Multi-trait GWAS using imputed high-density genotypes from whole-genome sequencing identifies genes associated with body traits in Nile tilapia

Table 4 Genes intercepted by a lead SNP associated with body traits based on multi-trait GWAS in Nile tilapia

Gene^a	LG^b	Position^c	N SNP^d	p-values^e		Genomic location	Traits
Gene^a	LG^b	Position^c	N SNP^d	Min	Max	Genomic location	Traits
CCDC102A	1	39,153,024	1	3.146E-12	3.474E-10	Intronic	ADG, BWH, WW, HW, HON, BLH
ADAMTS9	5	29,062,243	1	3.446E-11	–	Exonic	FW
SRGAP1	7	60,999,336–61,005,198	3	4.614E-09	4.614E-09	Intronic	HW
SLC4A2	9	14,670,077–14,674,835	2	5.225E-08	5.225E-08	Intronic	WW
MALRD1	9	16,267,509–16,328,834	2	1.678E-10	5.325E-08	Intronic	ADG, BWH, HON
PTPRN2	9	16,433,765–16,435,917	2	4.091E-09	4.758E-09	Intronic	ADG, HW
DMXL1	12	24,525,556	1	2.379E-11	–	Intronic	FW
MARCH8	13	17,730,096–17,730,605	1	2.012E-08	2.012E-08	Intronic	FY
MSH6	13	21,626,153–21,626,426	1	3.796E-08	3.796E-08	Exonic/Intronic	ADG
FUT8	15	14,457,958	1	4.861E-08	–	Intronic	ADG
TMEM121	15	14,662,118	1	9.425E-10	9.844E-09	Intronic	ADG, BWH, WW
MYO6	15	23,976,527	1	5.175E-08	–	Intronic	HON
HEG1	16	12,574,352	1	3.836E-08	–	Intronic	FY
DOCK9	16	17,284,162	1	1.673E-08	–	Intronic	HW
MYO16	16	20,105,934–20,116,545	2	3.340E-11	1.988E-09	Intronic/Exonic	ADG, BWH, WW, HON, BLH
NUP107	17	19,609,147–19,612,729	2	3.815E-08	4.102E-08	Intronic/Exonic	BWH, HON
KTN1	19	11,094,375	1	7.954E-09	–	Exonic	ADG

ADG average daily gain (g), BWH body weight at harvest (g), WW waste weight (g), HW head weight (g), HON gutted head-on weight (g), BLH Body length at harvest (cm), FW fillet weight (g), FY fillet yield (%)
^aGenes intercepted by at least one lead SNP based on O_niloticus_UMD_NMBU as reference genome for Oreochromis niloticus
^bLinkage group
^cIn base pairs
^dNumber of lead SNPs
^eMinimum (Min) and maximum (Max) p-value for coincident lead SNP for at least two traits

ISSN: 1471-2164