Screening for signatures of selection of Tianzhu white yak using genome-wide re-sequencing

Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in southwestern China

The Sichuan-Yunnan region is the main production area of yaks in southwestern China, with rich genetic resources of Yaks. Nevertheless, there have been limited study on the genetic characteristics of the entire yak populations in Tibet and southwestern China. In this study, we performed whole-genome resequencing to identify genetic variation information in a total of 198 individuals from six yak breeds (populations) in Sichuan (Muli yak, Jinchuan yak, Changtai yak, Maiwa yak), Yunnan (Zhongdian yak), and Tibet (Tibetan yak). The aim was to investigate the whole-genome genetic diversity, population genetic structure, and genome selection signatures. We observed that all six populations exhibit abundant genetic diversity. Except for Tibetan yaks, which showed low nucleotide diversity (0.00104), the remaining yak populations generally displayed high nucleotide diversity (0.00129-0.00153). Population genetic structure analysis revealed that, among the six yak populations, Muli yak exhibited greater differentiation from other yak populations and formed a distinct cluster independently. The Maiwa yak population displayed a complex genetic structure and exhibited gene exchange with Jinchuan and Changtai yaks. Positive selection signals were detected in candidate genes associated with growth (GNB4, HMGA2, TRPS1, and LTBP1), reproduction (PI4KB, DYNC1I1, and GRIP1), immunity (CD200 and IL1RAP), lactation (SNX13 and CPM), hypoxia adaptation (NDUFB6, PRKN, and MRPS9), hair (KRT24, KRT25, and KRT26), meat quality (SUCLG2), digestion and absorption (CLDN1), and pigment deposition (OCA2) using the integrated Pi and F ST methods. This study provides significant insights into understanding the whole-genome genetic characteristics of yak populations in Tibet and southwestern China.

Assessing genomic diversity and selective pressures in Bashan cattle by whole-genome sequencing data

Specific ecological environments and domestication have continuously influenced the physiological characteristics of Chinese indigenous cattle. Among them, Bashan cattle belongs to one of the indigenous breeds. However, the genomic diversity of Bashan cattle is still unknown. Published whole-genome sequencing (WGS) data of 13 Bashan cattle and 48 worldwide cattle were used to investigate the genetic composition and selection characteristics of Bashan cattle. The population structure analysis revealed that Bashan cattle harbored ancestries with East Asian taurine and Chinese indicine. Genetic diversity analysis implied the relatively high genomic diversity in Bashan cattle. Through the identification of containing >5 nsSNPs or frameshift mutations genes in Bashan cattle, a large number of pathways related to sensory perception were discovered. CLR, θπ ratio, FST, and XP-EHH methods were used to detect the candidate signatures of positive selection in Bashan cattle. Among the identified genes, most of the enriched signal pathways were related to environmental information processing, biological systems, and metabolism. We mainly reported genes related to the nervous system (HCN1, KATNA1, FSTL1, GRIK2, and CPLX2), immune (CD244, SLAMF1, LY9, and CD48), and reproduction (AKR1C1, AKR1C3, AKR1C4, and TUSC3). Our findings will be significant in understanding the molecular basis underlying phenotypic variation of breed-related traits and improving productivity in Bashan cattle.

Selection signatures for fiber production in commercial species: A review

Natural fibers derived from diverse animal species have gained increased attention in recent years due to their favorable environmental effects, long-term sustainability benefits, and remarkable physical and mechanical properties that make them valuable raw materials used for textile and non-textile production. Domestication and selective breeding for the economically significant fiber traits play an imperative role in shaping the genomes and, thus, positively impact the overall productivity of the various fiber-producing species. These selection pressures leave unique footprints on the genome due to alteration in the allelic frequencies at specific loci, characterizing selective sweeps. Recent advances in genomics have enabled the discovery of selection signatures across the genome using a variety of methods. The increased demand for 'green products' manufactured from natural fibers necessitates a detailed investigation of the genomes of the various fiber-producing plant and animal species to identify the candidate genes associated with important fiber attributes such as fiber diameter/fineness, color, length, and strength, among others. The objective of this review is to present a comprehensive overview of the concept of selection signature and selective sweeps, discuss the main methods used for its detection, and address the selection signature studies conducted so far in the diverse fiber-producing animal species.

Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in Qinghai, China

The Qinghai Province of China is located in the northeast region of the Qinghai-Tibetan Plateau (QTP) and carries abundant yak genetic resources. Previous investigations of archaeological records, mitochondrial DNA, and Y chromosomal markers have suggested that Qinghai was the major center of yak domestication. In the present study, we examined the genomic diversity, differentiation, and selection signatures of 113 Qinghai yak, including 42 newly sequenced Qinghai yak and 71 publicly available individuals, from nine yak breeds/populations (wild, Datong, Huanhu, Xueduo, Yushu, Qilian, Geermu, Tongde, and Huzhu white) using high-depth whole-genome resequencing data. We observed that most of Qinghai yak breeds/populations have abundant genomic diversity based on four genomic parameters (nucleotide diversity, inbreeding coefficients, linkage disequilibrium decay, and runs of homozygosity). Population genetic structure analysis showed that Qinghai yak have two lineages with two ancestral origins and that nine yak breeds/populations are clustered into three distinct groups of wild yak, Geermu yak, and seven other domestic yak breeds/populations. F _ST values showed moderate genetic differentiation between wild yak, Geermu yak, and the other Qinghai yak breeds/populations. Positive selection signals were detected in candidate genes associated with disease resistance (CDK2AP2, PLEC, and CYB5B), heat stress (NFAT5, HSF1, and SLC25A48), pigmentation (MCAM, RNF26, and BOP1), vision (C1QTNF5, MFRP, and TAX1BP3), milk quality (OPLAH and GRINA), neurodevelopment (SUSD4, INSYN1, and PPP1CA), and meat quality (ZRANB1), using the integrated PI, composite likelihood ratio (CLR), and F _ST methods. These findings offer new insights into the genetic mechanisms underlying target traits in yak and provide important information for understanding the genomic characteristics of yak breeds/populations in Qinghai.

Genome-wide detection of RNA editing events during the hair follicles cycle of Tianzhu white yak

BACKGROUND

The hair coat is available for the yak to live in the harsh environment of the plateau. Besides, improving the hair production of yak is necessary for its textile industry development. Hair grows from hair follicles (HFs). The HFs undergo periodic growth after birth and are regulated by the complex gene regulatory network. However, the molecular mechanism of HFs regeneration in the Tianzhu white yak remains unclear. RNA editing is a post-transcriptional mechanism that regulates gene expression and produces new transcripts. Hence, we investigated the influence of the A-to-I RNA editing events on the HFs cycle of the Tianzhu white yak.

RESULTS

We finally identified 54,707 adenosine-to-inosine (A-to-I) RNA editing sites (RESs) from RNA sequencing data of the HFs cycle in the Tianzhu white yak. Annotation results showed RESs caused missense amino acid changes in 7 known genes. And 202 A-to-I editing sites altered 23 target genes of 140 microRNAs. A total of 1,722 differential RESs were identified during the HFs cycle of Tianzhu white yak. GO and KEGG enrichment analysis revealed several signaling pathways and GO terms involved skin development, hair growth, and HFs cycle. Such as genes with differential RNA editing levels were significantly enriched in the peroxisome, metabolic pathways, Notch signaling pathway, and PPAR signaling pathway. Besides, the editing sites in HFs development-related genes FAS, APCDD1, WWOX, MPZL3, RUNX1, KANK2, DCN, DSC2, LEPR, HEPHL1, and PTK2B were suggested as the potential RESs involving HFs development.

CONCLUSION

This study investigated the global A-to-I RNA editing events during the HFs cycle of yak skin tissue and expanded the knowledge of A-to-I RNA editing on the HFs cycle. Furthermore, this study revealed that RNA editing-influenced genes may regulate the HFs cycle by participating in the HFs development-related pathways. The findings might provide new insight into the regulation of RNA editing in hair growth.

Genomic Diversity Profiling and Breed-Specific Evolutionary Signatures of Selection in Arunachali Yak

Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA (ddRAD) sequencing data of Arunachali yak animals was processed and 99,919 SNPs were considered for further analysis. The genomic diversity profiled based on nucleotide diversity, π (π = 0.041 in 200 bp windows), effective population size, Ne (Ne = 83) and Runs of homozygosity (ROH) (predominance of shorter length ROHs) was found to be optimum. Subsequently, 207 regions were identified to be under selective sweeps through de-correlated composite of multiple signals (DCMS) statistic which combined three individual test statistics viz. π, Tajima’s D and |iHS| in non-overlapping 100 kb windows. Mapping of these regions revealed 611 protein-coding genes including KIT, KITLG, CDH12, FGG, FGA, FGB, PDGFRA, PEAR1, STXBP3, olfactory receptor genes (OR5K3, OR5H6 and OR1E1) and taste receptor genes (TAS2R1, TAS2R3 and TAS2R4). Functional annotation highlighted that biological processes like platelet aggregation and sensory perception were the most overrepresented and the associated regions could be considered as breed-specific signatures of selection in Arunachali yak. These findings point towards evolutionary role of natural selection in environmental adaptation of Arunachali yak population and provide useful insights for pursuing genome-wide association studies in future.

Maternal genetic diversity, differentiation and phylogeny of three white yak breeds/populations in China

White yak is a unique economic livestock animal on the Qilian Mountains of Qinghai-Tibet Plateau (QTP). Here, 369 mitochondrial D-loop sequences from three Chinese white yak breeds/populations (Tianzhu, Menyuan and Huzhu) were comprehensively analyzed to indicate their maternal genetic diversity, differentiation and phylogenetic relationship. Our results showed that the haplotype diversity (Hd) was found to be highest in Tianzhu white yak (Hd ± SD = 0.9501 ± 0.0058), while the lowest was recorded in Huzhu white yak (Hd ± SD = 0.7178 ± 0.0474). Totally, the haplotype and nucleotide diversities of white yak were 0.9407 ± 0.0069 and 0.0187 ± 0.0094, respectively, indicating an abundant maternal genetic diversity in white yak. Estimates of F_ST (Fixation Index) values showed a high genetic differentiation between Tianzhu and Menyuan populations (F_ST = 0.2928, p < 0.05) as well as that between Tianzhu and Huzhu populations (F_ST = 0.2721, p < 0.05), but a moderate genetic differentiation between Menyuan and Huzhu populations (F_ST = 0.1352, p > 0.05) was observed. Cluster analysis based on F_ST values among populations indicated that the genetic relationship between Menyuan and Huzhu white yak was closer, but they had a far genetic relationship with Tianzhu white yak. Maternal phylogenetic analysis revealed that white yak represented two maternal lineages (I and II), suggesting two maternal origins. In addition, it is notable that taurine mtDNA haplotypes were detected in Tianzhu and Huzhu white yak populations, indicating taurine genetic introgression to some extent. Our study would provide useful information for the conservation and utilization of white yak.

Adaptation Mechanisms of Yak (Bos grunniens) to High-Altitude Environmental Stress

Living at a high altitude involves many environmental challenges. The combined effects of hypoxia and cold stress impose severe physiological challenges on endothermic animals. The yak is integral to the livelihood of the people occupying the vast, inhospitable Qinghai-Tibetan plateau and the surrounding mountainous region. Due to long-term selection, the yak exhibits stable and unique genetic characteristics which enable physiological, biochemical, and morphological adaptations to a high altitude. Thus, the yak is a representative model for mammalian plateau-adaptability studies. Understanding coping mechanisms provides unique insights into adaptive evolution, thus informing the breeding of domestic yaks. This review provides an overview of genetic adaptations in Bos grunniens to high-altitude environmental stress. Combined genomics and theoretical advances have informed the genetic basis of high-altitude adaptations.

Ultrasound-assisted thawing of frozen white yak meat: Effects on thawing rate, meat quality, nutrients, and microstructure

The objective of this study was to assess the effects of ultrasound-assisted thawing (UAT) on the quality of longissimus dorsi muscles from white yak meat (WYM). Ultrasonic power levels of 0, 200, 400, and 600 W (frequency of 20 kHz) were used to assist thawing. The thawing rate, meat quality, nutrient substances, volatile compounds, and microstructure of the WYM were determined. The results showed that ultrasonic thawing treatment reduced thawing times by 30.95-64.28% compared to control. The meat quality results revealed that the thawing loss, cooking loss, L* and b* values, and pH values decreased significantly while the a* value and cutting force increased significantly (P < 0.05) at the lower 400 W power level compared with the control. In addition, the free amino acid (FAA), mineral, and vitamin (especially water-soluble vitamins) contents were significantly (P < 0.05) increased with the ultrasound treatment. UAT significantly (P < 0.05) increased the content of volatile compounds, an effect that was highest in the UAT-400 W group. Partial least squares discrimination analysis (PLS-DA) showed that 2,4-heptadienal was critical in distinguishing the UAT groups from the control. When the ultrasonic power was lower than 400 W, the muscle cell area was significantly (P < 0.05) increased but decreased when higher power was used. Therefore, UAT improves the thawing efficiency and quality of frozen WYM, particularly at a power level of 400 W, and these findings have potential applications in the meat industry.

Genome-wide selection signatures analysis of litter size in Dazu black goats using single-nucleotide polymorphism

Litter size is considered to be the most important index for estimating domestic animal productivity. The number of indigenous goats in China with higher litter sizes than those of commercial breeds in other countries may be helpful for accelerating genetic improvements in goat breeding. We performed a genome-wide selective sweep analysis of 31 Dazu black goats with extreme standard deviation in litter size within the third fetus to identify significant genomic regions and candidate genes through different analyses. The analysis identified a total of 33,917,703 variants, including 32,262,179 SNPs and 1,655,524 indels. In addition, two novel candidate genes (LRP1B and GLRB), which are related to litter size, were obtained with π, Tajima's D, πA/πB, and F _ST at the individual level with a 95% threshold for each parameter. These two genes were annotated in five GO terms (localization, binding, macromolecular complex, membrane part, and membrane) and two pathways (long-term depression and neuroactive ligand-receptor interaction pathway). Regarding the result of linkage disequilibrium (LD) analysis, in LRP1B and GRID2, the high-yield Dazu black goats exhibit significantly different LD patterns from low-yield goats. Litter size variability has low heritability and is related to multiple complex factors found in domestic animals. Obtaining a clear explanation and significant signal by genome-wide selective sweep analysis with a small sample size is difficult. However, we investigated some candidate genes, particularly LRP1B and GLRB, which may provide useful information for further research.