Pig pangenome graph reveals functional features of non‑reference sequences

Background The reliance on a solitary linear reference genome has imposed a significant constraint on our compre-hensive understanding of genetic variation in animals.This constraint is particularly pronounced for non-reference sequences(NRSs),which have not been extensively studied.Results In this study,we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb.Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome.Furthermore,we observed that NRSs were rarely found within coding sequences,while NRS insertions were enriched in immune-related Gene Ontology terms.Notably,our investigation also unveiled a close association between novel genes and the immune capacity of pigs.We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs,and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X.Additionally,we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in South-ern Chinese pigs.Conclusions Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.

Effects of Dietary Picria felterrae Lour Extracts on Serum Biochemical Indexes and Immune Function of Guangxi Partridge Chickens

[Objective] This trial was to investigate the effect of dietary Picria felterrae Lour extracts on serum biochemical indexes and immune function of Guangxi Partridge chickens. [Method] Totally 500 individuals of 1-day-old Guangxi Partridge chickens were randomly divided into five groups, five replicates each group and 20 chicks each replicate. Groups A, B and C were treatment groups supplemented with 0.70%, 0.35% and0.175% P. felterrae extracts in the basal diet, respectively; group D was a medical control group supplemented with 0.01% colistin sulfate premix in the basal diet; and group E was a control group with basal diet. Serum samples were collected from 10 chickens in each group at 21, 35 and 49 days of age, to analyze the biochemical and immune indexes. [Result] It had no significant impact on serum TP and GLU contents of chickens by adding different levels of P. felterrae extracts in the basal diet（P 〉0.05）. However, at 21 and 35 days of age, the TBILI content of chickens in groups A, B and C were extremely lower or significantly lower than that in group E（ P〈0.01; P〈0.05）. At 35 days of age, the serum AKP activities in groups A, B and C were extremely higher than that in group E（P〈0.01）, and the serum GOT activities at 21 and 35 days of age in group C were significantly higher than that in group E（P〈0.05）. At 49 days of age, the serum Ig G content in groups A, B and C and the IL-2 content in group B and group C were significantly lower or extremely lower than that in group E（ P〈0.05; P〈0.01）; the T-AOC content in group B was significantly higher than that in group E（P〈0.05）; the GSH content in groups A, B and C were significantly higher than that in group E（ P〈0.05）. Adding different levels of P. felterrae extracts in the diet significantly decreased the TBILI content, reduced the Ig G, IL-2 and IL-6 contents, and improved the AKP and GOT activities and the T-AOC and GSH contents of Guangxi Partridge chicken. [Conclusion] Adding 0.35% P. felterrae extracts in the basal diet received the best effort.