Genetic regulation of m6A RNA methylation and its contribution in human complex diseases.

N6-methyladenosine (m6A) has been established as the most prevalent chemical modification in message RNA (mRNA), playing an essential role in determining the fate of RNA molecules. Dysregulation of m6A has been revealed to lead to abnormal physiological conditions and cause various types of human diseases. Recent studies have delineated the genetic regulatory maps for m6A methylation by mapping the quantitative trait loci of m6A (m6A-QTLs), thereby building up the regulatory circuits linking genetic variants, m6A, and human complex traits. Here, we review the recent discoveries concerning the genetic regulatory maps of m6A, describing the methodological and technical details of m6A-QTL identification, and introducing the key findings of the cis- and trans-acting drivers of m6A. We further delve into the tissue- and ethnicity-specificity of m6A-QTL, the association with other molecular phenotypes in light of genetic regulation, the regulators underlying m6A genetics, and importantly, the functional roles of m6A in mediating human complex diseases. Lastly, we discuss potential research avenues that can accelerate the translation of m6A genetics studies toward the development of therapies for human genetic diseases.

Transcriptome analysis of multiple tissues reveals the potential mechanism of death under acute heat stress in chicken.

BACKGROUND: Acute heat stress could induce high mortality and cause huge economic losses in the poultry industry. Although many studies have revealed heat stress-induced injuries of multiple tissues, the main target tissue and molecular mechanism of death under acute heat stress was largely unknown. This study systematically compared the transcriptome data of five main visceral tissues in chickens to reveal the response of multiple tissues to acute heat stress and determine the main target tissue of acute heat stress, further revealing the injuries of main target tissue and their potential mechanism by combing pathological section and qRT-PCR technologies. RESULTS: The transcriptome data of five visceral tissues revealed that acute heat stress broadly caused inflammatory response and damaged tissues metabolic homeostasis. Among the five tested visceral tissues, the number of differentially expressed genes in the lung was the highest, and their fold changes were the greatest, indicating that the lung was the main target tissue of acute heat stress. The results of pathological section revealed severe inflammation, emphysema and pulmonary hemorrhage in the lung under acute heat stress. Our study found that some pro-inflammatory genes, including CNTFR, FURIN, CCR6, LIFR and IL20RA, were significantly up-regulated both in the heat-stress and heat-death groups, and their fold changes in the heat-death group were significantly greater than that in the heat-stress group. We also found an anti-inflammatory gene, AvBD9, exhibiting an extremely high expression in the heat-stress group but a low expression in the heat-death group. CONCLUSIONS: Our study found that acute heat stress caused multiple tissue injuries broadly and the lung was the main target tissue of acute heat stress in chicken. Acute heat stress caused a severe inflammatory response, emphysema, and pulmonary haemorrhage, The severe inflammatory response in the heat-death group was related to the up-regulation of pro-inflammatory genes and down-regulation of anti-inflammatory genes.

Genetic structure and characteristics of Tibetan chickens.

Tibetan chicken is one of the most common and widely distributed highland breeds, and is often used as a model organism for understanding genetic adaptation to extreme environments in Tibet. Despite its apparent geographical diversity and large variations in plumage patterns, the genetic differences within breed were not accounted for in most studies and have not been systematically investigated. In order to reveal and genetically differentiate the current existing TBC sub-populations that might have major implications for genomic research in TBCs, we systematically evaluated the population structure and demography of current TBC populations. Based on 344 whole-genome sequenced birds including 115 Tibetan chickens that were mostly sampled from family-farms across Tibet, we revealed a clear separation of Tibetan chickens into 4 sub-populations that broadly aligns with their geographical distribution. Moreover, population structure, population size dynamics, and the extent of admixture jointly suggest complex demographic histories of these sub-populations, including possible multiple origins, inbreeding, and introgressions. While most of the candidate selected regions found between the TBC sub-populations and Red Jungle fowls were nonoverlapping, 2 genes RYR2 and CAMK2D were revealed as strong selection candidates in all 4 sub-populations. These 2 previously identified high altitude associated genes indicated that the sub-populations responded to similar selection pressures in an independent but functionally similar fashion. Our results demonstrate robust population structure in Tibetan chickens that will help inform future genetic analyses on chickens and other domestic animals alike in Tibet, recommending thoughtful experimental design.

Identification of candidate genes related to highland adaptation from multiple Chinese local chicken breeds by whole genome sequencing analysis.

Understanding the genetic mechanism of highland adaptation is of great importance for breeding improvement of Tibetan chickens (TBC). Some studies of TBC have identified some candidate genes and pathways from multiple subgroups, but the related genetic mechanisms remain largely unknown. Different genetic backgrounds and the independent genetic basis of highland adaptation make it difficult to identity the selective region of highland adaptation with all TBC samples. In this study, we conducted pre-analysis in a large-scale population to select a TBC subgroup with the purest and highest level of highland-specific lineage for the further analysis. Finally, the 37 samples from a TBC subgroup and 19 Lahsa White chickens were used to represent the highland group for further analysis with 80 samples from five Chinese local lowland breeds as controls. Population structure analysis revealed that highland adaptation significantly affected population stratification in Chinese local chicken breeds. Genome-wide selection signal analysis identified 201 candidate genes associated with highland adaptation of TBC, and these genes were significantly enriched in calcium signaling, vascular smooth muscle contraction and the cellular response to oxidative stress pathways. Additionally, we identified a narrow 1.76 kb region containing an overlapping region between HBZ and an active enhancer, and our identified region showed a highly significant signal. The highland group selected the haplotype with high activity to improve the oxygen-carrying capacity, thus being adapted to a hypoxic environment. We also found that STX2 was significantly selected in the highland group, thus potentially reducing the oxidative stress caused by hypoxia, and that STX2 exhibited the opposite effects on highland adaptation and reproductive traits. Our findings advance our understanding of extreme environment adaptation of highland chickens, and provide some variants and genes beneficial to TBC genetic breeding improvement.

A genome-wide single nucleotide polymorphism scan reveals genetic markers associated with fertility rate in Chinese Jing Hong chicken.

The function of the sperm storage tubules is directly correlated with the fertility of laying hens. However, little is known about the molecular mechanisms regulating the fertility traits in chicken. To identify genetic markers associated with reproductive traits, we calculated fertility rate at 61 to 69 wk (51 D) of Jing Hong chickens parent generation as the phenotype and the genotype were detected by the chicken 600K Affymetrix Axiom High Density single nucleotide polymorphisms (SNP)-array. The genome-wide association study using 190 Jing Hong hens showed that the 20 SNP in chromosomes 3 and 13 were significantly associated with fertility rate. To verify these results, a total of 1900 Jing Hong laying hens from 2 populations (P1 and P2) were further genotyped by polymerase chain reaction-restriction fragments length polymorphisms method. The association analysis results revealed that 12 polymorphisms (AX-75769978, AX-76582632, AX-75730546, AX-75730496, AX-75730588, AX-76530282, AX-76530329, AX-76529310, AX-75769906, AX-75755394, AX-80813697 and AX-76582809) out of 20 showed highly significant effects (P < 0.0001) on fertility rate in P1, P2 and P1+P2. Six haplotypes (TTAA, TTGG, TTAG, CTAA, CTGG, and CTAG) were inferred based on significant loci (AX-75730546 and AX-76530282) also showed significant association with fertility rate, where haplotype CTAG was shown to be markedly associated with the significantly highest (P < 0.0001) fertility rate (in P1, 86.42 ± 0.59; P2, 85.98 ± 0.59 and P1+P2, 86.16 ± 0.42) followed by other haplotypes for the irrespective of population studied. Collectively, we report for the first time that 12 SNP in the chromosomes 3 and 13 were significantly associated with fertility rate during the later stage of egg production, which could be used as the potential genetic markers that would be able to facilitate in the selection and improvement of fertility rate through chicken breeding.

Identification of novel variants and candidate genes associated with porcine bone mineral density using genome-wide association study.

Pig leg weakness not only causes huge economic losses for producers but also affects animal welfare. However, genes with large effects on pig leg weakness have not been identified and suitable methods to study porcine leg weakness are urgently needed. Bone mineral density (BMD) is an important indicator for determining leg soundness in pigs. Increasing pig BMD is likely to improve pig leg soundness. In this study, porcine BMD was measured using an ultrasound bone densitometer in a population with 212 Danish Landrace pigs and 537 Danish Yorkshires. After genotyping all the individuals using GeneSeek Porcine 50K SNP chip, genetic parameter estimation was performed to evaluate the heritability of BMD. Genome-wide association study and haplotype analysis were also performed to identify the variants and candidate genes associated with porcine BMD. The results showed that the heritability of BMD was 0.21 in Landrace and 0.31 in Yorkshire. Five single-nucleotide polymorphisms on chromosome 6 identified were associated with porcine BMD at suggestive significance level. Two candidate quantitative trait loci (74.47 to 75.33 Mb; 80.20 to 83.83 Mb) and three potential candidate genes (ZBTB40, CNR2, and Lin28a) of porcine BMD were detected in this study.