Plant Gene and Traits 2024, Vol.15, No.4, 207-219 http://genbreedpublisher.com/index.php/pgt 213 signature metabolites in different tea phylogenetic groups, aiding in the selection of varieties with desirable quality traits (Yu et al., 2020). 7.3 Outcomes of using genomics in tea breeding and lessons learned The application of genomic tools in tea breeding has led to several significant outcomes. The haplotype-resolved genome assembly of an Oolong tea cultivar, Tieguanyin, has provided insights into the genetic diversity and evolutionary history of tea plants, revealing extensive intra- and interspecific introgressions that contribute to modern cultivar diversity (Figure 3) (Zhang et al., 2021). This genetic information is crucial for targeted breeding programs aimed at enhancing specific quality traits. Figure 3 Genome-wide patterns of genetic introgression to modern tea cultivars from their close relatives (Adopted from Zhang et al., 2021) Image caption: a, Cytonuclear conflicts between nuclear and chloroplast phylogenetic trees among 14 resequenced Camellia section Thea species with C. oleifera included as the outgroup. b, SplitsTree network for Camellia accessions from section Thea. c, Detection of introgression events between C. sinensis and close relatives using the f3 test. Z scores were adjusted based on a Benjamini-Hochberg false discovery-rate correction method, and significant introgression is indicated with purple if adjusted (adj) Z score < -1.96. d, Distribution of 95th percentile fd outliers using modified fd statistics (y axis) in six groups of cultivated tea populations (x axis). The white dot in the center of each violin plot represents the median value, and the bounds of each box indicate first (25%) and third (75%) quartiles. Minima and maxima are present in the lower and upper bounds of the whiskers, respectively, and the width of whiskers are densities of modified fd statistics. P values were calculated using two-sided Fisher’s exact test without multiple comparisons. e, Amount of unique and shared introgressed sequences (in Mb) among six groups of cultivated tea populations. f, Distribution of introgressed loci along chromosomes (chr) 1-15, with the colored bar indicating the maximum of modified fd statistics in each 100-kb non-overlapping window (Adopted from Zhang et al., 2021) Genomic selection has demonstrated moderate to high prediction accuracies for various quality traits, suggesting its potential for implementation in breeding programs (Lubanga et al., 2021). The identification of quantitative trait loci (QTLs) related to important agronomic traits, such as the timing of bud flush, has also been achieved, providing markers for selection in breeding (Tan et al., 2022). However, the integration of genomic tools in tea breeding is not without challenges. The complexity of tea quality traits, influenced by multiple genes and environmental interactions, necessitates comprehensive and multi-faceted approaches. Additionally, the high cost and technical expertise required for genomic analyses can be limiting factors for widespread adoption. 8 Biotechnological Advances inCamellia Breeding 8.1 Genetic engineering and genome editing tools (e.g., CRISPR-Cas9) for trait improvement Genetic engineering and genome editing tools, particularly CRISPR-Cas9, have revolutionized the field of plant breeding by enabling precise modifications to the genome. These tools allow for the targeted alteration of genes associated with desirable traits such as increased yield, stress resistance, and improved nutritional content.
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