Influence of Redd Distribution and Microhabitat Availability on the Distribution and Abundance of Young-of-the-year Trout in the Green River, Utah

Redd distribution, redd density, and physical habitat were used to explain the distribution and abundance of young-of-the-year (YOY) brown trout (Salmo trutta) and rainbow trout (Oncorhynchus mykiss) in the Green River, Utah. The importance of variables at both a microhabitat and macrohabitat scale were assessed using stepwise regression analysis. Availability of cover (rock and vegetation) and proximity to spawning sites were the most important variables used to explain the distribution and abundance of YOY brown trout and rainbow trout. In addition, YOY brown trout and rainbow trout occupied specific microhabitats and showed patterns of use for particular depths, substrates, and cover. However, the importance of variables differed by year, indicating that variables other than those measured were also influencing their distribution and abundance. The results of my study indicate that variables at both a microhabitat and macrohabitat scale may be important in explaining the distribution and abundance of YOY trout in streams. Therefore, to better understand the habitat requirements of stream fishes and to better explain their distribution and abundance in streams future, studies may need to incorporate both physical habitat variables and variables affecting recruitment

Modeling suggests gene editing combined with vaccination could eliminate a persistent disease in livestock

Recent breakthroughs in gene-editing technologies that can render individual animals fully resistant to infections may offer unprecedented opportunities for controlling future epidemics in farm animals. Yet, their potential for reducing disease spread is poorly understood as the necessary theoretical framework for estimating epidemiological effects arising from gene-editing applications is currently lacking. Here, we develop semistochastic modeling approaches to investigate how the adoption of gene editing may affect infectious disease prevalence in farmed animal populations and the prospects and time scale for disease elimination. We apply our models to the porcine reproductive and respiratory syndrome (PRRS), one of the most persistent global livestock diseases to date. Whereas extensive control efforts have shown limited success, recent production of gene-edited pigs that are fully resistant to the PRRS virus have raised expectations for eliminating this deadly disease. Our models predict that disease elimination on a national scale would be difficult to achieve if gene editing was used as the only disease control. However, from a purely epidemiological perspective, disease elimination may be achievable within 3 to 6 y, if gene editing were complemented with widespread and sufficiently effective vaccination. Besides strategic distribution of genetically resistant animals, several other key determinants underpinning the epidemiological impact of gene editing were identified

Genomic and phenotypic characterization of finger millet indicates a complex diversification history

Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub‐genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub‐genomes A and B using neighbor‐joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome‐wide association study found only a limited number of significant marker‐trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context‐specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet

Genetic architecture and major genes for backfat thickness in pig lines of diverse genetic backgrounds

Background Backfat thickness is an important carcass composition trait for pork production and is commonly included in swine breeding programmes. In this paper, we report the results of a large genome-wide association study for backfat thickness using data from eight lines of diverse genetic backgrounds. Methods Data comprised 275,590 pigs from eight lines with diverse genetic backgrounds (breeds included Large White, Landrace, Pietrain, Hampshire, Duroc, and synthetic lines) genotyped and imputed for 71,324 single-nucleotide polymorphisms (SNPs). For each line, we estimated SNP associations using a univariate linear mixed model that accounted for genomic relationships. SNPs with significant associations were identified using a threshold of p < 10(-6) and used to define genomic regions of interest. The proportion of genetic variance explained by a genomic region was estimated using a ridge regression model. Results We found significant associations with backfat thickness for 264 SNPs across 27 genomic regions. Six genomic regions were detected in three or more lines. The average estimate of the SNP-based heritability was 0.48, with estimates by line ranging from 0.30 to 0.58. The genomic regions jointly explained from 3.2 to 19.5% of the additive genetic variance of backfat thickness within a line. Individual genomic regions explained up to 8.0% of the additive genetic variance of backfat thickness within a line. Some of these 27 genomic regions also explained up to 1.6% of the additive genetic variance in lines for which the genomic region was not statistically significant. We identified 64 candidate genes with annotated functions that can be related to fat metabolism, including well-studied genes such as MC4R, IGF2, and LEPR, and more novel candidate genes such as DHCR7, FGF23, MEDAG, DGKI, and PTN. Conclusions Our results confirm the polygenic architecture of backfat thickness and the role of genes involved in energy homeostasis, adipogenesis, fatty acid metabolism, and insulin signalling pathways for fat deposition in pigs. The results also suggest that several less well-understood metabolic pathways contribute to backfat development, such as those of phosphate, calcium, and vitamin D homeostasis

Phenotypic and genetic diversity of Spanish tomato landraces

[EN] The structure of Spanish landraces of tomato (Solanum lycopersicum L) has been analyzed. This diversity has been evaluated using agro-morphological characteristics (43 descriptors), quality parameters (solid soluble contents and individual sugars and organic acids) and DNA markers (amplified fragment length polymorphisms, AFLP). A wide range of variation was found for all traits but in the DNA marker level. Certain common characteristics could be identified in populations of the same landrace in several of the dimensions analyzed, but generally, an overlap of the spectrum of variation of different landraces was found. The results indicate that in each landrace the populations are strongly selected using very basic morphological characteristics such as fruit shape, colour or ribbing, while other traits vary depending on each farmer preferences. Seed mixing and pollen contamination might introduce variation which would be purged by farmers at the morphological level, but would be maintained in quality and yield traits. Despite the introduction of spurious variation it would be still possible to identify certain relations between quality attributes and the morphological traits defining specific landraces. The existence of a wide level of variation in plant yield and quality profiles enables the development of selection programmes targeted to provide farmers with materials with economically viable yield and excellent organoleptic quality. The results also highlight the necessity to stress the efforts in morpho-agronomical and quality characterization over molecular characterization in the ex situ management of these resources, as well as not to underestimate the importance of intra-varietal variability. (C) 2013 Elsevier B.V. All rights reserved.This research was funded by the Generalitat Valenciana with the research projects GV-CAPA00-19 and GV/2007/003.Cebolla Cornejo, J.; Rosello Ripolles, S.; Nuez Viñals, F. (2013). Phenotypic and genetic diversity of Spanish tomato landraces. Scientia Horticulturae. 162:150-164. https://doi.org/10.1016/j.scienta.2013.07.044S15016416

Identification of species by multiplex analysis of variable-length sequences

The quest for a universal and efficient method of identifying species has been a longstanding challenge in biology. Here, we show that accurate identification of species in all domains of life can be accomplished by multiplex analysis of variable-length sequences containing multiple insertion/deletion variants. The new method, called SPInDel, is able to discriminate 93.3% of eukaryotic species from 18 taxonomic groups. We also demonstrate that the identification of prokaryotic and viral species with numeric profiles of fragment lengths is generally straightforward. A computational platform is presented to facilitate the planning of projects and includes a large data set with nearly 1800 numeric profiles for species in all domains of life (1556 for eukaryotes, 105 for prokaryotes and 130 for viruses). Finally, a SPInDel profiling kit for discrimination of 10 mammalian species was successfully validated on highly processed food products with species mixtures and proved to be easily adaptable to multiple screening procedures routinely used in molecular biology laboratories. These results suggest that SPInDel is a reliable and cost-effective method for broad-spectrum species identification that is appropriate for use in suboptimal samples and is amenable to different high-throughput genotyping platforms without the need for DNA sequencing

Genetic diversity analysis of common beans based on molecular markers

A core collection of the common bean (Phaseolus vulgaris L.), representing genetic diversity in the entire Mexican holding, is kept at the INIFAP (Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias, Mexico) Germplasm Bank. After evaluation, the genetic structure of this collection (200 accessions) was compared with that of landraces from the states of Oaxaca, Chiapas and Veracruz (10 genotypes from each), as well as a further 10 cultivars, by means of four amplified fragment length polymorphisms (AFLP) +3/+3 primer combinations and seven simple sequence repeats (SSR) loci, in order to define genetic diversity, variability and mutual relationships. Data underwent cluster (UPGMA) and molecular variance (AMOVA) analyses. AFLP analysis produced 530 bands (88.5% polymorphic) while SSR primers amplified 174 alleles, all polymorphic (8.2 alleles per locus). AFLP indicated that the highest genetic diversity was to be found in ten commercial-seed classes from two major groups of accessions from Central Mexico and Chiapas, which seems to be an important center of diversity in the south. A third group included genotypes from Nueva Granada, Mesoamerica, Jalisco and Durango races. Here, SSR analysis indicated a reduced number of shared haplotypes among accessions, whereas the highest genetic components of AMOVA variation were found within accessions. Genetic diversity observed in the common-bean core collection represents an important sample of the total Phaseolus genetic variability at the main Germplasm Bank of INIFAP. Molecular marker strategies could contribute to a better understanding of the genetic structure of the core collection as well as to its improvement and validation