Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences

Table 6 Overrepresented gene ontology terms for moderate impact^b, line-specific variants in Fayoumi and Leghorn lines

Fayoumi GO Term	Count	P-value^a
FN3	22	1.10E-03
Ribonucleotide binding	154	1.70E-03
Purine ribonucleotide binding	154	1.70E-03
Fibronectin, type III	22	8.10E-03
PTPc	8	1.70E-02
Nucleotide binding	177	2.10E-02
Protein kinase activity	61	2.60E-02
Leghorn GO Term	Count	P-value^a
ECM-receptor interaction	25	9.60E-05
Extracellular matrix	41	1.90E-04
Metal ion binding	270	2.30E-03
Proteinaceous extracellular matrix	37	1.30E-03
Extracellular region	94	2.30E-03
Cell division and chromosome partitioning	26	2.60E-02
Calcium ion binding	77	3.90E-02
Aminophospholipid transporter activity	7	4.30E-02
Phospholipid-translocating atpase activity	7	4.30E-02

Over-represented GO terms for moderate impact variants (fixed/segregating) and unique for the inbred Fayoumi and Leghorn lines. ^aBenjamini-Hochberg Corrected p-value cut-off α = 0.05. ^bModerate impact variants: non_synonymous_coding, codon_change, codon_insertion, codon_change_plus_codon_insertion, codon_deletion, codon_change_plus_codon_deletion, utr_5_deleted, utr_3_deleted

ISSN: 1471-2164