Doctoral Thesis
Identification of Quantitative Trait Loci (QTL) for Production Traits inJapanese Quail (Coturnix japonica)(Summary)

MOHAMMAD IBRAHIM HAQANI
Graduate School of Biosphere Science
Hiroshima University
September 2020

In the current study, growth performance and nonlinear growth curve functions,quantitative trait loci (QTLs) for growth- and egg-related traits of large- and normal-sized (LS vs.
NS) Japanese quail (Coturnix japonica) were investigated. Growth- and egg-related traits are themost important economic traits in poultry breeding industry. Bird growth is a vital quality criterion
involving changes in the size, shape, weight, and volume of the body. Growth variation wasevaluated by measuring body weight and fitting growth curve models to these measurements.
Growth curve models furnish useful information on bird management and health, age at sexual
maturity, appropriate slaughter age, and the effects of genetic improvements. Quail eggs are asuitable source of animal protein fulfilling the nutritional requirement of the growing world
population, because it contains all the essential amino acids for humans and provides significant
amount of several vitamins and minerals. External and internal egg-related traits are the mostimportant egg traits that influence the quality of eggs, hatching performance, body weight of newly
hatched chicks, propagation of the flocks, and finally breeding’s economy of poultry industry.
Production traits in poultry are complex traits controlled by multiple QTLs and influenced bygenetic and environmental factors and their interactions. QTL analysis for genetic bases ofvariation can increase the response of breeding programs via investigation of genotype andphenotype relationship basis using genomic DNA markers. In QTL analysis, the chromosomal
position of useful loci is identified based on DNA markers especially single nucleotide
polymorphisms (SNPs) markers. Next-generation sequencing (NGS) technologies brought newadvances in genotyping by sequencing (GBS) methods and related bioinformatics computing
resources. This progress caused to facilitate the large-scale discovery of SNPs and made it in a
rapid and cost-eơective manner. Restriction-site associated DNA sequencing (RAD-seq) is one of
the GBS methods that can identify, verify, and score thousands of SNPs simultaneously; reducecomplexity across genome; deliver high resolution population genomic data; and is convenient for
non-model species at a reasonable cost. The current investigation was designed to detect QTLs
underlying growth- and egg-related traits in Japanese quail using the RAD-seq. In general, 805
birds were used to construct the resource family for QTL analysis. Large-sized (LS) and normalsized (NS) quail strains were selected as parental generations. LS and NS quail were reciprocallycrossed. The offspring obtained from the cross between a LS male with three NS females, and aNS male with three LS females were called A and B, respectively. One hundred quail from eachof the LS and NS strains, 50 birds from each of their reciprocal F1 generations (A and B), 277 (138females and 139 males) F2 from F1 A and 228 (111 females and 117 males) F2 from F1 B wereused in this study. Based on these, three studies were performed.
Body weight and nonlinear growth curve analysis
The current investigation was organized to compare the nonlinear regression growthmodels and to fit the best predictive function using the live body weight data of the reciprocal F1
birds mentioned above. Body weight was measured weekly from hatching to 16 weeks of age. In
this study, Weibull, Logistic, Gompertz, Richards and Brody growth models were used todetermine the function that best defines growth. According to the goodness-of-fit criteria (higher
Adj. R2 and lower AIC and BIC), the Richards model showed the best fit in LS females and males(Adj. R2 = 0.999, 0.999, and AIC = 92.007, 81.742, and BIC = 96.173, 85.908, respectively). On
the other hand, the Gompertz exhibited the best fit in the NS quail (Adj. R2 = 0.999, 0.993, andAIC = 67.341, 79.516, and BIC = 70.674, 82.849, in females and males, respectively). The F1 Abirds presented the best fit to the Richards. On the contrary, F1 B quail expressed the best fit to theGompertz function. Weibull and Logistic exhibited the good fit next to the Richards and Gompertz.
While, Brody model presented the poorest fitability to the curve. As a result, both Gompertz andRichards were highly fitted models to describe growth in Japanese quail. Moreover, the growth
pattern of the F1 birds was suggested to be inherited from the male parental strain. To my best
knowledge, this is the first study that compared growth curves in the reciprocal F1 birds and theirparental quail strains. These results will be effective for the QTL analysis of growth curveparameters.
Identification of QTL for growth-related traits
This investigation was designed to identify QTLs for growth-related traits by constructing
a genetic linkage map based on SNP markers using RAD-seq in Japanese quail. A QTL mapping
population of 505 F2 birds was used as materials. Body weight was measured weekly from hatching
to 16 weeks of age. Five nonlinear regression growth models were analyzed, and the growth curveparameters of Richards and Gompertz were selected as the best model for describing a quail growth
curve of the F2 in A and B families, respectively. RAD-seq developed 125 and 109 SNP markers
that were informative between their parental strains in A and B families, respectively. Map
Manager QTX b20 software constructed 16 linkage groups of the SNP markers that spanned 795.9centiMorgan (cM) with an average marker interval of 7.3 cM in A family, and 21 linkage groupsof the SNP markers that spanned 640.0 cM with an average marker interval of 7.3 cM in B family.
QTL analyses of phenotypic traits using R/qtl package revealed 4 main-effect QTLs in A family
and 7 main and 2 epistatic QTLs in B family. Detected QTLs were located on chromosomes 1 and3 in A family and 2, 3, 5, 9, 19, and 20 in B family associated with all BW traits at genome-wide
significant at 1% and 5% and suggestive at 10% levels. No QTL was detected for BW in the second
week of age. This is the first report that identified QTLs for asymptotic weight and weight at
inflection point of the Gompertz parameters, and asymptotic weight, and age and weight at
inflection point of the Richards parameters in Japanese quail. These results highlighted thecombination of QTL studies and the RAD-seq method in Japanese quail and will aid future
breeding programs for identifying genes underlying QTLs and in the application of marker-assisted
selection.
QTL mapping on external and internal egg-related traits
This research was conducted to identify QTLs associated with egg-related traits byconstructing a genetic linkage map based on SNP markers using RAD-seq in Japanese quail. A
total of 2490 eggs were investigated from a QTL mapping population of 249 F2 females at two
different stages, at the first stage of egg-laying and 12 weeks of age. Five eggs were analyzed ateach stage. RAD-seq developed 118 SNP markers in A family and 100 SNP markers in B family,
and the markers were mapped in 13 and 17 linkage groups in each family, using Map Manager
QTX b20 software. The markers spaned 776.1 cM in A family and 628.6 cM in B family with anaverage spacing of 7.4 and 7.6 cM in each family. Main-effect QTLs in A and B families (9 vs. 2QTLs, respectively), for 27 phenotypic traits in each, were identified using “Simple intervalmapping” in R/qtl package. Main-effect QTLs included one for each yellowness of yolk color at
the age of 12 weeks and age at first egg on chromosome 2, one for egg long axis at the first stageof egg-laying on chromosome 4, one for each egg short axis and yolk weight at the first stage ofegg-laying on chromosome 6, one for egg weight, egg short axis, albumen weight, and yolk weightat the first stage of egg production on chromosome 10, one for egg shell weight at the first stageof egg-laying on chromosome 12, and one for each egg short axis and yolk diameter at the firststage of egg-laying on Z chromosome in A family. In B family, one QTL for lightness of yolkcolor at the first stage of egg production on chromosome 7, and one for lightness of yolk color at
12 weeks of age on chromosome 12 were identified. QTLs were detected at genome-widesignificant at 1% and 5% and suggestive at 10% levels. This is the first study that performed QTL
analysis on egg-related traits using RAD-seq.
In general, the findings of this investigation indicated that growth- and egg-related traits
are regulated by many QTLs at different growth stages associated with production in breeding
programs for poultry industries. The findings are useful for developing the Japanese quail QTL
database as well as applying to other Galliformes species, especially chickens. These results
highlighted the effectiveness of RAD-seq associated with QTLs targeted and the application ofmarker-assisted selection in the poultry industry, particularly in Japanese quail.