Identification of selection signatures in <scp><i>Capra hircus</i></scp> and <scp><i>Capra aegagrus</i></scp> in Iran

Taheri, Sadegh; Saedi, Naghmeh; Zerehdaran, Saeed; Javadmanesh, Ali

doi:10.1111/asj.13864

Cited by 3 publications

(2 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…PLINK V 1.9 (Purcell et al, 2007) was used for further filtering for both datasets (derived from this study and the publicly available data). Individuals with a genotyping call rate < 99%, SNPs with a genotyping call rate < 99%, and those exhibiting significant deviations from Hardy-Weinberg equilibrium (P-value <10 -6 ) were excluded from the analysis (Taheri et al, 2023). Following this filtering process, the genetic data from both groups were combined, and only the SNPs that were common to both groups were selected.…”

Section: Methodsmentioning

confidence: 99%

Population genomics of a naturalCannabis sativaL. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping

Dehnavi,

Damerum,

Taheri

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Future breeding and selection of Cannabis sativa L. for drug production and industrial purposes require a source of germplasm with wide genetic variation, such as that found in wild relatives and progenitors of highly cultivated plants. Limited directional selection and breeding have occurred in this crop, especially informed by molecular markers. Here, we investigated the population genomics of a natural cannabis collection of male and female individuals from differing climatic zones in Iran. Using Genotyping-By-Sequencing (GBS), we sequenced 228 genotypes from 35 populations. The results obtained from GBS were used to perform association analysis identifying links between genotype and important phenotypes, including inflorescence characteristics, flowering time, plant morphology, tetrahydrocannabinol (THC) content, cannabidiol (CBD) content and sex. Approximately 23,266 significant SNPs of high quality were detected to establish associations between markers and traits, and population structure showed that Iranian cannabis plants fall into five groups. A comparison of Iranian samples from this study to global data suggests that the Iranian population is distinctive and, in general, is closer to marijuana than to hemp, although some populations in this collection are closer to hemp. The GWAS results showed that novel genetic loci, not previously identified, contribute to sex, yield and chemotype traits in cannabis and are worthy of further study.

show abstract

Section: Methodsmentioning

confidence: 99%

Population genomics of a naturalCannabis sativaL. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping

Dehnavi,

Damerum,

Taheri

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…A combination of lnθπ ratio and F ST value screened the selected genomic regions. VCFtools software [ 112 ] calculated the lnθπ ratio and F ST value using a sliding window, with a window size of 100 kb and a step size of 10 kb. Select the regions that meet both the top 5% and bottom 5% of the lnθπ ratio, as well as the top 5% of the F ST value, as the selected regions, and jointly screen for stronger selection signals to obtain the target gene.…”

Section: Methodsmentioning

confidence: 99%

Population structure and adaptability analysis of Schizothorax o’connori based on whole-genome resequencing

Gao,

He,

Xiong

et al. 2024

BMC Genomics

View full text Add to dashboard Cite

Background Schizothorax o’connori is an endemic fish distributed in the upper and lower reaches of the Yarlung Zangbo River in China. It has experienced a fourth round of whole gene replication events and is a good model for exploring the genetic differentiation and environmental adaptability of fish in the Qinghai-Tibet Plateau. The uplift of the Qinghai-Tibet Plateau has led to changes in the river system, thereby affecting gene exchange and population differentiation between fish populations. With the release of fish whole genome data, whole genome resequencing has been widely used in genetic evolutionary analysis and screening of selected genes in fish, which can better elucidate the genetic basis and molecular environmental adaptation mechanisms of fish. Therefore, our purpose of this study was to understand the population structure and adaptive characteristics of S. o’connori using the whole-genome resequencing method. Results The results showed that 23,602,746 SNPs were identified from seven populations, mostly distributed on chromosomes 2 and 23. There was no significant genetic differentiation between the populations, and the genetic diversity was relatively low. However, the Zangga population could be separated from the Bomi, Linzhi, and Milin populations in the cluster analysis. Based on historical dynamics analysis of the population, the size of the ancestral population of S. o’connori was affected by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Glacial Age. The selected sites were mostly enriched in pathways related to DNA repair and energy metabolism. Conclusion Overall, the whole-genome resequencing analysis provides valuable insights into the population structure and adaptive characteristics of S. o’connori. There was no obvious genetic differentiation at the genome level between the S. o’connori populations upstream and downstream of the Yarlung Zangbo River. The current distribution pattern and genetic diversity are influenced by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Ice Age. The selected sites of S. o’connori are enriched in the energy metabolism and DNA repair pathways to adapt to the low temperature and strong ultraviolet radiation environment at high altitude.

show abstract

Identification of selective sweep and associated QTL traits in Iranian Ovis aries and Ovis orientalis populations

Taheri,

Javadmanesh,

Zerehdaran

2024

Front. Genet.

View full text Add to dashboard Cite

IntroductionIdentifying genomic regions under selection is the most challenging issue for improving important traits in animals. Few studies have focused on identifying genomic regions under selection in sheep. The aim of this study was to identify selective sweeps and to explore the relationship between these and quantitative trait loci (QTL) in both domestic and wild sheep species using single nucleotide polymorphism markers (SNPs).MethodsGenomic data were obtained from the NextGen project, which included genotyping 20 domestic and 14 wild sheep using the Illumina Ovine SNP50K BeadChip. The XP-EHH, iHS, and RSB methods were employed to detect signatures of positive selection.ResultsThe results of the iHS method indicated 405 and 275 selective sweeps in domestic and wild sheep, respectively. Additionally, RSB and XP-EHH analyses revealed approximately 398 and 479 selective sweeps in domestic and wild sheep, respectively. Some of the genes associated with important QTL traits in domestic sheep include ADGRB3, CADM1, CAPN2, GALNT10, MTR, RELN, and USP25, while in wild sheep, the relevant genes include ACAN, ACO1, GADL1, MGST3, and PRDM16. Selective sweeps identified in domestic sheep were associated with body weight, muscle weight, milk protein percentage, and milk yield. In contrast, selective sweeps found in wild sheep were linked to average daily gain, bone weight, carcass fat percentage, and dressing percentage.DiscussionThese results indicate that selection by humans and the environment have largely progressed in harmony, highlighting the importance of both economic and environmental traits for survival. Additionally, the identification of potential candidate genes associated with economic traits and genomic regions that have experienced selection can be utilized in sheep breeding programs. However, due to the incomplete information regarding the functional annotation of genes in sheep and the limited sample size, further research with a larger sample group is essential to gain a deeper understanding of the candidate genes linked to economic traits in both domestic and wild sheep. Advancing knowledge in this area can significantly enhance the effectiveness of breeding strategies. The quantitative trait loci identified in this study have the potential to be incorporated into breeding plans for both domestic and wild sheep.

show abstract

Identification of selection signatures in Capra hircus and Capra aegagrus in Iran

Cited by 3 publications

References 65 publications

Population genomics of a naturalCannabis sativaL. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping

Population genomics of a naturalCannabis sativaL. collection from Iran identifies novel genetic loci for flowering time, morphology, sex and chemotyping

Population structure and adaptability analysis of Schizothorax o’connori based on whole-genome resequencing

Identification of selective sweep and associated QTL traits in Iranian Ovis aries and Ovis orientalis populations

Contact Info

Product

Resources

About