Yong Jia

1. Barley PanTs Supplementary Data1-8_10-14.xlsx
Ten Datasets referred to in the main text (Supplementary Data 1-10), presented in tabular format as separate sheets in a joint Excel formatted file.
Supplementary Data 1: Basic statistics of the RTDs
Supplementary Data 2: Ordering of genotypes incorporated into the linear pan-genome.
Supplementary Data 3: Gene categories of GsRTD
Supplementary Data 4: Alternative splicing events for highly expressed transcripts from core-single-copy genes (average TPM > 10)
Supplementary Data 5: Gene copy number variation cluster significantly correlated with the gene expression.
Supplementary Data 6: C-repeat/DRE-Binding Factor (CBF) genes identifier in GsRTD and their location in the genome
Supplementary Data 7: Genotypes with the 141Mb 7H inversion and non-inversion
Supplementary Data 8: Differentially expressed genes in the 7H inversion.
Supplementary Data 10: Detailed example of a split pattern in Golden Promise
Supplementary Data 11: Barley cv. Morex Expression Atlas Metadata
Supplementary Data 12: GA-Pathway gene expression in PanTs experiment
Supplementary Data 13: Yield and agro data for Ga2ox3-7
Supplementary Data 14: Statistics GA2ox and 7

2. Supplementary Data9.csv A csv file containing genotype-specific co-expression network results (modules and community assignments) with annotation and MorexV3 gene IDs.

3. Supplementary Data15.txt This tab delimited text file is too large for inclusion in the main Supplementary Data file and contains the details of how genes/transcripts from the genotype specific RTDs map onto genes in PanBaRT20.

Phenotype and genotype data collected from the GRDC-funded project UMU2303-003RTX (Developing genetic tools to facilitate breeder use and deployment of high value acid soils tolerant chickpea germplasm). The genotype data consisted of approximately 4,300 high-quality SNP markers of 520 chickpea accessions. The phenotype data, including the tolerance index, plant growth data and yield-related traits, were collected from multiple trials across Australia from 2023 to 2025.