Analysis of the genetic variation in mitochondrial DNA, Y-chromosome sequences, and MC1R sheds light on the ancestry of Nigerian indigenous pigs
- Adeniyi C. Adeola1, 2,
- Olufunke O. Oluwole3,
- Bukola M. Oladele3,
- Temilola O. Olorungbounmi3,
- Bamidele Boladuro3,
- Sunday C. Olaogun4,
- Lotanna M. Nneji1, 2, 11,
- Oscar J. Sanke5,
- Philip M. Dawuda6,
- Ofelia G. Omitogun7,
- Laurent Frantz8, 9,
- Robert W. Murphy1, 10,
- Hai-Bing Xie1, 2,
- Min-Sheng Peng1, 2, 11Email author and
- Ya-Ping Zhang1, 2, 11, 12Email author
© The Author(s) 2017
Received: 30 December 2016
Accepted: 14 June 2017
Published: 26 June 2017
The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci that are involved in the determination of coat color. We investigated the genetic diversity of Nigerian indigenous pigs (NIP) by simultaneously analyzing variation in mitochondrial DNA (mtDNA), Y-chromosome sequence and the melanocortin receptor 1 (MC1R) gene.
Median-joining network analysis of mtDNA D-loop sequences from 201 NIP and previously characterized loci clustered NIP with populations from the West (Europe/North Africa) and East/Southeast Asia. Analysis of partial sequences of the Y-chromosome in 57 Nigerian boars clustered NIP into lineage HY1. Finally, analysis of MC1R in 90 NIP resulted in seven haplotypes, among which the European wild boar haplotype was carried by one individual and the European dominant black by most of the other individuals (93%). The five remaining unique haplotypes differed by a single synonymous substitution from European wild type, European dominant black and Asian dominant black haplotypes.
Our results demonstrate a European and East/Southeast Asian ancestry for NIP. Analyses of MC1R provide further evidence. Additional genetic analyses and archaeological studies may provide further insights into the history of African pig breeds. Our findings provide a valuable resource for future studies on whole-genome analyses of African pigs.
The origins of African pig breeds are highly controversial owing to a paucity of archaeological and genetic data for hypothesis testing [1, 2]. Previous genetic analyses of West African pigs revealed that they shared maternal and paternal haplotypes with European wild boars and pigs, but not with Near Eastern wild boars . The limited size of West African pig samples did not allow discriminating them from pigs domesticated in North Africa and/or from pigs introduced by the European colonizers during the 15th–19th centuries. Early Portuguese sailors circumnavigated Africa and, in doing so, they may have introduced a European gene pool into some West African pigs . However, this hypothesis has not been formally tested through genetic analysis. Some Iberian pigs are classified as black hairy and this pattern is common in indigenous West African pigs . However, the causal genetic variants that underlie the color phenotype in the latter pigs remain largely unexplored. Melanocortin receptor 1 (MC1R) is a major determinant in color phenotype . Functional mutations in MC1R result in different coat colors in domestic animals, such as cattle , horses , goats , sheep [8–10] and pigs [11–13]. Research on MC1R has provided valuable insights into the evolution of domesticated animals [13–15]. For instance, Linderholm et al.  showed that, among the alleles of MC1R, there is a novel black allele unique to Polynesian pigs. Therefore, we used this gene to investigate the genetic diversity and origin of hairy black Nigerian indigenous pigs (NIP) as well as data from mitochondrial DNA (mtDNA) and Y-chromosomes of NIP to provide insights into the origin of NIP.
Peripheral blood samples were collected from 204 NIP distributed in six Nigeria states after receiving appropriate permission from their owners (see Additional file 1: Table S1).
Analysis of mtDNA D-loop sequences
Our data involved the amplification and sequencing of 630-base pair (bp) fragments of mtDNA D-loop (the methods are detailed in Additional file 2; GenBank accession numbers: KU561971–KU562068 and KY055561–KY055663). The final dataset for analysis comprised 201 NIP (de novo) and 722 mtDNA D-loop sequences of pigs retrieved from GenBank (see Additional file 3: Table S2). All 923 sequences were aligned and trimmed to 464 bp, which corresponded to nucleotide positions between 112 and 575 of the reference sequence EF545567 . A median-joining network of 923 pig sequences was constructed using NETWORK 5.0 .
Paternal genetic data were also obtained from 57 Nigerian indigenous sires (see Additional file 1: Table S1) by sequencing 370 bp of intron 1 and part of the flanking exons 1 and 2 of the Y-linked gene UTY (ubiquitously transcribed tetratricopeptide repeat), which contains repeats (see methods in Additional file 2; GenBank accession numbers: KU561941–KU561970 and KY234314–KY234340). Single nucleotide polymorphisms (SNPs) in the UTY amplicon were used to diagnose Y-chromosome lineages HY1 and HY2 versus HY3 .
Analysis of MC1R sequences
Finally, we analyzed sequence variation in MC1R for 90 NIP (see Additional file 1: Table S1) by sequencing the entire MC1R-coding region i.e. 963 bp (see methods in Additional file 2; GenBank accession numbers: KX264504–KX264593).
Results and discussion
All of the 57 analyzed Nigerian sires were assigned to the HY1 haplotype only (data not shown), which occurs widely in both Europe and Asia . None of the NIP were assigned to HY3, which is unique to Asia and was detected at considerable high frequency in Kenyan pigs (35%) and Zimbabwean Mukota pigs (100%) . This might be due to the influence of East/Southeast Asian pigs on African pigs and, particularly the Mukota pigs from Zimbabwe, which closely resemble the Chinese lard pig, in terms of morphology. Our finding agrees with that of an earlier study that reported Western ancestry for West African pigs .
Direct selection for non-camouflage patterns was proposed to be an essential component of the selection of coat color loci in domestic animals , which may have been fostered by animal husbandry. Independent selective sweeps have been identified in Chinese and European pigs resulting in the dominant black color. For instance, in Polynesia and Europe, selection of pigs for the D124N substitution in MC1R resulted in a dominant black color, whereas selection for the L102P substitution in MC1R was responsible for the dominant black color in Chinese pigs [13–15]. These mutations have been used to differentiate Polynesian, European and Asian black pigs. Therefore, the high frequency of the European dominant black color haplotype in NIP suggests the occurrence of gene flow from local European pig breeds. The NIP individuals that carry the East Asian MC1R haplotype might have originated from European black pigs, which agrees with findings from a genome-wide analysis that showed that introgression of Asian haplotypes via anthropogenic hybridization and selection has influenced the genomic architecture of European pigs . Similarly, another possibility is a direct Asian introgression in NIP. Future investigations based on evidence from whole-genome sequence data should test these possibilities (Additional file 2).
In summary, this study reveals that NIP have mainly a European ancestry with some East/Southeast Asian ancestry, which may be due to direct introgression or through introgression from European pig breeds, themselves derived from introgression with Asian breeds. It also provides a first glimpse on MC1R variation across populations of indigenous pigs in one West Africa country. This study was designed to provide a valuable resource for future studies on whole-genome analyses of African pigs.
ACA, MSP, and YPZ conceived the work. ACA, OOO, BMO, TOO, BB, SCO, and OJS performed animal sampling, ACA and LMN performed the experiment. ACA and MSP performed data analysis. LMN provided technical assistance. ACA, LF, RWM, HBX, MSP, and YPZ were involved in the writing of the paper. All authors read and approved the final manuscript.
We are grateful to all volunteers who assisted in sampling. This work was supported by the Sino-Africa Joint Research Center, Chinese Academy of Sciences (SAJC201611 and SAJC201306) and the Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (the Large Research Infrastructure Funding). The Youth Innovation Promotion Association, Chinese Academy of Sciences provided support to MSP. In addition, this work was also supported, in part, by the Chinese Academy of Sciences President’s International Fellowship Initiative (2017VBA0003), and the manuscript preparation by a Natural Sciences and Engineering Research Council of Canada Discovery Grant A3148 to R.W.M.
The authors declare that they have no competing interests.
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