Animal Molecular Breeding 2024, Vol.14, No.5, 297-306 http://animalscipublisher.com/index.php/amb 300 The introduction of linkage mapping in the early 2000s significantly enhanced the precision of QTL mapping. These early linkage studies utilized F2 crosses between different chicken breeds, allowing researchers to track the inheritance of genetic markers along with phenotypic traits. This approach led to the discovery of multiple QTLs for egg production-related traits, including laying performance and egg quality. For example, a major QTL associated with egg number was identified on chromosome 1, providing insights into the genetic regulation of egg production (Lien et al., 2020). 3.2 Current approaches in QTL mapping for egg production Current approaches to QTL mapping have greatly benefited from the rapid advancements in high-throughput genotyping technologies, particularly genome-wide association studies (GWAS) and SNP array technologies. These tools enable the simultaneous analysis of thousands of genetic markers, providing a deeper understanding of the genetic architecture underlying egg production traits. GWAS has proven especially effective in identifying genetic loci associated with egg production traits, such as age at first egg, egg number, and egg weight. For instance, Figure 2 illustrates a linkage disequilibrium (LD) analysis of significant SNP regions on GGA1 associated with egg number during the third laying period (EN3), revealing high LD among multiple SNPs between 117.87 Mb and 118.36 Mb. This suggests that this region may contain key QTLs influencing egg number. Such analytical methods help researchers precisely locate candidate genes related to egg production and provide valuable targets for marker-assisted selection (MAS) and genomic selection. Recent studies have also identified significant SNPs on multiple chromosomes linked to egg number across different laying stages, offering accurate genetic targets and strategies for breeding improvement (Liu et al., 2019). Figure 2 Linkage Disequilibrium (LD) analyses of SNPs in the significant region (0.49 Mb) for egg number in period 3 (EN3). LD plot of significant SNPs on GGA1 from 117.87 Mb to 118.36 Mb. (Adapted from Liu et al., 2019) Image caption: The linkage disequilibrium (LD) analysis of single nucleotide polymorphisms (SNPs) in the significant region (0.49 Mb) for egg number during the third laying period (EN3). The LD matrix in the figure shows the associations between SNPs located on the GGA1 chromosome within the region from 117.87 Mb to 118.36 Mb. (Adapted from Liu et al., 2019) Additionally, modern QTL mapping has incorporated more refined statistical models, such as mixed linear models, that account for both fixed effects and random population structure, increasing the accuracy of QTL detection. These models are particularly useful in overcoming confounding factors like environmental effects and genetic background noise. Advanced studies have also begun combining QTL mapping with other genomic tools, such as transcriptome analysis, to identify candidate genes responsible for regulating egg production traits. These integrative approaches are enhancing our understanding of the molecular mechanisms underlying QTLs and their functional roles in egg production (Haqani et al., 2021).
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