Genome-Wide Association Study and Identification of Candidate Genes for Intramuscular Fat Fatty Acid Composition in Ningxiang Pigs.

Ningxiang pigs exhibit a diverse array of fatty acids, making them an intriguing model for exploring the genetic underpinnings of fatty acid metabolism. We conducted a genome-wide association study using a dataset comprising 50,697 single-nucleotide polymorphisms (SNPs) and samples from over 600 Ningxiang pigs. Our investigation yielded novel candidate genes linked to five saturated fatty acids (SFAs), four monounsaturated fatty acids (MUFAs), and five polyunsaturated fatty acids (PUFAs). Significant associations with SFAs, MUFAs, and PUFAs were found for 37, 21, and 16 SNPs, respectively. Notably, some SNPs have significant PVE, such as ALGA0047587, which can explain 89.85% variation in Arachidic acid (C20:0); H3GA0046208 and DRGA0016063 can explain a total of 76.76% variation in Elaidic Acid (C18:1n-9(t)), and the significant SNP ALGA0031262 of Arachidonic acid (C20:4n-6) can explain 31.76% of the variation. Several significant SNPs were positioned proximally to previously reported genes. In total, we identified 11 candidate genes (hnRNPU, CEPT1, ATP1B1, DPT, DKK1, PRKG1, EXT2, MEF2C, IL17RA, ITGA1 and ALOX5), six candidate genes (ALOX5AP, MEDAG, ISL1, RXRB, CRY1, and CDKAL1), and five candidate genes (NDUFA4L2, SLC16A7, OTUB1, EIF4E and ROBO2) associated with SFAs, MUFAs, and PUFAs, respectively. These findings hold great promise for advancing breeding strategies aimed at optimizing meat quality and enhancing lipid metabolism within the intramuscular fat (IMF) of Ningxiang pigs.

A Comprehensive Genomic Analysis of Chinese Indigenous Ningxiang Pigs: Genomic Breed Compositions, Runs of Homozygosity, and Beyond.

Ningxiang pigs are a renowned indigenous pig breed in China, known for their meat quality, disease resistance, and environmental adaptability. In recent decades, consumer demand for meats from indigenous breeds has grown significantly, fueling the selection and crossbreeding of Ningxiang pigs (NXP). The latter has raised concerns about the conservation and sustainable use of Ningxiang pigs as an important genetic resource. To address these concerns, we conducted a comprehensive genomic study using 2242 geographically identified Ningxiang pigs. The estimated genomic breed composition (GBC) suggested 2077 pigs as purebred Ningxiang pigs based on a ≥94% NXP-GBC cut-off. The remaining 165 pigs were claimed to be crosses, including those between Duroc and Ningxiang pigs and between Ningxiang and Shaziling pigs, and non-Ningxiang pigs. Runs of homozygosity (ROH) were identified in the 2077 purebred Ningxiang pigs. The number and length of ROH varied between individuals, with an average of 32.14 ROH per animal and an average total length of 202.4 Mb per animal. Short ROH (1-5 Mb) was the most abundant, representing 66.5% of all ROH and 32.6% of total ROH coverage. The genomic inbreeding estimate was low (0.089) in purebred Ningxiang pigs compared to imported western pig breeds. Nine ROH islands were identified, pinpointing candidate genes and QTLs associated with economic traits of interest, such as reproduction, carcass and growth traits, lipid metabolism, and fat deposition. Further investigation of these ROH islands and candidate genes is anticipated to better understand the genomics of Ningxiang pigs.

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.

A look under the hood of genomic-estimated breed compositions for brangus cattle: What have we learned?

The Brangus cattle were developed to utilize the superior traits of Angus and Brahman cattle. Their genetic compositions are expected to be stabilized at 3/8 Brahman and 5/8 Angus. Previous studies have shown more than expected Angus lineage with Brangus cattle, and the reasons are yet to be investigated. In this study, we revisited the breed compositions for 3,605 Brangus cattle from three perspectives: genome-wise (GBC), per chromosomes (CBC), and per chromosome segments (SBC). The former (GBC) depicted an overall picture of the "mosaic" genome of the Brangus attributable to their ancestors, whereas the latter two criteria (CBC and SBC) corresponded to local ancestral contributions. The average GBC for the 3,605 Brangus cattle were 70.2% Angus and 29.8% Brahman. The K-means clustering supported the postulation of the mixture of 1/2 Ultrablack (UB) animals in Brangus. For the non-UB Brangus animals, the average GBC were estimated to be 67.4% Angus and 32.6% Brahman. The 95% confidence intervals of their overall GBC were 60.4%-73.5% Angus and 26.5%-39.6% Brahman. Possibly, genetic selection and drifting have resulted in an approximately 5% average deviation toward Angus lineage. The estimated ancestral contributions by chromosomes were heavily distributed toward Angus, with 27 chromosomes having an average Angus CBC greater than 62.5% but only two chromosomes (5 and 20) having Brahman CBC greater than 37.5%. The chromosomal regions with high Angus breed proportions were prevalent, tending to form larger blocks on most chromosomes. In contrast, chromosome segments with high Brahman breed proportion were relatively few and isolated, presenting only on seven chromosomes. Hence, genomic hitchhiking effects were strong where Angus favorable alleles resided but weak where Brahman favorable alleles were present. The functions of genes identified in the chromosomal regions with high ( ≥ 75 % ) Angus compositions were diverse yet may were related to growth and body development. In contrast, the genes identified in the regions with high ( ≥ 37.5 % ) Brahman compositions were primarily responsible for disease resistance. In conclusion, we have addressed the questions concerning the Brangus genetic make-ups. The results can help form a dynamic picture of the Brangus breed formation and the genomic reshaping.

On the Secure Performance of Intelligent Reflecting Surface-Assisted HARQ Systems.

This paper analyzes the physical layer security performance of hybrid automatic repeat request (HARQ) systems with the assistance of an intelligent reflecting surface (IRS) and aims to reveal the primary factors that enhance PLS. First, closed-form expressions for the connection outage probability (COP) and secrecy outage probability (SOP) in HARQ with chase combining (HARQ-CC) are acquired using the generalized-K (KG) distribution. Then, these two critical metrics are derived while adopting HARQ with incremental redundancy (HARQ-IR), resorting to the mixture gamma (MG) distribution and the Mellin transform. Diversity and coding gain are also addressed through an asymptotic analysis of the COP and SOP. Finally, an evaluation of the numerical results demonstrates that a greater gain in the main channel and the wiretap channel can be produced by increasing the number of meta-surfaces rather than increasing the maximum transmission number, except for the higher signal-to-noise (SNR) region of HARQ-IR where the latter is preferred. This finding provides a significant guidance for the joint configuration of IRS and HARQ to achieve secure communication.

Genome-Wide Association Analysis Identified Variants Associated with Body Measurement and Reproduction Traits in Shaziling Pigs.

With the increasing popularity of genomic sequencing, breeders pay more attention to identifying the crucial molecular markers and quantitative trait loci for improving the body size and reproduction traits that could affect the production efficiency of pig-breeding enterprises. Nevertheless, for the Shaziling pig, a well-known indigenous breed in China, the relationship between phenotypes and their corresponding genetic architecture remains largely unknown. Herein, in the Shaziling population, a total of 190 samples were genotyped using the Geneseek Porcine 50K SNP Chip, obtaining 41857 SNPs for further analysis. For phenotypes, two body measurement traits and four reproduction traits in the first parity from the 190 Shaziling sows were measured and recorded, respectively. Subsequently, a genome-wide association study (GWAS) between the SNPs and the six phenotypes was performed. The correlation between body size and reproduction phenotypes was not statistically significant. A total of 31 SNPs were found to be associated with body length (BL), chest circumference (CC), number of healthy births (NHB), and number of stillborns (NSB). Gene annotation for those candidate SNPs identified 18 functional genes, such as GLP1R, NFYA, NANOG, COX7A2, BMPR1B, FOXP1, SLC29A1, CNTNAP4, and KIT, which exert important roles in skeletal morphogenesis, chondrogenesis, obesity, and embryonic and fetal development. These findings are helpful to better understand the genetic mechanism for body size and reproduction phenotypes, while the phenotype-associated SNPs could be used as the molecular markers for the pig breeding programs.

Optimization of HS-SPME-GC-MS for the Determination of Volatile Flavor Compounds in Ningxiang Pork.

This study attempts to explore the suitable conditions for the detection of volatile flavor compounds (VFCs) in Ningxiang pork by headspace solid-phase microextraction and gas chromatography-mass spectrometry (HS-SPME-GC-MS). Ningxiang pigs were harvested from a slaughterhouse and a longissimus dorsi sample was collected from each animal. The VFCs of Ningxiang pork can be strongly impacted by the detection conditions (columns, weight of meat samples, heat treatment time, equilibrium conditions, and extraction conditions) that need to be optimized. Our results also provided the optimal test conditions: weighing 5 g of meat samples, grinding for 30 s in a homogenizer, heat treatment at 100 °C for 30 min, equilibration at 70 °C for 30 min, and extraction at 100 °C for 50 min. Furthermore, the feasibility and representativeness of the test method were confirmed based on principal component analysis and a comparison of the three pork VFCs. These findings offer researchers a unified and efficient pretreatment strategy to research pork VFCs.

High-Discrimination Comparison Algorithm for the Comprehensive Evaluation of Innovation Ability in Colleges and Universities under Uncertain Information.

The innovation ability of students is one of the most important objectives that need to be cultivated in colleges and universities. The comprehensive evaluation of innovation ability discussed in the study can be divided into two stages: the first stage can be called preliminary evaluation and its main target is to identify students with innovative potential; in the second stage, the target objects found in the previous stage will be evaluated quantitatively and ranked. However, it is always difficult to quantitatively evaluate the innovation ability by using traditional algorithms. Based on the above analysis, the study proposes an algorithm to quantitatively evaluate the innovation ability with the help of management thought and fuzzy mathematics. Data are the basis of evaluation, and the accuracy of the data directly determines the quality of the algorithm; the data structure of the incompletely probabilistic fuzzy set is proposed in the study; the data structure can fully consider the fuzziness of the problem and the hesitation in the decision-making process; it can save the original detailed data to the maximum extent. Certainly, certain information may be lost or only the value range can be determined; there are usually some unknowns in the evaluation data, and the consistency optimization model is proposed for solving the problem. Usually, there are certain contradictions among the evaluation data; the definition of the consistency degree is proposed in the study; the consistency can be verified in time after all the unknowns are obtained, and the automatic adjustment module will be activated immediately if the value of the consistency degree exceeds the warning threshold. Finally, after verifying the data consistency, the solution can be obtained by solving the optimization model. Several experiments have been carried out to verify the effectiveness and high-discrimination ability of the algorithm proposed in the study; meanwhile, the superiority of the algorithm is further verified through comparisons with other outstanding algorithms.

A Closed-Loop Method for Multiperiod Intelligent Information Processing with Cost Constraints under the Fuzzy Environment.

From trivial matters in life to major scientific projects related to the fate of mankind, decision-making is everywhere. Whether high-quality decisions can be made often directly affects the development of affairs, especially when sudden disasters occur. As the basis of decision-making, data are crucial. The continuously probabilistic linguistic set, a data structure of the fuzzy mathematics, is selected in the paper to collect original data after careful comparisons, because this data structure can fully consider the hesitation of decision-makers and the fuzziness of complex problems. Although all alternatives are costly, the costs of different alternatives still vary greatly; obviously, the low-cost alternative is better than others when the same predetermined goal can be achieved, which is one of the research objectives and characteristics of this paper. Different from other researchers who only take the cost as one of the decision-making indicators, the algorithm proposed in the paper pays much more attention on the cost reduction. When dealing with an emergency, it is often difficult to solve the problem by taking measures only once; usually, multiple rounds of measures are needed. Each round of decision-making has both connections and differences, and the multiround decision-making model is proposed and built in the paper. Different from traditional linear structures, the model mainly adopts the closed-loop structure, which divides the whole process into multiple sub-decision-making points, the severities measured at the current time point will be compared with the values estimated at the latter time point, and then, the differences will be input into the system, the corresponding automatic adjustment modules will be activated immediately according to the values. The accuracy of the system can be verified and adjusted in time by the closed-loop control module. Finally, several experiments are carried out and the results show that the algorithm proposed in the paper is more effective and the cost is lower.

Rate Adaption for Secure HARQ-CC System with Multiple Eavesdroppers.

In this paper, we studied the secure transmission of a hybrid automatic repeat request with chase combining (HARQ-CC) system, under the existence of multiple eavesdroppers and limited latency. First, we analyzed some critical performance metrics, including connection outage probability (COP), secrecy outage probability (SOP) and effective secrecy throughput (EST). Then, to maximize the EST, three optimization problems of rate adaption were discussed: (i) optimizing the code rate with a given secrecy redundancy rate by a parameterized closed-form solution; (ii) optimizing the secrecy redundancy rate with a given code rate by a fixed-point method; (iii) optimizing both code rate and secrecy redundancy rate by an iterative optimization algorithm. We also considered COP and SOP constraints among the problems while corresponding solutions were deduced. Finally, numerical and simulated results verified our conclusions that the approximated SOP matches well with Monte-Carlo simulation for a strict reliable constraint, and that the optimized transmitting rate enhances EST efficiently with multiple eavesdroppers and retransmissions. Moreover, the influence of the number of eavesdroppers on secrecy performance was analyzed. Briefly, secrecy performance inevitably deteriorates with increasing number of eavesdroppers due to raised information leakage.