Development of an SNP Assay for Marker-Assisted Selection of Soil-Borne Rhizoctonia Solani AG-2-2-IIIB Resistance in Sugar Beet

Rhizoctonia solani, causing Rhizoctonia crown and root rot, is a major risk to sugar beet (Beta vulgaris L.) cultivation. The development of resistant varieties accelerated by marker-assisted selection is a priority of breeding programs. We report the identification of a single-nucleotide polymorphism (SNP) marker linked to Rhizoctonia resistance using restriction site-associated DNA (RAD) sequencing of two geographically discrete sets of plant materials with different degrees of resistance/susceptibility to enable a wider selection of superior genotypes. The variant calling pipeline utilized SAMtools for variant calling and the resulting raw SNPs from RAD sequencing (15,988 and 22,439 SNPs) were able to explain 13.40% and 25.45% of the phenotypic variation in the two sets of material from different sources of origin, respectively. An association analysis was carried out independently on both the datasets and mutually occurring significant SNPs were filtered depending on their contribution to the phenotype using principal component analysis (PCA) biplots. To provide a ready-to-use marker for the breeding community, a systematic molecular validation of significant SNPs distributed across the genome was undertaken to combine high-resolution melting, Sanger sequencing, and rhAmp SNP genotyping. We report that RsBv1 located on Chromosome 6 (9000093 bp) is significantly associated with Rhizoctonia resistance (p < 0.01) and able to explain 10% of the phenotypic disease variance. The related SNP assay is thus ready for marker-assisted selection in sugar beet breeding for Rhizoctonia resistance.

Inter-island local adaptation in the Galápagos Archipelago: genomics of the Galápagos blue-banded goby, Lythrypnus gilberti

The Galápagos Archipelago is a place where terrestrial adaptive radiations of finches, mockingbirds, and tortoises have been studied extensively. In contrast, little is known about the potential for marine species to diverge among islands. The overall degradation of coral reefs in the Galápagos makes understanding the mechanisms and factors of speciation, the engine of biodiversity, important, and timely. While speciation in marine archipelagos has been described in the past, such as for cone snails in Cabo Verde Archipelago and limpets in Hawaii, adaptive radiations in the marine environment are still rare and poorly understood. In this study, we focused on the Galápagos blue-banded goby, Lythrypnus gilberti, a small endemic fish that is found in shallow subtidal rocky habitats. Using RAD sequencing, we analyzed 19,504 loci that were either neutral, or potentially under directional selection. As expected, considering the small geographic range, population structure based on neutral markers was weak. For loci under directional selection, however, marked differences between islands suggested potential for local adaptation. Our data suggest that for marine species, where dispersal barriers are less apparent, mechanisms of local adaptation may also be at play in the Galápagos Archipelago.

Genomics Facilitates Evaluation and Monitoring of McCloud River Redband Trout ( Oncorhynchus mykiss stonei )

The McCloud River Redband Trout (MRRT; Oncorhynchus mykiss stonei ) is a unique subspecies of rainbow trout that inhabits the isolated Upper McCloud River of Northern California. A major threat to MRRT is introgressive hybridization with non-native rainbow trout from historical stocking and contemporary unauthorized introductions . To help address this concern, we collected RAD-sequencing data on 308 total individuals from MRRT and other California O. mykiss populations and examined population structure using Principal Component and admixture analyses. Our results are consistent with previous studies; we found that populations of MRRT in Sheepheaven, Swamp, Edson, and Moosehead creeks are nonintrogressed. Additionally, we saw no evidence of introgression in Dry Creek, and suggest further investigation to determine if it can be considered a core MRRT conservation population. Sheepheaven Creek was previously thought to be the sole historical lineage of MRRT, but our analysis identified three: Sheepheaven, Edson, and Dry creeks, all of which should be preserved. Finally, we discovered diagnostic and polymorphic SNP markers for monitoring introgression and genetic diversity in MRRT. Collectively, our results provide a valuable resource for the conservation and management of MRRT.

Phylogenetic relationships of stress resistant fish in Harapan Rainforest Jambi based on DNA barcode

DNA barcode as an effective tool for identification and reveal phylogenetic relationships in fish. The purpose of this study was to analysis DNA sequence, genetic distance and reveal phylogenetic relationships of stress resistance fish (blackfish) in Harapan Rainforest Jambi base on DNA barcode. The research was conducted from April to August 2016 in Harapan Rainforest Jambi, Integrated Laboratory, Jambi University and Biotechnology Laboratory of the Primate Study Centre-IPB University. DNA extraction was done on five blackfish species from Harapan Rainforest Jambi, namely Nandus nebulosus, Pristolepis grootii, Trichopodus leerii, Channa striata and Channa micropeltes. As a comparison, we used stress intolerance fish (whitefish) from Harapan Rainforest Jambi, i.e., Balantiocheilos melanopterus and Hemibagrus nemurus from the gene-bank NCBI with acession number KT001040,1. DNA Extraction was performed according to Quick-Star Tissue Protocol from Qiagen. COI gene amplification with modification at denaturation and anneling temperatures. Visualization DNA band using a horizontal electrophoresis machine from Bio Rad. Sequencing DNA send to 1st Base Malaysia. DNA sequence used Biodit and MEGA X software. The alignment of the DNA bands in MEGA X produces DNA sequence along 588 bp, where 350 bp conserve and 238 bp variable sites. The composition of the base nucleotides were (T/U) =29%, C=28.6%, A=25%, and G=17.3%. The closest genetic distance was between Channa striata and Channa micropeltes (0.190) and the farthest was found on Nandus nebulosus and Hemibagrus nemurus (0.303). The phylogeny tree shows that the blackfishes are separated from whitefishes. The group of blackfish is divided into Channidae group (Channa striata, Channa micropeltes) and non-Channidae group (Nandus nebulosus, Trichopodus leerii, Pristolepis grootii).

Development of SNP markers derived from RAD sequencing for Atlantic salmon (Salmo salar L.) inhabiting the rivers of southern England

The rivers of the Hampshire Basin, southern England contain a genetically unique group of Atlantic salmon that have suffered dramatic declines in numbers over the last 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 94 single nucleotide polymorphism (SNP) loci for salmon from this region and investigate their applicability and variability in both target (i.e. southern English) and non-target populations. The SNP loci will be useful for population genetic and assignment studies on Atlantic salmon within the UK and beyond.