Profiling of skeletal muscle tissue for long non-coding RNAs related to muscle metabolism in the QingYu pig at the growth inflection point

Luo, Jia,Shen, Linyuan,Gan, Mailin,Jiang, Anan,Chen, Lei,Ma, Jideng,Jin, Long,Liu, Yihui,Tang, Guoqing,Jiang, Yanzhi,Li, Mingzhou,Li, Xuewei,Zhang, Shunhua,Zhu, Li Asian Australasian Association of Animal Productio 2021 Animal Bioscience Vol.34 No.8

Objective: Investigation of muscle growth at different developmental stages is an appropriate strategy for studying the mechanisms underlying muscle development and differences in phenotypes. In particular, the muscle development mechanisms and the difference between the fastest and slowest growth rates. Methods: In this study, we used a growth curve model to fit the growth inflection point (IP) of QingYu pigs and compared differences in the long non-coding RNA (lncRNA) transcriptome of muscle both at the growth IP and plateau phase (PP). Results: The growth curve of the QingYu pig had a good fit (R² = 0.974) relative to a typical S-curve and reached the IP at day 177.96. At the PP, marbling, intramuscular fat, and monounsaturated fatty acids had increased significantly and the percentage of lean muscle and polyunsaturated fatty acids had decreased. A total of 1,199 mRNAs and 62 lncRNAs were differentially expressed at the IP compared with the PP. Additional to gene ontology and Kyoto encyclopedia of genes and genomes pathway analyses, these differentially expressed protein coding genes were principally related to muscle growth and lipid metabolism. Conclusion: Our results suggest that the identified differentially expressed lncRNAs, could play roles in muscle growth, fat deposition and regulation of fatty acid composition at the IP and PP.

Single nucleotide polymorphism-based analysis of the genetic structure of Liangshan pig population

Liu, Bin,Shen, Linyuan,Guo, Zhixian,Gan, Mailing,Chen, Ying,Yang, Runling,Niu, Lili,Jiang, Dongmei,Zhong, Zhijun,Li, Xuewei,Zhang, Shunhua,Zhu, Li Asian Australasian Association of Animal Productio 2021 Animal Bioscience Vol.34 No.7

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

Coat colour phenotype of Qingyu pig is associated with polymorphisms of melanocortin receptor 1 gene

Xiaoqian Wu,Zhendong Tan,Linyuan Shen,Qiong Yang,Xiao Cheng,Kun Liao,Lin Bai,Surong Shuai,Mingzhou Li,Xuewei Li,Shunhua Zhang,Li Zhu 아세아·태평양축산학회 2017 Animal Bioscience Vol.30 No.7

Objective: Qingyu pig, a Chinese indigenous pig breed, exhibits two types of coat colour phenotypes, including pure black and white with black spotting respectively. Melanocortin receptor 1 (MC1R) and agouti signaling protein (ASIP) are two widely reported pivotal genes that significantly affect the regulation of coat colour. The objectives of this study were to investigate whether the polymorphisms of these two genes are associated with coat colour and analyze the molecular mechanism of the coat colour separation in Qingyu pig. Methods: We studied the phenotype segregation and used polymerase chain reaction amplification and Sanger sequencing to investigate the polymorphism of MC1R and ASIP in 121 Qingyu pigs, consisting of 115 black and 6 white with black spotted pigs. Results: Coat colour of Qingyu pig is associated with the polymorphisms of MC1R but not ASIP. We only found 2 haplotypes, EQY and Eqy, based on the 13 observed mutations from MC1R gene. Among which, Eqy presented a recessive inheritance mode in black spotted Qingyu pigs. Further analysis revealed a g.462-463CC insertion that caused a frameshift mutation and a premature stop codon, thus changed the first transmembrane domain completely and lost the remaining six transmembrane domains. Altogether, our results strongly support that the variety of Qingyu pig’s coat colour is related to MC1R. Conclusion: Our findings indicated that black coat colour in Qingyu pig was dominant to white with black spotted phenotype and MC1R gene polymorphism was associated with coat colour separation in Qingyu pig.

Estimation of Growth Curves and Suitable Slaughter Weight of the Liangshan Pig

Luo, Jia,Lei, Huaigang,Shen, Linyuan,Yang, Runlin,Pu, Qiang,Zhu, Kangping,Li, Mingzhou,Tang, Guoqing,Li, Xuewei,Zhang, Shunhua,Zhu, Li Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.9

The Liangshan pig is a traditional Chinese small-sized breed; it has a relatively long feeding period and low meat production ability but superior meat quality. This study utilized three non-linear growth models (Von Bertalanffy, Gompertz, and logistic) to fit the growth curve of Liangshan pigs from an unselected, random-bred pig population and estimate the pigs most suitable slaughter weight. The growth development data at 20 time points of 275 Liangshan pigs (from birth to 250 d) were collected. To analyze the relative gene expression related to development, seven slaughter weight phases (50, 58, 66, 74, 82, 90, and 98 kg) (20 pigs per phase) were examined. We found that the Liangshan pig growth curve fit the typical S-curve well and that their growth turning point was 193.4 days at a weight of 62.5 kg, according to the best fit Von Bertalanffy model based on the goodness of fit criteria. Furthermore, we estimated that the most suitable slaughter weight was 62.5 to 74.9 kg based on the growth curve and the relative expression levels of growth-related genes.

Estimation of Growth Curves and Suitable Slaughter Weight of the Liangshan Pig

Jia Luo,Huaigang Lei,Linyuan Shen,Runlin Yang,Qiang Pu,Kangping Zhu,Mingzhou Li,Guoqing Tang,Xuewei Li,Shunhua Zhang,Li Zhu 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.9

The Liangshan pig is a traditional Chinese small-sized breed; it has a relatively long feeding period and low meat production ability but superior meat quality. This study utilized three non-linear growth models (Von Bertalanffy, Gompertz, and logistic) to fit the growth curve of Liangshan pigs from an unselected, random-bred pig population and estimate the pigs most suitable slaughter weight. The growth development data at 20 time points of 275 Liangshan pigs (from birth to 250 d) were collected. To analyze the relative gene expression related to development, seven slaughter weight phases (50, 58, 66, 74, 82, 90, and 98 kg) (20 pigs per phase) were examined. We found that the Liangshan pig growth curve fit the typical S-curve well and that their growth turning point was 193.4 days at a weight of 62.5 kg, according to the best fit Von Bertalanffy model based on the goodness of fit criteria. Furthermore, we estimated that the most suitable slaughter weight was 62.5 to 74.9 kg based on the growth curve and the relative expression levels of growth-related genes.

Genetic parameter estimation for reproductive traits in QingYu pigs and comparison of carcass and meat quality traits to Berkshire×QingYu crossbred pigs

Luo Jia,Yang Yiting,Liao Kun,Liu Bin,Chen Ying,Shen Linyuan,Chen Lei,Jiang An’an,Liu Yihui,Li Qiang,Wang Jinyong,Li Xuewei,Zhang Shunhua,Zhu Li 아세아·태평양축산학회 2020 Animal Bioscience Vol.33 No.8

Objective: The QingYu pig is well known for its excellent meat quality attributes in Sichuan province, China. In order to improve its production efficiency, the determination of genetic factors contributing to quantifiable economic traits of livestock is important. Moreover, the cross-breeding of QingYu pigs with western breeds possessing strong growth attributes is an efficient way to improve the performance of this breed. Methods: Here, the genetic parameters of several important reproductive traits of QingYu pigs were estimated, include total number born (TNB), number born alive, litter birth weight, individual birth weight, number of piglets weaned, litter weaning weight, and individual weaning weight. The data was analyzed using the ASReml 3.0 software (NSW Inc., Sydney, Australia). Furthermore, the effects of crossing Berkshire with QingYu (BQ) pigs on carcass and meat quality traits, as well as the effects of slaughter weight on carcass and meat quality of BQ were characterized. Results: QingYu pigs exhibited superior reproductive traits. The TNB available to QingYu pigs was more than 8 per parity. The observed repeatability of the reproductive traits of the QingYu pigs was between 0.10 and 0.23. The significantly correlated genetic and phenotypic of reproduction traits were consistent. Interestingly, the BQ pigs exhibited improved carcass quality, with a significant increase in loin muscle area, lean percentage and reduction in sebum percentage. As a result, BQ had higher L45min, lower cooking scores, and lower drip loss. In addition, the loin muscle area, body length, and sebum percentage were significantly higher in 90 and 100 kg animals. Cooking loss showed a significant increase at 80 kg, and marbling increased significantly from 90 kg. Conclusion: The results of this study suggest that QingYu pigs exhibit excellent reproductive properties and heritability of these traits. Crossing with Berkshire is an efficient strategy to improve the carcass and meat quality of QingYu pigs for commercial operations. Furthermore, it appears as though the optimal slaughter weight of BQ pigs is at approximately 90 kg.