MTME Rice Breeding Data | Data.NSW

This data was used in the manuscript 'Genomic selection for genotype performance and stability using information on multiple traits and multiple environments' by J. Bancic, B. Ovenden, G. Gorjanc and D.J. Tolhurst (https://doi.org/10.1007/s00122-023-04305-1).

This paper develops a single-stage genomic selection (GS) approach which incorporates information on multiple traits and multiple environments within a partially separable factor analytic framework. The factor analytic linear mixed model is an effective method for analysing multi-environment trial (MET) datasets, but is yet to be extended to GS for multiple traits and multiple environments. The advantage of using all sources of information is that breeders can utilise genotype by environment by trait interaction (GETI) to obtain more accurate predictions across correlated traits and environments. The partially separable factor analytic linear mixed model (SFA-LMM) developed in this paper is based on a three-way separable structure, which includes a factor analytic matrix between traits, a factor analytic matrix between environments and a genomic relationship matrix between genotypes. An additional specific variance matrix is then added to enable a different genotype by environment interaction (GEI) pattern for each trait and a different genotype by trait interaction (GTI) pattern for each environment. The results show that the SFA-LMM and all other factor analytic linear mixed models provide a better fit than the completely separable approaches. Selection from the SFA-LMM is then demonstrated using a selection index based on measures of genotype performance and stability. This research represents an important continuation in the advancement of plant breeding analyses, particularly with the advent of high-throughput phenotypic datasets involving a very large number of traits and environments.

These datasets include the phenotypic data, marker data and genomic relationship matrix used in the analysis. Phenotypic data includes grain yield, days to flowering, mature plant height and grain protein. Marker data was derived from Diversity Arrays next generation sequencing (DArTSeq).

This research was conducted as collaboration between The Roslin Institute (University of Edinburgh) and the Australian Rice Breeding Program. The Australian Rice Breeding Program is funded under the Australian Rice Partnership II project, a partnership between NSW Department of Primary Industries, AgriFutures and SunRice.

Data Source:

Data.NSW

Tags

Data and Resources

CSV

Phenotypic Data

This file contains phenotypic data (grain yield in tonnes per hectare, days to flowering from date of sowing, mature plant height in cm, grain protein...

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CKAN Data API

Access resource data via a web API with powerful query support. Further information in the main CKAN Data API and DataStore documentation.

Code examples:

curl JavaScript PowerShell Python R

Querying

Get 5 results containing "jones" in any field:

curl https://uatweb.datansw.links.com.au/data/api/action/datastore_search \
  -H"Authorization:$API_TOKEN" -d '
{
  "resource_id": "434e3031-c7ad-46c3-b9b6-405d703b7d33",
  "limit": 5,
  "q": "jones"
}'

const resp = await fetch(`https://uatweb.datansw.links.com.au/data/api/action/datastore_search`, {
    method: 'POST',
    headers: {
        'content-type': 'application/json',
        authorization: API_TOKEN
    },
    body: JSON.stringify({
        resource_id: '434e3031-c7ad-46c3-b9b6-405d703b7d33',
        limit: 5,
        q: 'jones'
    })
})
await resp.json()

$json = @'
{
  "resource_id": "434e3031-c7ad-46c3-b9b6-405d703b7d33",
  "limit": 5,
  "q": "jones"
}
'@
$response = Invoke-RestMethod https://uatweb.datansw.links.com.au/data/api/action/datastore_search`
  -Method Post -Body $json -Headers @{"Authorization"="$API_TOKEN"}
$response.result.records

(using the ckanapi client library)

from ckanapi import RemoteCKAN

rc = RemoteCKAN('https://uatweb.datansw.links.com.au/data/', apikey=API_TOKEN)
result = rc.action.datastore_search(
    resource_id="434e3031-c7ad-46c3-b9b6-405d703b7d33",
    limit=5,
    q="jones",
)
print(result['records'])

library(httr2)

req <- request("https://uatweb.datansw.links.com.au/data/api/action/datastore_search")
result <- req %>% 
    req_headers(Authorization = API_TOKEN) %>% 
    req_body_json(list(
        resource_id = '434e3031-c7ad-46c3-b9b6-405d703b7d33',
        limit = 5,
        q = 'jones'))
    req_perform %>% 
    resp_body_json

Get results with either "watershed" or "survey" as subject and "active" as its stage:

curl https://uatweb.datansw.links.com.au/data/api/action/datastore_search \
-H"Authorization:$API_TOKEN" -d '
{
"resource_id": "434e3031-c7ad-46c3-b9b6-405d703b7d33",
  "filters": {
    "subject": ["watershed", "survey"],
    "stage": "active"
  }
}'

const resp = await fetch(`https://uatweb.datansw.links.com.au/data/api/action/datastore_search`, {
    method: 'POST',
    headers: {
        'content-type': 'application/json',
        authorization: API_TOKEN
    },
    body: JSON.stringify({resource_id: '434e3031-c7ad-46c3-b9b6-405d703b7d33', filters: {
        subject: ['watershed', 'survey'],
        stage: 'active'
    }})})
await resp.json()

$json = @'
{
  "resource_id": "434e3031-c7ad-46c3-b9b6-405d703b7d33",
  "filters": {
    "subject": ["watershed", "survey"],
    "stage": "active"
  }
}
'@
$response = Invoke-RestMethod https://uatweb.datansw.links.com.au/data/api/action/datastore_search`
  -Method Post -Body $json -Headers @{"Authorization"="$API_TOKEN"}
$response.result.records

from ckanapi import RemoteCKAN

rc = RemoteCKAN('https://uatweb.datansw.links.com.au/data/', apikey=API_TOKEN)
result = rc.action.datastore_search(
    resource_id="434e3031-c7ad-46c3-b9b6-405d703b7d33",
    filters={
      "subject": ["watershed", "survey"],
      "stage": "active",
    },
)
print(result['records'])

library(httr2)

req <- request("https://uatweb.datansw.links.com.au/data/api/action/datastore_search")
result <- req %>% 
    req_headers(Authorization = API_TOKEN) %>% 
    req_body_json(list(
        resource_id='434e3031-c7ad-46c3-b9b6-405d703b7d33', 
        filters = list(
            subject = list("watershed", "survey"), 
            stage = "active")))
    req_perform %>% 
    resp_body_json

Using the API with this Web Browser

Some API endpoints may be accessed using a GET query string.

Query example (first 5 results)

https://uatweb.datansw.links.com.au/data/api/action/datastore_search?resource_id=434e3031-c7ad-46c3-b9b6-405d703b7d33&limit=5

Query example (results containing 'jones')

https://uatweb.datansw.links.com.au/data/api/action/datastore_search?resource_id=434e3031-c7ad-46c3-b9b6-405d703b7d33&q=jones

CSV

Marker Data

This file contains filtered and centred marker data on 267 rice genotypes derived from DArTSeq genotyping. A total of 3,895 polymorphic markers were used.

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CSV

Genomic Relationship Matrix

This genomic relationship matrix was constructed from the filtered and centred molecular marker data.

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CKAN Data API

Access resource data via a web API with powerful query support. Further information in the main CKAN Data API and DataStore documentation.

Code examples:

curl JavaScript PowerShell Python R

Querying

Get 5 results containing "jones" in any field:

curl https://uatweb.datansw.links.com.au/data/api/action/datastore_search \
  -H"Authorization:$API_TOKEN" -d '
{
  "resource_id": "486d096f-e715-4ccb-b0ee-bea4cab1911f",
  "limit": 5,
  "q": "jones"
}'

const resp = await fetch(`https://uatweb.datansw.links.com.au/data/api/action/datastore_search`, {
    method: 'POST',
    headers: {
        'content-type': 'application/json',
        authorization: API_TOKEN
    },
    body: JSON.stringify({
        resource_id: '486d096f-e715-4ccb-b0ee-bea4cab1911f',
        limit: 5,
        q: 'jones'
    })
})
await resp.json()

$json = @'
{
  "resource_id": "486d096f-e715-4ccb-b0ee-bea4cab1911f",
  "limit": 5,
  "q": "jones"
}
'@
$response = Invoke-RestMethod https://uatweb.datansw.links.com.au/data/api/action/datastore_search`
  -Method Post -Body $json -Headers @{"Authorization"="$API_TOKEN"}
$response.result.records

(using the ckanapi client library)

from ckanapi import RemoteCKAN

rc = RemoteCKAN('https://uatweb.datansw.links.com.au/data/', apikey=API_TOKEN)
result = rc.action.datastore_search(
    resource_id="486d096f-e715-4ccb-b0ee-bea4cab1911f",
    limit=5,
    q="jones",
)
print(result['records'])

library(httr2)

req <- request("https://uatweb.datansw.links.com.au/data/api/action/datastore_search")
result <- req %>% 
    req_headers(Authorization = API_TOKEN) %>% 
    req_body_json(list(
        resource_id = '486d096f-e715-4ccb-b0ee-bea4cab1911f',
        limit = 5,
        q = 'jones'))
    req_perform %>% 
    resp_body_json

Get results with either "watershed" or "survey" as subject and "active" as its stage:

curl https://uatweb.datansw.links.com.au/data/api/action/datastore_search \
-H"Authorization:$API_TOKEN" -d '
{
"resource_id": "486d096f-e715-4ccb-b0ee-bea4cab1911f",
  "filters": {
    "subject": ["watershed", "survey"],
    "stage": "active"
  }
}'

const resp = await fetch(`https://uatweb.datansw.links.com.au/data/api/action/datastore_search`, {
    method: 'POST',
    headers: {
        'content-type': 'application/json',
        authorization: API_TOKEN
    },
    body: JSON.stringify({resource_id: '486d096f-e715-4ccb-b0ee-bea4cab1911f', filters: {
        subject: ['watershed', 'survey'],
        stage: 'active'
    }})})
await resp.json()

$json = @'
{
  "resource_id": "486d096f-e715-4ccb-b0ee-bea4cab1911f",
  "filters": {
    "subject": ["watershed", "survey"],
    "stage": "active"
  }
}
'@
$response = Invoke-RestMethod https://uatweb.datansw.links.com.au/data/api/action/datastore_search`
  -Method Post -Body $json -Headers @{"Authorization"="$API_TOKEN"}
$response.result.records

from ckanapi import RemoteCKAN

rc = RemoteCKAN('https://uatweb.datansw.links.com.au/data/', apikey=API_TOKEN)
result = rc.action.datastore_search(
    resource_id="486d096f-e715-4ccb-b0ee-bea4cab1911f",
    filters={
      "subject": ["watershed", "survey"],
      "stage": "active",
    },
)
print(result['records'])

library(httr2)

req <- request("https://uatweb.datansw.links.com.au/data/api/action/datastore_search")
result <- req %>% 
    req_headers(Authorization = API_TOKEN) %>% 
    req_body_json(list(
        resource_id='486d096f-e715-4ccb-b0ee-bea4cab1911f', 
        filters = list(
            subject = list("watershed", "survey"), 
            stage = "active")))
    req_perform %>% 
    resp_body_json

Using the API with this Web Browser

Some API endpoints may be accessed using a GET query string.

Query example (first 5 results)

https://uatweb.datansw.links.com.au/data/api/action/datastore_search?resource_id=486d096f-e715-4ccb-b0ee-bea4cab1911f&limit=5

Query example (results containing 'jones')

https://uatweb.datansw.links.com.au/data/api/action/datastore_search?resource_id=486d096f-e715-4ccb-b0ee-bea4cab1911f&q=jones

R Script

R Script Used for Modelling

This file contains the R Script for the models described in the manuscript

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PDF

Manuscript: Genomic selection for genotype performance an...

This is the published manuscript for this paper

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PDF

Supplementary material: Genomic selection for genotype pe...

This is the supplementary material file for the published manuscript

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Data Preview: Genomic Relationship Matrix

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Additional Information

Field	Value
Title	MTME Rice Breeding Data
Date Published	13/12/2022
Last Updated	08/05/2023
Publisher/Agency	Department of Primary Industries (DPI)
Licence	Creative Commons Attribution
Update Frequency	Never/Static
Contact Point	Department of Primary Industries nsw.agriculture@dpi.nsw.gov.au
Temporal Coverage	01/10/2016 - 01/06/2018
Data Portal	Data.NSW