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Journal of Integrative Agriculture  2019, Vol. 18 Issue (10): 2338-2350    DOI: 10.1016/S2095-3119(19)62731-0
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Mitochondrial DNA diversity and origin of indigenous pigs in South China and their contribution to western modern pig breeds
WANG Chen1, CHEN Yao-sheng1, HAN Jian-lin2, 3, MO De-lin1, LI Xiu-jin1, LIU Xiao-hong1 
1 State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
2 CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
3 International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
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Indigenous pigs in South China are valuable genetic resources with many specific and unique characters, which have played an important role in the establishment of some western modern pig breeds.  However, the origin and genetic diversity of indigenous pigs in South China have not been fully understood.  In the present study, we sequenced 534 novel mitochondrial DNA (mtDNA) D-loop and assembled 54 complete mitogenome sequences for all 17 indigenous pig breeds from Fujian, Guangdong, Guangxi and Hainan in South China.  These data were analyzed together with previously published homologous sequences relevant to this study.  We found that all 13 coding genes of the mitogenomes were under purifying selection, but ND1 had the most variable sites and CYTB contained the most non-synonymous SNPs.  Phylogenetic analysis showed that all indigenous pigs in South China were clustered into the D haplogroup with D1a1, D1b, D1c and D1e sub-haplogroups found to be dominant.  Haplotype and nucleotide diversities of D-loop sequences ranged from 0.427 to 0.899 and from 0.00342 to 0.00695, respectively, among which all pigs in Guangdong had the lowest diversity.  The estimates of pairwise FST, gene flow (Nm) and genetic distance (Da) indicated that most of these indigenous pig breeds differentiated from each other significantly (P<0.05).  Among the western modern breeds, Berkshire and Yorkshire had significant Asian matrilineal footprints from indigenous pigs in South China, especially the Spotted pigs distributed in Guangdong and Guangxi.  The neutrality test (Fu’s FS) indicated that indigenous pigs from Fujian and Guangxi had gone through recent population expansion events (P<0.05).  It is concluded that indigenous pigs in South China were most likely derived from the Mekong region and the middle and downstream regions of Yangtze River through Guangxi and Fujian.  Our findings provide a complete and in-depth insight on the origin and distribution pattern of maternal genetic diversity of indigenous pigs in South China.
Keywords:  pig        South China        mitogenome        D-loop        genetic diversity  
Received: 09 May 2018   Accepted: 29 September 2019
Fund: This work was supported by the Basic Work of Science and Technology Project, China (2014FY120800) and the Science and Technology Project of Guangdong Province, China (2014YT02H042, 2014B020202001).
Corresponding Authors:  Correspondence LIU Xiao-hong, Tel/Fax: +86-20-39332940, E-mail:   
About author:  WANG Chen, E-mail:;

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WANG Chen, CHEN Yao-sheng, HAN Jian-lin, MO De-lin, LI Xiu-jin, LIU Xiao-hong. 2019. Mitochondrial DNA diversity and origin of indigenous pigs in South China and their contribution to western modern pig breeds. Journal of Integrative Agriculture, 18(10): 2338-2350.

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