Genome-wide analysis of Hanwoo and Chikso populations using the BovineSNP50 genotyping array

Abstract

Hanwoo and Chikso are classified as Korean native cattle breeds that are currently registered with the Food and Agriculture Organization. However, there is still a lack of genomic studies to compare Hanwoo to Chikso populations. The objective of this study was to perform genome-wide analysis of Hanwoo and Chikso populations, investigating the genetic relationships between these two populations. We genotyped a total of 319 cattle including 214 Hanwoo and 105 Chikso sampled from Gangwon Province Livestock Technology Research Institute, using the Illumina Bovine SNP50K Beadchip. After performing quality control on the initially generated datasets, we assessed linkage disequilibrium patterns for all the possible SNP pairs within 1 Mb apart. Overall, average r values in Hanwoo (0.048) were lower than Chikso (0.074) population. The genetic relationship between the populations was further assured by the principal component analysis, exhibiting clear clusters in each of the Hanwoo and Chikso populations, respectively. Overall heterozygosity for Hanwoo (0.359) was slightly higher than Chikso (0.345) and inbreeding coefficient was also a bit higher in Hanwoo (- 0.015) than Chikso (- 0.035). The average F value was 0.036 between Hanwoo and Chikso, indicating little genetic differentiation between those two breeds. Furthermore, we found potential selection signatures including LRP1B and NTRK2 genes that might be implicated with meat and reproductive traits in cattle. In this study, the results showed that both Hanwoo and Chikso populations were not under severe level of inbreeding. Although the principal component analysis exhibited clear clusters in each of the populations, we did not see any clear evidence that those two populations are highly differentiated each other.

Evaluation of the physicochemical, metabolomic, and sensory characteristics of Chikso and Hanwoo beef during wet aging

“…During wet aging, a * values of rump from both breeds significantly decreased (Figure 1c), following the results of the study performed by Ma et al [21]. This was possibly due to the reduced color stability by the oxidation of myoglobin and lipids [20].…”

“…This was possibly due to the reduced color stability by the oxidation of myoglobin and lipids [20]. It was also reported that extended vacuum storage would deteriorate color stability and bloom development of meat [21]. Meanwhile, a major difference in meat color between Hanwoo and Chikso rump was found in a * value.…”

“…Korean native cattle are classified as four indigenous cattle breeds: Hanwoo, Chikso, Heugu, and Jeju black [1]. Among them, Korean native cattle, especially Hanwoo is a, are well-known breed to consumers owing to itstheir superior meat quality, such as excellent tenderness, high degree of marbling, and desirable flavor [21]. Korean native cattle can be divided into four indigenous cattle breeds: Hanwoo with yellow-brown hair, Chikso with tiger bands, Heugu, and Jeju black with black fur, according to the Domestic Animal Diversity Information System of the United Nations, Food and Agriculture Organization [2].…”

“…Moreover, information on the meat quality of Chikso beef and its differentiated characteristics from common Hanwoo beef is scarce. Recently, Chikso has gained attention owing to its unique flavor characteristics to consumers who prioritize desirable meat flavor and seek new meat products [21]. Previous studies have reported flavor differences between cooked Hanwoo and Chikso beef through sensory assessment or instrumental analyses [45,56].…”

Genome‐wide association study and pathway analysis for fat deposition traits in nellore cattle raised in pasture–based systems

“…Song et al. (2018) observed that this gene was associated with carcass quality traits in native Korean cattle (Hanwoo and Chikso). LRP1B mediates the lipid transport process of apolipoprotein E, which is involved in cholesterol transport, and also participates in other physiological processes, such as the transport of nutrients and vitamins, and neurological development (May et al., 2007).…”