{"doi":"10.1111/pbi.14077","title":"Genomic signatures of barley breeding for environmental adaptation to the new continents","abstract":"Crops expanding from their centres of domestication towards a wide range of agroclimatic regions has led to significant phenotypic and genetic divergence between cultivated forms. Since its domestication in the Fertile Crescent about 10 000 years ago, barley accompanied the spread of agriculture into Europe during the 5th and 6th millennia BC. It was subsequently introduced to North America and Australia by European settlers in the 17th and 18th centuries. The Australian growing season is effectively determined by the soil moisture availability, which is different from that in many European and North American countries where barley is grown over the summer half of the year with frequent rainfall events. Breeding activities are expected to have shaped the barley genomes and selected genes for adaptation to the relevant agroclimatic conditions. Elucidating the genetic basis for adaptation to contrasting agroclimatic conditions will advance our understanding of crop adaptation and guide breeders in selecting varieties for future changing environments. In this study, we sequenced and de novo assembled the genomes of two early barley varieties bred out in Australia, namely “Clipper”, and “Stirling” (Figure S1A, Methods S1). The assembly length of the Clipper and Stirling genomes are 4.28 Gb and 4.26 Gb with a contig N50 of 39.4 Mb and 36.9 Mb, respectively, (Table S1). In-situ Hi-C sequencing anchored 97% of sequences to seven chromosomes in both assemblies (Figure S1B,C). The whole-genome shotgun sequence of 56 barley cultivars from Australia, Europe, and North America was first mapped to the Clipper reference genome to investigate the modern barley cultivars' phylogenetic relationships and population structures (Methods S2). Australian and North American barley show diverse genetic differentiation patterns (Figure S2, Table S2-S6). The various genetic differentiation patterns across chromosomes may reflect the breeding selection targeting different genomic regions in Australia and North America. Barley breeding in Australia centred on selecting varieties with fast development, that is, early flowering, to escape terminal heat during the maturation stage (He et al., 2022). We examined gene Presence/Absence variants (PAVs) between European, Australian, and North American barley. We found that selecting early flowering and photoperiod-sensitivity in Australia has enriched phenology gene alleles with specific PAVs (Methods S3). Seventy genes in Australian barley show a significant change in the presence frequency compared with European barley (Table S7), with 17 genes in the flowering pathways, including genes involved in photoperiod and circadian clock (HvCK2a and HvCO16), vernalisation (HvCBF10A), and meristem response and development (HvSOC1, HvBM5, HvBM7) (Figure S2E). We further compared the genomes of seven barley cultivars (i.e., Clipper and Stirling from Australia, Igri, Barke and RGT Planet from Europe, and Morex and Hockett from North America) for the haplotypes of ten potential genes that may be associated with flowering time and responsiveness to photoperiod and light intensity (Methods S4). Among the ten genes, we identified five genes with a dominant haplotype in Australian varieties (Figure 1a). We revealed two distinctive haplotypes for HvPhyC. Clipper, Stirling, Morex, Hockett and RGT Planet share a haplotype (H1) characterized by an SNP mutation (G) in exon 1 and a 24 bp deletion in exon 4 (Figure 1a), and this haplotype is dominant in Australian varieties. For HvCry1b, Australian dominant haplotype H1 is characterized by a 7-bp insertion in exon 1 and an SNP (T) in exon 2. All European or North American cultivars carry haplotype (H2) with a 7-bp deletion and an SNP (G) (Figure 1a). A discriminant analysis revealed a proportion of Australian barley accessions having an overlapping genetic composition of HvCry1b not with European but with African barley (Methods S5, Figure S3), suggesting a possible non-European orig","journal":"Plant Biotechnology Journal","year":2023,"id":333406,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":23,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9536,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1060720,"name":"Penghao Wang","orcid":"0000-0002-3751-3921","position":1,"is_corresponding":false},{"id":1060721,"name":"Tefera Tolera Angessa","orcid":"0000-0002-2400-1732","position":2,"is_corresponding":false},{"id":1060722,"name":"Xiaoqi Zhang","orcid":"0000-0003-0707-0928","position":3,"is_corresponding":false},{"id":1060723,"name":"K. J. Chalmers","orcid":"0000-0002-9687-8680","position":4,"is_corresponding":false},{"id":1060724,"name":"Gaofeng Zhou","orcid":"0000-0003-0921-8666","position":5,"is_corresponding":false},{"id":1060725,"name":"Camilla Beate Hill","orcid":"0000-0002-6754-5553","position":6,"is_corresponding":false},{"id":1060726,"name":"Yong Jia","orcid":"0000-0002-0394-3966","position":7,"is_corresponding":false},{"id":1060727,"name":"Craig G. Simpson","orcid":"0000-0002-1723-1492","position":8,"is_corresponding":false},{"id":703697,"name":"John Fuller","orcid":"0000-0003-4729-2867","position":9,"is_corresponding":false},{"id":77745,"name":"Alka Saxena","orcid":"0000-0001-5683-0618","position":10,"is_corresponding":false},{"id":1061184,"name":"Hadi Al Shamaileh","orcid":null,"position":11,"is_corresponding":false},{"id":1060728,"name":"Muhammad Munir Iqbal","orcid":"0000-0002-8603-5348","position":12,"is_corresponding":false},{"id":1060729,"name":"Brett Chapman","orcid":"0000-0003-4484-2253","position":13,"is_corresponding":false},{"id":619067,"name":"Parwinder Kaur","orcid":"0000-0003-0201-0766","position":14,"is_corresponding":false},{"id":292976,"name":"Olga Dudchenko","orcid":"0000-0001-9163-9544","position":15,"is_corresponding":false},{"id":18710,"name":"Erez Lieberman Aiden","orcid":"0000-0003-0634-6486","position":16,"is_corresponding":false},{"id":1060730,"name":"Gabriel Keeble‐Gagnère","orcid":"0000-0002-9165-0724","position":17,"is_corresponding":false},{"id":1061185,"name":"Sharon Westcott","orcid":null,"position":18,"is_corresponding":false},{"id":1061186,"name":"David Leah","orcid":null,"position":19,"is_corresponding":false},{"id":1060731,"name":"Josquin Tibbits","orcid":"0000-0002-4951-7540","position":20,"is_corresponding":false},{"id":809041,"name":"Robbie Waugh","orcid":"0000-0003-1045-3065","position":21,"is_corresponding":false},{"id":1060732,"name":"Peter Langridge","orcid":"0000-0001-9494-400X","position":22,"is_corresponding":false},{"id":56282,"name":"Rajeev K. Varshney","orcid":"0000-0002-4562-9131","position":23,"is_corresponding":false},{"id":1060733,"name":"Tianhua He","orcid":"0000-0002-0924-3637","position":24,"is_corresponding":false},{"id":80371,"name":"Chengdao Li","orcid":"0000-0002-9653-2700","position":25,"is_corresponding":false},{"id":1060719,"name":"Haifei Hu","orcid":"0000-0003-1070-213X","position":0,"is_corresponding":true}],"reference_count":6,"raw_metadata":null,"created_at":"2026-07-19T01:09:39.719497Z","pmid":"37497741","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}