- Identification of candidate genomic regions for chicken egg number traits based on. - genome-wide association study. - In the present study, in order to understand the molecular mechanisms underlying the dramatic differences of egg number between commercial egg-type chickens and indigenous chickens, we performed a genome-wide association study (GWAS) in a mixed linear model.. - Furthermore, we identified 32 candidate genes based on the function of the screened genes. - These genes were found to be mainly involved in regulating hormones, playing a role in the formation, growth, and development of follicles, and in the development of the reproductive system. - To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.. - The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.. - Full list of author information is available at the end of the article. - At present, a few candidate genes and regions related to egg number have been reported based on GWAS technology [9, 11–16]. - According to the QTL database QTLs related to chicken economic traits have been identified, 332 of which are associated with egg number.. - When K = 2, Rhode Island Red and one of the White Leghorn groups (WL_YQ) appeared as two differentiated clusters. - Genome-wide association study. - After correction, we found 148 SNPs that could be asso- ciated with egg number (57 significantly, 91 suggestively) (Additional file 1: Table S1). - The chi- square test was carried out to compare the allele fre- quencies of the significant SNPs identified in this region. - 2 QQ plot and Manhattan of the egg number traits. - In the top left of the QQ plot, λ is shown as 1.004. - Table 1 Genome-wide SNPs around significant peaks associated with egg number traits. - Table 1 Genome-wide SNPs around significant peaks associated with egg number traits (Continued). - of the solute carrier family 25 (SLC25A29) is involved in the transport of amino acids. - The results of the QQ plot and λ show that the correction effect is good, and there is no population stratification phenomenon.. - Four of the 148 QTLs in this study were those identi- fied in previous studies. - AX-76715084 is located 0.046 Mb upstream of the GRXCR1 (glutaredoxin and cysteine-rich domain con- taining 1) gene on chromosome 4. - Although these genes Table 1 Genome-wide SNPs around significant peaks associated with egg number traits (Continued). - Table 2 Details for 32 candidate genes that influence egg number traits in different ways. - Influencing the development of the reproductive system. - These genes mainly affect egg number in three ways (Table 2). - Some genes affect egg number traits by affecting the growth and development of follicles. - KITLG plays an important role in the growth and development of follicles [21, 48]. - Therefore, it is reasonable to speculate that KITLG has an important impact on egg number traits.. - It is believed to be involved in the growth and reproduction of livestock [49]. - Liu et al.. - identified three SNPs in the GHRHR promoter that are significantly related to egg number traits in Beijing You chickens [24]. - Group Breeds Abbreviation Sample size Average annual egg number n Total b. - This suggests that this region located on chromosome 12 and the ITPR1 gene may be important for chicken egg number traits. - However, there is no concrete literature to prove that they are associated with egg number traits in chickens, thus further research is still required. - At the same time, interestingly enough, a number of studies have detected regions associated with egg number traits on chromosome 5 [12, 15]. - In this study, we performed a GWAS based on the dif- ference of egg number between high productivity layers and Chinese indigenous chickens and identified a series of SNPs and candidate genes related to reproductive traits. - Four of the SNP effects overlapped with previously reported QTL regions, which supports the results of this study. - They were placed in the high egg productivity group in this study. - The details of the samples are presented in Table 3.. - GWAS analyses of the egg number were performed using a univariate mixed linear model in GEMMA [56].. - Therefore, in this study, we calculated the sum of the number of independent SNPs and LD blocks for correc- tion [59]. - This means that SNPs with P values below are considered and may be associated with egg number traits.. - ensembl.org/index.html) databases. - In addition, regions within 100 kb of a candidate SNP were searched for previously reported QTLs with egg number, egg production or reproductive traits in the chicken QTL database (https://www.animalgenome.org/. - The online version contains supplementary material available at https://doi.. - org/10.1186/s . - Genome-wide SNPs associated with egg number traits.. - Difference of the allele frequencies of the significant SNPs located at Mb on chromosome 5 between the high and low productivity groups.. - U and D represent that SNP located upstream and downstream of the gene, respectively. - U and D represent that SNP located upstream and downstream of the gene, respectively.. - https://doi.org/10.3382/ps . - https://doi.org . - https://doi.org/10.3382/ps/pey172.. - https://doi.. - org/10.1186/s x.. - https://doi.org/10.1017/S . - https://doi.org/10.1007/s . - Genetic effect of the prolactin receptor gene on egg production traits in chickens. - https://doi.org October.2.1.. - https://doi.org/10.3382/ps/peu023.. - https://doi.org/10.1186/s . - https://doi.org/10.. - https://doi.org/10.3389/. - https://doi.org/10.1111/jbg.12086.. - https://doi.org/10.13 71/journal.pone.0028600.. - https://doi.org/10.1371/. - https://doi.org/10.1016/j.anireprosci . - https://doi.org/10.1111/age.12456.. - org/10.1093/nar/gks1150.. - https://doi.org/10.1038/nrg2813.. - org/10.1093/jas/skx038.. - https://doi.org/10.1 007/s . - https://doi.org/10.1111/j x.. - Two mutations in the 5 ′ -flanking region of the KITLG gene are associated with litter size of dairy goats. - https://doi.org/10.1111/age.12277.. - https://doi.org/10.1016/j.gene . - Single-nucleotide polymorphisms in the promoter of the growth hormone-releasing hormone receptor gene are associated with growth and reproduction traits in chickens. - https://doi.org/10.1016/S . - https://doi.org/10.1016/j.jmb . - https://doi.org/10.1210/edrv-15-3-391.. - https://doi.org/10.1371/journal.pone.0094509.. - https://doi.org/10.1186/s y.. - https://doi.org/10.1095/biolreprod . - https://doi.org/10.1023/B:BIGI . - org/10.1074/jbc . - https://doi.org/10.1111/. - https://doi.org/10.1016/j.. - GnRH and GnRH receptors in the pathophysiology of the human female reproductive system. - org/10.1093/humupd/dmv059.. - https://doi.org/10.1 016/j.theriogenology . - https://doi.org/10.7150/jca.23769.. - https://doi.org August.28.12.. - https://doi.org/10.31 68/jds . - https://doi.org/10.1210/endo.141.12.. - Genome-wide association study revealed genomic regions related to white/red earlobe color trait in the Rhode Island red chickens. - https://doi.org/10.1101/gr . - 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