Fig. 4: Allelic and copy number variation of ABH.1.

a Haplotype analysis of ABH.1 using whole-genome re-sequencing data from 540 hexaploid and 157 tetraploid wheat accessions. Variants at the coding sequence of ABH.1 were clustered into seven major haplotypes (Hap1-Hap7), while 366 accessions lacked ABH.1 (Hap0). Introns and exons are represented by lines and black boxes, respectively. The coding nucleotide and amino acid sequences of Chinese Spring (CS) are shown in black font, and the bracketed numbers represent the relative positions of nucleotide or amino acid sequences concerning ATG or Met, respectively. Deletions are indicated by the symbol ‘-’. YM14, Yumai14; YBM, Yangbaimai. b Four major representative structural variations of the NE1 locus. Reads from these wheat samples were aligned to the Chinese Spring reference genome sequence IWGSC RefSeq v2.1, and coverage depth for each 5 kb window was computed. The coverage depth for each 5 kb window was then normalized based on the total coverage depth. Finally, the normalized depth for the target region (Chr5B:385.5-390.5 Mb) was presented in the form of a scatter plot, with each data point representing a 5 kb window. c Coverage depth of the ABH.1 gene in the published re-sequence dataset for 540 hexaploidy wheat accessions. The ABH.2 (TraesCS5B03G0565000) gene is situated downstream of ABH.1 (TraesCS5B03G0561800), with the sequencing coverage depth of ABH.2 used as an indicator of normal resequencing outcomes within this genomic region. Reads from wheat samples were aligned to the Chinese Spring RefSeq v2.1, and coverage depth was determined for each gene. The coverage depth for each gene was subsequently normalized by the total coverage depth, and the resulting normalized depth for the target gene was depicted in a scatter plot, with each data point representing a specific wheat accession. The n number is the sample size used to derive statistics. d The expression of ABH.1 was compared among the four CNV (copy number variation) groups (two-sided Student’s t test; centerline, median). RNA-seq data from 305 common wheat genomes (one biological replicate) were used to quantify ABH.1 expression for the four CNV groups. P-values are shown at the top of data points, and n, the sample size used to derive statistics, is listed at the bottom of the figure. TPM, transcripts per million. Source data are provided as a Source Data file.