Abstract
Maize (Zea mays) is the most widely grown crop species in the world and a classical model organism for plant research. The completion of a high-quality reference genome sequence and the advent of high-throughput sequencing have greatly empowered re-sequencing studies in maize. In this study, plants of maize inbred line B73 descended from two different sets of seed material grown for several generations either in the field or in the greenhouse were found to show a different growth phenotype and ionome under phosphate starvation conditions and moreover a different responsiveness towards mycorrhizal fungi of the species Glomus intraradices (syn: Rhizophagus irregularis). Whole genome re-sequencing of individuals from both sets and comparison to the B73 reference sequence revealed three cryptic introgressions on chromosomes 1, 5 and 10 in the line grown in the greenhouse summing up to a total of 5,257 single-nucleotide polymorphisms (SNPs). Transcriptome sequencing of three individuals from each set lent further support to the location of the introgression intervals and confirmed them to be fixed in all sequenced individuals. Moreover, we identified >120 genes differentially expressed between the two B73 lines. We thus have found a nearly-isogenic line (NIL) of maize inbred line B73 that is characterized by an altered growth phenotype under phosphate starvation conditions and an improved responsiveness towards symbiosis with mycorrhizal fungi. Through next-generation sequencing of the genomes and transcriptomes we were able to delineate exact introgression intervals. Putative de novo mutations appeared approximately uniformly distributed along the ten maize chromosomes mainly representing G:C -> A:T transitions. The plant material described in this study will be a valuable tool both for functional studies of genes differentially expressed in both B73 lines and for research on growth behavior especially in response to symbiosis between maize and mycorrhizal fungi.
Highlights
Maize (Z. mays) is an important cereal crop and has been a major plant model species for genetic research since the first half of the 20th century
Through whole genome and transcriptome comparison with the B73 reference genome and a set of B73 plants that were obtained more recently from the stock center and exclusively grown in the field, we show that the genome of this nearly isogenic line (NIL) harbors three well-delineated segments from a different maize genotype in a B73 background summing up to a total of 5,257 single-nucleotide polymorphisms (SNPs)
We have described here a nearly isogenic line (NIL) of maize inbred line B73
Summary
Maize (Z. mays) is an important cereal crop and has been a major plant model species for genetic research since the first half of the 20th century. It is an extremely diverse species whose genome abounds with single-nucleotide polymorphisms (SNPs) [1,2] as well as with copy number and presence-absence variation between inbred lines [2,3]. The genome of B73 had been sequenced to high quality using a map-based clone-by-clone strategy [8]. The B73 reference sequence provides the backbone for genome-wide association studies [9] and map-based cloning projects [10] for the crop and model plant maize
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
