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Likelihood ratio test statistic (LRT) profiles for growth and carcass quality traits on BTA6 (BFT = Backfat thickness; ADG = Average daily gain; CWT = Carcass weight; LMA = Longissimus dorsi muscle area; Marb = Marbling score; WT = Final weight). The upper and italicized lower numerical values under the marker names indicate relative positions in this study and in USDA-MARC bovine genome map (www.animalgenome.org), respectively.
Source publication
The purpose of this study was to detect quantitative trait loci (QTL) for growth and carcass quality traits on BTA6 in a population of Hanwoo cattle. Three hundred and sixty one steers were produced from 39 sires that were sired by 17 grandsires in the two Hanwoo farming branches of the National Livestock Research Institute of Korea, between Spring...
Contexts in source publication
Context 1
... BTA6 sex-average linkage map comprising seven markers spanned 175.3 K cM, whose length was larger than the distances in USDA MARC bovine genome map (http://www.animalgenome.org). However, marker orders were the same, and the relative distances between the markers ranging from 0 cM to 81 cM were not much different from the UDSA-MARC map, in which all of the QTL were detected in this study, i.e. for BFT, WT and ADG (Figure 1). The distal region of BTA6, however, was much larger compared to the MARC linkage map. ...
Context 2
... QTL were detected on BTA6 at the 5% chromosome-wise level for BFT, ADG, and WT. The most likely positions for the QTL were in the proximal regions; 0 cM, 35 cM, and 63 cM, and their relative positions were close to the markers, IL90, BMS518, and BM4621, respectively (Table 2 and Figure 1). The proportions of phenotypic variance due to QTL allelic variance for the three QTL were 30%, 15%, and 11%, respectively. ...
Context 3
... QTL for LMA was detected with limited statistical support (p = 0.086 at chromosome-wise level), at 67 cM, close to BM4621, where the QTL for WT was detected. Also, the most likely position (63 cM) of the QTL for CWT was the same as the QTL for WT (Table 2 and Figure 1). ...
Context 4
... et al. (2008) showed that the '12273_165' SNP was associated with WT, CWT, LMA, ADG at the 5% comparison-wise level, using the same population as this study. In similar or close to the SNP region, we also detected QTL for WT and ADG at the 5% chromosome-wise level, and LMA at the 10% chromosome-wise level (Table 2 and Figure 1). These results suggest that there is some evidence that alleles of causal genes responsible for growth and carcass traits are segregating in the Hanwoo population. ...
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Citations
... Hanwoo, Angus or composite breeds [13,14,18,19]; Hapmap-51248-BTA-51337 on BTA1; BFGL-NGS-119673, ARS-BFGL-NGS-8401, and BTB-00236217 on BTA5; BTB-00236217 and BTB-01744782 on BTA6; Hapmap34906-BES11_Con-tig369_1053 on BTA11; BTB-01493007 on BTA13; BTB-00566332 on BTA14;BTB-00634483 and Hapmap42533-BTA38667 on BTA16; ARS-BFGL-NGS-39535 on BTA29 (Table 7). Longissimus dorsi muscle area (LMA): A total of 18 SNPs were detected, of which seven SNPs at 5% GW level. ...
... 18 www.ajas.info Li et al (2017) Asian-Australas J Anim Sci 30: [8][9][10][11][12][13][14][15][16][17][18][19] identified (Table 10). The QTL for WWT and YWT were located at 42.74 to 42.87 Mb, near which a gene, GHR (33.90 to 34.07 Mb) was located. ...
... Hanwoo, Angus or composite breeds [13,14,18,19]; Hapmap-51248-BTA-51337 on BTA1; BFGL-NGS-119673, ARS-BFGL-NGS-8401, and BTB-00236217 on BTA5; BTB-00236217 and BTB-01744782 on BTA6; Hapmap34906-BES11_Con-tig369_1053 on BTA11; BTB-01493007 on BTA13; BTB-00566332 on BTA14;BTB-00634483 and Hapmap42533-BTA38667 on BTA16; ARS-BFGL-NGS-39535 on BTA29 (Table 7). Longissimus dorsi muscle area (LMA): A total of 18 SNPs were detected, of which seven SNPs at 5% GW level. ...
... 18 www.ajas.info Li et al (2017) Asian-Australas J Anim Sci 30: [8][9][10][11][12][13][14][15][16][17][18][19] identified (Table 10). The QTL for WWT and YWT were located at 42.74 to 42.87 Mb, near which a gene, GHR (33.90 to 34.07 Mb) was located. ...
Objective
A whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs) with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo.
Methods
The data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant.
Results
A total of 18 (0), 15 (3), 12 (8), 15 (18), 11 (7), and 21 (1) SNPs were detected at the 5% chromosome (genome) - wise level for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA) and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL) regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29) were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA).
Conclusion
The application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.
... Korean consumers prefer a beef of the Korean native cattle, Hanwoo, because the breed has good genetic characteristics in meat palatability and chewiness (Cho and Ko, 1998). In a previous study, we reported three QTL affecting backfat thickness, average daily gain, and final weight on BTA6 in a Hanwoo population by applying a linkage mapping method (Lee et al., 2010b). Also, Lee et al. (2008;2010c) reported that the genotypes of the 12273_165 SNP within the CCDC158 gene are significantly associated with carcass cold weight. ...
... Another reason of the inconsistency of QTL detection between the models may be small magnitude of QTL effects. Previously, we scanned BTA6 to find QTL for the carcass quality traits using an interval mapping approach in a Hanwoo population, but only one QTL was detected for BFT at the 5% chromosome-wise level (Lee et al., 2010b). Therefore, our results suggest that the application of multiple LD mapping approaches is beneficial in QTL detection, when QTL effect is of no great magnitude in an experiment with a small sample size. ...
... However, there was no report on candidate genes that were located on BTA6 (Cheong et al., 2007;Shin et al., 2007;Cho et al., 2008). Previously, we scanned BTA6 using an interval mapping method in Hanwoo paternal halfsib families (Lee et al., 2010b). Lee et al. (2010b) reported that one QTL for BFT were detected at the 5% chromosomewise level at 0 cM, which was close to the marker, IL90 (0 cM). ...
The purpose of this study was to detect QTL for carcass quality on bovine chromosome (BTA) 6 using a high density SNP map in a Hanwoo population. The data set comprised 45 sires and their 427 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers that were used for progeny testing in the Hanwoo Improvement Center in Seosan, Korea, were genotyped with the 2,535SNPs on BTA6 that were embedded in the Illumina bovine SNP 50K chip. Four different linkage disequilibrium (LD) mapping models were applied to detect significant SNPs for carcass quality traits; the fixed model with a single marker, the random model with a single marker, the random model with haplotype effects using two adjacent markers, and the random model at hidden state. A total of twelve QTL were detected, for which four, one, three and four SNPs were detected on BTA6 under the respective models (p
In whole genome association study, genomic selection, Determining of extent and
level of linkage disequilibrium (LD) is important in sample size and marker density. In this experiment, the blood and sperm samples were collected form 1089 Holstein bulls and 2030 markers on chromosome 6 were genotyped by using Illumina Bovine SNP50K BeadChip based on UMD3.1 genome assembly. Data were corrected for missing genotyped SNP and individual with unknown genotype by Plink. After correction 1606 markers remained (79%). The average observed heterozygosity was 0.37 and 80% of the markers had minor all frequency more than 0.2. The LD was calculated with rP2P and Dˊ by Haploview v4.2. The extent of LD in this study was 40 kb with rP2P=0.3. The rP2P value was decreasing to 0.2 (moderate level) in 80kb and 0.1 (background level) in 300 kb. The effective population size has been decreased to 100 individual in 10 generations ago. The 49 haplotype blocks with
range 18-472 kb were detected that covering the 10.6 Mb of whole chromosome. These results showed that between 4000-70000 markers or one marker per 40-75 kb will be need for whole genome association study in this Holstein population.
The purpose of this study was to improve mapping power and resolution for the QTL influencing carcass quality in Hanwoo, which was previously detected on the bovine chromosome (BTA) 6. A sample of 427 steers were chosen, which were the progeny from 45 Korean proven sires in the Hanwoo Improvement Center, Seosan, Korea. The samples were genotyped with the set of 2,535 SNPs on BTA6 that were imbedded in the Illumina bovine 50 k chip. A linkage disequilibrium variance component mapping (LDVCM) method, which exploited both linkage between sires and their steers and population-wide linkage disequilibrium, was applied to detect QTL for four carcass quality traits. Fifteen QTL were detected at 0.1% comparison-wise level, for which five, three, five, and two QTL were associated with carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA), and marbling score (Marb), respectively. The number of QTL was greater compared with our previous results, in which twelve QTL for carcass quality were detected on the BTA6 in the same population by applying other linkage disequilibrium mapping approaches. One QTL for LMA was detected on the distal region (110,285,672 to 110,633,096 bp) with the most significant evidence for linkage (p<10(-5)). Another QTL that was detected on the proximal region (33,596,515 to 33,897,434 bp) was pleiotrophic, i.e. influencing CWT, BFT, and LMA. Our results suggest that the LDVCM is a good alternative method for QTL fine-mapping in detection and characterization of QTL.
