Population genomic data reveal genes related to important traits of quail

Abstract

BackgroundJapanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics, and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution, and functional studies.ResultsHere, we present a quail genome assembly spanning 1.04 Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and 2 sex chromosomes Z/W). Our genomic data have resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey), and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHβ), which is correlated with different FSHβ levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type, and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z, which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs.ConclusionsThis study provided a high-quality quail reference genome, identified quail-specific genes, and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color, which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary processes within the Phasianidae family.

The quail genome: insights into social behaviour, seasonal biology and infectious disease response

“…Coturnix japonica 2.0 assembly metrics were comparable to previous assemblies of Galliformes, and superior to other genomes of other quail species [38,39] in ungapped (contigs) sequence length metrics (Table 1). Specifically, in comparison to recently published genomic data from the Japanese quail [39], our genome is substantially less fragmented (contig N50 of 0.511 Mb vs 0.027 Mb), has been assigned to more chromosomes and has more complete annotation with ncRNA, mRNA and pseudogenes predicted. Our estimate of total interspersed repetitive elements was 19% genome-wide based on masking with Windowmasker [40].…”

Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird

“…The achieved BUSCO scores and contig N50 values of the peacock genome were on par or better than many other bird genome assemblies including some of the recently published genomes from Galliformes order (Rhinoceros hornbill, Yellow-thoated sandgrouse, Kea, Chinese bamboo partridge, Mikado Pheasant etc.) ( Zhang G. et al, 2014 ; Lee et al, 2018 ; Tiley et al, 2018 ; Wu et al, 2018 ). For peacock, two genomic libraries with similar insert sizes were used along with a high (136X) sequence coverage.…”

Genome-Wide Association Study to Identify SNPs and Haplotypes Associated with Reproductive Performance and Egg Quality Traits in Geese

“…Sichuan White is a popular Chinese goose breed reared for both meat and eggs. While egg laying and egg quality traits have been studied intensively in avians, including chickens [29,30], ducks [15,31], and quail [32], few studies have examined traits other than those associated with egg laying in the goose genome [13].…”