mtDNA Diversity and Phylogenetic State of Korean Cattle Breed, Chikso

Abstract

In order to analyze the genetic diversity and phylogenetic status of the Korean Chikso breed, we determined sequences of mtDNA cytochrome b (cyt b) gene and performed phylogenetic analysis using 239 individuals from 5 Chikso populations. Five non-synonymous mutations of a total of 15 polymorphic sites were identified among 239 cyt b coding sequences. Thirteen haplotypes were defined, and haplotype diversity was 0.4709 ranging from 0.2577 to 0.6114. Thirty-five haplotypes (C1–C35) were classified among 9 Asia and 3 European breeds. C2 was a major haplotype that contained 206 sequences (64.6%) from all breeds used. C3–C13 haplotypes were Chikso-specific haplotypes. C1 and C2 haplotypes contained 80.5% of cyt b sequences of Hanwoo, Yanbian, Zaosheng and JB breeds. In phylogenetic analyses, the Chikso breed was contained into B. taurus lineage and was genetically more closely related to two Chinese breeds than to Korean brown cattle, Hanwoo. These results suggest that Chikso and Hanwoo have a genetic difference based on the mtDNA cyt b gene as well as their coat color, sufficient for classification as a separate breed.

Short Communication: Genetic diversity and phylogenetic analysis of two Indonesian local cattle breeds based on cytochrome b gene sequences

“…Among the two investigated breeds, the compositional frequency of A base was the highest (30.2%) among three other bases (T, 27.2%; C, 26.00%; G, 16.3%). The nucleotide composition in this study was similar to published studies in cattle (Kim et al 2013), sheep (Pakpahan et al 2016;Sofla et al 2017) and chicken (Adamu et al 2016), suggesting that composition of A+T nucleotides in those animals was higher than C+G nucleotides.…”

Exploring genetic diversity and phylogenic relationships of Chinese cattle using gene mtDNA 16S rRNA

“…Previous studies reported a base composition bias towards A + T in the mtDNA D-loop region (Lei et al, 2006;Yang et al, 2014) and in the cyt b gene (Cai et al, 2007;Kim et al, 2013) in cattle. In fact, earlier research (Perna and Kocher, 1995;Saccone et al, 1999Saccone et al, , 2000 indicated that mitochondrial genomes of many organisms including mammals were guanine and cytosine (GC) poor.…”

Genetic Variation of Eight Indonesian Swamp-Buffalo Populations Based on Cytochrome b Gene Marker

“…The results of previous studies reported that there were 4 transition substitutions (C>T) in Cyt b gene sequence of swamp buffaloes in Asian mainland (Thailand and Peninsular Malaysia), but transversion substitution was not found (Lau et al, 1998). Also, Kim et al (2013) found fifteen transition substitutions in the Korean cattle from fifteen polymorphic sites identified. In contrast, in the Pakistani river buffaloes (Nili-Ravi, Kundi) there were 79 transition substitutions (g.33A>G and g.46C>T) and 43 transver- Bbc BK BD KL KN TR NTB BTN NAD 1 1 --------1 1.27 2 -9 10 6 2 ----27 34.18 3 -1 -------1 1.27 4 -1 -------1 1.27 5 ---6 4 10 10 5 3 38 48.10…”

“…The main reason for using mitochondrial DNA marker because the mitochondrial genome has a relatively small size (± 16500 bp), and a rapid evolutionary rate, which causes high intra-species diversity (Avise, 1994). Mammalian mitochondrial DNAs show several special features such as an absence of intron, maternal inheritance, all offsprings from the same female parent having the same mitochondrial DNA sequence, the existence of single copy of orthologous genes, the lack of recombination events and a high mutation rate (Linacre & Tobe, 2011;Kim et al, 2013). Mitochondrial DNAs of the animal contain thirteen protein-coding genes and are considered as strong markers for genetic variation analysis such as at the family, genus, and species levels (Arif & Khan, 2009;Doosti et al, 2014).…”

“…Previous studies on genetic variation and phylogeography based on mitochondrial Cyt b gene marker in livestock have been reported, such as in goats (Pakpahan et al, 2016), Romanian cattle (Xuan et al, 2010), Korean cattle (Kim et al, 2013), Pakistani cattle (Hussain et al, 2018), Indonesian local cattle (Hartatik et al, 2015;Hartatik et al, 2018), Nili-Ravi and Kundi buffaloes in Pakistan (Saif et al, 2012), and Southeast Asian buffaloes (Lau et al, 1998;Yindee et al, 2010;Lei et al, 2011;Zhang et al, 2011;Zhang et al, 2016). Study related to genetic variation and genetic relationships of Indonesian local swamp buffaloes was reported by Sukri et al (2014) that from eight Indonesian local swamp-buffalo populations (Madiu, Aceh, Blitar, Riau, Kalimantan, Tator, Bali, Lombok, and Bima), it was found 19.87% variable sites consisted of 16 haplotypes and 7 different haplogroups unique based on their geographical regions.…”