Genome-wide association study for birth, weaning and yearling weight in Colombian Brahman cattle

Martínez, Rodrigo; Bejarano, Diego; Gómez, Yolanda; Dasoneville, Romain; Jiménez, Ariel; Even, Gael; Sölkner, Johann; Mészáros, Gabor

doi:10.1590/1678-4685-GMB-2016-0017

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Animal Genetics • Genet. Mol. Biol. 40 (2) • Apr-Jun 2017 • https://doi.org/10.1590/1678-4685-GMB-2016-0017 copy

Genome-wide association study for birth, weaning and yearling weight in Colombian Brahman cattle

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

Genotypic and phenotypic data of 1,562 animals were analyzed to find genomic regions that potentially influence the birth weight (BW), weaning weight at seven months of age (WW) and yearling weight (YW) of Colombian Brahman cattle, with genotyping conducted using Illumina Bead chip array with 74,669 SNPs. A Single Step Genomic BLUP (ssGBLP), approach was used to estimate the proportion of variance explained by each marker. Multiple regions scattered across the genome were found to influence weights at different ages, also dependent on the trait component (direct or maternal). The most interesting regions were connected to previously identified QTLs and genes, such as ADAMTSL3, CAPN2, CAPN2, FABP6, ZEB2 influencing growth and weight traits. The identified regions will contribute to the development and refinement of genomic selection programs for Zebu Brahman cattle in Colombia.

Keywords:
Bos indicus; SNP; QTL; GWAS; body weight

Traits	Mean	S. D.	C. V.	Min	Max	h2_d
BW	33.06	3.60	10.89	19	68	0.26
WW	198.31	25.99	13.11	143	266	0.18
YW	257.46	25.47	9.89	205	340	0.22

Trait type	Chromosome	Region^a a The region is defined as the location of the most important SNPs ± 0.5 Mb	Number of characterized genes in the region^b b Source: NCBI, October 2015, annotation release 104	Weight and growth-relevant QTLs
Direct and maternal	BTA2	17.34 −18.42	5	QTL:1549 ^c c QTL number identification on QTLdatabase (www.animalgenome.org/cgi-bin/) , “Body depth”
				QTL:1550, “Body form composite index”
				QTL:3491, “Hip height”
				QTL:1553, “Stature”
				QTL:1323, “Body weight (birth)”
		51.52 – 52.55	1	QTL:10670, “Body weight (birth)”
				QTL:10665, “Carcass weight”
				QTL:1310, “Body weight (slaughter)”
	BTA17	49.40 – 53.40	5	QTL:23867, “Metabolic body weight”
				QTL:23868, “Metabolic body weight”
				QTL:23870, “Body weight (weaning)”
Direct only	BTA16	27.83 – 28.86	9	QTL:11025, “Body weight (birth)”
				QTL:11026, “Body weight (weaning)”
				QTL:4482, “Body weight (weaning)”
				QTL:4486, “Pre-weaning average daily gain”
Maternal only	BTA1	1.62 – 2.65	9	QTL:24744, “Weaning weight-maternal milk”
				QTL:5265, “Residual feed intake”
	BTA7	73.22 – 74.28	10	No weight and growth-related QTL
	BTA16	58.20 – 60.56	6	No weight and growth-related QTL

Trait type	Chromosome	Region^a a The region is defined as the location of the most important SNPs ± 0.5 Mb	Number of characterized genes in the region^b b Source: NCBI, October 2015, annotation release 104	Weight and growth-relevant QTLs
Direct and maternal	BTA7	56.96 – 57.99	2	QTL:10807^c c QTL number identification on QTLdatabase (www.animalgenome.org/cgi-bin/) , “Body weight (yearling)”
				QTL:10806, “Longissimus muscle area”
				QTL:10805, “Carcass weight”
				QTL:10808, “Body weight (weaning)”
				QTL:10810, “Body weight (birth)”
	BTA8	1.63 – 2.65	2	QTL:10821, “Body weight (weaning)”
				QTL:10820, “Height (mature)”
				QTL:10819, “Longissimus muscle area”
				QTL:10817, “Carcass weight”
		78.35 – 79.40	7	No matching QTLs
	BTA14	57.26 – 58.34	4	No QTLs
	BTA20	2.70 – 3.74	6	QTL:1357, “Body weight (birth)”
				QTL:11099, “Body weight (birth)”
				QTL:11098, “Carcass weight”
				QTL:11097, “Body weight (weaning)”
				QTL:11094, “Carcass weight”
				QTL:11096, “Body weight (yearling)”
	BTA28	1.91 – 2.97	4	No QTLs

Trait type	Chromosome	Region^a a The region is defined as the location of the most important SNPs ± 0.5 Mb	Number of characterized genes in the region^b b Source: NCBI, October 2015, annotation release 104	Weight and growth-relevant QTLs
Direct and maternal	BTA1	155.24 - 156.42	4	No matching QTLs
	BTA16	11.35 – 12.42	0	QTL:11019 ^c c QTL number identification on QTLdatabase (www.animalgenome.org/cgi-bin/) , “Body weight (yearling)”
				QTL:11022, “Carcass weight”
				QTL:11021, “Longissimus muscle area”
				QTL:11023, “Weaning weight-maternal milk”
				QTL:1355, “Carcass weight”
				TL:23153, “Body weight (weaning)”
	BTA19	9.39 – 10.49	17	QTL:11075, “Body weight (mature)”
				QTL:11076, “Body weight (yearling)”
Maternal only	BTA1	17.76 - 18.82	3	QTL:10639, “Weaning weight-maternal milk”
				QTL:10638, “Body weight (birth)”
	BTA14	51.05 – 52.15	1	QTL:23842, “Body weight (weaning)”
				QTL:23846, “Body weight (weaning)”
				QTL:23843, “Body weight (birth)”
				QTL:23844, “Body weight (birth)”
				QTL:23845, “Body weight (birth)”
				QTL:23265, “Carcass weight”
				QTL:23849, “Metabolic body weight”
				QTL:23850, “Metabolic body weight”
	BTA21	23.48 - 24.62	10	QTL:22801, “Average daily gain”
				QTL:11118, “Fat thickness at the 12th rib”
				QTL:2641, “Body weight (birth)”
				QTL:11123, “Body weight (mature)”
				QTL:11122, “Height (mature)”
				QTL:11120, “Height (yearling)”
	BTA28	42.28 – 43.47	11	QTL:22763, “Body weight (birth)”

Sociedade Brasileira de Genética Rua Cap. Adelmio Norberto da Silva, 736, 14025-670 Ribeirão Preto SP Brazil, Tel.: (55 16) 3911-4130 / Fax.: (55 16) 3621-3552 - Ribeirão Preto - SP - Brazil
E-mail: editor@gmb.org.br

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[1] Send correspondence to Rodrigo Martínez. Colombian Corporation of Agricultural Research, Tibaitatá Research Center, Km 14 way Bogotá to Mosquera, CP 250047, Colombia. E-mail: ramartinez@corpoica.org.co.