Single Nucleotide Polymorphisms associated with growth and carcass traits located on QTL Regions previously associated with Bovine Respiratory Disease
Received: October 14, 2017
Accepted: November 08, 2017
Published: December 01, 2017
Genet.Mol.Res. 16(4): gmr16039843
The objective of the current study was to evaluate single nucleotide polymorphisms (SNP) for potential growth and carcass trait associations located in two previously described quantitative trait loci (QTL) regions associated with bovine respiratory disease. A population of 323 crossbred steers sired by five purebred sire breeds between 2010-2013 (Angus, Braford, Braunvieh, Charolais, and Simmental) were evaluated from birth until harvest. Eighty-two SNP were evaluated in the current study for potential significant associations with growth and carcass traits (58 on BTA6 and 24 on BTA20). A total of nine unique SNP (rs41595713, rs42403565, rs42571566, rs42900130, rs41931108, rs42480445, rs43451134, rs42524450, rs41626155) were significantly associated (P < 0.05) with specific growth traits such as birth weight, weaning weight and hip height. Six of these significant SNP were located on BTA6 and three were located on BTA20. When evaluating the carcass traits hot carcass weight (HCW), yield grade (YG), marbling score (MARB), and rib eye area (REA) a total of nine unique SNP (rs42900130, rs42961882, rs43446022, rs41931108, rs41595713, rs41653357, rs43036576, rs42823614, rs42512588) were significantly associated (P < 0.05) with carcass traits. For both of these regions, animals inheriting differing genotypes from the previously described SNP, had significantly different levels of performance for specific growth and carcass traits. Although multiple SNP were identified as significant with growth and carcass traits, these SNP identified herein must be validated in a larger more diverse population prior to implementation into marker assisted selection programs
The bovine genome has been extensively evaluated for regions that may contain genes and variants that contribute to the performance of economically important traits in beef cattle. Specifically, BTA6 and BTA20 have been hotspots for QTL associated with growth, performance, carcass quality and composition and bovine respiratory disease (BRD) (http://bovinegenome.org/bovineqtl_v2/findQTL.html). Previous studies evaluating disease susceptibility have identified QTL regions associated with BRD susceptibility and growth traits located on BTA6 and BTA20 (Li et al., 2004; Casas et al., 2010; Snelling et al., 2010). However, it has also been reported that BTA6 and BTA20 have been shown to harbor the majority of the significant single nucleotide polymorphisms (SNP) associated with growth (Snelling et al., 2010) as well as many carcass traits (Casas et al., 2003; Saatchi et al., 2014).
Previous work has also demonstrated the negative correlative effects that BRD can have on carcass traits such as hot carcass weight (HCW) and performance traits like average daily gain (Schneider et al., 2009). Additionally, it has been reported that selection for BRD resistance may have little effect on HCW, longissimus muscle area (LMA), and fat due to the low genetic correlation estimates. However, results indicated favorable genetic correlations existed for birth weight (BW) and marbling score (MS) with both affected and unaffected animals (Schneider et al., 2010). An additional study reported that steers with clinical signs of BRD had less internal fat, and lower MS compared to the steers with no clinical sign of BRD at time of slaughter (Gardner et at., 1999). Thus, the objective of the current study was to evaluate SNP located on previously described QTL regions of BTA6 and BTA20 that overlap with BRD for potential associations with growth and, carcass traits in a population of crossbred steers sent to the feedlot and harvested at a commercial packing facility.
Material and Methods
All animals were treated and maintained in accordance with the principles and guidelines outlined in the Guide for the Care and Use of Agricultural Animals in Research and Teaching. The animals utilized in the current study were comprised of 323 crossbred steers born at the Louisiana State University Ag Center Central Research Station in Baton Rouge, LA and LSU Ag Center Hill Farm in Homer, LA from 2010 to 2013. Calves were born during the spring calving season and were managed until weaning, or approximately six to seven months of age. Calves were sired by Charolais, Braunvieh, Simmental, Angus or Braford bulls. The dam breeds at the LSU Ag Center utilized for this study have been previously described during the characterization of the Germplasm Evaluation VIII studies (Wheeler et al., 2011). The dams utilized by the LSU Ag Center Hill Farm in Homer, LA were comprised of various breed backgrounds (Table 1).
|Sire Breed||Total Number of Animals|
Table 1: Total number of animals for each sire breed.
Steers that met shipping criteria were vaccinated and shipped to commercial feedlots in Texas and Oklahoma. When the finishing process was completed, animals were sent to a commercial packing plant where carcass quality and composition traits were recorded. These trait measurements included hot carcass weight (HCW), marbling score (MS), rib eye area (REA), back fat thickness (BF) and yield grade (YG).
DNA Extraction and Genotyping
Ear notches were collected from all calves at birth for future DNA extraction. Extraction of DNA was conducted using a saturated salt procedure previously described by Miller et al. (1998). DNA stock solutions were diluted to 25 ng/μl concentrations for future genotyping reactions. Fifty-eight SNP were selected from a previously described QTL region with SNP associated with incidence of BRD spanning between 40-80 Mbp on BTA6 (Li et al., 2004) (Miller et al., 2016). Twenty-four SNP were selected from a previously described QTL region with SNP associated with incidence of BRD spanning 0-30 Mbp on BTA20 (Casas et al., 2011; Miller et al., 2016). Single nucleotide polymorphisms were selected using the QTL database (http://www.animalgenome.org/cgi-bin/QTLdb/index). Single nucleotide polymorphisms, allele substitutions, and upstream and downstream genomic sequences are reported in Tables 2 and 3. Single nucleotide polymorphism genotyping was performed by Neogen, Inc. (Lincoln, Nebraska) via the Sequonom platform.
|SNP ID||Allele Substitution||Forward Sequence||Reverse Sequence|
Table 2: Single nucleotide polymorphisms ID, allele substitutions, and upstream and downstream genomic sequences utilized for amplification and visualization of genotypes for BTA20.
|SNP ID||Allele Substitution||Forward Sequence||Reverse Sequence|
Table 3: Single nucleotide polymorphisms ID, allele substitutions, and upstream and downstream genomic sequences utilized for amplification and visualization of genotypes for BTA6.
The Mixed Model procedure of SAS (version 9.4, SAS Institute, Cary, NC) was utilized to evaluate potential SNP associations located on BTA 6 and BTA 20 with growth traits, carcass composition and quality traits. Only the SNPs with more than one genotype were included in the analysis. The LSMEANS function, along with the pre-planned pairwise comparisons procedure, was utilized to evaluate if significant differences existed between individuals inheriting differing genotypes for SNP identified as significant for specific traits. Dependent variables in the model included birth weight (BW), weaning weight (WW), hip height (HH), HCW, YG, MS, REA, and BF. Independent variables included sire breed, SNP genotype and birth year. Sire breed (year) was fit into the model as a random nested variable to account for confounding effects of sire breeds among the four years. Significance was set at P < 0.05.
Analyses of SNPs revealed significant genotypic effects for growth traits, and carcass traits in both QTL regions. When evaluating growth traits, multiple SNP were significantly associated with BW, WW and HH as shown in Table 4. Specifically, four SNP (rs41595713, rs42403565, rs42571566, rs42900130) located on BTA6 and two on BTA20 (rs41931108, rs42480445) were significantly associated (P <0 .05) with BW (Table 4). Animals inheriting the heterozygous (TC, AG) and minor homozygous (CC, GG) allele genotypes from SNP rs41595713, rs42480445, and rs42900130 had significantly (P < 0.05) heavier BW than those inheriting the major homozygous allele genotype (Table 5). Animals inheriting the heterozygous (CG, CT, GA) allele genotype from SNP rs41931108, rs42403565 and rs42571566 had significantly heavier BW than those inheriting the major or minor homozygous allele genotypes (Table 5). Breed was also a significant (P < 0.0001) contributing factor for BW effects with regards to SNP rs42571566 (Table 4).
Note: 1BW=Birth weight; 2WW=Weaning weight; 3HH=Hip Height4Representation of the major allele is located on the left.
Table 4: Level of significance and frequency of animals from each genotype associated with birth weight, weaning weight and hip height.
Note: a,b Differing superscripts indicate a difference of means at P < 0.05 within rows; 1BW=Birth weight; 2WW=Weaning weight; 3HH=Hip Height; 4Representation of the major allele is located on the left.
Table 5: Single nucleotide polymorphisms associated with growth traits and least square means estimate comparisons between reported genotypes for birth weight, weaning weight and hip height.
When evaluating WW, two SNP located on BTA20 (rs41931108, rs42524450) and one SNP located on BTA6 (rs43451134) were identified as significant (P < 0.05) (Table 4). Animals inheriting the minor homozygous (GG) and major homozygous (CC) allele genotypes from SNP rs41931108 had significantly (P < 0.05) heavier WW than those inheriting the heterozygous allele genotype for this marker (Table 5). Animals inheriting the heterozygous (CT) and minor homozygous (TT) allele genotypes from SNP rs42524450 had significantly (P < 0.05) heavier WW than animals inheriting the major homozygous allele genotype (Table 4). Animals inheriting the major homozygous (TT) allele genotype from SNP rs43451134 had significantly (P < 0.05) heavier WW than animals inheriting the heterozygous and minor homozygous allele genotypes (Table 5). A single SNP marker on BTA6 was identified as being significantly (P < 0.05) associated with HH (Table 4). Animals inheriting the minor (TT) and major (CC) homozygous allele genotypes from SNP rs41626155 had higher (P < 0.05) HH than those inheriting the heterozygous allele genotype (Table 5).
When evaluating carcass traits, multiple SNP were significantly associated with HCW, YG, MS and REA as shown in Table 6. A total of four SNP, three located on BTA6 (rs42900130, rs42961882 and rs43446022) and one located on BTA 20 (rs41931108), were significantly associated with HCW (Table 4.5). Animals inheriting the major homozygous (AA, TT, GG) allele genotype from SNP rs42900130 rs42961882 and rs43446022 had significantly (P < 0.05) heavier HCW than those inheriting the heterozygous and minor homozygous allele genotypes (Table 7) Animals inheriting the minor homozygous (GG) allele genotype from rs41931108 had significantly (P < 0.05) heavier HCW than those inheriting the heterozygous and major homozygous allele genotypes (Table 7). A single SNP located on BTA20 was significantly (P < 0.05) associated with YG (Table 4.5). Animals inheriting the heterozygous (TC) and minor homozygous (CC) allele genotypes from SNP rs41595713 had a significantly (P < 0.05) higher YG than animals inheriting the major homozygous allele genotype (Table 7).
Note: 1HCW=Hot carcass weight; 2YG=Yield grade; 3MARB=Marbling score; 4REA=Rib eye area; 5Representation of the major allele is located on the left.
Table 6: Level of significance and frequency of animals from each genotype associated with hot carcass weight, yield grade, marbling score and rib eye area.
Note: a, b Differing superscripts indicate a difference of means at P < 0.05 within rows; 1HCW=Hot carcass weight; 2YG=Yield grade; 3MARB=Marbling score; 4REA=Rib eye area; 5Representation of the major allele is located on the left.
Table 7: Single nucleotide polymorphisms associated with carcass traits and least square means estimate comparisons between reported genotypes for hot carcass weight, yield grade, marbling score and rib eye area.
A single unique SNP located on BTA6 (rs41653357) and another unique SNP located on BTA 20 (rs43036576) were significantly (P < 0.05) associated with MS (Table 6). Animals inheriting the heterozygous (AC) and major homozygous (AA) allele genotypes from SNP rs41653357 had significantly (P < 0.05) greater MS than animals inheriting the minor homozygous allele genotype (Table 7). Animals inheriting the major homozygous (AA) allele genotype from SNP rs43036576 had significantly (P < 0.05) greater MS than animals inheriting the heterozygous and minor allele genotypes (Table 7). A single SNP marker located on both BTA6 (rs42823614) and BTA20 (rs42512588) was significantly (P < 0.05) associated with REA (Table 6). Animals inheriting the major homozygous (CC, AA) allele genotype from SNP rs42512588 and rs42823614 had significantly (P < 0.05) larger REA than those inheriting the heterozygous and minor homozygous allele genotypes (Table 7). Breed effects were also a significant (P < 0.0001) contributing factor for REA when evaluating rs42512588 and rs42823614 (Table 6).
A total of ten unique SNP located on BTA6 were significantly (P < 0.05) associated with growth, and carcass traits. Six out of the ten unique SNP were significantly associated with growth traits including BW, WW and HH. These results are in agreement with reports that identified significant SNP for BW and WW on BTA6 (Lu et al., 2013). Previous reports also identified SNP located on BTA6 significantly associated with HH which agrees with the study herein (Bolormaa et al., 2014).
Four SNP located on BTA6 were identified as being significantly associated with carcass traits including HCW, MS and REA. These results were in agreement with reports that identified significant SNP for HCW on BTA6 and a second report that identified significant SNP associated with REA located on BTA6 (Lu et al., 2013; Casas et al., 2000). Previous reports also identified significant SNP for MS located on BTA 6 (Lee et al., 2012), which is in agreement with the results presented in the present study. The current study identified no significantly associated SNP for YG located on BTA6. Furthermore, it was previously reported that significant markers associated with BF were identified on BTA 6 (Li et al., 2004), however, the current study did not identify any significant SNP associated with BF on BTA6.
Of the ten unique SNP identified on BTA6, two were significantly associated with more than one trait in the current study. Marker rs42900130 was significantly (P < 0.05) associated with BW and HCW. Furthermore, marker rs42823614 was significantly (P < 0.05) associated with REA and was also identified as an SNP significantly associated with incidence of BRD in previous studies (Miller et al., 2016).A total of six unique SNP located on BTA20 were significantly (P < 0.05) associated with growth traits, carcass traits and incidence of BRD. Three of the eleven unique SNP were significantly associated with growth traits including BW and WW. These results are in agreement with previous reports that identified significant QTL regions associated with BW and WW on BTA20 (Saatchi et al., 2014). However, the current study failed to validate previous reports that identified SNP on BTA 20 significantly associated with HH (Bolormaa et al., 2014).
Three SNP identified in the current study located on BTA20 were significantly associated with carcass traits including HCW, YG, MS and REA. These results are in agreement with reports that identified significant QTL regions on BTA20 associated with HCW (McClure et al., 2010). The study herein is also in agreement with reports that identified significant SNP for YG, MS and REA located on BTA20 (Saatchi et al., 2014; Garcia et al., 2010). The current study was not in agreement with reports that previously identified SNP on BTA20 that were significant for BF (Garrett et al., 2008).
Of the six unique SNP identified on BTA20, three were significantly associated with more than one trait. Marker rs41595713 was significantly (P < 0.05) associated with BW and YG. Marker rs41931108 was significantly (P < 0.05) associated with BW, WW and HCW. Furthermore, marker rs42512588 was significantly (P < 0.05) associated with REA in the current study, which was also one of the markers identified as significantly associated with incidence of BRD in a previous study (Miller et al., 2016).
Although, several SNP markers located on BTA6 and BTA20 were identified as significantly associated with a variety of economically important traits, two SNP were significantly associated with both REA and BRD incidence on BTA6 and 20 (Miller et al., 2016). These preliminary results verified the initial hypothesis that SNP cold be significant for a variety of traits in a single QTL region and that single SNP could have potential effects on multiple traits. Furthermore, results from the current study would indicate that these two QTL regions located on BTA6 and 20 warrant further investigation to identify SNP significantly associated with multiple economically important traits in beef cattle. Although multiple SNP were identified in the current study, additional experimentation utilizing larger populations of crossbred steers validating markers reported herein and many more markers needs to be conducted prior to implementation into marker assisted selection programs. Additionally, SNP location and function need to be evaluated to determine if the SNP is located on a functional portion of a gene or is being inherited due to genetic linkage because of close genomic proximity to a causative SNP.
The study was approved and funded by the Louisiana Agricultural Experiment Station and the Utah State Agricultural Experiment Station through the use of State and Federal Hatch funds.
About the Authors
Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan UT, USA
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