Research articles
 

By Dr. Matthew D Garcia , Ms. Rebecca Hill , Dr. Glen Gentry , Dr. Kenneth Bondioli , Ms. Jennifer Bailey , Mr. Michael Canal
Corresponding Author Dr. Matthew D Garcia
Louisiana State University/School of Animal Sciences, 105 jb francioni - United States of America 70803
Submitting Author Dr. Matthew D Garcia
Other Authors Ms. Rebecca Hill
Louisiana State University/School of Animal Sciences, - United States of America

Dr. Glen Gentry
Louisiana State University, - United States of America

Dr. Kenneth Bondioli
Louisiana State University/School of Animal Sciences, - United States of America

Ms. Jennifer Bailey
Louisiana State University/School of Animal Sciences, - United States of America

Mr. Michael Canal
Louisiana State University/School of Animal Sciences, - United States of America

GENETICS

SNP, Candidate Gene, Growth, Carcass

Garcia MD, Hill R, Gentry G, Bondioli K, Bailey J, Canal M. Evaluation of Candidate Genes and Subsequent Effects Growth and Carcass Traits in Multi-Generational Sired and Modern Sired Angus Females. WebmedCentral GENETICS 2014;5(6):WMC004655
doi: 10.9754/journal.wmc.2014.004655

This is an open-access article distributed under the terms of the Creative Commons Attribution License(CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Submitted on: 25 Jun 2014 06:19:14 PM GMT
Published on: 26 Jun 2014 07:09:19 AM GMT

Abstract


The objective of the current study was to evaluate phenotypic differences and SNP located on three candidate genes for possible associations with growth and carcass traits in a population of Angus cows sired by modern phenotype Angus bulls and multi-generational Angus bulls born from 1960-2006. Quantitative analyses revealed that modern sired Angus cows had significantly larger (P< 0.05) weaning weights, levels of intramuscular fat, levels of back fat, but were not significantly different when comparing rib eye area. The only trait that the multi-generational Angus sired cows were significantly larger (P < 0.05) than the modern sired Angus was in birth weight, which is not optimal due to its strong correlation with dystocia during the parturition process. When evaluating SNP located on the DGAT1, LEPR and CAST gene were also evaluated in the same population for possible SNP associations with growth and carcass traits. While significant SNP were identified on both the DGAT1 and LEPR genes no SNP located on the CAST gene were significantly associated with any traits in the current study. Specifically, when evaluating growth traits three SNP  (rs134375381, rs135263435, rs43348659) located on the LEPR and three SNP (rs136875432, rs132699547, rs135423283)  located on the DGAT1 gene were significantly associated ( P < 0.05) or exhibited a statistical trend ( P < 0.1) with birth weight and weaning weight respectively. When evaluating carcass traits, a statistical trend( P < 0.1) was observed for the trait of back fat thickness for two SNP (rs134375381,rs135263435) located on the LEPR gene. Furthermore, the two SNP associated with back fat thickness were also associated with birth weight, thus revealing that SNP have the potential to be associated with multiple traits. Results of the current study revealed that modern germplasm is more beneficial to be utilized in current production schemes and that multiple SNP from multiple candidate genes can be associated with both growth and carcass traits. However, prior to utilizing the identified SNP in the current study in selection strategies, the effect of SNP must be verified in other populations, other environments and subsequently many more SNP on numerous candidate genes identified prior to implementation into marker assisted selection strategies.

Introduction


Dramatic improvement in the Angus breed for carcass quality and composition traits has been observed over many years (Northcutt et al., 1993). The mature weight for Angus cows ranging from five to 12 years in age increased from 519kg in 1963 (Northcutt et al., 1993) to 630kg in 2011 (McHugh et al., 2011).Parnell and associates (1997) observed that yearling weights for Angus females comprised of lines selected for high and low yearling growth rates were 2.11 kg and -2.54 kg, respectively. During this time, it was noted that high line females achieved puberty at an earlier age and had significantly longer gestation periods than low line females (Archer et al., 1998).

Three known candidate genes leptin receptor LEPR, calpastatin CAST, and DGAT1 were selected based on their previously recorded associations with growth and carcass traits in Angus cattle (McClure et al., 2010; Pintos et al., 2011). The objective of the current study was to evaluate SNP located on three candidate genes for possible associations with growth and carcass traits.

Materials and Methods


Experimental Animals

Twenty-five purebred Angus females sired by modern phenotype bulls and twenty-two multi-generation sired purebred Angus heifers produced from modern purebred Angus cows were utilized in this study. Multi-generational calves were produced via artificial insemination on modern Angus females utilizing frozen-thawed semen from thirteen sires born from 1960 through 2006. The Select Synch protocol (Geary et al., 2000) was utilized prior to artificial insemination with aged frozen/thawed semen to synchronize modern Angus females. Females that did not respond to the Select Synch protocol were given an injection of prostaglandin (PGF2a) (Pfizer Animal Health, New York, NY) and artificial insemination was repeated during the next observed estrus.

Specifically, females evaluated in the current study were comprised of twenty-two multigenerational Angus females born in 2010, eleven modern sired Angus females born in 2008, eight modern sired Angus females born in 2009, and six modern sired Angus females born in 2011. Modern Angus females were produced via artificial insemination or a single pasture bull clean-up system. All Angus females were born and managed at Louisiana State University Agriculture Center Central Research Station located in Baton Rouge, Louisiana. All females were maintained on natural pastures and developed until puberty on adapted Ryegrass pastures until first breeding.Individual animal weights were collected at birth and weaning.

Blood Collection and DNA Extraction


Blood samples were collected from all Angus females via jugular venipuncture. Blood was transferred into 20mL tubes and centrifuged at 4000rpm at 4°C for 20 minutes. White blood cell buffy coats were extracted and transferred to 250mL micro-centrifuge tubes. Genomic DNA was isolated and purified from buffy coats using a previously described saturated salt procedure (Miller et al., 1988).

SNP Selection and Genotyping

Previously reported single nucleotide polymorphisms (SNPs) on candidate genes LEPR, CAST, and DGAT1 were collected from the dbSNP website (http://www.ncbi.nlm.nih.gov/projects/SNP/). Single nucleotide polymorphisms were selected by identifying SNP that were evenly distributed over the entire length of each candidate gene. The justification for this selection method was to account for possible linkage associations with potential causative mutations located on the candidate genes. Selected SNP, forward and reverse primers and allele substitutions for LEPR, CAST, and DGAT1 are reported in Table 1.1, Table 1.2, and Table 1.3. Single nucleotide polymorphism genotyping was conducted by NeoGen (Lincoln, Nebraska) utilizing Sequenom genotyping technology (Illumina Inc., San Diego, California).

Ultrasound Measurements

Carcass quality and composition measurements were measured via ultrasound technology by a certified technician. Carcass traits were measured with a 3.5MHz linear probe utilizing Designer Genes BioProbe 1049 software (Harrison, AR) setting 90N-25F2.1. Measurements included fat thickness at the 12th and 13th rib, ribeye area, and intramuscular fat percentage.

Statistical Analysis

The LSMEANS function of SAS was utilized to evaluate potential differences in performance among modern sired Angus females versus multi-generational sired Angus females. The traits that were evaluated included birth weight, weaning weight, intramuscular fat, ribeye area, and back fat thickness. The Mixed Model procedure of SAS version 9.3 (SAS Institute Inc., Cary, North Carolina) was utilized for statistical analysis. The model included fixed effects for sire, dam generation group, and individual candidate gene SNP. Sire within generation group was also fitted as a random nested variable to account for potential confounding affects observed in the data. Random variables fit in the model included variables of birth weight, weaning weight, back fat thickness, ribeye area, and intramuscular fat and were fit in the model to test for potential associations between SNP and the previously described traits. All statistical analyses were conducted using similar methodologies reported in previous studies (White et al., 2005). Single nucleotide polymorphisms with more than one genotype represented were included in the analysis. Any SNP with only one genotype were excluded from the analysis due to a lack of marker effects. Due to a limited sample population statistical significance was evaluated at (P < 0.05) and statistical trend was evaluated at (P < 0.10).

Results


Evaluation of weaning weights revealed that modern sired Angus females had significantly higher(P < 0.05)  weaning weights than multi-generation sired Angus females (Figure 1.2). Mean intramuscular fat and back fat thickness were significantly higher (P < 0.05) for modern sired Angus females when compared with multi-generation sired Angus females (Figure 1.3; Figure 1.5). However, when evaluating ribeye area no significant difference was detected between modern sired Angus females and multi-generation sired Angus females (Figure 1.4). The single trait that the multigenerational sired Angus female excelled in over modern sired females was birth weight with multi-generational females having a significantly (P < 0.05) larger birth weight than modern sired females. However, this increase in birth weight is not deemed beneficial in the beef industry as it is highly correlated to dystocia during the parturition process.

Three unique SNP located within LEPR were associated with birth weight (rs135263435, rs43348659, and rs134375381) (Table 3.4). Marker rs135263435 significantly (P = 0.03) influenced birth weight performance. Animals inheriting the homozygous genotype GG for marker rs135263435 had birth weights that were higher than birth weights of animals that inherited the heterozygous genotype GA (Table 1.5). A trend (P = 0.07) was observed for marker rs43348659 influencing birth weight performance. Animals inheriting the homozygous genotype AA for marker rs43348659 had birth weights that were higher than birth weights of animals that inherited the heterozygous genotype AC (Table 1.5). A trend (P = 0.07) was observed for marker rs134375381 influencing birth weight performance. Animals inheriting the homozygous genotype GG for marker rs134375381 had birth weights that were higher than birth weights of animals that inherited the heterozygous genotype GT (Table 1.5).

Three unique SNP located within DGAT1 were associated with weaning weight (rs136875432, rs135423283, and rs132699547) (Table 1.4). A trend (P = 0.10) was observed for marker rs136875432 influencing weaning weight performance. Animals inheriting the homozygous genotype GG for marker rs136875432 had weaning weights that were higher than weaning weights of animals that inherited the heterozygous genotype GA (Table 1.5). A trend (P = 0.10) was observed for marker rs135423283 influencing weaning weight performance. Animals inheriting the homozygous genotype TT for marker rs135423283 had weaning weights that were higher than weaning weights of animals that inherited the heterozygous genotype GT (Table 1.5). A trend (P=0.10) was observed for marker rs132699547 influencing weaning weight performance. Animals inheriting the homozygous genotype GG for marker rs132699547 had weaning weights that were higher than weaning weights of animals that inherited the heterozygous genotype CG (Table 1.5). No SNP located on CAST were significantly associated with birth weight or weaning weight. Two unique SNP located within LEPR were associated with back fat thickness (rs134375381 and rs135263435) (Table 1.6). A trend (P = 0.10) was observed for marker rs134375381 influencing back fat thickness. Animals inheriting the heterozygous genotype GT for marker rs134375381 had back fat thicknesses that were larger than back fat thicknesses of animals that inherited the homozygous genotype GG (Table 1.7).A trend (P = 0.10) was observed for marker rs135263435 influencing back fat thickness. Animals inheriting the heterozygous genotype GA for marker rs135263435 had back fat thicknesses that were larger than back fat thickness of animals that inherited the homozygous genotype GG (Table 1.7). No selected SNP located on CAST or DGAT1 were significantly associated with back fat thickness. No selected SNP located on LEPR, CAST, or DGAT1 were significantly associated with intramuscular fat or ribeye area in this population.

Discussion


The hypothesis that multi-generational Angus females would have lower levels of performance for growth and production traits was validated in the current study. However, a second hypothesis that multi-generation Angus would have more favorable carcass quality traits was disproven. The multi-generation sired Angus females had less desirable carcass traits when compared to modern sired Angus females for back fat thickness and intramuscular fat. This indicated a selection change for increased growth rate and increased carcass size in the modern sired Angus females. These trends have been reported in many previous studies (Enns et al., 2008; Parnell et al., 1997; McClure et al., 2010) and indicate that genetic selection for production traits have made progress over the generations. Furthermore, the current study validates that modern germplasm from modern animals is more beneficial to utilize for the improvement of modern herds due to the large amount of genetic improvement that has been made over the founding beef breed populations.

The current study identified three markers (rs136875432, rs135423283, and rs132699547) associated with weaning weight located on the DGAT1 gene. Effects of DGAT1 markers on weaning weight have previously been reported and are in agreement that DGAT1 is a viable candidate gene for growth and performance traits (McClure et al., 2010). Furthermore, LEPR markers rs135263435 andrs134375381 were observed to be associated with birth weight and back fat thickness, indicating that a single marker could be associated with multiple traits. The effects of LEPR markers on back fat thickness have previously been previously reported and are also in agreement with the current study that LEPR is a viable candidate gene that warrants further evaluation (Buchanan et al., 2002; Schenkel et al., 2005).

The current study identified multiple markers significantly associated with economically important traits in beef cattle. However, prior to utilization further experimentation must be conducted. Validation of SNP identified in the current study must be validated in other populations and other environments. Secondly, a greater number of SNP and a greater number of candidate genes must be evaluated in order to properly identify significant marker associations and identify SNP that account for the largest degree of variability for the trait of interest. Finally, proper utilization of SNP significantly associated with economically important traits is essential. Specifically, multiple trait interaction must be evaluated so that detrimental effects on other performance traits are minimized. Identification of all SNP associated with a trait and those SNPs potential trait interactions and evaluation of markers associated with multiple traits in putative genomic regions is necessary as selection for individual markers or traits can be antagonistic to other important traits.

Identification of all markers associated with birth weight, weaning weight, ribeye area, and back fat thickness on candidate genes or in previously described regions of the genome associated with performance traits would allow increased accuracy of selection for beef producers trying to incorporate increased performance, profit, and sustainability into their herds. The identification of the causative mutations accounting for the largest amount of variability for economically important traits of interest would allow for increased accuracy of selection in addition to focused genotyping of markers essential for selection for these specific traits. The current study has identified three SNP on LEPR associated with birth weight and back fat thickness and three SNP on DGAT1 associated with weaning weight that with validation in other populations could prove a valuable asset to future MAS programs.

Literature Cited


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Source(s) of Funding


State Hatch Funds

Competing Interests


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