Post-genotyping optimization of dataset formation could affect genetic diversity parameters: an example of analyses with alpine goat breeds

Abstract

Background Local breeds retained unique genetic variability important for adaptive potential especially in light of challenges related to climate change. Our first objective was to perform, for the first time, a genome-wide diversity characterization using Illumina GoatSNP50 BeadChip of autochthonous Drežnica goat breed from Slovenia, and five and one local breeds from neighboring Austria and Italy, respectively. For optimal conservation and breeding programs of endangered local breeds, it is important to detect past admixture events and strive for preservation of purebred representatives of each breed with low or without admixture. In the second objective, we hence investigated the effect of inclusion or exclusion of outliers from datasets on genetic diversity and population structure parameters. Results Distinct genetic origin of the Drežnica goat was demonstrated as having closest nodes to Austrian and Italian breeds. A phylogenetic study of these breeds with other goat breeds having SNP data available in the DRYAD repository positioned them in the alpine, European and global context. Swiss breeds clustered with cosmopolitan alpine breeds and were closer to French and Spanish breeds. On the other hand, the Drežnica goat, Austrian and Italian breeds were closer to Turkish breeds. Datasets where outliers were excluded affected estimates of genetic diversity parameters within the breed and increased the pairwise genetic distances between most of the breeds. Alpine breeds, including Drežnica, Austrian and Italian goats analyzed here, still exhibit relatively high levels of genetic variability, homogeneous genetic structure and strong geographical partitioning. Conclusions Genetic diversity analyses revealed that the Slovenian Drežnica goat has a distinct genetic identity and is closely related to the neighboring Austrian and Italian alpine breeds. These results expand our knowledge on phylogeny of goat breeds from easternmost part of the European Alps. The here employed outlier test and datasets optimization approaches provided an objective and statistically powerful tool for removal of admixed outliers. Importance of this test in selecting the representatives of each breed is warranted to obtain more objective diversity parameters and phylogenetic analysis. Such parameters are often the basis of breeding and management programs and are therefore important for preserving genetic variability and uniqueness of local rare breeds.

Discovering novel clues of natural selection on four worldwide goat breeds

“…Arianna Manunza 1,4* , Johanna Ramirez Diaz 1,4 , Brian L Sayre 2 , Paolo Cozzi 1 , Tania Bobbo 1 , Tatiana Deniskova 3 , Arsen Dotsev 3 , Natalia Zinovieva 3 & Alessandra Stella 1 In goat breeds, the domestication followed by artificial selection for economically important traits have shaped genetic variation within populations, leading to the fixation of specific alleles for specific traits. This led to the formation and evolution of many different breeds specialised and raised for a particular purpose.…”

“…Different methodologies that can be applied to detect selection signatures 5 , generally based on the comparison of statistics on genotypes at intra-populations versus inter-populations level. Two main categories of statistics have been developed at (1) 4 These authors contributed equally: Arianna Manunza and Johanna Ramirez Diaz. * email: arianna.manunza@ibba.cnr.it Population relationships, clustering and outlier variant detection.…”

“…In small local breed, genomic information has been exploited to investigate the ability to respond to environmental changes and challenges. This subdivision is generally based on the assumption that strong selection pressure applied to commercial breeds lead to negative impacts on their ability to adapt in comparison with traditional breeds, due to stronger connection to their original environments 4 . The role of the natural selection in shaping the genetic architecture of the highly selected, transboundary breeds has not yet been investigated.…”

Distributional Response of the Rare and Endangered Tree Species Abies chensiensis to Climate Change in East Asia

“…Over the past 100 years, the average temperature in the alpine region has risen by nearly 2 °C, which is almost twice as large as the average global increase; however, the last 30 years have seen a particularly rapid rise, with frequent severe weather events [ 1 , 2 ]. As temperatures warm, future climate change will not only alter surface temperature and precipitation patterns [ 3 ], but will also affect ecosystems and biomes, leading to changes in the physiological metabolism, geographical distribution, and population size of plants, particularly those of alpine origin [ 4 , 5 ].…”

Genetic Diversity, Population Structure and Phylogeny of Indigenous Goats of Mongolia Revealed by SNP Genotyping

“…Decisions might be supported by the compilation of databases containing objective information about the genotypes of these breeds: their genetic risks, phylogenetic relationships, as well as knowledge of the socioeconomic processes that can affect the risks of these breeds [5,6]. SNP genotyping is widely recognized as the most appropriate tool due to the availability of commercial SNP arrays that give unified comparable data [7].…”