Genomics and Applied Biology 2024, Vol.15, No.3, 142-152 http://bioscipublisher.com/index.php/gab 146 4.2 Identification of key genes responsible for desirable traits Identifying key genes responsible for target traits such as growth, disease resistance, and drought tolerance is the foundation of functional genomics. In Eucommia ulmoides, several studies have focused on quantitative trait loci (QTL) analysis and identified candidate genes related to growth traits. For instance, one study identified 89 putative QTLs associated with growth traits, including 25 related to tree height, 32 related to ground diameter, and 15 related to crown diameter (Jin et al., 2020). Another study used single nucleotide polymorphism (SNP) markers to construct a high-density genetic map, identifying 44 QTLs related to growth traits and 33 candidate genes involved in energy storage, signal transduction, hormones, and metabolic pathways (Liu et al., 2022). These findings provide a solid foundation for improving the genetic basis of Eucommia ulmoides through genome-assisted breeding. 4.3 Case study: genetic improvement of stress resistance through genomics-assisted breeding A notable case study in the genetic improvement of stress resistance through genomics-assisted breeding can be seen in the application of genomic selection (GS) in various crops and tree species. GS uses genetic markers covering the whole genome to predict breeding values with high accuracy, thereby facilitating the rapid selection of superior genotypes (Goddard and Hayes, 2007; Crossa et al., 2017). In Eucommia ulmoides, the integration of functional genomics with breeding programs has led to the identification of key genes and QTLs associated with stress resistance traits. For instance, the MYB transcription factor family in E. ulmoides has been studied for its role in regulating rubber biosynthesis and stress responses, providing valuable insights for breeding programs aimed at enhancing stress resistance (Hu et al., 2023) (Figure 2). By leveraging these genomic tools and insights, breeders can develop E. ulmoides varieties with improved stress resistance, contributing to the sustainability and productivity of this economically important tree species. 5 Genomic Tools and Resources for E. ulmoides 5.1 Overview of current genomic databases and resources for E. ulmoides The genomic resources for Eucommia ulmoides have significantly expanded in recent years, providing valuable data for both basic and applied research. A high-quality chromosome-level genome assembly for the female E. ulmoides was obtained using PacBio and Hi-C technologies, resulting in a 1.01 Gb genome with 17 pseudochromosomes and 31 665 protein-coding genes. This assembly also facilitated the reassembly of the male genome, enhancing its scaffold N50 to 48.30 Mb and increasing the number of predicted genes by 11 266 (Du et al., 2023). Additionally, a high-quality haploid genome assembly was generated, improving the scaffold N50 to 53.15 Mb and providing insights into rubber biosynthesis and genome evolution (Li et al., 2020). These genomic assemblies are crucial for understanding the genetic basis of important traits and for advancing breeding programs. 5.2 High-throughput sequencing platforms and bioinformatics tools for functional analysis High-throughput sequencing platforms such as Illumina, PacBio, and Hi-C technologies have played a crucial role in generating comprehensive genomic and transcriptomic data for Eucommia ulmoides. For example, the Illumina platform was used for sequencing the transcriptomes of male and female flower buds, identifying 75 065 unigenes and a large number of single nucleotide polymorphisms (SNPs) (Liu et al., 2016). PacBio and Hi-C technologies were employed to produce high-quality genome assemblies, which are essential for detailed functional genomics studies (Li et al., 2020; Du et al., 2023). Bioinformatics tools such as Trinity have been used for de novo assembly of large datasets, and various annotation pipelines have been analyzed to provide in-depth insights into gene function and regulation for functional analysis of Eucommia ulmoides (Liu et al., 2016). 5.3 Importance of genome-wide association studies (GWAS) and quantitative trait loci (QTL) mapping Genome-wide association studies (GWAS) and quantitative trait loci (QTL) mapping are pivotal for identifying genetic variants associated with important traits in E. ulmoides. A high-density genetic map constructed using genotyping-by-sequencing (GBS) identified 191 095 SNPs and mapped 10 103 SNP markers across 17 linkage groups, covering 90% of the genome. This map facilitated the detection of 44 QTLs associated with growth traits, providing a foundation for marker-assisted selection (Liu et al., 2022). Another study updated the genetic linkage
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