Substitution and Haplotype Diversity Analysis on The Partial Sequence of The Mitochondrial DNA Cyt b of Indonesian Swamp Buffalo (Bubalus bubalis)

Abstract

This research aims to investigate the substitution pattern of nucleotide base and haplotype diversity of Indonesian swamp buffalo (Bubalus bubalis) based on the mitochondrial DNA cyt b partial gene sequence. 17 samples were chosen from 7 different regions with each uniquely represents Indonesian biogeography which comprise Aceh, Riau, Madiun, Blitar, Lombok, South Borneo and Tana Toraja. The result of cyt b gene sequence alignment showed the presence of transition and transversion substitutions and the absence of insertion and deletion. The amount of transitions was found to be higher than that of transversions and the amount of substitution in pyrimidine was also higher than that in purine. The highest amount of transitions happened in base TC which is a silent substitution. The result of median joining network analysis showed that Indonesian haplotype Bubalus bubalis could be classified into 16 haplotypes which form different haplogroups unique to their geographical region. The result of median joining network analysis also indicated that the genetic relationships of swamp buffaloes (Bubalus bubalis) in Indonesia are highly influenced by their geographical locations.

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

“…In the present study, it was found 856 (98.96%) conservation sites and 9 (1.04%) variable sites. Cyt b genes sequences of Indonesian swamp buffaloes in this study were more conservative than those reported by Sukri et al (2014) that found lower variable sites. The use of different Cyt b genes references from the GenBank influenced the results.…”

“…A total of 78 Cyt b genes sequences of local swamp buffaloes from 8 different populations were observed in this study. Previous studies reported that from 17 Cyt b gene sequences of Indonesian swamp buffaloes, 80.13% were found to be conserved sites and 19.87% were found to be variable sites (Sukri et al, 2014). In the present study, it was found 856 (98.96%) conservation sites and 9 (1.04%) variable sites.…”

“…The number of haplotypes of Cyt b gene sequences of eight Indonesian swamp-buffaloe populations in this study was higher than that reported by Saputra et al (2013) that they only found three haplotypes of seven Indonesian swamp-buffaloe populations based on the 21 Cytochrome Oxidase subunit I (COI) gene sequences. The higher haplotypes number of Cyt b gene sequences of Indonesian swamp buffalo was reported by Sukri et al (2014) as many as 16 haplotypes from 17 Cyt b gene sequences. Meanwhile, in Thailand swamp buffalo there were 14 haplotypes from 62 Cyt b gene sequences (Yindee et al, 2010).…”

“…The use of different Cyt b genes references from the GenBank influenced the results. Cyt b gene sequence reference used in this study was from swamp buffalo (Bubalus bubalis carabanesis); meanwhile Sukri et al (2014) used Cyt b genes sequences reference from African buffalo (Syncerus caffer).…”

“…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. Meanwhile, Amin et al (2015) reported that four local swamp-buffalo populations in Central Indonesia (Bali, Toraja, Lombok, and Bima) had close genetic relationships, which they only consisted of one main cluster and two sub-clusters.…”