Format

Send to

Choose Destination
BMC Genomics. 2015 Dec 29;16:1115. doi: 10.1186/s12864-015-2342-2.

Whole mitochondrial genomes unveil the impact of domestication on goat matrilineal variability.

Author information

1
Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. licia.colli@unicatt.it.
2
Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. licia.colli@unicatt.it.
3
Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. hovirag.lancioni@unipg.it.
4
Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. cardinali_irene@libero.it.
5
Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. anna.olivieri@unipv.it.
6
Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. marcocapo87@yahoo.it.
7
Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. marcocapo87@yahoo.it.
8
Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. marcopellecchia@koineambiente.com.
9
Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. Marcin.Rzepus@unicatt.it.
10
Institute of Food Science and Nutrition - ISAN, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. Marcin.Rzepus@unicatt.it.
11
Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. zamani_wahid@yahoo.com.
12
Department of Environmental Sciences, Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Noor, Mazandaran, 46414-356, Iran. zamani_wahid@yahoo.com.
13
Natural Resources Faculty, University of Guilan, Guilan, 41335-1914, Iran. naderi@guilan.ac.ir.
14
Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. francesca.gandini01@universitadipavia.it.
15
School of Applied Sciences, University of Huddersfield, Huddersfield, HD1 3DH, UK. francesca.gandini01@universitadipavia.it.
16
Agricultural Biotechnology Research Institute of Iran (ABRII), North Branch, Rasht, 41635-4115, Iran. smf.vahidi@gmail.com.
17
Department of Animal Production, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt. safsoof23@hotmail.com.
18
Laboratorio di Genetica, Istituto per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, 40064, Italy. ettore.randi@isprambiente.it.
19
Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, DK-9000, Denmark. ettore.randi@isprambiente.it.
20
Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. vincenza.battaglia@unipv.it.
21
Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy. mariateresa.sardina@unipa.it.
22
Dipartimento Scienze Agrarie e Forestali, Università degli Studi di Palermo, Palermo, 90128, Italy. baldassare.portolano@unipa.it.
23
Environmental Sciences Department, Gorgan University of Agriculture and Natural Resources, Gorgan, 49138-15739, Iran. hamid.r.rezaei@gmail.com.
24
Natural History Museum of Crete, University of Crete, Iraklio, Crete, 71409, Greece. lyberis@nhmc.uoc.gr.
25
Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. frederic.boyer@ujf-grenoble.fr.
26
Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. eric.coissac@inria.fr.
27
Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. francois.pompanon@ujf-grenoble.fr.
28
Université Grenoble Alpes, Laboratoire d'Ecologie Alpine, Grenoble, 38041, France. pierre.taberlet@ujf-grenoble.fr.
29
Institute of Zootechnics, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. paolo.ajmone@unicatt.it.
30
Research Center on Biodiversity and Ancient DNA - BioDNA, Università Cattolica del S. Cuore, Piacenza, 29122, Italy. paolo.ajmone@unicatt.it.
31
Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Perugia, 06123, Italy. alessandro.achilli@unipv.it.
32
Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, 27100, Italy. alessandro.achilli@unipv.it.

Abstract

BACKGROUND:

The current extensive use of the domestic goat (Capra hircus) is the result of its medium size and high adaptability as multiple breeds. The extent to which its genetic variability was influenced by early domestication practices is largely unknown. A common standard by which to analyze maternally-inherited variability of livestock species is through complete sequencing of the entire mitogenome (mitochondrial DNA, mtDNA).

RESULTS:

We present the first extensive survey of goat mitogenomic variability based on 84 complete sequences selected from an initial collection of 758 samples that represent 60 different breeds of C. hircus, as well as its wild sister species, bezoar (Capra aegagrus) from Iran. Our phylogenetic analyses dated the most recent common ancestor of C. hircus to ~460,000 years (ka) ago and identified five distinctive domestic haplogroups (A, B1, C1a, D1 and G). More than 90 % of goats examined were in haplogroup A. These domestic lineages are predominantly nested within C. aegagrus branches, diverged concomitantly at the interface between the Epipaleolithic and early Neolithic periods, and underwent a dramatic expansion starting from ~12-10 ka ago.

CONCLUSIONS:

Domestic goat mitogenomes descended from a small number of founding haplotypes that underwent domestication after surviving the last glacial maximum in the Near Eastern refuges. All modern haplotypes A probably descended from a single (or at most a few closely related) female C. aegagrus. Zooarchaelogical data indicate that domestication first occurred in Southeastern Anatolia. Goats accompanying the first Neolithic migration waves into the Mediterranean were already characterized by two ancestral A and C variants. The ancient separation of the C branch (~130 ka ago) suggests a genetically distinct population that could have been involved in a second event of domestication. The novel diagnostic mutational motifs defined here, which distinguish wild and domestic haplogroups, could be used to understand phylogenetic relationships among modern breeds and ancient remains and to evaluate whether selection differentially affected mitochondrial genome variants during the development of economically important breeds.

PMID:
26714643
PMCID:
PMC4696231
DOI:
10.1186/s12864-015-2342-2
[Indexed for MEDLINE]
Free PMC Article

Publication type, MeSH terms, Substance, Secondary source ID

Publication type

MeSH terms

Substance

Secondary source ID

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center