Genome-wide association study using the Bayes C method for important traits in dairy yield in Colombian Holstein Cattle

Flórez, Juan Carlos Rincón; Herrera, Albeiro López; Zuluaga, Jose Julián Echeverri

doi:10.4025/actascianimsci.v40i1.39015

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Acta Scientiarum. Animal Sciences

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ANIMAL BREEDING AND REPRODUCTION • Acta Sci., Anim. Sci. 40 • 2018 • https://doi.org/10.4025/actascianimsci.v40i1.39015 copy

Genome-wide association study using the Bayes C method for important traits in dairy yield in Colombian Holstein Cattle

Associação genômica usando o método Bayes C para características importantes na produção leiteira em Gado Holandês na Colômbia.

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT.

The objective of this study was to determine the genome association between markers of bovine LD BeadChip with dairy important traits. Information of breeding program of the Universidad Nacional de Colombia was used. BLUP-EBVs were used for dairy yield (DY), fat percentage (FP), protein percentage (PP) and somatic cell score (SCS). 150 animals were selected for blood or semen DNA extraction and genotyping with BovineLD BeadChip (Illumina). Autosomal information was retained and the editing information was performed using Plink v1.07 software. The effects of SNPs were determined by Bayes C with GS3 software. The minor allele frequency for most of the markers on the bead chip was high, which increases the probability of finding important loci segregating in the population. Estimations of fraction markers with an effect were close to zero in almost all cases. The most important markers were mapped by trait using ENSEMBL. A total of 6,510 autosomal SNPs were retained, out of which only a proportion with effect was taken from the mixed function of Bayes C. Important genes as ANKS1B, CLCN1, NMBR and CTSD, were found for each trait for AL, FP, PP and SCS respectively. Finally, Bayes C estimation allowed to identify specific SNPs possibly associated with QTLs.

Keywords:
dairy cattle; GWAS; QTLs, single nucleotide polymorphism

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[1] *Author for correspondence. E-mail: rincon.juan@utp.edu.co.

Chromosome	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15
Number of SNPs	390	341	310	301	305	306	282	292	268	269	275	224	209	18	219
Chromosome	16	17	18	19	20	21	22	23	24	25	26	27	28	29	X
Number of SNPs	205	190	176	180	205	184	163	150	176	134	142	138	124	134	206

Trait	Rs code	Chromosome / position	MAF	Gene/consequence	Function
DY	Rs110718748	5 / 63899453	0.40	ANKS1B/intronic variant	There are different isoforms of the gene with neuronal regulation functions, regulation of global protein synthesis, APP regulated.
	Rs41607880	4 / 89380482	0.49	TMEM229A/close intergenic variant	Activity with binding transcription factors to specific DNA sequence
	Rs110425841	22/ 60508872	0.14	PODXL2/Intronic variant and upstream of ABTB1	PODXL2: transmembrane proteins binding to glycosaminoglycans ABTB1: Elongation factor activity in translation.
	Rs43483670	6/ 103079093	0.23	MAPK10/Intronic variant	JUN kinase activity and MAP kinase (Signaling)
	Rs41913085	11/ 19125116	0.45	VIT/Nearby intergenic variant	glycosaminoglycan binding
FP	Rs109245784	4/ 107540967	0.29	CLCN1/Intronic variant	Chloride channels activity
	Rs41571534	19/ 26182297	0.19	WSCD1/Nearby intergenic variant	sulfotransferase activity, milk fat
	Rs41670205	2/ 55831708	0.45	LRP1B/Intronic variant	Activity in cell surface proteins that bind and internalize ligands in the process of receptor - mediated endocytosis. Calcium and low - density lipoprotein binding.
	Rs43655765	11/ 2350093	0.49	SNRNP200 / Synonymous variant.	Small nuclear ribonucleoprotein (determining role in splicing)
	Rs110897514	17/ 20336068	0.43	PCDH18 / Nearby intergenic variant	Calcium dependent cell adhesion protein
PP	Rs29014693	9/ 80015418	0.45	NMBR / Nearby intergenic variant	Involved in many biological functions such as feeding, pituitary, gastric and pancreatic secretion, cell development and differentiation, among others.
	Rs41772701	15/ 57260972	0.47	CAPN5 / Intronic variant	Endopeptidase activity calcium dependent cysteine type.
	Rs29023352	4/ 118676822	0.38	INSIG1 / Nearby intergenic variant	Intermediary in cholesterol synthesis control. Plays a role in the growth and differentiation of tissue involved in metabolic control.
	Rs41576177	24/ 32677985	0.38	OSBPL1A / Intronic variant	It binds to phospholipids and cholesterol.
	Rs41624303	5/ 82878525	0.26	Arntl2 / Intronic variant	Activity in protein dimerization and activity of binding transcription factors to specific DNA sequence
SCS	Rs109548201	29: 50361506	0.28	CTSD / Downstream variant (9PB)	Acid protease activity in intracellular protein breakdown. Involved in the pathogenesis of several diseases.
	Rs41589068	5: 30275164	0.25	Among NCKAP5L and TMBIM6 / Intergenic	TMBIM6: Apoptosis modulator, calcium homeostasis. NCKAP5L; Activity associated to signaling mechanisms.
	Rs41797394	16: 33121540	0.39	Locus uncharacterized near EFCAB2	EFCAB2 Binding activity to calcium ions
	Rs41602750	5: 93871154	0.44	MGST1 / Nearby intergenic variant	Glutathione peroxidase activity and homodimerization
	Rs109119975	15: 31153296	0.41	Intergenic variant near to immunological important gene cluster PVRL1, THY1, C1QTNF5	PVRL1: protein homodimerization activity. THY1: binding and activating protein kinase, cell-cell interaction and cell ligand. C1QTNF5: Plays a role in cell adhesion, related to tumor necrosis factor.

Trait	rs code	Location	QTL type associated
DY	Rs110718748	In the interval attributed to a QTL. Direct association reported	Dairy yield, % fat, pregnancy and calving ease.
	Rs41607880	Close to a QTL (< 1Mb).	Milk production, fat and protein production, delivery first estrus interval, consumption.
	Rs110425841	In the interval attributed to a QTL.	Fatty acids in milk and somatic cell score, weight.
	Rs43483670	Close to a QTL (< 1.5 Mb)	Meat quality
	Rs41913085	In the interval attributed to a QTL. Direct association reported	Reproductive traits and content of Beta-lactoglobulin.
FP	Rs109245784	No QTL reported in the region.
	Rs41571534	In the interval attributed to a QTL.	Myristoleic acid content, EBV for milk fat production, percentage of linoleic acid in milk,
	Rs41670205	Close to a QTL (< 1 Mb).	Protein production, grade of milk.
	Rs43655765	In the interval attributed to a QTL.	Logissimus lean muscle area, pentadecanoic acid content.
	Rs110897514	Close to a QTL (<0.5 Mb).	Production of milk fat, energy production in milk, fat percentage and protein production.
PP	Rs29014693	Close to a QTL (< 0.5 Mb).	Capric acid content.
	Rs41772701	Close to a QTL (< 0.5 Mb).	Relationship Omega 3 / Omega 6 content of docosahexaenoic acid
	Rs29023352	Close to a QTL (< 0.5 Mb).	Birth weight
	Rs41576177	Close to a QTL (< 1.5 Mb).	Fertility rates and feed conversion
	Rs41624303	Close to a QTL (< 1.5 Mb).	C22:1 fatty acid content
SCS	Rs109548201	Close to a QTL (< 0.5 Mb).	Lignoceric acid content, iron content.
	Rs41589068	In the interval attributed to a QTL.	Udder height, croup lenght, cell-mediated immune response, protein percentage in milk, fat production.
	Rs41797394	Close to a QTL (< 1.5 Mb).	Paratuberculosis susceptibility, early embryonic survival.
	Rs41602750	No QTL reported in the region.
	Rs109119975	Close to a QTL (< 0.5 Mb)	Somatic cell score, udder composition index, subcutaneous fat, milk production.