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

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

doi:10.3390/genes12050735

Mohammad Ibrahim Haqani, Atsushi Takenouchi + Show 7 more

Open Access

https://doi.org/10.3390/genes12050735

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Abstract

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.

Highlights

Tremendous progress has been made in poultry egg production and breeding programs over the past decades, leading to the fast-growing livestock industry
The LS birds presented the highest values for EW1, ELA1, ESA1, AW1, YW1, ESW1, EW2, ESA2, AW2, and ESW2 traits
The present study revealed nine quantitative trait loci (QTL) for 10 egg-related traits (EW1, ELA1, ESA1, ESS1, YD1, AW1, YW1, ESW1, YC-b*2, and at first egg (AFE)) in 138 F2 female Japanese quails

Summary

Introduction

Tremendous progress has been made in poultry egg production and breeding programs over the past decades, leading to the fast-growing livestock industry. Several DNA markers, such as single nucleotide polymorphisms (SNPs) [4], restriction fragment length polymorphisms [5], amplified fragment length polymorphisms (AFLPs) [6], and simple sequence length polymorphisms (or microsatellite) [7], have been used to identify the chromosomal positions of loci. Among these markers, SNPs play a crucial role in genetics, biomedicine, ecology, and evolutionary studies [8,9,10,11]. Restriction-site associated DNA sequencing (RAD-seq) is a GBS method that can simultaneously identify, verify, and score thousands of SNPs, reduce complexity across genomes, deliver high-resolution population genomic data, and be convenient for non-model species at a reasonable cost [20,21,22,23]

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