Fine mapping quantitative trait loci affecting milk production traits on bovine chromosome 6 in a Chinese Holstein population.

To fine map the previously detected quantitative trait loci (QTLs) affecting milk production traits on bovine chromosome 6 (BTA6), 15 microsatellite markers situated within an interval of 14.3 cM spanning from BMS690 to BM4528 were selected and 918 daughters of 8 sires were genotyped. Two mapping approaches, haplotype sharing based LD mapping and single marker regression mapping, were used to analyze the data. Both approaches revealed a quantitative trait locus (QTL) with significant effects on milk yield, fat yield and protein yield located in the segment flanked by markers BMS483 and MNB209, which spans a genetic distance of 0.6 cM and a physical distance of 1.5 Mb. In addition, the single marker regression mapping also revealed a QTL affecting fat percentage and protein percentage at marker DIK2291. Our fine mapping work will facilitate the cloning of candidate genes underlying the QTLs for milk production traits.

Mei G ，Yin C ，Ding X ，Zhang Q ... -  《Journal of Genetics and Genomics》

Interval and composite interval mapping of somatic cell score, yield, and components of milk in dairy cattle.

Single-marker, interval-mapping (IM) and composite interval mapping (CIM) were used to detect quantitative trait loci (QTL) controlling milk, fat and protein yields, and somatic cell score (SCS). A granddaughter design was used to combine molecular genetic information with predicted transmitting abilities (PTA) and estimated daughter yield deviations (DYD) from eight Dairy Bull DNA Repository Holstein families. Models that included and excluded weights accounting for the uncertainty of the response variable were evaluated in each trait, family and phenotype (DYD and PTA) combination. The genotypic information consisted of 174 microsatellite markers along 29 Bos taurus autosomes. The average number of informative markers per autosome was three and the number of informative sons per family and marker varied between 21 and 173. Within-family results from the least squares single-marker analyses were used in expectation-maximization likelihood IM and CIM implemented with QTL Cartographer. Different CIM model specifications, offering complementary control on the background QTL outside the interval under study, were evaluated. Permutation techniques were used to calculate the genome-wide threshold test statistic values based on 1,000 samples. Results from the DYD and PTA analyses were highly consistent across traits and families. The minor differences in the estimates from the models that accounted for or ignored the uncertainty of the DYD (variance) and PTA (inverse of reliability) may be associated to the elevated and consistent precision of the DYD and PTA among sons. The CIM model best supported by the data had 10 markers controlling for background effects. On autosome (BTA) three, a QTL at 32 cM influencing protein yield was located in family five and a QTL at 74 cM for fat yield was located in family eight. Two map positions associated with SCS were detected on BTA 21, one at 33 cM in family one and the other at 84 cM in family three. A QTL for protein yield was detected between 26 and 36 cM on BTA six, family six, and a QTL for milk yield was detected at 116 cM on BTA seven in family three. The IM and CIM approaches detected a QTL at 3 cM on BTA 14 influencing fat yield in family four. Two map positions on BTA 29 were associated with significant variation of milk (0 cM) and fat yield (14 cM) in family seven. These results suggest the presence of one QTL with pleiotropic effects on multiple traits or multiple QTL within the marker interval. Findings from this study could be used in subsequent fine-mapping work and applied to marker-assisted selection of dairy production and health traits.

Rodriguez-Zas SL ，Southey BR ，Heyen DW ，Lewin HA ... -  《JOURNAL OF DAIRY SCIENCE》

Detection of quantitative trait loci affecting milk production traits on 10 chromosomes in Holstein cattle.

Sons (n = 71 to 75) of each of six Holstein sires were genotyped at 69 microsatellite loci covering a total of 676 cM on chromosomes 3, 5, 9, 10, 13, 15, 17, 20, 23, and 26. Estimates of quantitative trait loci (QTL) effect and location were made using a least squares interval mapping approach based on daughter yield deviations of sons for 305 d milk, fat, and protein yield and fat and protein percentage. Thresholds for statistical significance of QTL effects were determined from interval mapping of 10,000 random permutations of the data across the bull sire families and within each sire family separately. Analyses combining data across sires indicated the presence of QTL affecting milk, fat, and protein yield on chromosomes 20 and 26 and a QTL affecting fat and protein percentage on chromosome 3. Analyses within each sire family separately indicated the presence of segregating QTL in at least one family on 7 of the 10 chromosomes. Statistically significant estimates of QTL effects on breeding value ranged from 438 to 658 kg of milk, from 17.4 to 24.9 kg of fat, 13.0 to 17.0 kg of protein, 0.04 to 0.17% fat, and 0.07 to 0.10% protein.

Plante Y ，Gibson JP ，Nadesalingam J ，Mehrabani-Yeganeh H ，Lefebvre S ，Vandervoort G ，Jansen GB ... -  《JOURNAL OF DAIRY SCIENCE》

Detection of quantitative trait loci affecting milk production traits on bovine chromosome 6 in a Chinese Holstein population by the daughter design.

Fourteen microsatellite markers with a coverage of 63.5 cM on bovine chromosome 6 were selected, and 26 sire families with 2,260 daughters were analyzed for mapping quantitative trait loci (QTL) affecting 5 milk production traits in a Chinese Holstein population. In the analyses across 26 families and within the largest significant families with a one-QTL model fitted, a QTL near BMS470 was detected that affected fat yield at the 5% experiment-wide significance level. When a 2-QTL model was fitted in the across-family analysis, it was found that there might exist 2 QTL affecting the 3 yield traits, although the exact or empirical thresholds for the significance testing were unknown. In all analyses, the results for milk yield and protein yield were generally consistent, which might have resulted from the same genetic background for milk and protein yield.

Chen HY ，Zhang Q ，Yin CC ，Wang CK ，Gong WJ ，Mei G ... -  《-》

Fine mapping and association analysis of a quantitative trait locus for milk production traits on Bos taurus autosome 4.

To fine map a quantitative trait locus (QTL) affecting milk production traits previously associated with microsatellite RM188, we implemented an interval mapping analysis by using microsatellite markers in a large Israeli Holstein half-sib sire family, and linkage disequilibrium (LD) mapping in a large set of US Holstein bulls. Interval mapping located the target QTL to the near vicinity of RM188. For the LD mapping, we identified 42 single nucleotide polymorphisms (SNP) in 15 genes in a 12-Mb region on bovine chromosome 4. A total of 24 tag SNP were genotyped in 882 bulls belonging to the University of California Davis archival collection of Holstein bull DNA samples with predicted transmitted ability phenotypes. Marker-to-marker LD analysis revealed 2 LD blocks, with intrablock r(2) values of 0.10 and 0.46, respectively; outside the blocks, r(2) values ranged from 0.002 to 0.23. A standard additive/dominance model using the generalized linear model procedure of SAS and the regression module of HelixTree software were used to test marker-trait associations. Single nucleotide polymorphism 9 on ARL4A, SNP10 on XR_027435.1, SNP12 on ETV1, SNP21 on SNX13, and SNP24 were significantly associated with milk production traits. We propose the interval encompassing ARL4A and SNX13 genes as a candidate region in bovine chromosome 4 for a concordant QTL related to milk protein traits in dairy cattle. Functional studies are needed to confirm this result.

Rincón G ，Islas-Trejo A ，Casellas J ，Ronin Y ，Soller M ，Lipkin E ，Medrano JF ... -  《-》