Journal standards and trends in crop genomics

Myles Axton

Chief Editor

Nature Genetics

ICRISAT

Hyderabad, India

February 18th 2015

Maciej Tomczak

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Your best work yet

Gloucester Old Spot by John Miles,1834. Gloucester Museums Service Art Collection.

Organizing the paper

Writing the paper

Organizing the paper

HYPOTHESIS EVIDENCE

METHOD

Nipponbare rice genome contains active and inactive

transposable elements (TEs) Repeats are present in genome Genomic sequencing

Active TEs will show little intrafamily divergence There are repeats with various levels of identity,

including identical interspersed repeats Computational search for repeats, filtering by sequence

identity %

Nipponbare rice genome contains an active MITE

named mPing Sequence of 430bp with 26 identical copies in

available Nipponbare sequence

Manual inspection of 1257 repeat families in Nipponbare

sequence

mPing element is actively transposing 42 new mPing insertion sites in cell culture DNA Transposon display technique used with rice cell culture

DNA

mPing is related to other TEs Identified the larger Ping and Pong elements in the

Nipponbare genomic sequence Computational search of Nipponbare sequence using the

mPing sequence

mPing is mechanistically related to Ping mPing is a derived from Ping by deletion Sequence comparison among copies of two types of

element

mPing is mechanistically related to Pong Pong is more distantly related to mPing than is Ping Sequence comparison among copies of three types of

element

Ping is not the source of transposase for mPing Ping is not present in the sequenced indica (93-11)

genome Sequence analysis of (93-11) by BLAST with Ping

sequence

Pong is actively transposing New Pong insertions in cell culture DNA Transposon display technique used with rice cell culture

DNA

mPing has been differentially active in rice strains

from different latitudes mPing element has undergone more extensive

amplification in temperate rice strains Transposon display technique used with DNA from diverse

rice strains

Jiang, N. et al An active DNA transposon family in rice. Nature 421:163-167, 2003.

Navigating the editorial process

Tayfun Özçelic

Genetics and genomics in Nature journals

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Trends in agricultural genomics

Rachel Meyer

From reference genomes to genome diversity

Drought resistance through deep root trait

Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions

Yusaku Uga et al.

•Cloning of DRO1 deep rooting QTL

•DRO1 is negatively regulated by auxin and controls cell elongation such that the deep root allele induces asymmetrical growth downward

•DRO1 QTL crossed into shallow rooting rice confers increased drought resistance

Tuning tomato productivity with florigen alleles

Optimization of crop productivity in tomato using induced mutations in the florigen pathway

Soon Ju Park et al. Nat. Genet. (2014) doi:10.1038/ng.3131

02 November 2014

Soil is familiar

Cornell University Cooperative Extension

But we do not understand enough about soil to keep ourselves alive

Phillip Beesley http://philipbeesleyarchitect.com/

Nature Plants

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Nature Outlook on Rice

Access to data

Eve Stockton

Access to phenotype data as well as genotypes

journal.pbio.1001595

Author responsibilities

Birgit Woelker

Avoid distorting citations

• Conversion of hypothesis to fact through citation alone BMJ 339, 2680 (2009)

Avoid fabrication and falsification

• Same photo, ‘different’ genotype

Nature Genetics 2007 Intra- and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways

Science May 2010 Small RNA Duplexes Function as Mobile Silencing Signals Between Plant Cells

90o

Display unprocessed data

Nature Genetics 36, 55 - 62 (2004)

“p53* (second row) shows the normalized amount of p53 in the four samples.

Normalization was done after densitometric analyses of p53 (third row) and GFP (fourth row) band intensities in each lane, using Scion Image and NIH Image software. “

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Thank you!

Alexander Davis