Whole genome sequencing revealed genetic diversity, population structure, and selective signature of Panou Tibetan sheep

BACKGROUND

The detection of selective traits in different populations can not only reveal current mechanisms of artificial selection for breeding, but also provide new insights into phenotypic variation in new varieties and the search for genes associated with important traits. Panou sheep is a cultivated breed of Tibetan sheep in China with stable genetic performance, consistent appearance and fast growth and development after decades of artificial selection and cultivation. Due to long-term adaptation to the high altitude, cold and hypoxic environment in the plateau area, they may have formed a unique gene pool that is different from other Tibetan sheep breeds. To explore the genetic resources of Panou sheep, we used next-generation sequencing technology for the first time to investigate the genome-wide population structure, genetic diversity, and candidate signatures of positive selection in Panou sheep.

RESULTS

Comparative genomic analysis with the closely related species Oula sheep (a native breed of Tibetan sheep in China) was used to screen the population selection signal of Panou sheep. Principal component analysis and neighbor joining tree showed that Panou sheep and Oula sheep had differences in population differentiation. Furthermore, analyses of population structure, they came from the same ancestor, and when K = 2, the two populations could be distinguished. Panou sheep exhibit genetic diversity comparable to Oula sheep, as shown by observed heterozygosity, expected heterozygosity and runs of homozygosity. Genome-wide scanning using the Fst and π ratio methods revealed a list of potentially selected related genes in Panou sheep compared to Oula sheep, including histone deacetylase 9 (HDAC9), protein tyrosine kinase 2 (PTK2), microphthalmia-related transcription factor (MITF), vesicular amine transporter 1 (VAT1), trichohyalin-like 1 (TCHHL1), amine oxidase, copper containing 3 (AOC3), interferon-inducible protein 35 (IFI35).

CONCLUSIONS

The results suggest that traits related to growth and development and plateau adaptation may be selection targets for the domestication and breeding improvement of Tibetan sheep. This study provides the fundamental footprints for Panou sheep breeding and management.

The Distribution and Origins of Pyrus hopeiensis-"Wild Plant With Tiny Population" Using Whole Genome Resequencing

Pyrus hopeiensis is a valuable but endangered wild resource in the genus Pyrus. It has been listed as one of the 120 wild species with tiny population in China. The specie has been little studied. A preliminary study of propagation modes in P. hopeiensis was performed through seed propagation, hybridization, self-crossing trials, bud grafting, branch grafting, and investigations of natural growth. The results showed that the population size of P. hopeiensis was very small, the distribution range was limited, and the habitat was extremely degraded. In the wild population, natural hybridization and root tiller production were the major modes of propagation. Whole genome re-sequencing of the 23 wild and cultivated accessions from Pyrus species collected was performed using an Illumina HiSeq sequencing platform. The sequencing depth range was 26.56x-44.85x and the average sequencing depth was 32x. Phylogenetic tree and principal component analyses (PCA) based on SNPs showed that the wild Pyrus species, such as PWH06, PWH07, PWH09, PWH10, PWH13, and PWH17, were closely related to both P. hopeiensis HB-1 and P. hopeiensis HB-2. Using these results in combination with morphological characteristics, it speculated that P. hopeiensis populations may form a natural hybrid group with frequent gene exchanges between and within groups. A selective elimination analysis on the P. hopeiensis population were performed using Fst and π radio and a total of 381 overlapping genes including SAUR72, IAA20, HSFA2, and RKP genes were obtained. These genes were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) function enrichment. And four KEGG pathways, including lysine degradation, sphingolipid metabolism, other glycan degradation, and betaine biosynthesis were significantly enriched in the P. hopeiensis population. Our study provided information on genetic variation, evolutionary relationships, and gene enrichment in P. hopeiensis population. These data will help reveal the evolutionary history and origin of P. hopeiensis and provide guidelines for subsequent research on the locations of functional genes.