Identifying Genetic Architecture of Carcass and Meat Quality Traits in a Ningxiang Indigenous Pig Population

Ningxiang pig is a breed renowned for its exceptional meat quality, but it possesses suboptimal carcass traits. To elucidate the genetic architecture of meat quality and carcass traits in Ningxiang pigs, we assessed heritability and executed a genome-wide association study (GWAS) concerning carcass length, backfat thickness, meat color parameters (L.LD, a.LD, b.LD), and pH at two postmortem intervals (45 min and 24 h) within a Ningxiang pig population. Heritability estimates ranged from moderate to high (0.30~0.80) for carcass traits and from low to high (0.11~0.48) for meat quality traits. We identified 21 significant SNPs, the majority of which were situated within previously documented QTL regions. Furthermore, the GRM4 gene emerged as a pleiotropic gene that correlated with carcass length and backfat thickness. The ADGRF1, FKBP5, and PRIM2 genes were associated with carcass length, while the NIPBL gene was linked to backfat thickness. These genes hold the potential for use in selective breeding programs targeting carcass traits in Ningxiang pigs.

Comprehensive transcriptional profiling of aging porcine liver

Background

Aging is a major risk factor for the development of many diseases, and the liver, as the most important metabolic organ, is significantly affected by aging. It has been shown that the liver weight tends to increase in rodents and decrease in humans with age. Pigs have a genomic structure, with physiological as well as biochemical features that are similar to those of humans, and have therefore been used as a valuable model for studying human diseases. The molecular mechanisms of the liver aging of large mammals on a comprehensive transcriptional level remain poorly understood. The pig is an ideal model animal to clearly and fully understand the molecular mechanism underlying human liver aging.

Methods

In this study, four healthy female Yana pigs (an indigenous Chinese breed) were investigated: two young sows (180-days-old) and two old sows (8-years-old). High throughput RNA sequencing was performed to evaluate the expression profiles of messenger RNA, long non-coding RNAs, micro RNAs, and circular RNAs during the porcine liver aging process. Gene Ontology (GO) analysis was performed to investigate the biological functions of age-related genes.

Results

A number of age-related genes were identified in the porcine liver. GO annotation showed that up-regulated genes were mainly related to immune response, while the down-regulated genes were mainly related to metabolism. Moreover, several lncRNAs and their target genes were also found to be differentially expressed during liver aging. In addition, the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks were assessed during liver aging.

Conclusions

Numerous age-related genes were identified and circRNA-miRNA co-expression networks that are active during porcine liver aging were constructed. These findings contribute to the understanding of the transcriptional foundations of liver aging and also provide further references that clarify human liver aging at the molecular level.

Comprehensive transcriptional profiling of porcine brain aging

The brain as an important organ can be affected largely by aging, and the comprehensive transcriptional underpinnings of brain aging remain poorly understood. Here, we performed a high throughput RNA sequencing to evaluate the expression profiles of messenger RNA (mRNA), long non-coding RNAs (lncRNAs), micro RNAs (miRNAs), and circular RNAs (circRNAs) in porcine brain. We have identified 714 mRNAs, 38lncRNAs, 41miRNAs, and 148circRNAs were age-related genes in the porcine cerebral cortex. The lncRNAs, miRNAs and circRNAs have effect on the age of porcine brain due to the much changes of expression level as noncoding RNAs. The up-regulated genes were significantly enriched for stress response, reproductive regulatory process, immune response and metabolic process, and the down-regulated genes were related to neurologic function, stress response and signaling pathway. The synaptic transmission pathway may be the key role in aging of porcine brain that it was co-enriched for in both differentially expressed mRNAs and lncRNAs. Moreover, some lncRNAs and their target genes were also differentially expressed during brain aging. We further assessed the multi-group cooperative control relationships and constructed circRNA-miRNA co-expression networks during brain aging. We also selected 2 mRNAs, 2 lncRNAs, 2 miRNAs, and 1 circRNAs to perform the q-PCR, and the expression patterns were highly consistent between the two methods confirming the high reproducibility and reliability of the gene expression profiling in our study. In conclusion, our findings will contribute to understand the transcriptional underpinnings of brain aging and provide a foundation for future studies on the molecular mechanisms underlying brain aging.

Growth, carcass characteristics and meat quality of Chinese indigenous Yanan pig crossbred with Duroc and Berkshire genotypes

The objective of the present study was to evaluate the effects of crossbreeding on the growth, carcass characteristics and meat quality of Chinese native Yanan (YN) pig breed and related crossbreeds, including Duroc × Yanan (DY) and Duroc × (Berkshire × Yanan) (DBY). In total, 60 pigs (20 per breed) were used in the study. The results showed that both crossbreeds, especially DBY pigs, exhibited improved growth and carcass characteristics compared with those of purebred YN pigs. Moreover, the two crossbreeds, especially DBY pigs, produced acceptable meat-quality characteristics (normal pH and meat-colour values, high intramuscular fat content and water-holding capacity, acceptable muscle-fibre parameters, and strong pork flavour) similar to those of YN pigs. M. longissimus lumborum contained eight essential amino acids, with high contents in all pigs. C18:1, C16:0, C18:0, and C18:2 were the main fatty acids in M. longissimus lumborum in the three breeds, and a polyunsaturated:saturated fatty acid ratio of ~0.2 was observed in DBY and YN pigs. These results indicated that DBY pigs exhibit an acceptable total production performance and could be extensively used in commercial pig production to provide high-quality niche products.

Carcass quality, physico-chemical parameters, muscle fibre traits and myosin heavy chain composition of m. longissimus lumborum from Puławska and Polish Large White pigs

In 54 Puławska pigs and 60 Polish Large White pigs (PLW), slaughtered at 30 and 100 kg body weight, carcass and meat quality of m. longissimus lumborum were studied. Analysis revealed that in both examined body weight groups, hot carcass weight, carcass yield percentage, meat content, and weight of ham and carcass ham percentage were significantly lower and backfat thickness higher for Puławska pigs compared to PLW pigs, while PLW pigs exhibited significantly longer carcasses, greater loin eye area, and, in the case of lighter pigs, smaller proportion of loin in the carcass. Muscles of Puławska pigs, in the lighter group, had higher IMF content and a* value, while in the heavier group they exhibited higher pH(45), pH(24) and a* values, lower L*, drip loss, WHC, and thermal loss compared with PLW pigs. PLW pigs had higher WB and hardness values and more glycolytic muscles characterised by higher TNF.

Carcass and meat quality traits of four commercial pig crossbreeds in China

We evaluated carcass and meat quality traits of two Chinese native crossbreeds Landrace x Meishan (LM) and Duroc x (Landrace x Meishan) (DLM) and two foreign crossbreeds Duroc x (Landrace x Yorkshire) (DLY) and PIC (an imported five-way crossbreed). One hundred and twenty weaned pigs (half castrated males and half females) were reared and slaughtered at a predestinated slaughter age. The general carcass and meat quality traits were measured and analyzed. The DLY and PIC crosses had significantly heavier live weights (93.39 and 96.33 kg, P < 0.01), significantly higher dressing percentages (80.65 and 79.39%, P < 0.05), significantly bigger loin areas (42.69 and 43.91 cm(2), P < 0.001), and significantly more lean carcasses (65.78 and 66.40%, P < 0.001) than LM and DLM. On the other hand, LM had a significantly lower live weight (70.29 kg, P < 0.01), significantly thicker back fat (3.54 cm, P < 0.001), significantly less lean carcasses (46.82%, P < 0.001), and significantly less ham and breech (26.53%, P < 0.05) than the other crossbreeds. Among meat quality parameters, LM had the highest intramuscular fat content (5.02%, P < 0.001) and the smallest fiber area (3126.45 μm(2), P < 0.01). However, PIC showed the lowest pH(1) (5.82, P < 0.01) and pH(2) (5.63, P < 0.01), the highest drip loss (2.89%, P < 0.01), and the lowest intramuscular fat (1.35%, P < 0.001). We concluded that LM and DLM had good meat quality traits but poorer carcass traits than DLY and PIC; DLY had good carcass and meat quality traits; PIC had good carcass traits, but it had less intramuscular fat, lower pH and higher drip loss.