| Domestic buffalo is an important livestock in southern China.It is usually used in farming of paddy field and plays an important role in the development and dissemination of rice planting culture.Buffalo was domesticated from the wild Asian buffalo 3,000 to 6,000 years ago,mainly distributed in the tropical and subtropical regions of South Asia,Southeast Asia and East Asia.Mitochondrial DNA(mtDNA),Y-chromosome microsatellite(Y-STR)and Y-chromosome single nucleotide polymorphism(Y-SNP)are the most effective molecular genetic markers for studying the animals’ maternal and paternal origin.Molecular genetic studies of buffalo in recent years have shown an independent domestication of swamp and river buffalo.River buffalo was domesticated in the western part of the Indian subcontinent.Several studies on mtDNA,Y-SNP and genome chip data of swamp buffalo suggested that swamp buffalo was domesticated in southwest China,southwest China-Southeast Asia border area and Northern Thailand.These studies agree that the domestication area of swamp buffalo is in the southwest of China and the north of Southeast Asia.In order to analyze the origin and domestication of swamp buffalocomprehensively,more than 800 swamp buffalo samples from China,Vietnam,Thailand,Laos,Myanmar and India were collected.Mitochondrial D-loop region,Cytb gene,mtDNA genome sequences and Y-STR were acquiredby sequencing and fluorescence microsatellite capillary electrophoresis.The genetic diversity,maternal origin,paternal origin and domestication location and time of swamp buffalo were analyzed and discussed respectively.The following results were obtained:(1)Swamp buffaloes have very rich mtDNA genetic diversity and weak phylogeography structure.Swamp buffalo revealed 10 mtDNA haplogroups: SA1,SA2,SA3,SB1,SB2,SB3,SB4,SC,SD and SE,of which SA1 was the main haplogroup and SC,SD,SE and SA3 were rare haplogroups.(2)The swamp buffalo was domesticated in 7,000-3,000 years ago.SA1 haplogrooup was domesticated about 6,400 years ago in the middle and lower reaches of the Yangtze River valley in China,and later expanded along the L1 and L2 routes to the upper reaches of the Yangtze River and Southeast China,and finally reached Southeast Asia.During the process of migration,several late domestication activities took place in the upper reaches of the Yangtze River valley(SB3,about 4,100 years ago),southwest China and north-east Asia(SB1 and SB2,about 3,300 years ago).The first large-scale population expansion("secondary domestication")of the SA2 haplogroup occurred in southwestern China about 3,300 years ago.This multiple non-independent domestication model of domestication-migration-domestication was first found in swamp buffaloes.The large-scale transmission of rice after domestication is closely related to the domestication of swamp buffalo.(3)The divergence time between river buffalo and swamp buffalo was 913±78 Kya.The divergence time between river buffalo R 1 and R 2 haplogroup was 82±18 Kya.The divergence time of A and B haplogrooup was 189.6±27.2 Kya.The differentiation of haplogroup SA,SB,SD and SE occurred in the Riss Glacial of 200-130 Kya.The phylogenetic model of buffalo is influenced by the glacial period.In the cold climate of the glacial period with the decrease of suitable habitats,buffalos were long isolated and differentiated into different haplogroups.Individuals survived in refuges during glacial period were domesticated into domestic buffalo in the warmer post-glacial period.(4)Y-STR analysis revealed that there were four paternal origins(Y1-Y4)in swamp buffaloes.Y1 was the main paternal origin.The Yangtze River valley might be the domestication center of Y1.The southwest China-Southeast Asia border was important sites for paternal origin of swamp buffalo. |
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