{"doi":"10.1101/2024.12.02.626474","title":"Molecular evolution of a reproductive barrier in maize and related species","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>\n                  Three cross-incompatibility loci each control a distinct reproductive barrier in both domesticated maize (\n                  <jats:italic>Zea mays</jats:italic>\n                  ssp.\n                  <jats:italic>mays</jats:italic>\n                  ) and its wild teosinte relatives. These three loci,\n                  <jats:italic>Teosinte crossing barrier1</jats:italic>\n                  (\n                  <jats:italic>Tcb1</jats:italic>\n                  ),\n                  <jats:italic>Gametophytic factor1</jats:italic>\n                  (\n                  <jats:italic>Ga1</jats:italic>\n                  ), and\n                  <jats:italic>Ga2</jats:italic>\n                  , each play a key role in preventing hybridization between incompatible populations and are proposed to maintain the barrier between domesticated and wild subspecies. Each locus encodes both a silk-active and a matching pollen-active pectin methylesterase (PMEs). To investigate the diversity and molecular evolution of these gametophytic factor loci, we identified existing and improved models of the responsible genes in a new genome assembly of maize line P8860 that contains active versions of all three loci. We then examined fifty-two assembled genomes from seventeen species to classify haplotype diversity and identify sites under diversifying selection during the evolution of these genes. We show that\n                  <jats:italic>Ga2</jats:italic>\n                  , the oldest of these three loci, was duplicated to form\n                  <jats:italic>Ga1</jats:italic>\n                  at least 12 million years ago.\n                  <jats:italic>Tcb1</jats:italic>\n                  , the youngest locus, arose as a duplicate of\n                  <jats:italic>Ga1</jats:italic>\n                  before or around the time of diversification of the\n                  <jats:italic>Zea</jats:italic>\n                  genus. We find evidence of positive selection during evolution of the functional genes at an active site in the pollen-expressed PME and predicted surface sites in both the silk- and pollen-expressed PMEs. The most common allele at the\n                  <jats:italic>Ga1</jats:italic>\n                  locus is a conserved\n                  <jats:italic>ga1</jats:italic>\n                  allele (\n                  <jats:italic>ga1-Off</jats:italic>\n                  ), which is specific haplotype containing three full-length PME gene copies, all of which are non-coding due to conserved stop codons and are between 610 thousand and 1.5 million years old. We show that the\n                  <jats:italic>ga1-Off</jats:italic>\n                  allele is associated with and likely generates 24-nt siRNAs in developing pollen-producing tissue, and these siRNAs map to functional\n                  <jats:italic>Ga1</jats:italic>\n                  alleles. In previously-published crosses, the\n                  <jats:italic>ga1-Off</jats:italic>\n                  allele was associated with reduced function of the typically dominant functional alleles for the Ga1 and Tcb1 barriers. Taken together, this seems to be an example of a type of epigenetic trans-homolog silencing known as paramutation functioning at a locus controlling a reproductive barrier.\n                </jats:p>","journal":null,"year":null,"id":681110,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1779543,"name":"Garnet Phinney","orcid":null,"position":1,"is_corresponding":false},{"id":615087,"name":"Arun S. Seetharam","orcid":"0000-0002-6789-9298","position":2,"is_corresponding":false},{"id":1779545,"name":"Matthew M.S. Evans","orcid":"0000-0002-6076-8607","position":3,"is_corresponding":false},{"id":330995,"name":"Elizabeth A. Kellogg","orcid":"0000-0003-1671-7447","position":4,"is_corresponding":false},{"id":668414,"name":"Junpeng Zhan","orcid":"0000-0001-7353-7608","position":5,"is_corresponding":false},{"id":255908,"name":"Blake C. Meyers","orcid":"0000-0003-3436-6097","position":6,"is_corresponding":false},{"id":32886,"name":"Daniel J. Kliebenstein","orcid":"0000-0001-5759-3175","position":7,"is_corresponding":false},{"id":68281,"name":"Jeffrey Ross‐Ibarra","orcid":"0000-0003-1656-4954","position":8,"is_corresponding":false},{"id":1779541,"name":"Elli Cryan","orcid":"0009-0006-8018-6686","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"Molecular evolution of a reproductive barrier in maize and related species","abstract":"<jats:title>Abstract</jats:title>\n                <jats:p>\n                  Three cross-incompatibility loci each control a distinct reproductive barrier in both domesticated maize (\n                  <jats:italic>Zea mays</jats:italic>\n                  ssp.\n                  <jats:italic>mays</jats:italic>\n                  ) and its wild teosinte relatives. These three loci,\n                  <jats:italic>Teosinte crossing barrier1</jats:italic>\n                  (\n                  <jats:italic>Tcb1</jats:italic>\n                  ),\n                  <jats:italic>Gametophytic factor1</jats:italic>\n                  (\n                  <jats:italic>Ga1</jats:italic>\n                  ), and\n                  <jats:italic>Ga2</jats:italic>\n                  , each play a key role in preventing hybridization between incompatible populations and are proposed to maintain the barrier between domesticated and wild subspecies. Each locus encodes both a silk-active and a matching pollen-active pectin methylesterase (PMEs). To investigate the diversity and molecular evolution of these gametophytic factor loci, we identified existing and improved models of the responsible genes in a new genome assembly of maize line P8860 that contains active versions of all three loci. We then examined fifty-two assembled genomes from seventeen species to classify haplotype diversity and identify sites under diversifying selection during the evolution of these genes. We show that\n                  <jats:italic>Ga2</jats:italic>\n                  , the oldest of these three loci, was duplicated to form\n                  <jats:italic>Ga1</jats:italic>\n                  at least 12 million years ago.\n                  <jats:italic>Tcb1</jats:italic>\n                  , the youngest locus, arose as a duplicate of\n                  <jats:italic>Ga1</jats:italic>\n                  before or around the time of diversification of the\n                  <jats:italic>Zea</jats:italic>\n                  genus. We find evidence of positive selection during evolution of the functional genes at an active site in the pollen-expressed PME and predicted surface sites in both the silk- and pollen-expressed PMEs. The most common allele at the\n                  <jats:italic>Ga1</jats:italic>\n                  locus is a conserved\n                  <jats:italic>ga1</jats:italic>\n                  allele (\n                  <jats:italic>ga1-Off</jats:italic>\n                  ), which is specific haplotype containing three full-length PME gene copies, all of which are non-coding due to conserved stop codons and are between 610 thousand and 1.5 million years old. We show that the\n                  <jats:italic>ga1-Off</jats:italic>\n                  allele is associated with and likely generates 24-nt siRNAs in developing pollen-producing tissue, and these siRNAs map to functional\n                  <jats:italic>Ga1</jats:italic>\n                  alleles. In previously-published crosses, the\n                  <jats:italic>ga1-Off</jats:italic>\n                  allele was associated with reduced function of the typically dominant functional alleles for the Ga1 and Tcb1 barriers. Taken together, this seems to be an example of a type of epigenetic trans-homolog silencing known as paramutation functioning at a locus controlling a reproductive barrier.\n                </jats:p>","is_dataset_classified":null,"base_score":0.0,"endowment":0.0,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"26207759","pmcid":null,"openalex_id":"https://openalex.org/W4404940414","authors":[],"funders":[],"total_grants":0,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[],"oa_status":"green","license":"cc-by","oa_locations":[{"url":"https://www.biorxiv.org/content/biorxiv/early/2024/12/03/2024.12.02.626474.full.pdf","host_type":"repository"},{"url":"https://www.biorxiv.org/content/biorxiv/early/2024/12/03/2024.12.02.626474.full.pdf","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/2024.12.02.626474","host_type":"publisher"},{"url":"https://doi.org/10.1101/2024.12.02.626474","host_type":"repository"}],"fields_of_study":["Genetic Mapping and Diversity in Plants and Animals","Plant Reproductive Biology","Chromosomal and Genetic Variations"],"mesh_terms":[],"keywords":["Biology","Evolutionary biology"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Life in Land"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-17T16:57:57.019976Z","pmid":null,"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":[]}