Molecular Plant Breeding 2024, Vol.15, No.4, 198-208 http://genbreedpublisher.com/index.php/mpb 201 Figure 2 DXS2 alters carotenoid biosynthesis in maize kernels, and changes in allele frequency of the favorable DXS2 allele during maize domestication and improvement (Adopted from Fang et al., 2019) Image caption: (a) LOD profiles of the QTL cluster qKC7-1 for carotenoid-related traits. (b) Fine mapping of qKC7-1 and gene structure of DXS2. Numbers near markers denote the number of recombinants. Dark-gray and light-gray shading represents exons and UTRs, respectively. The red diamond indicates the 51-bp InDel in exon 1 of DXS2. The red bars in exon 1 indicate the targeting sites for sgRNA. (c) Sequences of DXS2 in a CR-dxs2 plant and its wide type (WT). Nucleotides in red denote the sgRNA targets, and boxed nucleotides indicate the protospacer-adjacent motif (PAM, i.e. NGG). (d) Kernel performance for CR-dxs2 and WT. Scale bar, 0.5 cm. (e) Comparison of kernel carotenoids between CR-dxs2 and WT. Error bars indicate SE based on five biological replicates. *P < 0.05, **P < 0.01, Student’s t-test. (f) DXS2-based candidate-gene association analysis for kernel color and the linkage disequilibrium (LD) patterns for all identified variants (MAF≥0.05) at the DXS2 locus. The most significant TE-PAV is shown in red. The intensity of gray shading indicates the extent of LD (r2) between TE-PAV and the other variants identified in this region. The gene structure is shown on the x-axis. Dark-gray and light-gray shading represents exons and UTRs, respectively. (g) Comparison of DXS2 expression in TE+ and TE− genotypes. (h) The effect of TE-PAV in an association mapping panel. (i) Correlation of kernel total carotenoid content with the relative expression of DXS2 in kernels at 15 DAP. Dot color: red, TE−; green, TE+. (j) Expression pattern of DXS2 in endosperms at different developmental stages. NIL, near-isogenic line. (k) Changes in the frequency of the TE during maize domestication and improvement (Adopted from Fang et al., 2019) 4.2 Marker-assisted selection (MAS) Marker-assisted selection (MAS) leverages molecular markers linked to desirable traits to accelerate the breeding process. This technique allows for the precise selection of individuals carrying the target traits, thereby reducing
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