Alanine-specific appetite in slow growing chickens is associated with impaired glucose transport and TCA cycle

BMC Genomics

Table 3 Single nucleotide polymorphisms (SNP) with deleterious effect^a. The SNPs identified in amino acid and glucose sensor/transporter genes in slow (SG) compared to fast (FG) growing chickens

Ligand	Transporter/Sensor	Aliases	Deleterious SNP (Chromosome: Position)	Reference Allele	Mutated Allele	SIFT score	Amino Acid Change	n (Slow Growing Chickens)	n (Fast Growing Chickens)	P value (Fisher’s Exact Test)
Amino Acid	LPAR5	GPR92	1:77028001	T	C	0.00	N/D	5	3	0.44
	LPAR5	GPR92	1:77028838	C	A	0.04	A/S	1	0	1
	SLC38A1	SNAT1	1:30954991	C	T	0.02	G/S	1	0	1
	SLC38A2	SNAT2	1:30989563	A	C	0.01	I/S	0	2	0.44
	SLC38A2	SNAT2	1:30989536	C	T	0.00	G/E	0	1	1
	SLC7A11	–	4:29145636	G	A	0.00	P/L	0	1	1
	SLC7A5	LAT1	11:18195549	A	G	0.03	L/S	0	2	0.44
	SLC9A3R2	–	14:6272328	C	A	0.00	G/V	3	1	0.52
	T1R1	TAS1R1	21:564781	C	T	0.01	G/S	0	1	1
	T1R3	TAS1R3	21:2330035	G	A	0.03	H/Y	1	0	1
			21:2330503	G	C	0.00	A/G	1	0	1
			21:2328338	T	G	0.00	H/P	0	1	1
	Gust	GNAT3	1:11285686	T	G	0.00	H/P	1	0	1
	GRM7	mGluR7	12:19071629	C	A	0.00	C/F	1	0	1
	GRM7	mGluR7	12:19098074	A	G	0.00	S/P	1	0	1
Glucose	SLC5A10	SGLT5	14:5173852	C	T	0.01	S/L	1	0	1
	SLC2A4RG^b	GEF	20:9813052	A	T	0.00	V/E	5	0	0.007
	YWHAQ	HS1	3:96684296	A	T	0.00	L/Q	3	2	1
	OGDH	AKGDH	22:4630844	G	A	0.03	R/C	1	4	0.20
	OGDH	AKGDH	22:4641871	C	T	0.00	D/H	4	3	1

Abbreviations: GEF GLUT4 enhancer factor, GLUT4 sodium/glucose cotransporter 4, GPR92 G protein receptor 92, GRM7 Glutamate Metabotropic Receptor 7, Gust α-gustducin, HS1 Herpes Simplex 1, LPAR5 lysophosphatidic acid receptor 5, OGDH Oxoglutarate Dehydrogenase, SGLT5 sodium/glucose cotransporter 5, SLC38A1, 2 solute carrier family 38 member 1, 2, SLC7A11, 5 solute carrier family 7 member 11, 5, SLC5A10 solute carrier family 5 member 10, SLC2A4RG solute carrier family 2 regulator, T1R1/3 taste receptor family 1 type 1/3, SNAT1,2 Sodium-coupled neutral amino acid transporter 1, 2, YWHAQ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta, A Alanine, C Cysteine, D Aspartic acid, E Glutamic Acid, F Phenylalanine, G Glycine, H Histidine, I Isoleucine, L Leucine, N Asparagine, P Proline, Q Glutamine, R Arginine, S Serine, T Threonine, V Valine, W Tryptophan, Y Tyrosine
^aThe table shows the 20 SNPs showing deleterious effect based on Variant Effector Predictor analysis (SIFT score < .05). Overall, the genomic analysis identified over 900,000 variants on average in each individual (n = 5) with an accuracy of 99.9% (Phred score ≥ 30), of which 186 SNPs were on genes of interest (Table S2 in Additional file 1)
^bGlucose transporter SLC2A4RG presented one SNP (from A to T) with an allelic frequency significantly (P < 0.01) associated to growth rate (SG compared to FG) in chickens

ISSN: 1471-2164