High-resolution genetic mapping of maize pan-genome sequence anchors

In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a ‘pan-genome’, which is essential to fully understand the genetic control of phenotypes. However, the pan-genome’s complexity hinde...

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Detalles Bibliográficos
Autores: Fei Lu, Romay, M.C., Glaubitz, J.C., Bradbury, P., Elshire, R., Wang, T., Yu Li, Yongxiang Li, Semagn, K., Xuecai Zhang, Hernandez, A., Mikel, M.A., Soifer, I., Barad, O., Buckler, E.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2015
País:México
Institución:Centro Internacional de Mejoramiento de Maíz y Trigo
Repositorio:Repositorio Institucional de Publicaciones Multimedia del CIMMYT
OAI Identifier:oai:repository.cimmyt.org:10883/19719
Acceso en línea:https://hdl.handle.net/10883/19719
Access Level:acceso abierto
Palabra clave:AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
SINGLE NUCLEOTIDE POLYMORPHISM
GENOMES
PHENOTYPES
MAIZE
GENETIC MAPS
INBRED LINES
MACHINE LEARNING
Descripción
Sumario:In addition to single-nucleotide polymorphisms, structural variation is abundant in many plant genomes. The structural variation across a species can be represented by a ‘pan-genome’, which is essential to fully understand the genetic control of phenotypes. However, the pan-genome’s complexity hinders its accurate assembly via sequence alignment. Here we demonstrate an approach to facilitate pan-genome construction in maize. By performing 18 trillion association tests we map 26 million tags generated by reduced representation sequencing of 14,129 maize inbred lines. Using machine-learning models we select 4.4 million accurately mapped tags as sequence anchors, 1.1 million of which are presence/absence variations. Structural variations exhibit enriched association with phenotypic traits, indicating that it is a significant source of adaptive variation in maize. The ability to efficiently map ultrahigh-density pan-genome sequence anchors enables fine characterization of structural variation and will advance both genetic research and breeding in many crops.

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