Population genetic data (COI, ddRAD) of Sialis
lutaria (Insecta, Megaloptera) from the Emscher
catchment (Germany)

https://bdj.pensoft.net/article/141997/

#COI #DNAbarcoding #ddRAD #PopulationGenetics

Population genetic data (COI, ddRAD) of Sialis lutaria (Insecta, Megaloptera) from the Emscher catchment (Germany)

In urban river systems, fragmentation of habitats and in-stream dispersal barriers play a major role in shaping the population genetic structure of freshwater macroinvertebrate species. In small, fragmented populations, effects of genetic drift and inbreeding are enhanced, which can lead to increased population differentiation and genetic diversity loss. One formerly strongly degraded and fragmented stream system in a highly urbanised area is the Emscher catchment in North Rhine-Westphalia, Germany. Major restoration efforts have led to an improvement of water and habitat quality over the past 20 years also in the formerly polluted tributaries, for example, the Boye catchment. However, the analysis of the population structure of two different amphipod and isopod species has revealed that some populations are still strongly isolated, indicating persisting gene flow barriers. In contrast, the effects are expected to be less pronounced in merolimnic species, which have an adult winged life stage, such as the alderfly Sialis lutaria (Linnaeus, 1758) . However, this species was much less abundant in the Boye catchment and not found in adjacent catchments (only 9 of 41 sampling sites), reducing the power of possible analyses.As no population genetic studies of S. lutaria have to our knowledge been published so far and genetic resources are generally scarce for this species, we generated and present here population genetic data for 70 S. lutaria specimens for the mitochondrial cytochrome c oxidase I (COI) gene and, more importantly, high resolution genomic single nucleotide polymorphism (SNP) data for 71 specimens, generated with double-digest restriction site-associated sequencing (ddRAD-seq). These data can be valuable for further studies, analysing the population genetic structure, dispersal pathways and potential gene flow barriers for S. lutaria on a larger geographic scale. Additional to presenting the data, we also give first insights in the population structure on a small geographic scale (area of approx. 15 km2). While the population differentiation was generally low, as expected on this small scale, we still found that gene flow was not equally strong between all populations, but that one population played a central role as a source and sink population, which cannot only be explained by the distance between populations.

Biodiversity Data Journal
Genome-Wide Identification of SNPs and Their Annotation in Indian Gir Cattle - #ddRAD #girbreed #milkproductiontraits #SNPs #Zebucattle #genome - https://link.springer.com/article/10.3103/S0095452724040042
Genome-Wide Identification of SNPs and Their Annotation in Indian Gir Cattle - Cytology and Genetics

Abstract The study was carried out in Gir cattle for identification of genome wide SNPs and then to annotate the identified high-quality SNPs to the milk production traits. A total of 99 517 SNPs were identified with respect to the Bos indicus reference genome. Upon annotation of SNPs identified with respect to Bos indicus reference genome, 984 SNPs located in 175 candidate genes related with milk production traits, notably Acetyl-CoA carboxylase β gene, which affects milk composition traits by regulation of fatty acid oxidation in the mitochondria; Growth hormone receptor gene which have role in milk yield and its composition traits; LEP gene, involved in energy partitioning and metabolism, were among others. This study provides the first analysis of ddRAD sequences to discover SNPs in Indian Gir cattle breed, aligned to indicine reference genome. The variants mined in this study can be incorporated in existing SNP chips and thus, play an important role in understanding the genetic structure of our cattle in order to design appropriate breed improvement programmes.

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