| The Asian buffalo has the greatest impact on the development of human agriculture and society that lives in the world’s most densely populated regions of East Asia,Southeast Asia and South Asia.They are the most important means of production for traditional farming families,which not only provide a strong traction for agricultural cultivation,but also provide meat,milk,leather,and fertilizer.There are billions of people relying on water buffalo for their livelihoods than any other domestic animals.Asian water buffalo is divided into two subspecies,the swamp type and the river type.The former is mainly distributed in East Asia and Southeast Asia,and the latter is mainly distributed in South Asia.Due to the lack of archaeological and historical records,the origin of swamp buffalo domestication remains controversial.The research of Asian buffalo genome has just started in a few years,and its genetic information resources and the genetic mechanism of important economic traits almost blank.In this study,a total of 230 buffalo individuals from 14 countries and 39 sampling sites on the Eurasian continent were re-sequenced and population genetics analyzed,revealing the evolutionary history of the Asian buffalo and the regions affected by domestication selection in the genome.We use the next-generation sequencing technology based on the Illumina PE150 platform,a total of 6.3TB of clean data was obtained,with an average sequencing depth of 10.5×.The mapping ratio and coverage rate mapped with the reference genome were above 98% of most individuals.We obtained 18,732,366 SNPs in swamp buffalo,23,722,820 SNPs in river buffalo,and 33,516,506 SNPs in the combined population,as well as the summary genomic region where the buffalo SNPs are located.The genetic structure analysis based on the SNP data of the buffalo genome: gene flow analysis shows that the buffaloes distributed in Yunnan,Indochina,and northern India have gene flow and hybridization,which may be related to the local tea-horse trade that have existed for thousands years.Previous studies mostly believed that the domesticated swamp buffalo comes from Southwest China and the northern Indo-China Peninsula because of the high genetic diversity in this area.Our results found that the high genetic diversity of the swamp buffalo population in this area is the result of gene flow infiltration of river buffalo,and the archaeological evidence is still blank.Combining with the archaeological studies of East Asia and Southeast Asia,we believe that the migration of the swamp buffalo and the proliferation of the Austronesian have a high degree of overlap.It is speculated that the origin of its domestication should be located in the southeast coast of China.Analysis of selected genes in the swamp buffalo genome: A total of 801 candidate genes were screened through the combination of the three tests of π,iHS and CLR.Among them,82 genes were detected by the three tests simultaneously,237 genes were detected by the iHS and CLR tests,99 genes were detected by the iHS and π tests,and 380 genes were detected by the CLR and π tests.The KEGG pathway enrichment analysis was performed on the genes in the selective sweep analysis of swamp buffalo,and a total of 22 significantly enriched(P<0.05)KEGG pathways were obtained.Total of 153 GO terms were significantly enriched(P<0.05).Comparing the results of KEGG enrichment and GO enrichment,we found that the biological functions of swamp buffalo to selectively eliminate gene sets mainly focus on skeletal muscle and cardiac muscle function,nerve conduction and behavior,energy metabolism,and immunity.The development of skeletal muscle is related to strength and endurance,and the function of myocardium is related to the transport of blood oxygen.They are all indispensable for maintaining exercise function.The swamp buffalo is a domestic animal that is known for its strong strength and endurance,which means that the candidate genes in these enriched entries may be a key factor in improving the strength and endurance of people in the process of domesticating the swamp buffalo.Analysis of selected genes in the river-type buffalo genome: A total of 542 eligible river buffalo candidate genes were screened through the combination of π,iHS and CLR tests.Among them,62 genes were detected by three tests,147 genes were detected by iHS and CLR tests,65 genes were detected by iHS and π tests,and 265 genes were detected by CLR and πtests.The KEGG pathway enrichment analysis was performed on the genes in the river buffalo’s selective sweep area,and 8 pathways were significantly enriched(P≤0.05).There were 106 GO entries that were significantly enriched(P<0.05)in the GO enrichment analysis of genes in the selective sweep area of river buffalo,and some genes were extremely enriched(P<0.01).Comparing the river buffalo candidate genes with the cattle QTL,62 of the genes were found to have quantitative trait annotations.Combining the results of KEGG and GO enrichment analysis,PPI analysis,and QTL correlation analysis,we found that the river buffalo’s selective sweep genes mainly involves biological functions in several aspects such as servicing function,lactation,and resistance to heat stress.This study thoroughly explored the genetic basis of Asian buffalo population structure,genetic diversity,gene flow,domestication and important economic traits from the whole genome level,and re-deconstructed the evolutionary history and domestication process of Asian buffalo.The high-quality population genomic data of Asian buffalo obtained in this study is also helpful for mining the unique genetic information resources of Asian buffalo,analyzing the genetic mechanism of important economic traits of buffalo,exploring the molecular mechanism of buffalo domestication origin and phenotypic-geographic difference.It provides valuable data resources for the genetic improvement and utilization of important economic traits of Asian water buffalo. |
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