Association of host genetics with intestinal microbial relevant to body weight in a chicken F2 resource population

Ji, Jun; Luo, Chenglong; Zou, Xian; Lv, Xiaoyan; Xu, Ye-Chun; Shu, Dingming; Qu, Hao

doi:10.3382/ps/pez199

Cited by 29 publications

(27 citation statements)

References 56 publications

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“…To date, GWAS has been widely used to map an increasing number of QTL, SNPs and candidate regions associated with FI, BWG, and FCR in beef cattle 19,20 and swine 8,21 . In chickens, several GWAS have revealed many genes and genomic regions associated with production 11,14,[22][23][24] , morphological traits 13,25 , aggressive behavior 10 , disease resistance 26 , and even with the intestinal microbial interaction 27 . Despite advances in knowledge of regions of interest in the chicken genome, few GWAS has been carried out to evaluate the genetic architecture of FE traits, and most of them ignore dominance, epistasis and sex interactions effects.…”

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confidence: 99%

Exploring the genetic architecture of feed efficiency traits in chickens

Marchesi

Ono

Cantão

et al. 2021

Sci Rep

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Chicken feed efficiency (FE) traits are the most important economic traits in broiler production. Several studies evaluating genetic factors affecting food consumption in chickens are available. However, most of these studies identified genomic regions containing putative quantitative trait loci for each trait separately. It is still a challenge to find common gene networks related to these traits. Therefore, here, a genome-wide association study (GWAS) was conducted to explore candidate genomic regions responsible for Feed Intake (FI), Body Weight Gain (BWG) and Feed Conversion Ratio (FCR) traits and their gene networks. A total of 1430 broilers from an experimental population was genotyped with the high density Affymetrix 600K SNP array. A total of 119 associated SNPs located in 20 chromosomes were identified, where some of them were common in more than one FE trait. In addition, novel genomic regions were prospected considering the SNPs dominance effects and sex interaction, identifying putative candidate genes only when these effects were fit in the model. Relevant candidate genes such as ATRNL1, PIK3C2A, PTPRN2, SORCS3 and gga-mir-1759 were highlighted in this study helping to elucidate the genomic architecture of feed efficiency traits. These results provide new insights on the mechanisms underlying the consumption and utilization of food in chickens.

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confidence: 99%

Exploring the genetic architecture of feed efficiency traits in chickens

Marchesi

Ono

Cantão

et al. 2021

Sci Rep

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“…Our previous study showed that the loci rs16775833 was associated with β-diversity, being located within the DMRT1 gene cluster, which might influence the BW of chickens ( Ji et al., 2019 ). The DMRT1 gene family is widely known for its involvement in sex determination in many organisms ( Lambeth et al., 2014 , Ayers et al., 2015 ).…”

Section: Discussionmentioning

confidence: 99%

“…Microbial QTL plots showed the association of a functional LCT SNP (rs4988235) with the abundance of Bifidobacterium ( Bonder et al., 2016 ). In a previous study, we showed that the locus rs16775833 within the DMRT gene cluster accounted for approximately 21% of the variation in the population structure of the gut microbiota by GWAS ( Ji et al., 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Effects of the DMRT1 genotype on the body weight and gut microbiota in the broiler chicken

Luo

et al. 2020

Poultry Science

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Intestinal microbiota is a critical determinant of growth and risk of metabolic diseases. Our previous studies showed that the locus rs16775833 within the DMRT1 gene is significantly associated with variation in the population structure of the gut microbiota, which is involved in determining the BW of the chicken. To assess the accuracy of correlation of rs16775833 located in the DMRT1 gene on microbial population and BW in birds, 2 genotypes GG and TT in the rs16775833 were identified in Chinese Yellow broiler breeders. We found that BW in the TT genotype group was significantly higher than in the GG genotype group at 7 and 13 wk of age in 777 female chickens. A full-length 16S rRNA sequencing approach was used to further evaluate the fecal bacterial composition of female broilers in 11 TT genotype chickens with high weight ( HW-TT ) and 11 GG genotype chickens with low weight ( LW-GG ) at 91 D of age. Partial least squares discriminant analysis revealed that the microbiota of the HW-TT and LW-GG females were clearly separated into 2 clusters. Furthermore, we identified 13 significantly different ( P < 0.05) microbes at the genus level and 17 significantly different ( P < 0.05) species between the HW-TT and LW-GG groups. Our data show that rs16775833 can modulate the microbial community structure and is associated with the BW of birds. To our knowledge, this is the first time that DMRT1 has been identified as a specific host factor, which is not only involved in sex determination but also has an effect on microbial function that might regulate animal growth.

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“…Overall, it seems both host genetic variations and intestinal microbiota composition could explain variations in individual Salmonella Enteritidis carriage in chicken. Furthermore, genetic studies on other phenotypic traits, such as digestive e ciency [22], body weight [23] or feather-pecking in laying hens [24] showed that host genetic variations in uence the intestinal microbiota composition in chicken. In these studies, authors identi ed several QTLs and single nucleotide polymorphisms (SNPs) associated with speci c bacterial species that may explain the phenotype and calculated heritabilities of these bacteria abundances.…”

Section: Introductionmentioning

confidence: 99%

Impact of Host Genetics on Caecal Microbiota Composition and on Salmonella Carriage in Chicken

Cazals¹,

Estellé²,

Bruneau³

et al. 2020

Preprint

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Background Salmonella Enteritidis (SE) is one of the major causes of human foodborne intoxication through the consumption of contaminated poultry products. Genetic selection of animals more resistant to Salmonella carriage and the modulation of gut microbiota are two promising ways of decreasing individual Salmonella carriage. This study aims to identify the main genetic and microbial factors controlling the individual levels of Salmonella carriage in chickens (Gallus gallus) in controlled experimental conditions. Two-hundred and forty animals from the White Leghorn inbred lines, N and 61, were infected by SE at 7 days of age. After infection, animals were kept in isolators to reduce the recontamination of birds by Salmonella. Caecal contents were sampled at 12 days post-infection and used for DNA extraction. Microbiota DNA was used to measure individual counts of SE by digital PCR and to determine the bacterial taxonomic composition through a 16S rRNA gene high-throughput sequencing approach. Results Results confirmed that the N line is more resistant to Salmonella carriage than the 61 line, and that intra-line variability is higher for the 61 line. Furthermore, the 16S analysis showed strong significant differences in microbiota taxonomic composition between the two lines. Out of 617 Operational Taxonomic Units (OTUs), over 390 were differentially abundant between the two lines. Furthermore, within the 61 line, we found a difference in the microbiota taxonomic composition between high and low Salmonella carriers, with 39 differentially abundant OTUs. Finally, via metagenome functional prediction based on 16S data, we identified several metabolic pathways potentially associated to microbiota taxonomic differences (e.g. butyrate metabolism) between high and low carriers. Conclusions Overall, this study demonstrates that the caecal microbiota composition of the N and 61 lines is influenced by the host genetics, which could be one of the reasons why these lines differ for their Salmonella carriage in experimental infection conditions.

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Association of host genetics with intestinal microbial relevant to body weight in a chicken F2 resource population

Cited by 29 publications

References 56 publications

Exploring the genetic architecture of feed efficiency traits in chickens

Exploring the genetic architecture of feed efficiency traits in chickens

Effects of the DMRT1 genotype on the body weight and gut microbiota in the broiler chicken

Impact of Host Genetics on Caecal Microbiota Composition and on Salmonella Carriage in Chicken

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