Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

Haqani, Mohammad Ibrahim; Nomura, Shigeru; Nakano, Michiharu; Goto, Tatsuhiko; Nagano, Atsushi J.; Takenouchi, Atsushi; Nakamura, Yatsuka; Ishikawa, Akira; Tsudzuki, Masaoki

doi:10.1007/s00438-021-01806-w

Cited by 5 publications

(12 citation statements)

References 99 publications

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“…Thus, the F 2 quail reference population we developed was a convenient model for conducting this GWAS for meat productivity. This implemented approach was in line with the creation and wide implementation of F 2 reference populations for molecular genetic studies in various poultry species, e.g., in chickens [ 22 , 78 ], turkeys [ 79 ], ducks [ 48 ], and quails [ 35 , 36 , 38 , 41 , 47 ]. This enabled an increase in the power and sensitivity of detecting QTLs, when forming a sample of experimental birds for the GWAS analysis (despite a relatively low sample size).…”

Section: Discussionmentioning

confidence: 96%

“…Among the disadvantages of this microsatellite-assisted approach, certain complications in mapping and identifying the respective genes should be noted. Over the last years, there has been a rise in the number of studies that employ SNPs as genetic markers and genome-wide SNP genotyping [ 10 , 35 ]. Using this technique and the genome-wide association study (GWAS) approach in quail, significant SNPs and putative genes have been identified in terms of their association with performance traits [ 36 , 37 ], behavior [ 38 , 39 ], plumage color [ 10 ], reproductive traits [ 40 ], and egg quality [ 41 , 42 ].…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail

Volkova,

Romanov,

Abdelmanova

et al. 2024

Genes

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The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the domestic quail. A total of 146 males from an F2 reference population resulting from crossing a fast (Japanese) and a slow (Texas White) growing breed were examined. Using the genotyping-by-sequencing technique, genomic data were obtained for 115,743 SNPs (92,618 SNPs after quality control) that were employed in this GWAS. The results identified significant SNPs associated with the following traits at 8 weeks of age: body weight (nine SNPs), daily body weight gain (eight SNPs), dressed weight (33 SNPs), and weights of breast (18 SNPs), thigh (eight SNPs), and drumstick (three SNPs). Also, 12 SNPs and five candidate genes (GNAL, DNAJC6, LEPR, SPAG9, and SLC27A4) shared associations with three or more traits. These findings are consistent with the understanding of the genetic complexity of body weight-related traits in quail. The identified SNPs and genes can be used in effective quail breeding as molecular genetic markers for growth and meat characteristics for the purpose of genetic improvement.

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Section: Discussionmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail

Volkova,

Romanov,

Abdelmanova

et al. 2024

Genes

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“…The differences among the results of these studies may be explained by the different durations of egg production. In our previous report, we identified a QTL for growth-related traits on chromosome 1 using the same Japanese quail strains 16 . Similarly, in the present study, two associations were found on the same locus (150,370,977 bp) on chromosome 1 for BW 4 and 5.…”

Section: Discussionmentioning

confidence: 99%

“…Reference 2 identified 22 QTLs for body weight, egg weight, number of eggs laid, and age of the first egg using SNP markers. References 16 , 17 discovered four QTLs for body weight and nine QTLs for egg-related traits using the RAD-seq method. Moreover, microsatellite markers have been used to detect QTLs for traits associated with body weight traits 18 – 23 , growth and egg production 3 , 24 , and egg-laying curves 25 .…”

Section: Introductionmentioning

confidence: 99%

Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

Haqani,

Nakano,

Nagano

et al. 2023

Sci Rep

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This study was designed to perform an association analysis and identify SNP markers associated with production traits of Japanese quail using restriction-site-associated DNA sequencing. Weekly body weight data from 805 quail were collected from hatching to 16 weeks of age. A total number of 3990 eggs obtained from 399 female quail were used to assess egg quality traits. Egg-related traits were measured at the beginning of egg production (first stage) and at 12 weeks of age (second stage). Five eggs were analyzed at each stage. Traits, such as egg weight, egg length and short axes, eggshell strength and weight, egg equator thickness, yolk weight, diameter, and colour, albumen weight, age of first egg, total number of laid eggs, and egg production rate, were assessed. A total of 383 SNPs and 1151 associations as well as 734 SNPs and 1442 associations were identified in relation to quail production traits using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. The GLM-identified SNPs were located on chromosomes 1–13, 15, 17–20, 24, 26–28, and Z, underlying phenotypic traits, except for egg and albumen weight at the first stage and yolk yellowness at the second stage. The MLM-identified SNPs were positioned on defined chromosomes associated with phenotypic traits except for the egg long axis at the second stage of egg production. Finally, 35 speculated genes were identified as candidate genes for the targeted traits based on their nearest positions. Our findings provide a deeper understanding and allow a more precise genetic improvement of production traits of Galliformes, particularly in Japanese quail.

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“…Recently, the whole genome sequence of quail [ 4 , 5 ] has been analyzed using population genomics [ 6 ]. Quantitative trait loci (QTLs) for growth, egg, and meat traits have been revealed so far [ 7 , 8 , 9 , 10 ]. Accumulating knowledge about the loci underlying economic traits is essential for understanding the complex genetic basis of animal production [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

Establishment of Wild-Derived Strains of Japanese Quail (Coturnix japonica) in Field and Laboratory Experiments

Goto

Konno

2023

Biology

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Domestic quail are used as both farm and laboratory animals. As the wild ancestor of quails is “endangered,” field studies are needed to conserve them. If wild-derived strains of quail are established, they will be unique genetic resources for both farm and laboratory animals. The purpose of the present study was to conduct a field study and create wild-derived quail strains using the breeding stocks in Tokachi, Hokkaido, Japan. Field observations from 2019 to 2022 indicate that wild quails migrate and stay at reproductive sites from late April to late October. Our estimations of the approximate ages of the observed and captured quails imply that adult males have intermittent reproductive opportunities from May to August. Morphological traits collected from adult and juvenile quails in the 2019–2022 population were similar to those previously reported for Japan’s 1914 and 1970 populations. Using natural mating of captured wild males and domestic (Dom) females, we established the W50 and W75 strains, which possessed 50% and 75% genetic contributions from the wild stocks. These unique genetic resources can be applied for future conservation and experimental use to understand the domestication history and genetic basis of quantitative traits.

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Quantitative trait loci for growth-related traits in Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

Cited by 5 publications

References 99 publications

Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail

Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail

Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing

Establishment of Wild-Derived Strains of Japanese Quail (Coturnix japonica) in Field and Laboratory Experiments

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