title: Generation of an integrated Hieracium genomic and transcriptomic resource enables exploration of small RNA pathways during apomixis initiation.
abstract: Application of apomixis, or asexual seed formation, in crop breeding would allow rapid fixation of complex traits, economizing improved crop delivery. Identification of apomixis genes is confounded by the polyploid nature, high genome complexity and lack of genomic sequence integration with reproductive tissue transcriptomes in most apomicts.
  
  
  
  A genomic and transcriptomic resource was developed for Hieracium subgenus Pilosella (Asteraceae) which incorporates characterized sexual, apomictic and mutant apomict plants exhibiting reversion to sexual reproduction. Apomicts develop additional female gametogenic cells that suppress the sexual pathway in ovules. Disrupting small RNA pathways in sexual Arabidopsis also induces extra female gametogenic cells; therefore, the resource was used to examine if changes in small RNA pathways correlate with apomixis initiation. An initial characterization of small RNA pathway genes within Hieracium was undertaken, and ovary-expressed ARGONAUTE genes were identified and cloned. Comparisons of whole ovary transcriptomes from mutant apomicts, relative to the parental apomict, revealed that differentially expressed genes were enriched for processes involved in small RNA biogenesis and chromatin silencing. Small RNA profiles within mutant ovaries did not reveal large-scale alterations in composition or length distributions; however, a small number of differentially expressed, putative small RNA targets were identified.
  
  
  
  The established Hieracium resource represents a substantial contribution towards the investigation of early sexual and apomictic female gamete development, and the generation of new candidate genes and markers. Observed changes in small RNA targets and biogenesis pathways within sexual and apomictic ovaries will underlie future functional research into apomixis initiation in Hieracium.
authors.affiliation: Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia.
authors.forename: David S
authors.initials: DS
authors.lastname: Rabiger
authors.affiliation: Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia.
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Taylor
authors.affiliation: Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Bellenden Street, Crace, Australian Capital Territory, 2911, Australia.
authors.forename: Andrew
authors.initials: A
authors.lastname: Spriggs
authors.affiliation: Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia.
authors.forename: Melanie L
authors.initials: ML
authors.lastname: Hand
authors.affiliation: Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia.
authors.forename: Steven T
authors.initials: ST
authors.lastname: Henderson
authors.affiliation: Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia.
authors.forename: Susan D
authors.initials: SD
authors.lastname: Johnson
authors.affiliation: Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia.
authors.forename: Karsten
authors.initials: K
authors.lastname: Oelkers
authors.affiliation: Australian Centre for Plant Functional Genomics, University of Adelaide PMB 1, Glen Osmond, South Australia, 5064, Australia.
authors.forename: Maria
authors.initials: M
authors.lastname: Hrmova
authors.affiliation: Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Saito
authors.affiliation: Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan.
authors.forename: Go
authors.initials: G
authors.lastname: Suzuki
authors.affiliation: Division of Natural Science, Osaka Kyoiku University, Osaka, 582-8582, Japan.
authors.forename: Yasuhiko
authors.initials: Y
authors.lastname: Mukai
authors.affiliation: School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, Queensland, 4072, Australia.
authors.forename: Bernard J
authors.initials: BJ
authors.lastname: Carroll
authors.affiliation: Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Private Bag 2, Glen Osmond, South Australia, 5064, Australia. anna.koltunow@csiro.au.
authors.forename: Anna M G
authors.initials: AM
authors.lastname: Koltunow
mesh_terms: D060832:Apomixis / Q000235:genetics* / Q000502:physiology; D019659:Asteraceae / Q000235:genetics* / Q000502:physiology; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D056771:Ovule / Q000235:genetics / Q000502:physiology; D018749:RNA, Plant / Q000235:genetics*; D012639:Seeds / Q000235:genetics / Q000502:physiology
chemical_list: D018749:RNA, Plant