Polymorphisms in major milk protein genes (LALBA, MBLG, CSN1S1 and CSN3) and milk fat genes (DGAT1 and SCD1) and association with milk production and fatty acid traits in indigenous White Fulani and Borgou cattle breeds in Benin

Abstract

Polymorphism in milk protein and fat genes is an important tool for breed characterization, genetic association as well as genetic diversity studies. However, there is no data available on genetic polymorphisms of major milk protein genes as well as their association with milk production traits in indigenous Borgou and White Fulani cattle breeds in Benin. The aim of this study was to assess the polymorphism in LALBA, MBLG, CSN1S1, CSN3, DGAT1 and SCD1 genes, their association with milk production and fatty acid traits as well as the genetic diversity, gene flow and phylogenetic relationships among Borgou and White Fulani cattle breeds in Benin. The genetic polymorphisms were assessed in 98 Borgou and 100 White Fulani cattle using polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) and Sanger sequencing methods. The milk components were determined using MilkoScan FT 6000 Series mid-range infrared and the fatty acid composition analysis was done by gas chromatography mass spectrometry (GC-MS). The results showed that White Fulani produced higher (P<0.001) test-day milk yield (1.14 vs 0.80 kg), fat content (5.49 vs 4.51 %), fat yield (57.13 vs 36.52 g) and test-day protein yield (40.4 vs 30.05 g) compared to Borgou. On the other hand, Borgou presented higher (P<0.001) content of milk urea nitrogen, oleic acid (C18:1 cis-9), linoleic acid (C18:2 cis-9, cis-12), C18 desaturation index (P<0.05), total index and higher (P<0.001) contents of polyunsaturated fatty acids (PUFA) than White Fulani. Six single nucleotide polymorphisms were found in CSN3 gene (g.13065 C>T, g.13068 C>T, g.13104 A>C, g.13111 A>G, g.13165 A>G and g.13173 A>T). The SNPs showed significant effect in Borgou only. Thus, the CSN3 g.13065 C>T genotypes were significantly associated with protein % (P<0.05), lactose % (P<0.01), test day fat and protein yields (P<0.05). The CSN3 g.13068 C>T and CSN3 g.13173 A>T genotypes were significantly associated with protein % (P<0.05) and lactose % (P<0.01). Moreover, the g.13111 A>G was associated with fat % and test-day fat yield (P<0.01) while the CSN3 xx g.13165 A>G was associated with fat% (P<0.05), protein % and lactose % (P<0.01) in Borgou. The AG genotype of MBLG g.5940G>A was significantly associated with higher fat (6.8% vs 4.6% vs 4.5, P<0.05) and total solids (16.8% vs 13.7% vs 13.5%, P<0.05) contents compared to AA and GG genotypes, respectively in Borgou. The AG genotype of CSN1S1 g.10430 G>A was associated with higher (P<0.05) test-day milk yield (1.18 kg) compared to AA genotype (0.67 kg) and GG genotype (0.78 kg). The TT genotype of CSN1S1 g.10359 T>C was associated with higher (P<0.01) test-day milk yield and higher (P<0.05) test-day fat and protein yields in White Fulani. Moreover, the GG genotype of CSN1S1 g.10430 G>A was associated with higher (P<0.01) test-day milk yield in White Fulani. The SCD1 VV genotype was associated with higher (P<0.05) protein and lactose contents and lower (P<0.05) C18:1 cis-9 content in White Fulani. The SCD1 AV genotype was associated with higher C14 and total indices; and the SCD1 V allele was associated with decrease in C14 index in Borgou. In White Fulani breed, the DGAT1 K allele was associated with increased total saturated fatty acids (SFA), and decreased C18 index, total index and total monounsaturated fatty acids. Borgou presented higher (P<0.01) observed heterozygosity (Hob) and unbiased gene diversity (Hex) (0.329, 0.353) than White Fulani (0.286, 0.302). The population differentiation () was 0.017 and significantly different from zero (P<0.01). High level of gene flow (Nem=14.104), a low Nei’s DA genetic distance (0.017) and a very closer phylogenetic relationship were observed between both breeds. Borgou milk is better in terms of human health compared to White Fulani. The identified alleles and single nucleotide polymorphisms (SNPs) associated with milk production and fatty acid traits could serve as potential genetic markers to improve milk production and fatty acids traits in Borgou and White Fulani cattle breeds in Benin. To allow sustained genetic improvement, care must be taken to prevent the gene flow and loss of genetic diversity between both breeds.