Lex Bird Breeding System published in Nature Genetics

Image: Arjan Haverkamp (via Wikipedia)

The high quality genome assembly of a wild wading bird, the ruff Philomachus pugnax, generated by Edinburgh Genomics, has been used to reveal the genetics of a striking natural polymorphism affecting plumage, behaviour and mating success. The work is published today in Nature Genetics - DOI: 10.1038/ng.3443.

Edinburgh Genomics collaborated closely with colleagues in Sheffield, Canada, USA, Netherlands, Russia and Austria to analyse the genomic basis of the fascinating system of male morphs in the ruff, a wading bird. We found that the three different male types – a standard “independent” morph that displays to females on a fiercely defended territory, a “satellite” morph that is not territorial, and a “faeder” morph that behaves like a female – are determined by alleles at a single locus, a “supergene”. In satellite and faeder males, a large segment of the chromosome is inverted compared to wild type territorial males, and further complex rearrangements within the inversion distinguish these two. The large inversion disables an essential gene (explaining the relative rarity of the alternate morphs) and traps a series of genes involved in plumage colouration and androsteroid metabolism. The international team also determined that different male ruff morphs have differing androsteroid levels during mating, correlating with the genetic findings.

Edinburgh Genomics collaborated by generating deep genome coverage from standard and mate-pair libraries of a focal individual on our HiSeq2500 v4 instruments. These data, along with PacBio reads, were used to assemble the 1.2 gigabase genome. We also generated a RADSeq genetical genomic map from a controlled pedigree to pin down the satellite/faeder inversion locus, and used deep sequencing data from many additional birds of known genotype to reveal the pattern and likely process of rearrangement. The genome assembly and annotation was carried out by Dr Judith Risse of Edinburgh Genomics, who is first joint author on the Nature Genetics manuscript. The project in Edinburgh was led by Mark Blaxter.