Dominance effects of ion transport and ion transport regulator genes on the final weight and backfat thickness of Landrace pigs by dominance deviation analysis

Genome-wide analysis reveals that the cytochrome P450 family 7 subfamily B member 1 gene is implicated in growth traits in Rasa Aragonesa ewes

Sheep are very well adapted to changing environments and are able to produce and reproduce with low inputs in feed and water better than other domestic ruminants. Indeed, the ewe body condition score (BCS) and live weight (LW) play a significant role in productive and reproductive performance. This work conducts a genome-wide association study (GWAS) to detect genetic variants associated with growth traits in 225 adult ewes of the Rasa Aragonesa breed by using the genotypes from 50 k and HD Illumina Ovine BeadChip. These ewes were measured for LW, BCS and growth rate (GR) for 2 years, from January to September. Corrected phenotypes for BCS, LW and GR were estimated and used as input for the GWAS. Only one single nucleotide polymorphism (SNP) rs425509273 in chromosome 9 (OAR9), associated with the GR, overcame the genome-wise significance level. One, three and nine SNPs were associated at the chromosome-wise level (FDR 10%) for traits BCS, LW and GR, respectively. The cytochrome P450 family 7 subfamily B member 1 (CYP7B1) candidate gene, located 83 kb upstream from SNP rs425509273 in OAR9, was partially isolated and Sanger-sequenced. Fifteen polymorphisms comprising 12 SNPs, two indels and one polyC, were detected in promoter, exon 1, 3, 5, and intron 1-3 region. The SNP association analysis of the polymorphisms located close to the transcription start site (TSS) showed that a 22 bp insertion located at -58 nucleotides from the TSS (indel (-58)), a polyC (-25), and two A/G SNPs (SNP3 (-114) and SNP5 (-63)) were associated with the GR trait, whereas only the indel (-58) was associated with the BCS trait. The haplotype analysis confirmed these results. The functional characterisation of the polymorphisms at CYP7B1 gene in liver by real-time quantitative PCR analysis confirmed that the mutations in the promoter region affected CYP7B1 gene expression. Our results demonstrated the involvement of the CYP7B1 gene promoter on GR and BCS traits in Rasa Aragonesa. These findings suggest that variations in ovine CYP7B1 may serve as potential genetic markers to be used in breeding programmes to improve growth characteristics that could influence reproductive traits.

Heterozygosity and homozygosity regions affect reproductive success and the loss of reproduction: a case study with litter traits in pigs

Runs of heterozygosity (ROHet) and homozygosity (ROH) harbor useful information related to traits of interest. There is a lack of investigating the effect of ROHet and ROH on reproductive success and the loss of reproduction in mammals. Here, we detected and characterized the ROHet and ROH patterns in the genomes of Chinese indigenous pigs (i.e., Jinhua, Chun’an, Longyou Black, and Shengxian Spotted pigs), revealing the similar genetic characteristics of indigenous pigs. Later, we highlighted the underlying litter traits-related ROHet and ROH using association analysis with linear model in these four indigenous pig breeds. To pinpoint the promising candidate genes associated with litter traits, we further in-depth explore the selection patterns of other five pig breeds (i.e., Erhualian, Meishan, Minzhu, Rongchang, and Diqing pigs) with different levels of reproduction performance at the underlying litter traits-related ROHet and ROH using F_ST and genetic diversity ratio. Then, we identified a set of known and novel candidate genes associated with reproductive performance in pigs. For the novel candidate genes (i.e., CCDC91, SASH1, SAMD5, MACF1, MFSD2A, EPC2, and MBD5), we obtained public available datasets and performed multi-omics analyses integrating transcriptome-wide association studies and comparative single-cell RNA-seq analyses to uncover the roles of them in mammalian reproductive performance. The genes have not been widely reported to be fertility-related genes and can be complementally considered as prior biological information to modify genomic selections models that benefits pig genetic improvement of litter traits. Besides, our findings provide new insights into the function of ROHet and ROH in mammals.

Genome-Wide DNA Methylation Patterns of Muscle and Tail-Fat in DairyMeade Sheep and Mongolian Sheep

Simple Summary

DNA methylation is an important epigenetic modification and plays an important role in the regulation of gene expression. The study of DNA methylation will help to explore the effects of epigenetic modifications, other than DNA sequence variation, on biological phenotypes and physiological functions, promoting the revolution of livestock selection and breeding practices. DairyMeade sheep (thin-tailed) and Mongolian sheep (fat-tailed) have large differences in their dairy and meat production performances, as well as their tail phenotype, thus providing us with good materials for genomic DNA methylation studies. The below results provided a genome-wide DNA methylation landscape of muscle and tail-fat tissues between DairyMeade sheep and Mongolian sheep and a series of differentiated methylation regions (DMRs) in which CAMK2D may play a crucial role in fat metabolism and meat quality traits. These results may help us to understand how DNA methylation affects the economic traits of domestic animals like sheep.

Abstract

This study aimed to explore the genome-wide DNA methylation differences between muscle and tail-fat tissues of DairyMeade sheep (thin-tailed, lean carcass) and Mongolian sheep (fat-tailed, fat-deposited carcass). Whole-genome bisulfite sequencing (WGBS) was conducted and the global DNA methylation dynamics were mapped. Generally, CGs had a higher DNA methylation level than CHHs and CHGs, and tail-fat tissues had higher CG methylation levels than muscle tissues. For DNA repeat elements, SINE had the highest methylation level, while Simple had the lowest. When dividing the gene promoter region into small bins (200 bp per bin), the bins near the transcription start site (±200 bp) had the highest CG count per bin but the lowest DNA methylation levels. A series of DMRs were identified in muscle and tail-fat tissues between the two breeds. Among them, the introns of gene CAMK2D (calcium/calmodulin-dependent protein kinase II δ) demonstrated significant DNA methylation level differences between the two breeds in both muscle and tail-fat tissues, and it may play a crucial role in fat metabolism and meat quality traits. This study may provide basic datasets and references for further epigenetic modification studies during sheep genetic improvement.

Estimates of genomic inbreeding and identification of candidate regions that differ between Chinese indigenous sheep breeds

Background

A run of homozygosity (ROH) is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents. Genomic inbreeding can be quantified based on ROH. Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands. We carried out ROH analyses in five Chinese indigenous sheep breeds; Altay sheep (n = 50 individuals), Large-tailed Han sheep (n = 50), Hulun Buir sheep (n = 150), Short-tailed grassland sheep (n = 150), and Tibetan sheep (n = 50), using genotypes from an Ovine Infinium HD SNP BeadChip.

Results

A total of 18,288 ROH were identified. The average number of ROH per individual across the five sheep breeds ranged from 39 (Hulun Buir sheep) to 78 (Large-tailed Han sheep) and the average length of ROH ranged from 0.929 Mb (Hulun Buir sheep) to 2.544 Mb (Large-tailed Han sheep). The effective population size (Ne) of Altay sheep, Large-tailed Han sheep, Hulun Buir sheep, Short-tailed grassland sheep and Tibetan sheep were estimated to be 81, 78, 253, 238 and 70 five generations ago. The highest ROH-based inbreeding estimate (F_ROH) was 0.0808 in Large-tailed Han sheep, whereas the lowest F_ROH was 0.0148 in Hulun Buir sheep. Furthermore, the highest proportion of long ROH fragments (> 5 Mb) was observed in the Large-tailed Han sheep breed which indicated recent inbreeding. In total, 49 ROH islands (the top 0.1% of the SNPs most commonly observed in ROH) were identified in the five sheep breeds. Three ROH islands were common to all the five sheep breeds, and were located on OAR2: 12.2–12.3 Mb, OAR12: 78.4–79.1 Mb and OAR13: 53.0–53.6 Mb. Three breed-specific ROH islands were observed in Altay sheep (OAR15: 3.4–3.8 Mb), Large-tailed Han sheep (ORA17: 53.5–53.8 Mb) and Tibetan sheep (ORA5:19.8–20.2 Mb). Collectively, the ROH islands harbored 78 unique genes, including 19 genes that have been documented as having associations with tail types, adaptation, growth, body size, reproduction or immune response.

Conclusion

Different ROH patterns were observed in five Chinese indigenous sheep breeds, which reflected their different population histories. Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding. Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds. Our findings contribute to the understanding of genetic diversity and population demography, and help design and implement breeding and conservation strategies for Chinese sheep.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00608-9.

Expression analysis and single-nucleotide polymorphisms of SYNDIG1L and UNC13C genes associated with thoracic vertebral numbers in sheep (Ovis aries)

The objective of the current study was to analyze expression levels of synapse differentiation inducing 1-like (SYNDIG1L) and unc-13 homolog C (UNC13C) genes in different tissues, while single-nucleotide polymorphisms (SNPs) of two genes were associated with multiple thoracic vertebrae traits in both Small-tailed Han sheep (STH) and Sunite sheep (SNT). The expression levels of SYNDIG1L and UNC13C were analyzed in the brain, cerebellum, heart, liver, spleen, lung, kidney, adrenal gland, uterine horn, longissimus muscle, and abdominal adipose tissues of two sheep breeds with different thoracic vertebral number (TVN) sheep (T13 groups and T14 groups) by real-time quantitative polymerase chain reaction (RT-qPCR). Meanwhile, the polymorphisms of UNC13C gene g.52919279C>T and SYNDIG1L gene g.82573325C>A in T14 and T13 were genotyped by the Sequenom MassARRAY^® SNP assay, and association analysis was performed with the TVN. The results demonstrated that UNC13C gene was extensively expressed in 11 tissues. The expression of UNC13C gene in longissimus muscle of T14 groups of STH was significantly higher than that of T13 groups (P<0.05). SYNDIG1L gene was overexpressed in brain and cerebellum tissues, and the expression level of UNC13C gene in the brain and cerebellum of T13 groups in SNT was significantly higher than that of T14 groups (P<0.01). Association analysis showed that SNPs found in the UNC13C gene had no significant effects on TVN for both two genes. The polymorphism of SYNDIG1L g.82573325C>A was significantly correlated with the TVN in both STH (P<0.05) and SNT (P<0.01). Taken together, the SYNDIG1L gene was related to thoracic vertebral development, and this variation may be potentially used as a molecular marker to select the multiple thoracic vertebrae in sheep.

Discovery of significant porcine SNPs for swine breed identification by a hybrid of information gain, genetic algorithm, and frequency feature selection technique

Background

The number of porcine Single Nucleotide Polymorphisms (SNPs) used in genetic association studies is very large, suitable for statistical testing. However, in breed classification problem, one needs to have a much smaller porcine-classifying SNPs (PCSNPs) set that could accurately classify pigs into different breeds. This study attempted to find such PCSNPs by using several combinations of feature selection and classification methods. We experimented with different combinations of feature selection methods including information gain, conventional as well as modified genetic algorithms, and our developed frequency feature selection method in combination with a common classification method, Support Vector Machine, to evaluate the method’s performance. Experiments were conducted on a comprehensive data set containing SNPs from native pigs from America, Europe, Africa, and Asia including Chinese breeds, Vietnamese breeds, and hybrid breeds from Thailand.

Results

The best combination of feature selection methods—information gain, modified genetic algorithm, and frequency feature selection hybrid—was able to reduce the number of possible PCSNPs to only 1.62% (164 PCSNPs) of the total number of SNPs (10,210 SNPs) while maintaining a high classification accuracy (95.12%). Moreover, the near-identical performance of this PCSNPs set to those of bigger data sets as well as even the entire data set. Moreover, most PCSNPs were well-matched to a set of 94 genes in the PANTHER pathway, conforming to a suggestion by the Porcine Genomic Sequencing Initiative.

Conclusions

The best hybrid method truly provided a sufficiently small number of porcine SNPs that accurately classified swine breeds.

Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

Background

Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, single-trait GWAS, multi-trait GWAS and LONG-GWAS. The Illumina Bovine HD 770 K BeadChip was used to identify genomic single nucleotide polymorphisms (SNPs) in 1217 individuals.

Results

In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. Among these, 21 genes were promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2, and PRIM2 identified by single-trait analysis; SLC37A1, LAP3, PCDH7, MANEA, and LHCGR identified by multi-trait analysis; and P2RY1, MPZL1, LINGO2, CMIP, and WSCD1 identified by LONG-GWAS.

Conclusions

Multiple association analysis was performed for six growth traits at each growth stage. These findings offer valuable insights for the further investigation of potential genetic mechanism of growth traits in Simmental beef cattle.

Transcriptome Analysis Reveals Long Intergenic Non-Coding RNAs Contributed to Intramuscular Fat Content Differences between Yorkshire and Wei Pigs

Intramuscular fat (IMF) content is closely related to various meat traits, such as tenderness, juiciness, and flavor. The IMF content varies considerably among pig breeds with different genetic backgrounds. Long intergenic non-coding RNAs (lincRNAs) have been widely identified in many species and found to be an important class of regulators that can participate in multiple biological processes. However, the mechanism behind lincRNAs regulation of pig IMF content remains unknown and requires further study. In our study, we identified a total of 156 lincRNAs in the longissimus dorsi muscle of Wei (fat-type) and Yorkshire (lean-type) pigs using previously published data. These identified lincRNAs have shorter transcript length, longer exon length, lower exon number, and lower expression level as compared with protein-coding transcripts. We predicted potential target genes (PTGs) that are potentially regulated by lincRNAs in cis or trans regulation. Gene ontology and pathway analyses indicated that many potential lincRNAs target genes are involved in IMF-related processes or pathways, such as fatty acid catabolic process and adipocytokine signaling pathway. In addition, we analyzed quantitative trait locus (QTL) sites that differentially expressed lincRNAs (DE lincRNAs) between Wei and Yorkshire pigs co-localized. The QTL sites where DE lincRNAs co-localize are mostly related to IMF content. Furthermore, we constructed a co-expressed network between DE lincRNAs and their differentially expressed PTGs (DEPTGs). On the basis of their expression levels, we suggest that many DE lincRNAs can affect IMF development by positively or negatively regulating their PTGs. This study identified and analyzed some lincRNAs- and PTGs-related IMF development of the two pig breeds and provided new insight into research on the roles of lincRNAs in the two types of breeds.

Additive and heterozygous (dis)advantage GWAS models reveal candidate genes involved in the genotypic variation of maize hybrids to Azospirillum brasilense

Maize genotypes can show different responsiveness to inoculation with Azospirillum brasilense and an intriguing issue is which genes of the plant are involved in the recognition and growth promotion by these Plant Growth-Promoting Bacteria (PGPB). We conducted Genome-Wide Association Studies (GWAS) using additive and heterozygous (dis)advantage models to find candidate genes for root and shoot traits under nitrogen (N) stress and N stress plus A. brasilense. A total of 52,215 Single Nucleotide Polymorphism (SNP) markers were used for GWAS analyses. For the six root traits with significant inoculation effect, the GWAS analyses revealed 25 significant SNPs for the N stress plus A. brasilense treatment, in which only two were overlapped with the 22 found for N stress only. Most were found by the heterozygous (dis)advantage model and were more related to exclusive gene ontology terms. Interestingly, the candidate genes around the significant SNPs found for the maize-A. brasilense association were involved in different functions previously described for PGPB in plants (e.g. signaling pathways of the plant's defense system and phytohormone biosynthesis). Our findings are a benchmark in the understanding of the genetic variation among maize hybrids for the association with A. brasilense and reveal the potential for further enhancement of maize through this association.