Location: The Automated controlled-environment phenotyping at the Donald Danforth Plant Science Center Bellwether Foundation Phenotyping Facility

The Scanalyzer 3D platform consists of multiple digital imaging chambers connected to the Conviron growth house by a conveyor belt system, resulting in a continuous imaging loop. Plants are imaged from the top and/or multiple sides, followed by digital construction of images for analysis.

• RGB imaging allows visualization and quantification of plant color and structural morphology, such as leaf area, stem diameter and plant height.

• NIR imaging enables visualization of water distribution in plants in the near infrared spectrum of 900–1700 nm.

• Fluorescent imaging uses red light excitation to visualize chlorophyll fluorescence between 680 – 900 nm. The system is equipped with a dark adaptation tunnel preceding the fluorescent imaging chamber, allowing the analysis of photosystem II efficiency.

The LemnaTec software suite is used to program and control the Scanalyzer platform, analyze the digital images and mine resulting data. Data and images are saved and stored on a secure server for further review or reanalysis.

Experiments LT1A (TM015) and LT1B (TM016)

Duration: 10 days on LemnaTec platform

Experimental Design:

• 3 replicates of 190 BAP lines were grown in a randomized complete block design

• Watering regimes = 30% FC and 100% FC

• Drought conditions were imposed 10 days after planting

• Plants were imaged daily for 10 days (11-20 DAP) and sampled at 20 days after planting

• Experiment was repeated twice to phenotype the full BAP (Reps 1A and 1B)

see https://gist.github.com/dlebauer/6b7b0e181cc5ae5034b992f725712ba4#file-sorghum-lines-genomics-md

Field phenotyping

• Maricopa Agricultural Center (MAC), Arizona

• Kansas State University - coming 2017

Controlled-environment phenotyping

• Donald Danforth Plant Science Center, Missouri

Genomics

• HudsonAlpha Institute for Biotechnology, Alabama - coming 2017

Genomic data includes whole-genome resequencing data from the HudsonAlpha Institute for Biotechnology, Alabama for 384 samples for accessions from the sorghum Bioenergy Association Panel (BAP) and genotyping-by-sequencing (GBS) data from Kansas State University for 768 samples from a population of sorghum recombinant inbred lines (RIL).

Whole-genome resequencing

Experimental Design:

• 384 BAP samples were sequenced to an average depth of ~25x.

• Shotgun sequencing (127-bp paired-end) was done using an Illumina X10 instrument at the HudsonAlpha Institute for Biotechnology.

• Variant calling was done using a computational pipeline at the Danforth Center.

• See the Data Products page to get access to raw and derived data products.

Genotyping-by-sequencing

Experimental Design:

• 768 RIL samples were sequenced using a GBS approach.

Experiment LT1A (TM015)

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Experiment LT1B (TM016)

PI_521290 PI_524475 PI_525049 PI_52606 PI_526905 PI_527045 PI_533792 PI_533902 PI_533998 PI_534120 PI_534165 PI_535783 PI_535785 PI_535792 PI_535793 PI_535794 PI_535795 PI_535796 PI_540518 PI_542718 PI_550604 PI_561840 PI_562730 PI_562732 PI_562781 PI_562897 PI_562970 PI_562971 PI_562981 PI_562982 PI_562985 PI_562990 PI_562991 PI_562994 PI_562997 PI_562998 PI_563002 PI_563006 PI_563009 PI_563020 PI_563021 PI_563022 PI_563032 PI_563196 PI_563222 PI_563295 PI_563329 PI_563330 PI_563331 PI_563332 PI_563338 PI_563348 PI_563350 PI_563355 PI_564163 PI_566819 PI_568717 PI_569090 PI_569097 PI_569148 PI_569244 PI_569264 PI_569416 PI_569418 PI_569419 PI_569420 PI_569421 PI_569422 PI_569423 PI_569425 PI_569427 PI_569433 PI_569435 PI_569443 PI_569444 PI_569445 PI_569447 PI_569452 PI_569453 PI_569454 PI_569455 PI_569457 PI_569458 PI_569459 PI_569460 PI_569462 PI_569465 PI_569886 PI_570031 PI_570038 PI_570042 PI_570047 PI_570053 PI_570071 PI_570073 PI_570074 PI_570075 PI_570076 PI_570085 PI_570087 PI_570090 PI_570091 PI_570096 PI_570106 PI_570109 PI_570110 PI_570114 PI_570145 PI_570254 PI_570371 PI_570373 PI_570388 PI_570393 PI_570400 PI_570431 PI_573193 PI_576399 PI_576401 PI_583832 PI_585406 PI_585448 PI_585452 PI_585454 PI_585461 PI_585467 PI_585577 PI_585608 PI_585954 PI_585961 PI_585966 PI_586435 PI_586443 PI_586541 PI_593916 PI_619807 PI_619838 PI_620072 PI_620157 PI_63715 PI_641807 PI_641810 PI_641815 PI_641817 PI_641821 PI_641824 PI_641829 PI_641830 PI_641835 PI_641836 PI_641850 PI_641860 PI_641862 PI_641892 PI_641909 PI_642998 PI_643008 PI_643016 PI_646242 PI_646251 PI_646266 PI_651491 PI_651493 PI_651495 PI_651496 PI_651497 PI_653616 PI_653617 PI_655972 PI_655978 PI_655981 PI_655983 PI_656015 PI_656026 PI_656035 PI_656065 PI_92270 PI_329471 PI_329506 PI_329569 PI_337680 PI_452692 PI_455217 PI_152730 PI_329311 NTJ2 M81e CK60B B_Az9504 ICSV700 China 17

Season 1 sorghum (April - July 2016) Season 2 sorghum (August - November 2016) Durum wheat (January 2017 -

Season 1 soghum (April - July 2016)

Three hundred thirty one lines were planted in Season 1.

Planting maps

• Under the scanner system

• West the scanner system

Planting Design

Under scanner system

West of scanner system

Automated Phenotpying

The Lemnatec Scanalyzer Field Gantry System is the largest field crop analytics robot in the world. This high-throughput phenotyping field-scanning robot has a 30-ton steel gantry that autonomously moves along two 200-meter steel rails while continuously imaging the crops growing below it with a diverse array of cameras and sensors.

Twelve sensors are attached to the gantry system. Detailed information for each sensor including name, variable measured, and field of view are available here. The planned sensor missions and their objectives for 2016 are available here.

Manually Collected Field Data

emergence vigor emergence final stand counts plant heights node and tiller counts on marked plants phenology growth stage data leaf desiccation ratings radiation interception managements Incomplete harvest yield data

Season 2 soghum (August - November 2016)

One hundred and seventy-six lines were planted in Season 2.

Planting map

Under the scanner system

Planting Design

Under scanner system - same as season 1

Automated Phenotpying

same as season 1

Manually Collected Field Data

plant heights managements emergence vigor emergence final stand counts node and tiller counts on marked plants leaf length and width on marked plants, one date

Durum wheat

Experimental design

Automatically and manually collected field data plan