Identification of SNP markers associated with gut microbiome composition in chicken

Enteric microbiome composition and structure varies widely between individuals, and has been associated with multiple health conditions and differences in productivity in farm animals. Enteric microbial communities are clearly influenced by environmental factors and food, but host genotype may also have an impact. This study is part of an effort to comprehensively profile interactions between chicken genetic variation and the composition of the gut microbial ecosystem on a genome-wide scale. We collected blood and caecal lumen contents from 150 indigenous Indian Kadaknath chickens and 150 commercial-type Cobb400 broilers, raised in groups together under the same farm conditions. All chickens were genotyped with the 600K Affymetrix HD SNP array and the caecal lumen microbiome was defined using Illumina 16s rDNA amplicon sequencing. Single marker regression genome- wide association analysis was conducted. Using this dataset, we identified significant associations at genome-wide level (P<0.05 Bonferroni corrected) between host genetic variation and gut microbiome composition.