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

Morris, Katrina M.; Hindle, Matthew; Boitard, Simon; Burt, David W.; Danner, Angela; Eöry, Lél; Forrest, H. S.; Gourichon, David; Gros, Jérôme; Hillier, LaDeana W.; Jaffredo, Thierry; Khoury, Hanane; Lansford, Rusty; Leterrier, Christine; Loudon, A. S. I.; Mason, Andrew S.; Meddle, Simone; Minvielle, Francis; Minx, Patrick; Pitel, Frédérique; Seiler, J.; Shimmura, Tsuyoshi; Tomlinson, Chad; Vignal, Alain; Webster, Robert G.; Yoshimura, Takashi; Warren, Wesley C.; Smith, Jacqueline

doi:10.1186/s12915-020-0743-4

Cited by 54 publications

(46 citation statements)

References 123 publications

(172 reference statements)

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“…2018) and Japanese quail (Morris et al . 2020) were developed. As our experiment with several full‐ and half‐sib families and approximately 1000 animals across three generations can be seen as a powerful linkage mapping design, we developed a further linkage map.…”

Section: Discussionmentioning

confidence: 99%

Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica)

et al. 2020

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SummaryA large F2 cross with 920 Japanese quail was used to map QTL for phosphorus utilization, calcium utilization, feed per gain and body weight gain. In addition, four bone ash traits were included, because it is known that they are genetically correlated with the focal trait of phosphorus utilization. Trait recording was done at the juvenile stage of the birds. The individuals were genotyped genome‐wide for about 4k SNPs and a linkage map constructed, which agreed well with the reference genome. QTL linkage mapping was performed using multimarker regression analysis in a line cross model. Single marker association mapping was done within the mapped QTL regions. The results revealed several genome‐wide significant QTL. For the focal trait phosphorus utilization, a QTL on chromosome CJA3 could be detected by linkage mapping, which was substantiated by the results of the SNP association mapping. Four candidate genes were identified for this QTL, which should be investigated in future functional studies. Some overlap of QTL regions for different traits was detected, which is in agreement with the corresponding genetic correlations. It seems that all traits investigated are polygenic in nature with some significant QTL and probably many other small‐effect QTL that were not detectable in this study.

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Section: Discussionmentioning

confidence: 99%

Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica)

et al. 2020

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“…We have compared these sequences with Japanese quail protein sequences that were available in databases. The most recently published quail genome is by Morris et al (2020). They stated that the genome sequence of Coturnix japonica is close to completion.…”

Section: Calpeptin Does Not Inhibit Myofibrillogenesismentioning

confidence: 99%

Myofibril assembly and the roles of the ubiquitin proteasome system

et al. 2020

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De novo assembly of myofibrils in vertebrate cross-striated muscles progresses in three distinct steps, first from a minisarcomeric alignment of several nonmuscle and muscle proteins in premyofibrils, followed by insertions of additional proteins and increased organization in nascent myofibrils, ending with mature contractile myofibrils. In a search for controls of the process of myofibril assembly, we discovered that the transition from nascent to mature myofibrils could be halted by inhibitors of three distinct functions of the ubiquitin proteasome system (UPS). First, inhibition of pathway to E3 Cullin ligases that ubiquitinate proteins led to an arrest of myofibrillogenesis at the nascent myofibril stage. Second, inhibition of p97 protein extractions of ubiquitinated proteins led to a similar arrest of myofibrillogenesis at the nascent myofibril stage. Third, inhibitors of proteolytic action by proteasomes also blocked nascent myofibrils from transitioning to mature myofibrils. In contrast, inhibitors of autophagy or lysosomes did not affect myofibrillogenesis. To probe for differences in the effects of UPS inhibitors during myofibrillogenesis, we analyzed by fluorescence recovery after photobleaching the exchange rates of two selected sarcomeric proteins (muscle myosin II heavy chains and light chains). In the presence of p97 and proteasomal inhibitors, the dynamics of each of these two myosin proteins decreased in the nascent myofibril stage, but were unaffected in the mature myofibril stage. The increased stability of myofibrils occurring in the transition from nascent to mature myofibril assembly indicates the importance of dynamics and selective destruction in the muscle myosin II proteins for the remodeling of nascent to mature myofibrils.

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“…In addition, the Japanese quail shows close phylogenetic relatedness to chickens with similar length of genome, chromosome number, and morphology of chromosomes. Therefore, a high rate of contiguity, assembly statistics, gene content, chromosomal organization, and synteny conservation exists between the two species [ 42 , 80 ]. Knaga et al [ 31 ] reported QTL for the egg number and egg production rate at positions 36 to 42 cM on chromosome 1 using 30 microsatellite markers.…”

Section: Discussionmentioning

confidence: 99%

Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

Haqani

Nomura

Nakano

et al. 2021

Genes

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This research was conducted to identify quantitative trait loci (QTL) associated with egg-related traits by constructing a genetic linkage map based on single nucleotide polymorphism (SNP) markers using restriction-site associated DNA sequencing (RAD-seq) in Japanese quail. A total of 138 F2 females were produced by full-sib mating of F1 birds derived from an intercross between a male of the large-sized strain with three females of the normal-sized strain. Eggs were investigated at two different stages: the beginning stage of egg-laying and at 12 weeks of age (second stage). Five eggs were analyzed for egg weight, lengths of the long and short axes, egg shell strength and weight, yolk weight and diameter, albumen weight, egg equator thickness, and yolk color (L*, a*, and b* values) at each stage. Moreover, the age at first egg, the cumulative number of eggs laid, and egg production rate were recorded. RAD-seq developed 118 SNP markers and mapped them to 13 linkage groups using the Map Manager QTX b20 software. Markers were spanned on 776.1 cM with an average spacing of 7.4 cM. Nine QTL were identified on chromosomes 2, 4, 6, 10, 12, and Z using the simple interval mapping method in the R/qtl package. The QTL detected affected 10 egg traits of egg weight, lengths of the long and short axes of egg, egg shell strength, yolk diameter and weight, albumen weight, and egg shell weight at the beginning stage, yellowness of the yolk color at the second stage, and age at first egg. This is the first report to perform a quail QTL analysis of egg-related traits using RAD-seq. These results highlight the effectiveness of RAD-seq associated with targeted QTL and the application of marker-assisted selection in the poultry industry, particularly in the Japanese quail.

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

Cited by 54 publications

References 123 publications

Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica)

Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica)

Myofibril assembly and the roles of the ubiquitin proteasome system

Mapping of Quantitative Trait Loci Controlling Egg-Quality and -Production Traits in Japanese Quail (Coturnix japonica) Using Restriction-Site Associated DNA Sequencing

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