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Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

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.

SUBMITTER: Mascher M

PROVIDER: S-EPMC4013074 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

Mascher Martin M Gerlach Nina N Gahrtz Manfred M Bucher Marcel M Scholz Uwe U Dresselhaus Thomas T

PloS one 20140507 5

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 i ...[more]

PMID: 24804793

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Project description:Genome-wide gene expression atlas of maize inbred line B73. Maize inbred B73 was used for constructing the gene atlas. Plants were grown in Plano silt loam soil at the West Madison Agricultural Research Station, Verona, WI during Summer 2008. During field preparation, 200 kg/acre of Urea (46-0-0) was applied. One day after planting, herbicides including Callisto (142 g/acre), Dual II (710 ml/acre), and Simazine (227 g/acre) were applied. For collection of seed tissues, shoots were covered before silk emergence avoiding any injury to the plants. Plants were self-pollinated on the same day to establish a common time initiation point for the harvest timeline. Greenhouse-grown plants were propagated by growing five plants per pot (30 cm top diameter, 28 cm height, 14.5 L volume) containing Metro-Mix 300 (Sun Gro Horticulture, Bellevue, WA, USA) with no additional fertilization. The growing conditions were 27 deg. C day and 24 deg. C night temperature with a 16h light (5:00am to 9:00pm) and 8h dark regime. Germinating seed tissue was generated by soaking seeds in distilled water in a Petri dish for 12h and then placing seeds between layers of moist paper towels for another 12h to allow germination. The field samples were collected between 8:00am and 10:00am, approximately 3 hours after sunrise. The greenhouse samples were collected between 8:00am and 9:00am, three hours after turning on the lights. Three biological replicates were collected for each tissue type. For all the tissues except germinating seeds, a biological replicate was constituted by collecting and pooling samples from three competitive randomly chosen plants. For germinating seed, ten randomly chosen seeds were pooled to form a biological replicate. The harvested tissues were immediately frozen in liquid nitrogen and stored at -80 deg. C. Total RNA was extracted using TRIZOL reagent (Invitrogen, http://www.invitrogen.com) following the manufacturer's protocol, and purified using RNeasy MinElute Cleanup Kit (Qiagen, http://www.qiagen.com) following the manufacturer's instructions. PLEXdb (http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Rajandeep S Sekhon. The equivalent experiment is ZM29 at PLEXdb. organism part name: 24H_Germinating Seed(3-replications); organism part name: 6DAS_GH_Coleoptile(3-replications); organism part name: 6DAS_GH_Primary Root(3-replications); organism part name: V1_GH_Primary Root(3-replications); organism part name: VE_Whole Seedling(3-replications); organism part name: VE_Primary Root(3-replications); organism part name: V1_Pooled Leaves(3-replications); organism part name: V1_Stem and SAM(3-replications); organism part name: V4_Stem and SAM(3-replications); organism part name: V3_Stem and SAM(3-replications); organism part name: V3_First Leaf and Sheath(3-replications); organism part name: V3_Topmost Leaf(3-replications); organism part name: V5_Shoot Tip(3-replications); organism part name: V5_First Internode(3-replications); organism part name: V5_Tip of stage-2 Leaf(3-replications); organism part name: V5_Base of stage-2 Leaf(3-replications); organism part name: V7_First Internode(3-replications); organism part name: V7_Tip of stage-2 Leaf(3-replications); organism part name: V7_Base of stage-2 Leaf(3-replications); organism part name: V9_Fourth Internode(3-replications); organism part name: V9_Eighth Leaf(3-replications); organism part name: V9_Eleventh Leaf(3-replications); organism part name: V9_Thirteenth Leaf(3-replications); organism part name: V9_Immature Leaves(3-replications); organism part name: V13_Immature Tassel(3-replications); organism part name: V18_Meiotic Tassel(3-replications); organism part name: V18_Immature Cob(3-replications); organism part name: VT_Thirteenth Leaf(3-replications); organism part name: R1_Pre-pollination Cob(3-replications); organism part name: R1_Silks(3-replications); organism part name: R1_Anthers(3-replications); organism part name: R1_Innermost Husk(3-replications); organism part name: R2_Thirteenth Leaf(3-replications); organism part name: R2_Outer Husk(3-replications); organism part name: R2_Innermost Husk(3-replications); organism part name: 2DAP_Whole Seed(3-replications); organism part name: 4DAP_Whole Seed(3-replications); organism part name: 6DAP_Whole Seed(3-replications); organism part name: 8DAP_Whole Seed(3-replications); organism part name: 10DAP_Whole Seed(3-replications); organism part name: 12DAP_Whole Seed(3-replications); organism part name: 12DAP_Endosperm(3-replications); organism part name: 14DAP_Whole Seed(3-replications); organism part name: 14DAP_Endosperm(3-replications); organism part name: 16DAP_Whole Seed(3-replications); organism part name: 16DAP_Endosperm(3-replications); organism part name: 16DAP_Embryo(3-replications); organism part name: 18DAP_Whole Seed(3-replications); organism part name: 18DAP_Endosperm(3-replications); organism part name: 18DAP_Embryo(3-replications); organism part name: 18DAP_Pericarp(3-replications); organism part name: 20DAP_Whole Seed(3-replications); organism part name: 20DAP_Endosperm(3-replications); organism part name: 20DAP_Embryo(3-replications); organism part name: 22DAP_Whole Seed(3-replications); organism part name: 22DAP_Endosperm(3-replications); organism part name: 22DAP_Embryo(3-replications); organism part name: 24DAP_Whole Seed(3-replications); organism part name: 24DAP_Endosperm(3-replications); organism part name: 24DAP_Embryo(3-replications)

Dataset Information

Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

Publications

Sequence and ionomic analysis of divergent strains of maize inbred line B73 with an altered growth phenotype.

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