Genome assembly anchored QTL map of bovine chromosome 14.

Bovine chromosome 14 (BTA14) has been widely explored for quantitative trait loci (QTL) and genes related to economically important traits in both dairy and beef cattle. We reviewed more than 40 investigations and anchored 126 QTL to the current genome assembly (Btau 4_0). Using this anchored QTL map, we observed that, in dairy cattle, the region spanning 0 - 10 Mb on BTA14 has the highest density QTL map with a total of 56 QTL, mainly for milk production traits. It is very likely that both somatic cell score (SCS) and clinical mastitis share some common QTL in two regions: 61.48 Mb - 73.84 Mb and 7.86 Mb - 39.55 Mb, respectively. As well, both ovulation rate and twinning rate might share a common QTL region from 34.16 Mb to 65.38 Mb. However, there are no common QTL locations in three pregnancy related phenotypes: non-return rate, pregnancy rate and daughter pregnancy rate. In beef cattle, the majority of QTL are located in a broad region of 15 Mb - 45 Mb on the chromosome. Functional genes, such as CRH, CYP11B1, DGAT1, FABP4 and TG, as potential candidates for some of these QTL, were also reviewed. Therefore, our review provides a standardized QTL map anchored within the current genome assembly, which would enhance the process of selecting positional and physiological candidate genes for many important traits in cattle.

Corticotropin releasing hormone is a promising candidate gene for marbling and subcutaneous fat depth in beef cattle.

The gene corticotropin releasing hormone (CRH) is mapped on bovine chromosome 14 (BTA14), where more than 30 fat-related quantitative trait loci (QTLs) have been reported in dairy and beef cattle. The gene product regulates secretion of adrenocorticotrophin hormone, the hypothalamic-pituitary-adrenal axis, and multiple hypothalamic functions; therefore, we hypothesized that CRH is a promising candidate gene for beef marbling score (BMS) and subcutaneous fat depth (SFD) in a Wagyu x Limousin F2 population. Two pairs of primers were designed and a total of 5 single nucleotide polymorphisms (SNPs) were identified: g.9657C>T, c.10718G>C, c.10841G>A, c.10893A>C, and c.10936G>C (AAFC03076794.1). Among the 4 cSNPs, c.10718G>C, c.10841G>A, and c.10936G>C are missense mutations leading to amino acid changes from arginine to proline, from serine to asparagine, and from aspartic acid to histidine, respectively. These 5 SNPs were genotyped on ~250 F2 progeny, but only 4 were selected as tagging SNPs for association analysis because no historical recombination was observed between c.10718G>C and c.10893A>C. Statistical analysis showed that g.9657C>T, c.10718G>C, and c.10936G>C and their haplotypes had significant effects on SFD, but only c.10936G>C was significantly associated with BMS. The SNP in the promoter (g.9657C>T) led to gain/loss of a CpG site and 4 potential regulatory binding sites. Different haplotypes among the 4 cSNPs significantly affected mRNA secondary structures but were not associated with phenotypes. Overall, our results provide further evidence that CRH is a promising candidate gene for a concordant QTL related to lipid metabolism in mammals.

A simplified QTL mapping approach for screening and mapping of novel AFLP markers associated with beef marbling.

Genome screening of quantitative trait loci (QTL) for a complex trait is usually costly and highly laborious, as it requires a large number of markers spanning the whole genome. Here we present a simplified approach for screening and mapping of QTL-linked markers for beef marbling using a WagyuxLimousin F(2) reference population. This simplified approach involves integration of the amplified fragment length polymorphism (AFLP) with DNA pooling and selective genotyping and comparative bioinformatics tools. AFLP analysis on two high and two low marbling DNA pools yielded ten visually different markers. Among them, four were confirmed based on individual AFLP validation. Sequencing and in silico characterization assigned two of these AFLP markers to bovine chromosomes 1 (BTA1) and 13 (BTA13), which are orthologous to human chromosomes HSA21q22.2 and HSA10p11.23 with both regions harboring QTL for obesity-related phenotypes. Both AFLP markers showed significantly large additive genetic effects (0.28+/-0.11 on BTA1 and 0.54+/-0.21 on BTA13) on beef-marbling score (BMS) (P<0.05). Overall, this approach is less time consuming, inexpensive and in particular, suitable for screening and mapping QTL-linked markers when targeting one or a few complex traits.