August 17, 2012

Qualifying diversity in bovine cattle

There is a new open access paper for all those with interest in the genetic history of cows:

Deirdre C. Purfield et al., Runs of homozygosity and population history in cattle. BMC Genetics, 2012. Open access ··> LINK [doi:10.1186/1471-2156-13-70]

The runs of homozygosity (ROH) are used to qualify the nature of the inbreeding (endogamy) process where it exists. When the ROHs are short (for example among Malagassy Zebu), that indicates that the genome has been recombined and fragmented many times, while when the ROH are longer, it can be inferred that inbreeding process is recent, as happened in Jersey and Guernsey, who applied strict cattle regulations since the 19th century.

Fig. 6 - minimally annotated by me
Figure 6 Average sum of Runs of Homozygosity (ROH) per bovine SNP50 animal <20 Mb in length within breed VS average sum of ROH >20 Mb in length. Breeds that originate from the same geographical area tend to cluster together with African Bos taurus breeds showing low levels for both measures, except for the Somba, Oulmès Zaer and Lagune breeds where elevated levels were clearly highly influenced by long ROH whereas the zebu breeds showed intermediate values of ROH but these were more strongly influenced by shorter ROH

The full names of the breeds are:
  • African taurines: Baoule (BAO), Lagoude (LAG), N'Dama (NDA), Oulmès Zaer (OUL),  Somba (SOM)
  • African hybrids: Kuri (KUR), Sheko (SHK)
  • African zebu: Zebu Bororo (ZBO, Zebu Fulani (ZFU), Zebu from Madagascar (ZMA)
  • British Isles: Angus (ANG), Guernsey (GNS), Hereford (HFD), Jersey (JER), Red Angus (RGU)
  • Northern Europe: Bretonne Pied Noire (BPN), Holstein-Friesian (HOL), Maine-Anjou (MAN) Maraichine from Parthenaise (MAR), Monbeliard (MON), Normande (NOR), Norwegian Red Cattle (NRC), French Pied Rouge Lowland (PRP)
  • Central/SW France: Aubrac (AUB), Charolais (CHL), Charolais from UK (CHA), Gascon (GAS), Limousin (LMS), Salers (SAL)
  • Alpine: Abondance (ABO), French Brown Swiss (BRU), Brown Swiss (BSW), Piedmontese (PMT), Romagnola (RMG), Tarine (TAR), Vosgienne (VOS)
  • Zebus: Beef Master (BMA), Brahman (BRM), Gir (GIR), Nelore (NEL), Santa Gertrudis (SGT)

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