Aditi Sharma

Genome-wide association study identifies major loci for carcass weight on BTA14 in Hanwoo (Korean cattle).

This genome-wide association study (GWAS) was conducted to identify major loci that are significantly associated with carcass weight, and their effects, in order to provide increased understanding of the genetic architecture of carcass weight in Hanwoo. This genome-wide association study identified one major chromosome region ranging from 23 Mb to 25 Mb on chromosome 14 as being associated with carcass weight in Hanwoo. Significant Bonferroni-corrected genome-wide associations (P<1.52×10−6) were detected for 6 Single Nucleotide Polymorphic (SNP) loci for carcass weight on chromosome 14. The most significant SNP was BTB-01280026 (P = 4.02×10−11), located in the 25 Mb region on Bos taurus autosome 14 (BTA14). The other 5 significant SNPs were Hapmap27934-BTC-065223 (P = 4.04×10−11) in 25.2 Mb, BTB-01143580 (P = 6.35×10−11) in 24.3 Mb, Hapmap30932-BTC-011225 (P = 5.92×10−10) in 24.8 Mb, Hapmap27112-BTC-063342 (P = 5.18×10−9) in 25.4 Mb, and Hapmap24414-BTC-073009 (P = 7.38×10−8) in 25.4 Mb, all on BTA 14. One SNP (BTB-01143580; P = 6.35×10−11) lies independently from the other 5 SNPs. The 5 SNPs that lie together showed a large Linkage disequilibrium (LD) block (block size of 553 kb) with LD coefficients ranging from 0.53 to 0.89 within the block. The most significant SNPs accounted for 6.73% to 10.55% of additive genetic variance, which is quite a large proportion of the total additive genetic variance. The most significant SNP (BTB-01280026; P = 4.02×10−11) had 16.96 kg of allele substitution effect, and the second most significant SNP (Hapmap27934-BTC-065223; P = 4.04×10−11) had 18.06 kg of effect on carcass weight, which correspond to 44% and 47%, respectively, of the phenotypic standard deviation for carcass weight in Hanwoo cattle. Our results demonstrated that carcass weight was affected by a major Quantitative Trait Locus (QTL) with a large effect and by many SNPs with small effects that are normally distributed.

Hanwoo cattle: origin, domestication, breeding strategies and genomic selection

Hanwoo (Korean cattle) is the native, taurine type of cattle breed of Korea and its history as a draft animal dates back to 5000 Years. In earlier times Hanwoo was used extensively for farming, transportation. Over the period of time, Hanwoo has changed to be meat type cattle. Full-scale production of Hanwoo as meat-type cattle has occurred since 1960s with the rapid growth of the Korean economy. Hanwoo is one of the most economically important species in Korea as it is a significant source of nutrition to the Korean people. Hanwoo beef is the most cherished food of Korea. One of the main goals of researchers is to increase the meat quality, quantity and taste of the beef. In this review we describe the origin, domestication of Hanwoo cattle and breeding program initiated from 1980’s. Moreover the advent of technological advancement had provided us a platform to perform genome wide selection on economic traits and its implementation into traditional breeding programs.

Stories and Challenges of Genome Wide Association Studies in Livestock - A Review.

Undoubtedly livestock is one of the major contributors to the economy of any country. The economic value of livestock includes meat, dairy products, fiber, fertilizer etc. Understanding and identifying the associations of quantitative trait loci (QTL) with the economically important traits is believed to substantially benefit the livestock industry. The past two decades have seen a flurry of interest in mapping the QTL associated with traits of economic importance on the genome. With the availability of single nucleotide polymorphism chip of various densities it is possible to identify regions, QTL and genes on the genome that explain the association and its effect on the phenotype under consideration. Remarkable advancement has been seen in genome wide association studies (GWAS) since its inception till the present day. In this review we describe the progress and challenges of GWAS in various livestock species.

Mutations in calpastatin and μ-calpain are associated with meat tenderness, flavor and juiciness in Hanwoo (Korean cattle): molecular modeling of the effects of substitutions in the calpastatin/μ-calpain complex.

The objective of this study was to evaluate the effects of seven single nucleotide polymorphisms (SNPs) in Calpain 1 and Calpastatin genes previously associated with meat tenderness attributes in other cattle breeds in Korean Hanwoo cattle. The Hanwoo resource population was used to study association of 7 SNPs with beef tenderness, flavor, juiciness, intramuscular fat and shear force. In this association study, CAST:c.182A>G (+0.14, P=0.04) and CAST:c.1985G>C (-0.12, P=0.02) had significant effects on juiciness, but no effects on other traits. In contrast, CAPN1:c.1589G>A was associated with meat tenderness (P=0.01) and juiciness (P=0.04). The CAPN1:c.1589G>A (Val530Ile) SNP marker displayed significant effect on the meat tenderness score which is strongly supported by molecular modeling of the CAPN1:c.1589G>A (Val530Ile) variant that inhibits CAST protein from binding more strongly than the wild-type protein, which may explain its effect on meat tenderness.

Genetic Diversity and Relationships of Korean Chicken Breeds Based on 30 Microsatellite Markers

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (FIT) in native chicken was 0.234±0.025. Over 30.7% of FIT was contributed by within-population deficiency (FIS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds

Genome-wide Association Study for Warner-Bratzler Shear Force and Sensory Traits in Hanwoo (Korean Cattle).

Significant SNPs associated with Warner-Bratzler (WB) shear force and sensory traits were confirmed for Hanwoo beef (Korean cattle). A Bonferroni-corrected genome-wide significant association (p<1.3×10−6) was detected with only one single nucleotide polymorphism (SNP) on chromosome 5 for WB shear force. A slightly higher number of SNPs was significantly (p<0.001) associated with WB shear force than with other sensory traits. Further, 50, 25, 29, and 34 SNPs were significantly associated with WB shear force, tenderness, juiciness, and flavor likeness, respectively. The SNPs between p = 0.001 and p = 0.0001 thresholds explained 3% to 9% of the phenotypic variance, while the most significant SNPs accounted for 7% to 12% of the phenotypic variance. In conclusion, because WB shear force and sensory evaluation were moderately affected by a few loci and minimally affected by other loci, further studies are required by using a large sample size and high marker density.

Validation of genetic polymorphisms on BTA14 associated with carcass trait in a commercial Hanwoo population

The objective of this study was to validate the association of significant SNPs identified from a previous genome-wide association study with carcass weight (CWT) in a commercial Hanwoo population. We genotyped 13 SNPs located on BTA14 in 867 steers from Korea Hanwoo feedlot bulls. Of these 13 SNPs, five SNPs, namely rs29021868, rs110061498, rs109546980, rs42404006 and rs42303720, were found to be significantly associated (P < 0.001) with CWT. These five significant markers spanned the 24.3 to 29.4 Mb region of BTA14. The most significant marker (rs29021868) for CWT in this study had a 13.07 kg allele substitution effect and accounted for 2.4% of the additive genetic variance in the commercial Hanwoo population. The SNP marker rs109546980 was found to be significantly associated with both CWT (P < 0.001) and eye muscle area (P < 0.001) and could potentially be exploited for marker-assisted selection in Hanwoo cattle. We also genotyped the ss319607402 variation, which maps to intron2 of PLAG1 gene and which is already reported to be associated with height, to identify any significant association with carcass weight; however, no such association was observed in this Hanwoo commercial population.

Accuracy of genomic breeding value prediction for intramuscular fat using different genomic relationship matrices in Hanwoo (Korean cattle)

Objective Intramuscular fat is one of the meat quality traits that is considered in the selection strategies for Hanwoo (Korean cattle). Different methods are used to estimate the breeding value of selection candidates. In the present work we focused on accuracy of different genotype relationship matrices as described by forni and pedigree based relationship matrix. Methods The data set included a total of 778 animals that were genotyped for BovineSNP50 BeadChip. Among these 778 animals, 72 animals were sires for 706 reference animals and were used as a validation dataset. Single trait animal model (best linear unbiased prediction and genomic best linear unbiased prediction) was used to estimate the breeding values from genomic and pedigree information. Results The diagonal elements for the pedigree based coefficients were slightly higher for the genomic relationship matrices (GRM) based coefficients while off diagonal elements were considerably low for GRM based coefficients. The accuracy of breeding value for the pedigree based relationship matrix (A) was 13% while for GRM (GOF, G05, and Yang) it was 0.37, 0.45, and 0.38, respectively. Conclusion Accuracy of GRM was 1.5 times higher than A in this study. Therefore, genomic information will be more beneficial than pedigree information in the Hanwoo breeding program.

Demographic Trends in Korean Native Cattle Explained Using Bovine SNP50 Beadchip

Linkage disequilibrium (LD) is the non-random association between the loci and it could give us a preliminary insight into the genetic history of the population. In the present study LD patterns and effective population size (Ne) of three Korean cattle breeds along with Chinese, Japanese and Mongolian cattle were compared using the bovine Illumina SNP50 panel. The effective population size (Ne) is the number of breeding individuals in a population and is particularly important as it determines the rate at which genetic variation is lost. The genotype data in our study comprised a total of 129 samples, varying from 4 to 39 samples. After quality control there were ~29,000 single nucleotide polymorphisms (SNPs) for which r2 value was calculated. Average distance between SNP pairs was 1.14 Mb across all breeds. Average r2 between adjacent SNP pairs ranged between was 0.1 for Yanbian to 0.3 for Qinchuan. Effective population size of the breeds based on r2 varied from 16 in Hainan to 226 in Yanbian. Amongst the Korean native breeds effective population size of Brindle Hanwoo was the least with Ne = 59 and Brown Hanwoo was the highest with Ne = 83. The effective population size of the Korean cattle breeds has been decreasing alarmingly over the past generations. We suggest appropriate measures to be taken to prevent these local breeds in their native tracts.

Accuracy of Imputation of Microsatellite Markers from BovineSNP50 and BovineHD BeadChip in Hanwoo Population of Korea

Until now microsatellite (MS) have been a popular choice of markers for parentage verification. Recently many countries have moved or are in process of moving from MS markers to single nucleotide polymorphism (SNP) markers for parentage testing. FAO-ISAG has also come up with a panel of 200 SNPs to replace the use of MS markers in parentage verification. However, in many countries most of the animals were genotyped by MS markers till now and the sudden shift to SNP markers will render the data of those animals useless. As National Institute of Animal Science in South Korea plans to move from standard ISAG recommended MS markers to SNPs, it faces the dilemma of exclusion of old animals that were genotyped by MS markers. Thus to facilitate this shift from MS to SNPs, such that the existing animals with MS data could still be used for parentage verification, this study was performed. In the current study we performed imputation of MS markers from the SNPs in the 500-kb region of the MS marker on either side. This method will provide an easy option for the labs to combine the data from the old and the current set of animals. It will be a cost efficient replacement of genotyping with the additional markers. We used 1,480 Hanwoo animals with both the MS data and SNP data to impute in the validation animals. We also compared the imputation accuracy between BovineSNP50 and BovineHD BeadChip. In our study the genotype concordance of 40% and 43% was observed in the BovineSNP50 and BovineHD BeadChip respectively.