Rice Genomics and Genetics 2024, Vol.15, No.4, 164-177 http://cropscipublisher.com/index.php/rgg 170 MIKC*-type MADS-box transcription factors and RopGEF genes, with a correlation coefficient (PCC) of gene expression higher than 0.85, indicating strong functional redundancy among these genes. Figure 3 (c) illustrates an example of overcoming functional redundancy in the RSL gene family within the bHLH gene family, by comparing root hair length among wild-type, single mutants, and double knockout mutants, particularly noting significant root hair shortening in the double knockout mutants. These findings provide crucial insights into understanding gene functions in organisms and how gene editing technologies can be leveraged for agricultural biotechnology improvements (Figure 3). Figure 3 Validation and case studies of functional redundancy using CAFRI-Rice (Adopted from Hong et al., 2020) Image caption: a: Functional dominance of three characterized anther/pollen genes predicted by CAFRI-Rice The left and right phylogenetic heatmaps indicate the functional dominance of the RUPO and MATL genes, respectively. In the nearest gene clade, there are one and two sister nodes, or genes which show different expression patterns than the two queried genes. The phylogenetic heatmap of MTD1, which is located in the center, represents the functional dominance regardless of the nearest gene clade as ‘unique’ clade gene; b: Functional redundancy of two characterized anther/pollen genes predicted by CAFRI-Rice. The phylogenetic heatmap on the left indicates the functional redundancy of two S-clade MIKC*-type MADS box transcription factors. The phylogenetic heatmap on the right presents the functional redundancy among four RopGEF genes. Both analyses yielded high PCC values (above 0.85), implying strong redundancy; c: Example of overcoming the functional redundancy among the RSL class I genes within the bHLH gene family. The two RSL class I genes that exhibited a predicted functional redundancy by CAFRI-Rice are highlighted in red. The middle panel provides root hair photographs from wild-type plants, single mutants, and double knockout mutants. The white bar in the picture represents 500 μm (Adopted from Hong et al., 2020) 5.2 Marker-assisted selection and genomic selection Marker-assisted selection (MAS) and genomic selection (GS) are pivotal in modern rice breeding programs. The development of molecular markers is essential for these techniques, enabling the identification of desirable traits at the genetic level. Advances in high-throughput sequencing and genotyping technologies have facilitated the discovery of numerous molecular markers linked to important agronomic traits. These markers are instrumental in accelerating the breeding process by allowing for the early selection of superior genotypes. For example, the development of introgression lines using molecular markers has enabled the incorporation of favorable alleles
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