Comprehensive analysis of the mitochondrial <scp>DNA</scp> diversity in Chinese cattle

Xia, Xiaoting; Qu, Kaixing; Zhang, G.; Jia, Yanqing; Ma, Zengyi; Zhao, Xiaomin; Huang, Yongzhen; Chen, H.; Huang, Bizhi; Lei, Chuzhao

doi:10.1111/age.12749

Cited by 40 publications

(27 citation statements)

References 24 publications

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“…I1 was the predominant mtDNA haplogroup, whereas the haplogroup I2 was rare and T3 and T4 only detected in limited Longlin and Nandan cattle. The composition of the mtDNA haplogroups in Guangxi breeds were congruent with those previously presented [13,15]. Moreover, the haplotype H34 was shared by Weizhou, Longlin, and Nandan,…”

Section: Discussionsupporting

confidence: 83%

“…Recently, within the Bos indicus lineage, a novel sub-haplogroup, named I1a, has been described by Chen et al [4] on the basis of mitogenome haplotypes. Subsequent study based on mitogenome also confirmed the dominant position of this sub-haplogroup in Chinese local breeds [13].…”

Section: Introductionmentioning

confidence: 74%

“…Several previous studies have examined the genetic diversity and origin of Guangxi cattle breeds using both mitochondrial and Y-chromosome data. Early studies using mtDNA control region have suggested that both Nandan and Longlin have Bos indicus and Bos taurus mtDNA haplotypes while Weizhou only harbor Bos indicus haplotypes [13][14][15]. Another study based on the polymorphism of Y-chromosome (Y-SNP and Y-STR) showed that all the three Guangxi breeds belonged to the Bos indicus Y3 lineage [16].…”

Section: Introductionmentioning

confidence: 99%

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Mitogenome Diversity and Maternal Origins of Guangxi Cattle Breeds

Xia

Huang

Wang

et al. 2019

Animals

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Guangxi Province is located in the southernmost region of China, adjacent to the hotspot that is considered to be the putative migratory corridor or domestication area for Chinese indicine cattle. Here, we investigated the evolutionary status of Guangxi native breeds, Longlin (n = 21), Nandan (n = 18), and Weizhou cattle (n = 17) using mitogenome sequencing. Our results show that Bos indicus sub-haplogroup I1a predominates in Guangxi cattle breeds. Population structure by multidimensional-scaling analysis significantly differentiates Weizhou from the other two breeds (Longlin and Nandan). Moreover, the mtDNA haplotype composition and FST values indicate that the formation of Longlin and Nandan breeds may have been affected by Indian indicine, whereas, Weizhou island might have preserved pure Chinese indicine cattle due to its geographical isolation. We speculate that following the initial entry of zebu into southern China, the subsequent introgression of Indian indicine may have influenced the matrilineal origin of local breeds in southwestern China.

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Section: Discussionsupporting

confidence: 83%

Section: Introductionmentioning

confidence: 74%

Section: Introductionmentioning

confidence: 99%

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Mitogenome Diversity and Maternal Origins of Guangxi Cattle Breeds

Xia

Huang

Wang

et al. 2019

Animals

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“…employed to analyze genetic tree and genetic diversity of cattle breeds (Yang et al, 2014;Sharma et al, 2015;Villegas Castagnasso et al, 2015;Srirattana et al, 2017;Pramod et al, 2018;Xia et al, 2019).…”

Section: For This Reason D-loop Mitochondrial Is Oftenmentioning

confidence: 99%

Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds

Jakaria

Musyaddad

Rahayu

et al. 2019

J. Indonesian Trop. Anim. Agric.

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This study aimed to investigate the diversity of the complete sequence of D-loop mitochondrial DNA (mtDNA) in Bali and Sumba Ongole (SO) cattlebreeds. A total of 24 blood samples were collected from Bali cattle (19 heads) and SO cattle (5 heads), and were extracted and then analyzed to obtain the sequence of D-loop mt DNA.Multiple alignments of the whole sequence of D-loop mtDNA were determined using clustal W. Genetic distance was calculated using a p-distance method, while the genetic tree was constructed using neighbor-joining (NJ) based on MEGA 6. Haplotype number, haplotype diversity (Hd) and nucleotide diversity (Pi) were analyzed using DnaSP version 6. As a result, the sequence of D-loop mtDNA in Bali cattle (921-1119 bp) and SO cattle (913 bp) was reported to have 8 and 4 haplotypes. Hd and Pi of Bali cattle reached 0.625±0.139 and 0.0266±0.0145, respectively, which wwere different from that of SO cattle, namely 0.900±0.1610 and 0.0064±0.0015, respectively. Specifically, we found 22 bp-repetitive nucleotide in Bali cattle, existing 3-9 times with a length of 66-198 bp present in D-loop mtDNA. This unique feature did not exist in SO cattle. Genetic distance and genetic tree determined according to sequence in hypervariability (HV-1) region of D-loop mtDNA (166 bp) resulted in satisfied separation, successfully classifying Bos javanicus, Bos indicus, and Bos taurus cluster.

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“…Of the 37 genes, 13 code for proteins (polypeptides), 22 code for transfer RNA (tRNA), and two code for the small (12S) and large (16S) subunits of ribosomal RNA (rRNA). The D-loop region (Loftus et al, 1994;Bradley et al, 1996;Mannen et al, 1998;Kikkawa et al, 2003;Lai et al, 2006;Lei et al, 2006;Xia et al, 2019) and the cytochrome b (cyt b) gene (Lau et al, 1998;Sultana et al, 2003;Cai et al, 2003;Souza et al, 2009;Stock et al, 2009;Yap et al, 2010) of mtDNA have been widely used in cattle to characterize genetic diversity and phylogenetic performance among individuals and populations. The mtDNA 16S rRNA gene is also an advanced genetic marker for animal genetic diversity and phylogenetic studies.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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Abstract. The objective of this research was to characterize the genetic diversity and phylogenetic diversity among 12 cattle breeds (10 Chinese breeds and two foreign taurine breeds as controls) utilizing gene mtDNA 16S rRNA. The complete sequences of the mtDNA 16S rRNA genes of the 251 animals were 1570 bp long. The mean percentages of the four nitrogen bases were 37.8 % for adenine (A), 23.7 % for thymine (T), 20.9 % for cytosine (C), and 17.6 % for guanine (G). The mtDNA 16S rRNA gene base percentages had a strong bias towards A + T. All detected nucleotide variations in gene mtDNA 16S rRNA were either transitions (62.3 %) or transversions (37.7 %); no indels (insertions and deletions) were found. A total of 40 haplotypes were constructed based on these mutations. A total of 36 haplotypes of these 40 haplotypes were present in 10 Chinese cattle breeds. The haplotype diversity of all Chinese cattle populations was 0.903±0.077, while the nucleotide diversity was 0.0071±0.0039. Kimura's two-parameter genetic distances between pairs of the studied 12 breeds ranged from 0.001 to 0.010. The phylogenetic analysis assigned the 10 Chinese breeds to two distinct lineages that likely differed in their percentage of Bos taurus and Bos indicus ancestry.

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Comprehensive analysis of the mitochondrial DNA diversity in Chinese cattle

Cited by 40 publications

References 24 publications

Mitogenome Diversity and Maternal Origins of Guangxi Cattle Breeds

Mitogenome Diversity and Maternal Origins of Guangxi Cattle Breeds

Diversity of D-loop mitochondrial DNA (mtDNA) sequence in Bali and Sumba Ongole cattle breeds

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

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