A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes

Abstract

The helmeted guinea fowl Numida meleagris belongs to the order Galliformes. Its natural range includes a large part of sub‐Saharan Africa, from Senegal to Eritrea and from Chad to South Africa. Archaeozoological and artistic evidence suggest domestication of this species may have occurred about 2,000 years BP in Mali and Sudan primarily as a food resource, although villagers also benefit from its capacity to give loud alarm calls in case of danger, of its ability to consume parasites such as ticks and to hunt snakes, thus suggesting its domestication may have resulted from a commensal association process. Today, it is still farmed in Africa, mainly as a traditional village poultry, and is also bred more intensively in other countries, mainly France and Italy. The lack of available molecular genetic markers has limited the genetic studies conducted to date on guinea fowl. We present here a first‐generation whole‐genome sequence draft assembly used as a reference for a study by a Pool‐seq approach of wild and domestic populations from Europe and Africa. We show that the domestic populations share a higher genetic similarity between each other than they do to wild populations living in the same geographical area. Several genomic regions showing selection signatures putatively related to domestication or importation to Europe were detected, containing candidate genes, most notably EDNRB 2 , possibly explaining losses in plumage coloration phenotypes in domesticated populations.

MLH1 focus mapping in the guinea fowl (Numida meleagris) give insights into the crossover landscapes in birds

“…In the recent genome assembly publication of the guinea fowl, the diploid number of the species was considered as not established [31], but close to 2n = 78 as reported from mitotic metaphases [32]. In our SC spreads we observed consistently 37 autosomal pairs plus the ZW bivalent, and therefore established a diploid number of 76.…”

“…The guinea fowl chromosome #5 is the product of a fusion, with the short arm corresponding to chromosome #6 and the long arm to chromosome #7 of the chicken. [31,32]. These features are reflected in the macro-SC karyotypes where the four largest SCs share similar relative length and arm ratios, and the SC6 of the guinea fowl is comparatively larger than the chicken SC6 but similar in length to SC5 (Fig 3; Table 1).…”

“…To further enhance the knowledge on the recombination landscape in Galliformes we turned to the guinea fowl as this species belongs to Numididae, a family that ranks among the oldest gallinaceous birds. Despite a divergence time of about 47 My, the chicken and guinea fowl macrochromosomes are largely syntenic, with few interchromosomal rearrangements in Numididae [ 31 – 33 ]. Studying the crossover pattern in the guinea fowl would help to understand what effect, in any, evolutionary distances have on recombination patterns in birds.…”

Modulation of Morphology and Glycan Composition of Mucins in Farmed Guinea Fowl (Numida meleagris) Intestine by the Multi-Strain Probiotic Slab51®

“…Guinea fowls are ancestral birds. Currently, the bird bred for meat production is not morphologically selected with respect the wild conspecific specimens that live insub-Saharan Africa, and no appreciable morphological differences are shown between sexes, despite thatadult males are heavier than females [ 26 , 27 ]. Further studies, using a more representative and sexed population of guinea fowls, will be necessary to establish if also in this species the multi-strain probiotic Slab51 ® can guarantee high productive performances as observed in other species [ 28 ].…”

HGFDB: a collective database of helmeted guinea fowl genomics

“…However, only a handful of papers have been published on genetic diversity of HGF, mainly by microsatellite markers ( 7 ) or mtDNA ( 8 , 9 ). It was not until 2019 that the first draft HGF genome assembly obtained by short sequencing reads was published ( 10 ). Based on the third-generation long reads, optical and chromatin interaction mapping, our group has improved the HGF reference genome to the near-chromosome level with contig N50 of 68.3 Mb (Peng, M. et al ., In press).…”