Difference between revisions of "NSF BREAD"

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==Summary==
 
==Summary==
 
===Overview===
 
===Overview===
Dramatic increases in the speed and ability to collect precision phenotypic data are needed to decipher plant genomes and accelerate plant breeding. Over the past decade, the availability of genomic data has exploded while the methods to collect phenotypes have made minimal advancements. This has led to a dramatic imbalance in data sets connecting genotype to phenotype and highlighting phenotyping as the remaining major bottleneck in plant breeding programs. This project will advance the field of 3D graphics and modeling, data mining, and deep learning through integration of simultaneous ground truth phenotypic measurements and imaging with mobile technology.
+
Dramatic increases in the speed and ability to collect precision phenotypic data are needed to decipher plant genomes and accelerate plant breeding. Over the past decade, the availability of genomic data has exploded while the methods to collect phenotypes have made minimal advancements. This has led to a dramatic imbalance in data sets connecting genotype to phenotype and highlighting phenotyping as the remaining major bottleneck in plant breeding programs. This project will advance the field of 3D graphics and modeling, data mining, and deep learning through integration of simultaneous ground truth phenotypic measurements and imaging with mobile technology as well as work to extend already-existing tools like [[PhenoApps#Field Book|Field Book]].
  
 
By focusing on novel algorithms delivered through mobile apps, innovative phenotyping tools can be rapidly deployed through readily available and highly-penetrant mobile technology. This approach will enable rapid dissemination and broad usability. Collectively equipping thousands of breeders around the world with tools for rapid collection, processing and analysis of complex phenotypes will provide the foundation for increasing genetic gain that will ultimately result in improved productivity, food security, nutrition, and income of smallholder farmers and their families in developing countries.  
 
By focusing on novel algorithms delivered through mobile apps, innovative phenotyping tools can be rapidly deployed through readily available and highly-penetrant mobile technology. This approach will enable rapid dissemination and broad usability. Collectively equipping thousands of breeders around the world with tools for rapid collection, processing and analysis of complex phenotypes will provide the foundation for increasing genetic gain that will ultimately result in improved productivity, food security, nutrition, and income of smallholder farmers and their families in developing countries.  
 +
 
===Workflow===
 
===Workflow===
Add graphical app workflow (prelim data → algorithms → beta users → feedback and changes → implementation → beta test → release)
+
[[File:bread_workflow.png|900px]]
 +
 
 +
==Project team==
 +
{{Col-begin}}
 +
{{Col-break}}
 +
===Kansas State===
 +
* Jesse Poland
 +
** Trevor Rife
 +
* Mitch Neilsen
 +
 
 +
{{Col-break}}
 +
===Texas A&M===
 +
* Bruce Gooch
 +
 
 +
{{Col-break}}
 +
===Cornell===
 +
* Michael Gore
 +
** Jenna Hershberger
 +
 
 +
{{Col-break}}
 +
===CIMMYT===
 +
* Ravi Singh
 +
* Uttam Kumar
 +
 
 +
{{Col-break}}
 +
===IITA===
 +
* Ismail Rabbi
 +
{{Col-end}}
 +
 
 
==Wheat==
 
==Wheat==
 
===Summary===
 
===Summary===
 +
Wheat is one of the most important staple crops worldwide, providing 21% of the food calories and 20% of the protein for more than 4.5 billion people in 94 developing countries. In the developing world, wheat is a particularly important crop for food security as the primary staple for over 1.2 billion and an important food source for an additional 2.5 billion individuals living in poverty; men, women and children living on less than $2/day USD.  In addition, wheat is the primary income source for some 30 million poor wheat farmers and their families.
 +
 +
In the developing world, the demand for wheat is projected to increase 60% by 2050. However, during this same period, increasing temperatures induced by climate-change are expected to reduce wheat production in developing countries by 20–30%. As a result of growing populations, demand for wheat is growing at an annual rate of 1.7% but wheat yields are growing at only about 1% annually. The increased demand is leading to market volatility and increased prices, which has a greater relative impact on the poor and food insecure.  These combined factors are forecasted to double wheat prices.  As a result, the purchasing power of poor consumers will decrease, leading to food insecurity and creating conditions for widespread social unrest.  This scenario is aggravated by stagnating yields, soil degradation and loss of arable land, increasing fertilizer costs, loss of irrigation waters, and new virulent disease and pest strains.
 +
 
===Cycle===
 
===Cycle===
 +
{| class="wikitable" style="margin-center: auto; width: 95%;"
 +
|- style="text-align:center;"
 +
! style="width: 8.33%;" |January
 +
! style="width: 8.33%;" |February
 +
! style="width: 8.33%;" |March
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! style="width: 8.33%;" |April
 +
! style="width: 8.33%;" |May
 +
! style="width: 8.33%;" |June
 +
! style="width: 8.33%;" |July
 +
! style="width: 8.33%;" |August
 +
! style="width: 8.33%;" |September
 +
! style="width: 8.33%;" |October
 +
! style="width: 8.33%;" |November
 +
! style="width: 8.33%;" |December
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|- style="text-align:center;"
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|
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|
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|
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|
 +
|
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|
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|
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|
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|
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|
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|colspan="2" style="background-color:#A1D490;"|Planting
 +
|- style="text-align:center;"
 +
|
 +
|
 +
|
 +
|colspan="2" style="background-color:#D4A190;"|Harvest
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|- style="text-align:center;"
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|colspan="4" style="background-color:#90C3D4;"|Phenotyping
 +
|
 +
|
 +
|
 +
|
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|
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|
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|
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|}
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===Traits===
 
===Traits===
 
{| class="wikitable sortable"
 
{| class="wikitable sortable"
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| Rust quantification || 0 || None
 
| Rust quantification || 0 || None
 
|-
 
|-
| Seed size and shape  || 0 || [[#1KK|1KK]]
+
| Seed size and shape  || 0 || [[PhenoApps#1KK|1KK]]
 
|-
 
|-
 
| Leaf morphology || 0 || None
 
| Leaf morphology || 0 || None
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==Cassava==
 
==Cassava==
 
===Summary===
 
===Summary===
 +
Cassava (Manihot esculenta Crantz.) is a highly adaptable starchy root crop and the primary staple food for more than 800 million people, largely in sub-Saharan Africa, which accounts for more than 50% of
 +
the total cassava production globally.  This clonally propagated crop is also increasingly becoming a source of revenue from fresh and processed food, the production of starch-based products, biofuels and
 +
animal feed. The crop is cultivated in tropical and sub-tropical regions of Asia, Latin America and Africa. Currently, Nigeria is the largest world producer of cassava with a total output of 52.4 million MT,
 +
which was around 21% of the world total (252.2 million MT) in 2013. In Nigeria, cassava provides at least 80% of the daily caloric requirement for over 50% of the population.  Similarly, cassava provides food and income to more than 80% of the small holder households in Uganda.
 +
 +
Its ability to grow in marginal environments with erratic rainfall, poor soil fertility and under low intensity management has made it one of the most important food security crops in the African continent.  National and international cassava breeding efforts have made significant impact on cassava productivity, quality, and disease tolerance.  However, cassava breeding continues to be a challenging, particularly as cassava is a highly heterogeneous and heterozygous vegetative propagated crop with variable flowering, low seed set, and a long breeding cycle. It takes several years from making a cross to conducting large-plot, replicated, field trials and selection of parents for the next cycle of germplasm improvement.  As such, the rate of genetic gain per year for yield is very low (~1.2%).
 +
 
===Cycle===
 
===Cycle===
 +
{| class="wikitable" style="margin-center: auto; width: 95%;"
 +
|- style="text-align:center;"
 +
! style="width: 8.33%;" |January
 +
! style="width: 8.33%;" |February
 +
! style="width: 8.33%;" |March
 +
! style="width: 8.33%;" |April
 +
! style="width: 8.33%;" |May
 +
! style="width: 8.33%;" |June
 +
! style="width: 8.33%;" |July
 +
! style="width: 8.33%;" |August
 +
! style="width: 8.33%;" |September
 +
! style="width: 8.33%;" |October
 +
! style="width: 8.33%;" |November
 +
! style="width: 8.33%;" |December
 +
|- style="text-align:center;"
 +
|
 +
|
 +
|colspan="3" style="background-color:#A1D490;"|Planting
 +
|
 +
|
 +
|
 +
|colspan="3" style="background-color:#A1D490;"|Planting
 +
|
 +
|- style="text-align:center;"
 +
|
 +
|
 +
|
 +
| style="background-color:#D4A190;"|Harvest
 +
|
 +
|
 +
|
 +
|
 +
|
 +
| style="background-color:#D4A190;"|Harvest
 +
|
 +
|
 +
|- style="text-align:center;"
 +
| style="background-color:#90C3D4;"|Phenotyping
 +
|
 +
|
 +
| style="background-color:#90C3D4;"|Phenotyping
 +
|
 +
|
 +
| style="background-color:#90C3D4;"|Phenotyping
 +
|
 +
|
 +
| style="background-color:#90C3D4;"|Phenotyping
 +
|
 +
|}
 +
 
===Traits===
 
===Traits===
 
{| class="wikitable sortable"
 
{| class="wikitable sortable"
 
|-
 
|-
! Trait  !! Priority !! Status
+
! Trait  !! Priority !! Country !! Status
 
|-
 
|-
| Root size and shape || 0 || [[#1KK|1KK]]
+
| Root size and shape || 3 || NA || [[PhenoApps#1KK|1KK]]
 
|-
 
|-
| Cassava mosaic disease || 0 || None
+
| Cassava brown streak (root) || 1 || NA ||  [http://www.air.ug/mcrops/necrosis-app.html Necrosis Mobile App]
 
|-
 
|-
| Cassava brown streak disease   || 0 || None
+
| Cassava brown streak (leaf)   || 5 || NA ||  None
 
|-
 
|-
| Whitefly count || 0 || None
+
| Whitefly count || 2 || NA || [https://play.google.com/store/apps/details?id=aidev.cocis.makerere.org.whiteflycounter Whitefly Count App]
 
|-
 
|-
| Leaf morphology || 0 || None
+
| Leaf morphology || 8 || NA || None
 
|-
 
|-
| Plant architecture || 0 || None
+
| Plant architecture || 6 || NA || None
 
|-
 
|-
| Plant physiology || 0 || None
+
| Plant physiology || 7 || NA || None
 +
|-
 +
| Cassava mosaic disease || 4 || NA || None
 
|}
 
|}
  
==Progress==
+
===Potential Traits===
===Field Book===
+
{| class="wikitable sortable"
[http://wheatgenetics.org/field-book Field Book] was developed to eliminate paper note-taking from plant breeding programs and facilitate robust data collection and rapid data access. It is a standalone program that utilizes a straightforward interface that focuses on a single entry and trait at a time. The interface is dynamic and changes based on the type of trait being collected.  Data can be analyzed the same day they are collected, resulting in the ability to find and fix any mistakes made when collecting data. Field Book has been adopted by many U.S. and international breeding programs. It is the primary data collection software used by the [http://www.triticeaecap.org/ Triticeae Coordinated Agriculture Project], the [www.nextgencassava.org NextGen Cassava] project, many universities (KSU, Cornell, UNL, etc.), and even many private companies (Syngenta, Limagrain, and Bayer). As of April 2016, more than 1100 devices around the world have an active installation of Field Book.
+
|-
 
+
! Traits
===1KK===
+
! Importance
http://wheatgenetics.org/1kk
+
|-
 +
| Harvest index
 +
|
 +
|-
 +
| Postharvest physiological deteriation
 +
|
 +
|-
 +
| Root color (carotenoid content)
 +
|
 +
|-
 +
| Dry matter content
 +
| High
 +
|-
 +
| Sprouting vigor
 +
|
 +
|-
 +
| Root neck length
 +
|
 +
|-
 +
| Root peel and cortex vasculature thickness
 +
|
 +
|-
 +
| Soil type/fertility/environmental factors
 +
|
 +
|-
 +
| Dry season leaf retention
 +
|
 +
|}
  
 
==Notes==
 
==Notes==

Latest revision as of 18:09, 1 November 2017

The PhenoApps project will converge novel advances in image processing and machine vision to deliver transformative mobile applications through established breeder networks. User-friendly mobile apps for field-based high-throughput phenotyping that utilize novel image analysis algorithms will be built and deployed to model and extract plant phenotypes. To ensure both immediate, broad deployment and functionality on a diverse set of crops, breeder networks for cassava and wheat will be engaged, providing a diverse set of target plant phenotypes, environments, breeding programs and working cultures.

Summary

Overview

Dramatic increases in the speed and ability to collect precision phenotypic data are needed to decipher plant genomes and accelerate plant breeding. Over the past decade, the availability of genomic data has exploded while the methods to collect phenotypes have made minimal advancements. This has led to a dramatic imbalance in data sets connecting genotype to phenotype and highlighting phenotyping as the remaining major bottleneck in plant breeding programs. This project will advance the field of 3D graphics and modeling, data mining, and deep learning through integration of simultaneous ground truth phenotypic measurements and imaging with mobile technology as well as work to extend already-existing tools like Field Book.

By focusing on novel algorithms delivered through mobile apps, innovative phenotyping tools can be rapidly deployed through readily available and highly-penetrant mobile technology. This approach will enable rapid dissemination and broad usability. Collectively equipping thousands of breeders around the world with tools for rapid collection, processing and analysis of complex phenotypes will provide the foundation for increasing genetic gain that will ultimately result in improved productivity, food security, nutrition, and income of smallholder farmers and their families in developing countries.

Workflow

Bread workflow.png

Project team

Kansas State

  • Jesse Poland
    • Trevor Rife
  • Mitch Neilsen

Texas A&M

  • Bruce Gooch

Cornell

  • Michael Gore
    • Jenna Hershberger

CIMMYT

  • Ravi Singh
  • Uttam Kumar

IITA

  • Ismail Rabbi

Wheat

Summary

Wheat is one of the most important staple crops worldwide, providing 21% of the food calories and 20% of the protein for more than 4.5 billion people in 94 developing countries. In the developing world, wheat is a particularly important crop for food security as the primary staple for over 1.2 billion and an important food source for an additional 2.5 billion individuals living in poverty; men, women and children living on less than $2/day USD. In addition, wheat is the primary income source for some 30 million poor wheat farmers and their families.

In the developing world, the demand for wheat is projected to increase 60% by 2050. However, during this same period, increasing temperatures induced by climate-change are expected to reduce wheat production in developing countries by 20–30%. As a result of growing populations, demand for wheat is growing at an annual rate of 1.7% but wheat yields are growing at only about 1% annually. The increased demand is leading to market volatility and increased prices, which has a greater relative impact on the poor and food insecure. These combined factors are forecasted to double wheat prices. As a result, the purchasing power of poor consumers will decrease, leading to food insecurity and creating conditions for widespread social unrest. This scenario is aggravated by stagnating yields, soil degradation and loss of arable land, increasing fertilizer costs, loss of irrigation waters, and new virulent disease and pest strains.

Cycle

January February March April May June July August September October November December
Planting
Harvest
Phenotyping

Traits

Trait Priority Status
Spike count 0 None
Rust quantification 0 None
Seed size and shape 0 1KK
Leaf morphology 0 None
Plant architecture 0 None
Plant physiology 0 None

Cassava

Summary

Cassava (Manihot esculenta Crantz.) is a highly adaptable starchy root crop and the primary staple food for more than 800 million people, largely in sub-Saharan Africa, which accounts for more than 50% of the total cassava production globally. This clonally propagated crop is also increasingly becoming a source of revenue from fresh and processed food, the production of starch-based products, biofuels and animal feed. The crop is cultivated in tropical and sub-tropical regions of Asia, Latin America and Africa. Currently, Nigeria is the largest world producer of cassava with a total output of 52.4 million MT, which was around 21% of the world total (252.2 million MT) in 2013. In Nigeria, cassava provides at least 80% of the daily caloric requirement for over 50% of the population. Similarly, cassava provides food and income to more than 80% of the small holder households in Uganda.

Its ability to grow in marginal environments with erratic rainfall, poor soil fertility and under low intensity management has made it one of the most important food security crops in the African continent. National and international cassava breeding efforts have made significant impact on cassava productivity, quality, and disease tolerance. However, cassava breeding continues to be a challenging, particularly as cassava is a highly heterogeneous and heterozygous vegetative propagated crop with variable flowering, low seed set, and a long breeding cycle. It takes several years from making a cross to conducting large-plot, replicated, field trials and selection of parents for the next cycle of germplasm improvement. As such, the rate of genetic gain per year for yield is very low (~1.2%).

Cycle

January February March April May June July August September October November December
Planting Planting
Harvest Harvest
Phenotyping Phenotyping Phenotyping Phenotyping

Traits

Trait Priority Country Status
Root size and shape 3 NA 1KK
Cassava brown streak (root) 1 NA Necrosis Mobile App
Cassava brown streak (leaf) 5 NA None
Whitefly count 2 NA Whitefly Count App
Leaf morphology 8 NA None
Plant architecture 6 NA None
Plant physiology 7 NA None
Cassava mosaic disease 4 NA None

Potential Traits

Traits Importance
Harvest index
Postharvest physiological deteriation
Root color (carotenoid content)
Dry matter content High
Sprouting vigor
Root neck length
Root peel and cortex vasculature thickness
Soil type/fertility/environmental factors
Dry season leaf retention

Notes