Mineral ion content traits from McCouch Lab

[jaiswalp]

I just received a request to add the following traits from the Cornell group.

root hair density root cortex area root stele area root aerenchyma area number of metaxylem vessels days to booting panicle terminal primary branch length panicle internode length rachis thickness number of panicle internodes number of panicle branches per internode horizontal width of the root system root Al content root As content root B content root Ba content root Ca content root Cd content root Co content root Cr content root Cu content root Fe content root I content root K content root Li content root Mg content root Mn content root Mo content root Na content root Ni content root P content root Pb content root Rb content root S content root Se content root Si content root Sr content shoot Zn content shoot Al content shoot As content shoot B content shoot Ba content shoot Ca content shoot Cd content shoot Co content shoot Cr content shoot Cu content shoot Fe content shoot I content shoot Li content shoot Mg content shoot Mn content shoot Mo content shoot Ni content shoot Pb content shoot Rb content shoot S content shoot Se content shoot Si content shoot Sr content shoot Zn content

[marieALaporte]

Most of the traits listed should be pretty straightforward to add with the DP approach.

Le 2 juin 2017 à 13:12, Pankaj Jaiswal notifications@github.com a écrit :

I just received a request to add the following traits from the Cornell group.

root hair density root cortex area root stele area root aerenchyma area number of metaxylem vessels days to booting panicle terminal primary branch length panicle internode length rachis thickness number of panicle internodes number of panicle branches per internode horizontal width of the root system root Al content root As content root B content root Ba content root Ca content root Cd content root Co content root Cr content root Cu content root Fe content root I content root K content root Li content root Mg content root Mn content root Mo content root Na content root Ni content root P content root Pb content root Rb content root S content root Se content root Si content root Sr content shoot Zn content shoot Al content shoot As content shoot B content shoot Ba content shoot Ca content shoot Cd content shoot Co content shoot Cr content shoot Cu content shoot Fe content shoot I content shoot Li content shoot Mg content shoot Mn content shoot Mo content shoot Ni content shoot Pb content shoot Rb content shoot S content shoot Se content shoot Si content shoot Sr content shoot Zn content

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[austinmeier]

An excellent opportunity to try out the new "term genie replacement"?

[jaiswalp]

Suggested descriptions from the McCouch lab:

root hair density-->number of root hairs per root surface area root cortex area-->cross-sectional area of the root cortex root stele area-->cross-sectional area of the root stele root aerenchyma area-->cross-sectional area of the root aerenchyma number of metaxylem vessels-->number or metaxylem vessels in a cross section days to booting-->Number of days after transplanting when ~50% of plants from a plot replicate reach booting stage (visible flag leaf) panicle terminal primary branch length-->the length of the terminal primary branch on a panicle panicle internode length-->The distance between two nodes rachis thickness-->the diameter of the rachis number of panicle internodes-->the number of nodes in a panicle number of panicle branches per internode-->the average number of branches per node for all nodes within a panicle. horizontal width of the root system-->Maximum horizontal width of the whole root system root? and shoot ion content-->µg of ion/gram of dry weight plant tissue

[jaiswalp]

@austinmeier @marieALaporte go for it. How soon we can get these in.

[cooperl09]

The shoot-related terms will need be be shoot axis XYZ, as shoot is not a PO term. Their form can be added as a synonym.

[austinmeier]

@cooperl09 can we use shoot system (PO:0009006)?

[marieALaporte]

@jaiswalp The definitions will be created automatically by the tool. But according to the descriptions you gave, maybe the names of the traits will need to be slightly different (e.g. maximal width)

[cooperl09]

@austinmeier the shoot system PO:0009006 is the entire axial structure of the plant- I don't think it is appropriate here.

[jaiswalp]

sure. keep the original names as synonyms

[elsadebecker]

Hi, I'm the one that requested these terms. Such quick turnaround, wow! There are already a couple "shoot __ content" traits, for example TO:0020004, TO:0020114, and TO:0020003. As far as I can tell they don't refer to any specific shoot PO term yet.

[austinmeier]

@elsadebecker When you are measuring the "shoot x content" are you using the entire portion of the plant that is above ground?

[cooperl09]

TO:0020004, TO:0020114, and TO:0020003 are legacy terms and need to be fixed...

[elsadebecker]

@austinmeier yes, everything above ground was analyzed as shoot and everything below ground was analyzed as root

[austinmeier]

Excellent. I believe shoot system (PO:0009006) is appropriate in this case.

[cooperl09]

in that case they should be shoot system and root system. Thanks for clarifying

[elsadebecker]

Also, all panicle traits are from Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters, Crowell et al., 2016, and I took the descriptions from page 116 of the supplementary information pdf

[marieALaporte]

@elsadebecker the shoot Zn content appears twice in the list. I suppose one should be changed to root Zn content, correct?

[elsadebecker]

Yes, thanks!

[cooperl09]

Is there supposed to be a 'shoot (system) potassium K content' trait? Appears all the rest are done in both.

[elsadebecker]

I didn't request it because there was already TO:0020003, shoot potassium content

[cooperl09]

All the mineral content terms have been created, and will be available on our dev browser (http://dev.planteome.org/amigo) later today.

TO:1000025 | root system aluminum content TO:1000026 | root system arsenic content TO:1000027 | root system boron content TO:1000028 | root system barium content TO:1000029 | root system calcium content TO:1000030 | root system cadmium content TO:1000031 | root system cobalt content TO:1000032 | root system chromium content TO:1000033 | root system copper content TO:1000034 | root system iron content TO:1000035 | root system iodine content TO:1000036 | root system potassium content TO:1000037 | root system lithium content TO:1000038 | root system magnesium content TO:1000039 | root system manganese content TO:1000040 | root system molybdenum content TO:1000041 | root system sodium content TO:1000042 | root system nickel content TO:1000043 | root system phosphorus content TO:1000044 | root system lead content TO:1000045 | root system rubidium content TO:1000046 | root system sulfur content TO:1000047 | root system selenium content TO:1000048 | root system silicon content TO:1000049 | root system strontium content TO:1000050 | root system zinc content   |   TO:1000051 | shoot system aluminium content TO:1000052 | shoot system arsenic content TO:1000053 | shoot system boron content TO:1000054 | shoot system barium content TO:1000055 | shoot system calcium content TO:1000056 | shoot system cadmium content TO:1000057 | shoot system cobalt content TO:1000058 | shoot system chromium content TO:1000059 | shoot system copper content TO:1000060 | shoot system iron content TO:1000061 | shoot system iodine content TO:1000062 | shoot system lithium content TO:1000063 | shoot system magnesium content TO:1000064 | shoot system manganese content TO:1000065 | shoot system molybdenum content TO:1000066 | shoot system nickel content TO:1000067 | shoot system lead content TO:1000068 | shoot system rubidium content TO:1000069 | shoot system sulfur content TO:1000070 | shoot system selenium content TO:1000071 | shoot system silicon content TO:1000072 | shoot system strontium content TO:1000073 | shoot system zinc content

[cooperl09]

panicle trait requests have been moved to : #419

[cooperl09]

root related traits have been moved to #417

[elsadebecker]

These are all from chapter 3 of the dissertation Combining next-generation phenotyping and genome-wide association analysis to explore the genetic architecture of nutrient acquisition in domesticated Asian rice (Oryza sativa L.).

[cooperl09]

That link goes to a Cornell University web login page.... Cannot access it from here- would there be a published paper from the dissertation?

[elsadebecker]

No, there was never a paper published. Try this link instead? The proquest ID is 1426182399, if that helps.

[elsadebecker]

days to booting moved to #420

[elsadebecker]

number of metaxylem vessels moved to #421

[cooperl09]

Based on our meeting today, these have been completed, so I am closing this issue.