| Buffaloes are differentiated as Bubalus and Syncerus. Syncerus is not domesticated yet. Bubalus include a domesticated species and three wild species. All the domesticated buffalo worldwide originated from Bubalus. The domestic buffalo is classified into two types:river buffalo and swamp buffalo, Chinese buffalo belong to swamp buffalo. As a draft livestock, Chinese swamp buffalo has more than 7 000 years domestication and breeding history, playing a very important role in wet rice cultivation in southern China. Chinese swamp buffalo mainly spread in the vast areas of the south region of north latitude 36°, east region of east longitude 97°. The amount of Chinese buffalo is more than 22.75 million and ranked third all over the world. Chinese buffalo are divided into 24 native types with rich genetic diversity. But many of them are decreasing sharply in these years, some types are even at the brink of extinction. In order to protect and utilize Chinese domestic buffaloes' genetic resource perfectly, we investigated the Y-chromosome genetic diveristy and paternal origin of 243 bulls belonging to 13 populations (DDN, GZ, FA, BH, HZ, JH, ES, DH, FL, GX, HZi, XY and WZ) in Chinese swamp buffalo using 14 bovine Y-chromosome-specific microsatellites (Y-STR). The results are as follows: 1. Seven bovine Y-STRs can be used to study the buffalo genetic diversity and paternal origin.We tested the genetic diversity of 14 bovine Y-STRs of 243 male Chinese swamp buffalo across 13 populations, three markers (UMN0920, UMN0307 and UMN3008) amplified ladder-like or smear-like bands. While three markers (INRA008, UMN0103 and UMN0504) were monomorphic with a single allele and UMN1113 has three alleles but monomorphic. the remaining seven markers (INRA124, INRA189, BM861, UMN0304, PBR1F1, BC1.2 and UMN2001) were polymorphic with allele number ranging from 2 to 4. Two alleles (INRA18940bp and INRA18944bp) of them are tested first time in present study. 2. Analysis the MNA and SI of Y-STRs in Chinese BuffaloesIn MNA and Shannon index, HZ has the both highest value with an average of 3.25 and 0.496, respectively. ES and FL has the lowest MNA and Shannon index with an average value of 2.75 and 0.319 respectively. The rage of MNA and Shannon index value in other Chinese buffaloes'types are 2.83 to 3.10 and 0.325 to 0.493, respectively. 3. A great amount of variations were detected within Chinese swamp buffalo populations.Among 13 Chinese swamp buffalo populations, HZi had the highest differentiation with an average FST value of 0.2066 and JH showed the lowest differentiation with an average FST value of 0.0034. In all pairwise FST values, the following pairwise FST values were significantly (P< 0.05) differentiated:DDN with GZ, FA, HZ and NS; GZ with FA, HZ, DH and HZi; FA with BH and HZ; BH with HZ; DH with HZi and WZ; FL with HZi and WZ; HZi with XY and WZ; at last, XY with WZ. The results indicated that a great amount of variations were detected within Chinese swamp buffalo populations. 4. Chinese swamp buffaloes have high level of Y chromosome diversity.A total of 111 haplotypes, determined by the seven polymorphic Y-STR markers, were observed from 243 individuals in 13 Chinese swamp buffalo populations. The highest number of haplotypes was found in WZ which showed 33 haplotypes, The haplotype number of other Buffalo types are varied from 6 to 33 based on different sample sizes(except of ES, JH and HZi). The haplotype diversity values varied from 0.855±0.028 in DH to 0.976±0.013 in XY population, with the exception of extremely high value in populations ES (1.000±0.096) and HZi (1.000±0.096), which were resulted from the limited samples. These results indicated high level of Y chromosome diversity in Chinese swamp buffalo. 5. There are two paternal origins of Chinese Swamp buffaloes.MJ network was constructed based on the 111 Y-STR haplotypes of swamp buffaloes, which revealed two major distinct haplogroups, designated haplogroup I and haplogroupⅡ. There were more than 10 mutational step differences between haplogroup I and haplogroupⅡ, which indicating the high level of differentiation between the two haplogroups. HaplogroupⅡwas predominant (64.9%,72/111) with a high-frequency haplotype Y2 (9 individuals) located in the center. While haplogroup I was secondary (35.1%,39/111) with the highest-frequency haplotype Y1 (13 individuals) located in the center. Among the 13 Chinese swamp buffalo populations, however, ES belonged to haplogroup I, and JH belonged to haplogroupⅡonly, which limited by samlple size. The remaining populations included both haplogroups, indicating two paternal origins of the domestic swamp buffalo in China.
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