The dynamics of molecular, immune and physiological features of the host and the gut microbiome, and their interactions before and after onset of laying in two hen strains

Ponsuksili, Siriluck; Hadlich, Frieder; Perdomo‐Sabogal, Alvaro; Reyer, Henry; Oster, Michael; Trakooljul, Nares; Iqbal, Muhammad Arsalan; Schmucker, Sonja; Stefanski, Volker; Roth, Christoph; Silva, Amélia Camarinha; Huber, Korinna; Sommerfeld, Vera; Rodehutscord, M.; Wimmers, Klaus

doi:10.1016/j.psj.2022.102256

Cited by 2 publications

(6 citation statements)

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“…By comparing LB vs. LSL, our pairwise fixation index analysis identified 17 genes that were selected as candidates and highly differentiated between the two‐layer strains ( Z ( F ST ) ≥ 4). Several previous studies indicate that the immune and metabolic systems of both strains are acquired and maintained differently under high‐performance conditions (Iqbal et al, 2021 , 2022 ; Ponsuksili et al, 2022 ). In line with these results, our study shortlisted the CREBL2 on chromosome 1 as a candidate gene that was highly differentiated in the jejunum mucosa of LB and LSL strains with [ Z ( F ST ) = 4.65].…”

Section: Discussionmentioning

confidence: 96%

“…Our previous studies focused on the molecular and phenotypic characterization of the two laying hen strains LB and LSL. Interestingly, both lines have a similar performance on egg production but differ in body weight, immunity, bone metabolism, phytate degradation, and transcript abundance of genes that could be assigned to immune system processes and phosphorus metabolic processes (Habig et al, 2012 , 2014 ; Omotoso et al, 2021 ; Ponsuksili et al, 2022 ; Sommerfeld, Omotoso, et al, 2020 ). Therefore, genetic variation between the two strains of laying hens (LB and LSL) and in contrast to the Cobb 500 broiler (BR) meat chickens was the subject of the present study.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, the gene SLC13A2 (Solute Carrier Family 13 Member 2), which codes for the sodium‐coupled citrate transporter (Akhtar et al, 2022 ) is worth mentioning here. Our recent study showed that SLC13A2 is highly expressed in the intestinal mucosa, especially in the laying period (week 24), and was also identified as a biosignature associated with age and laying strain (LB vs. LSL; Ponsuksili et al, 2022 ). In the same study, we found that the expression of SLC13A2 in the intestinal mucosa was strongly negatively correlated with phosphorus utilization ( r = 0.73; Ponsuksili et al, 2022 ).…”

Section: Discussionmentioning

confidence: 99%

“…Our recent study showed that SLC13A2 is highly expressed in the intestinal mucosa, especially in the laying period (week 24), and was also identified as a biosignature associated with age and laying strain (LB vs. LSL; Ponsuksili et al, 2022 ). In the same study, we found that the expression of SLC13A2 in the intestinal mucosa was strongly negatively correlated with phosphorus utilization ( r = 0.73; Ponsuksili et al, 2022 ). Interestingly, based on the genetic variants, this study also selected SLC13A2 as a candidate gene that differs between laying lines and as an ASE gene for the LB laying strain at the 24th and 30th week; we speculate that SLC13A2 may be involved in the complex events that occur during the laying cycle and that it is strain specific during the selection process.…”

Section: Discussionmentioning

confidence: 99%

“…A multi‐omics study discovered that the LB and LSL layer lines use divergent intrinsic mechanisms that shape their immune and metabolic function (Iqbal et al, 2022 ). Another pan‐omics longitudinal integration study at different production periods from pre‐laying to the onset of laying indicated that they differed in their ability to activate immune and metabolic mechanisms, as well as unique gut‐microbiota interactions (Ponsuksili et al, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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RNA‐Seq‐based discovery of genetic variants and allele‐specific expression of two layer lines and broiler chicken

Iqbal

Hadlich

Reyer

et al. 2023

Evolutionary Applications

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Recent advances in the selective breeding of broilers and layers have made poultry production one of the fastest‐growing industries. In this study, a transcriptome variant calling approach from RNA‐seq data was used to determine population diversity between broilers and layers. In total, 200 individuals were analyzed from three different chicken populations (Lohmann Brown (LB), n = 90), Lohmann Selected Leghorn (LSL, n = 89), and Broiler (BR, n = 21). The raw RNA‐sequencing reads were pre‐processed, quality control checked, mapped to the reference genome, and made compatible with Genome Analysis ToolKit for variant detection. Subsequently, pairwise fixation index (FST) analysis was performed between broilers and layers. Numerous candidate genes were identified, that were associated with growth, development, metabolism, immunity, and other economically significant traits. Finally, allele‐specific expression (ASE) analysis was performed in the gut mucosa of LB and LSL strains at 10, 16, 24, 30, and 60 weeks of age. At different ages, the two‐layer strains showed significantly different allele‐specific expressions in the gut mucosa, and changes in allelic imbalance were observed across the entire lifespan. Most ASE genes are involved in energy metabolism, including sirtuin signaling pathways, oxidative phosphorylation, and mitochondrial dysfunction. A high number of ASE genes were found during the peak of laying, which were particularly enriched in cholesterol biosynthesis. These findings indicate that genetic architecture as well as biological processes driving particular demands relate to metabolic and nutritional requirements during the laying period shape allelic heterogeneity. These processes are considerably affected by breeding and management, whereby elucidating allele‐specific gene regulation is an essential step towards deciphering the genotype to phenotype map or functional diversity between the chicken populations. Additionally, we observed that several genes showing significant allelic imbalance also colocalized with the top 1% of genes identified by the FST approach, suggesting a fixation of genes in cis‐regulatory elements.

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Section: Discussionmentioning

confidence: 96%