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

Autor: Lu F; Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA., Romay MC; Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA., Glaubitz JC; Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA., Bradbury PJ; United States Department of Agriculture/Agricultural Research Service, Ithaca, New York 14850, USA., Elshire RJ; Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA., Wang T; Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China., Li Y; Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China., Li Y; Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China., Semagn K; International Maize and Wheat Improvement Center (CIMMYT), Nairobi 00621, Kenya., Zhang X; International Maize and Wheat Improvement Center (CIMMYT), Apdo 6-641, 06600 Mexico DF, Mexico., Hernandez AG; Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA., Mikel MA; 1] Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA [2] Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA., Soifer I; NRGENE, 3 Golda Meir St. Park HaMada, Ness Ziona 7403648, Israel., Barad O; NRGENE, 3 Golda Meir St. Park HaMada, Ness Ziona 7403648, Israel., Buckler ES; 1] Institute for Genomic Diversity, Cornell University, Ithaca, New York 14850, USA [2] United States Department of Agriculture/Agricultural Research Service, Ithaca, New York 14850, USA.
Jazyk: angličtina
Zdroj: Nature communications [Nat Commun] 2015 Apr 16; Vol. 6, pp. 6914. Date of Electronic Publication: 2015 Apr 16.
DOI: 10.1038/ncomms7914
Abstrakt: 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.
Databáze: MEDLINE