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.

Chickpea has become an increasingly popular healthy food worldwide. Aluminum (Al) toxicity is a major hurdle for chickpea cultivation and yield improvement in acidic soils. However, the genetic mechanism of Al-tolerance in chickpea remains poorly understood. Here, we performed a large-scale hydroponics screening and SNP chip array genotyping of 1154 diverse chickpea accessions. Root lengths after 6 days cultivation under hydroponics in control (T0: pH 4.2) and Al treatment (T1: pH4.2, 15/20 μM Al3+) were measured. Root tolerance index (RTI = T1/T0) ranking revealed significant variations in chickpea Al-tolerance, with common Australian chickpea cultivars positioned in the low to medium range. Genome-wide association analyses revealed eight QTLs on chromosomes ca1 (CaAlt1-1), ca3 (CaAlt3-1), ca4 (CaAlt4-1, CaAlt4-2), ca5(CaAlt5-1), ca6 (CaAlt6-1), and ca7 (CaAlt7-1, CaAlt7-2) associated with T1, implying a multigenic genetic basis for Al-tolerance in chickpea. Specifically, CaAlt7-2 was associated with both T1 and RTI, whilst CaAlt4-2 was detected for T1 uniquely in the HatTrick x CudiB22C population. Al- tolerant and sensitive haplotypes for the identified QTLs were also identified. Organic acid transporter genes CaMATE2, CaMATE4, and CaALMT1 were found in proximal genomic regions to CaAlt7-2, CaAlt4-1, and CaAlt6-1, respectively. Further qRT-PCR in parental chickpea lines (HatTrick, Slasher, Gunas, CudiB) confirmed that CaMATE2 and CaMATE4 were strongly induced upon Al treatment. Interestingly, CaMATE2 was preferentially expressed in the upper part of the root, whilst CaMATE4 preferentially in the root tips, implying a potential complementary role in Al resistance. Their direct roles in Al tolerance and the potential alternative candidate genes near the QTLs require further investigation. This first report of QTLs on Al-tolerance in chickpea has substantially advanced our understanding of the genetic basis of Al tolerance in chickpea and will facilitate the rapid breeding of Al-tolerant chickpea cultivars for previously un-accessible acidic soils.

Background
Grain colour is an important quality trait affecting the market value and consumer preference. Chickpeas with black-coloured seed coat is known for their beneficial high antioxidant and fibber content, yet the underlying molecular basis remains poorly understood.

Results
Here, we examined the grain colour trait of a panel of 261 diverse desi chickpea (Cicer arietinum) accessions and specially characterized the development of the black seed coat. We showed that the black colouration emerged on embryo tips at 30 days after flowering (DAF) and expanded to whole grain at 35 DAF. Genome-wide association analyses revealed a single major genetic locus CaBlk3-1 on chromosome Ca3 controlling black seed coat. Candidate gene screening within 0.5 Mb upstream and downstream of CaBlk3-1 identified a single MYB-encoding gene CaMYB114 related to anthocyanin biosynthesis. Phylogeny analyses showed that CaMYB114 was clustered with Arabidopsis MYB90, MYB113, MYB114, consistent with their role in anthocyanin production. Subsequent qRT-PCR analyses suggested that CaMYB114 was abundantly transcribed in black genotypes but weakly in the brown genotypes at 35 DAF, closely linked with black colour development. Genetic variation analyses of CaMYB114 identified a 12-bp deletion containing a GAGA motif in the 5UTR region of black chickpea genotype. A gene-specific marker targeting this deletion was developed to validate its link with the black seed coat in a larger chickpea germplasm collection.

Conclusions
We identified a single major QTL and the underlying candidate gene CaMYB114 closely associated with the black seed coat trait in chickpea. Our study has greatly improved our understanding of the genetic basis of chickpea black seed and will unlock the potential for breeding new chickpeas with desired grain colour to meet various market requirements.

Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.

Exploring structural variants in plant pangenomics: innovations and applications


Structural variants (SVs), which include large insertions, deletions, duplications, inversions, and translocations, have emerged as pivotal drivers of genomic diversity in plants. Unlike single-nucleotide changes, SVs can drastically alter gene content and genome architecture, thereby influencing phenotypic traits and adaptive potential (Hu et al., 2024a). The advent of plant pangenomes, which capture the full spectrum of genetic variation across multiple accessions of a species, has revolutionized our understanding of how SVs contribute to evolution and crop improvement (Hu et al., 2024b). By moving beyond a single reference genome, pangenomic analyses reveal missing genes and alleles, uncovering SV-linked traits that traditional single-reference genome-based approaches often overlook (Tong et al., 2025; Wang et al., 2023). This Research Topic focuses on these advances, highlighting studies that leverage pangenome frameworks to elucidate the roles of SVs in genetic diversity, environmental adaptation, and agronomic traits. We synthesize the findings of the contributions in this Research Topic and place them within the broader context of recent large-scale comparative studies in crops such as rice and barley, which also demonstrate the transformative impact of SV analysis on plant genomics.

Ribulose bisphosphate carboxylase (RuBisCO) is the primary regulator of carbon fixation in the plant kingdom. Although the large subunit (RBCL) is the site of catalysis, RuBisCO efficiency is also influenced by the sequence divergence of the small subunit (RBCS). This project compared the RBCS gene family in C3 and C4 grasses to identify genetic targets for improved crop photosynthesis. Triticeae/Aveneae phylogeny groups exhibited a syntenic tandem duplication array averaging 326.1 Kbp on ancestral chromosomes 2 and 3, with additional copies on other chromosomes. Promoter analysis revealed a paired I-box element promoter arrangement in chromosome 5 RBCS of H. vulgare, S. cereale, and A. tauschii. The I-box pair was associated with significantly enhanced expression, suggesting functional adaptation of specific RBCS gene copies in Triticaeae. H. vulgare-derived pan-transcriptome data showed that RBCS expression was 50.32% and 28.44% higher in winter-type accessions compared to spring types for coleoptile (p < 0.05) and shoot, respectively (p < 0.01). Molecular dynamics simulations of a mutant H. vulgare Rubisco carrying a C4-like amino acid substitution (G59C) in RBCS significantly enhanced the stability of the Rubisco complex. Given the known structural efficiency of C4 Rubisco complexes, G59C could serve as an engineering target for enhanced RBCS in economically crucial crop species which, in comparison, possess less efficient Rubisco complexes.

Chickpea (Cicer arietinum L.) is an important legume crop that has been subjected to intensive breeding, resulting in limited genetic diversity. Australia is the world's second largest producer and the leading exporter of chickpea; the genomic architecture of its cultivars remains largely unexplored. This knowledge gap hinders efforts to enhance their genetic potential for production, protection, and stress adaptation. To address this, we generated high-quality genome assemblies and annotations for 15 leading Australian chickpea cultivars using single-tube long-fragment read technology. The pan-genome analysis identified 34 345 gene families, including 13 986 dispensable families enriched for genes associated with key agronomic traits. Comparative genomic analysis revealed ~2.5 million single-nucleotide polymorphisms, nearly 200 000 insertions/deletions, and over 280 000 structural variations. These variations were found in key flowering time genes, seed weight-related genes, and disease resistance genes, providing insights into the genetic diversity underlying these critical traits. Haplotype analysis of key genes within the 'QTL-hotspot' region revealed the absence of superior haplotypes in Australian cultivars. Validation using Kompetitive allele-specific PCR markers confirmed these findings, highlighting the need to introduce beneficial haplotypes from diverse accessions to enhance drought tolerance in Australian chickpea cultivars. The genomic resources generated in this study provide valuable insights into chickpea genetic diversity and offer potential avenues for crop improvement.

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.