Extended Data Fig. 5: Identification of PsCIK2/3 as a candidate gene for Fa associated with fasciation.
a, Manhattan plot of GWAS based on the ZW6 genome reference, revealing a significant peak for fasciation between 0 and 40 Mb on chromosome 4; b, Close up of Manhattan plot of GWAS in the region of the peak in panel a; c, Bulked segregant mapping analyses (BSA) from sequencing fasciated and wild-type bulks of the F2 populations derived from the cross: Caméor (Fa/Fa) x JI0814 (fa/fa), and JI2822 (Fa/Fa) x JI0816 (fa/fa), further refining the genetic interval for Fa; d, Fine mapping of the Fa locus using two populations. In Caméor x JI0814 (Mapping 1), the region was narrowed down to chr4: 18,144,306-19,945,776 using 8 pairs of KASP markers (Supplementary Table 34); in the JI2822 x JI0816 population (Mapping 2), the interval was further confined chr4:18,180,969-19,506,907 (marker interval AX-183636277-AX183633456, Supplementary Table 18). e, Local detail of the fine-mapped genomic interval from panel d, showing 20 protein-coding genes, with Psat04G0031700 (encoding a Senescence-Associated Receptor-Like Kinase, PsCIK2/3) highlighted in orange; f, Population-based haplotype clustering analysis across the diversity panel for the 1.33Mb Fa region, identifying a cluster of fasciated accessions in Hap5; g, Haplotype clustering analysis of Psat04G0031700 (PsCIK2/3) reveals a 5 bp deletion associated with the fasciated phenotype, clustering all fasciated accessions into Hap3. h, Amino acid sequence alignment of PsCIK2/3 proteins from the wild-type line (JI2822, Fa, Psat04G0031700), the mutant line (JI0816, fa, Psat04G0031700-5bp), and the ortholog from Arabidopsis (AT2G23950.1, AtCIK2).
