Genome-wide Genetic Variation And Genetic Diversity Of Mitochondrial Genome In Bactrian Camel

The Bactrian camel includes various domestic(Camelus bactrianus)and wild breeds(Camelus ferns),and they are one of the few large livestock in the world that can survive in the Gobi desert.According to the archaeological research,the domestication of Bactrian camel probably occurred in 4500-5000 years ago;in the process of Bactrian camel domestication and breeding process,the rich local species resources were formed gradually.In order to make full use of Bactrian camel germplasm and provide important reference for genetics breeding and improvement of variety,we re-sequenced whole genome of 105 domestic bactrian camels from China,Mongolia,Kazakhstan,Russia and Iran,19 wild bactrian camels from Mongolia and 4 dromedary camels from Iran.After bioinformatics comparison analysis,we constructed genome-wide genetic variation maps in the level of different domestic Bactrian camel groups and wild Bactrian camel group.In addition,the genetic structure,phylogenetic relationship and genetic diversity of 11 domestic Bactrian camel population groups and 1 wild Bactrian camel population group from China,Mongolia and Russia,were studied in the level of the mitochondrial control region and cytochrome b gene,respectively.The main results were as follows:1.Genome-wide variation maps in Bactrian camel(1)A total of 4.24 Tb high-quality data and 1736x sequencing depth were obtained by whole genome re-sequencing in 105 domestic Bactrian camels from China,Mongolia,Russia,Kazakhstan and Iran,and 19 wild Bactrian camels from Mongolia.The average sequence depth of each Bactrian camel individual was 14x,and the average genomic coverage was 96.19%.A total of more than 90 million single nucleotide polymorphisms and more than 10 million insertions and deletions were identified;A genetic map of Bactrian camels was constructed for the first time,which provided abundant genetic markers for genetic breeding of Bactrian camels.(2)According to the phylogeny,principle component and population structure analysis,the germplasm resources of Bactrian camels were divided into two groups:the wild bactrian camel population group and the domestic bactrian camel population group;there were no significant differences in the domestic Bactrian camel population group among different regions and different geographical locations,which suggested that there was a certain gene flow in the different domestic Bactrian camel population groups.(3)Comparing with the domestic Bactrian camel groups,we also found that the wild Bactrian camel population group exhibited the lower nucleotide diversity in the whole genome region and exon region(pi values:1.43×10-3 and 0.97×10-3,respectively),which may be related to the current sharp decline in the number of wild Bactrian camel population group.2.Genetic diversity and population structure of Bactrian camels based on mitochondrial D-loop region(1)A total of 113 individuals from 12 domestic Bactrian camel population groups and 1 wild Bactrian camel group were sequenced and analyzed for their mitochondrial D-loop region.Twenty-five polymorphic sites and 15 haplotypes were discovered from 809 bp long sequences.The number of mutant bases accounted for 3.09%of the total number of nucleotides.(2)We found that the number of haplotypes varied from 2 to 6 in the 12 bactrian camel population groups;among them,the Heniin Hetsiin Huren camel group displayed the most haplotypes(h=6);however,the Zhungeer Bactrian camel group revealed the most abundant nucleotide diversity(?=0.0032)and haplotype diversity(Hd=0.9000 ±0.1610).(3)The phylogenetic and network analysis showed that the wild and domestic Bactrian camels were divided into two lineage distinctly,Lineage-A and Lineage-B.There were 13 haplotypes in the Lineage-A,and over 65.5%individuals belonged to three predominate haplotypes(H1,H2 and H3).There were 2 haplotypes in the Lineage-B,H14 and H15.3.Molecular phylogeny of the Bactrian camel based on mitochondrial Cytb gene sequences(1)A total of 92 domestic Bactrian camels from China,Mongolia and Russia,and 19 Mongolian wild Bactrian camels were sequenced and analyzed for their mitochondrial Cytb gene.Seventeen polymorphic sites were discovered from 1140 bp long sequences and accounting for the total number of nucleotides 1.22%.The average contents of T,A,G,and C were 27.77%,28.96%,15.07%,and 28.20%,respectively,and showed that the GC content(43.27%)was less than the AT content(56.73%).In this study,we detected only nucleotide substitutions,and no deletion or insertion mutations were observed.(2)We found that the 16 different haplotypes,of which 15 haplotypes(H1-H13,H15,and H16)belonged to domestic Bactrian camel population groups and only one haplotype belong to wild Bactrian camel group.In the all domestic Bactrian camel group,the Sunit Bactrian camel group displayed the highest nucleotide diversity(?=0.115×10-2)and haplotype diversity(Hd=0.889±0.075).(3)The genetic evolution of the mitochondrial Cytb gene in the domestic Bactrian camel populations varied in China,Mongolia and Russia.The most haplotypes(h=12)were found in the Chinese Bactrian camel population groups,with the highest haplotype diversity(Hd=0.679±0.064)and the nucleotide diversity(?=0.084×10-2).Therefore,it can be inferred that China may be one of the origins of domestic Bactrian camel.