Generation Challenge Programme >> Research Themes >> Capacity building

Comparative Genomics InfoCentre

2012-07-03T20:11:15-05:00

Comparative Genomics Research Initiative
Annual reports:2013 – read online | 2013 – download PDF (762.2 kB) | 2012 – read online | 2012 – download PDF (356.16 kB) | previous years
Multimedia information
- Podcasts – aluminium toxicity (sorghum) | Phosphorus efficiency (rice)
- Blogposts – comparative genomics in cereals | other genomics blogposts
- Videos
Rice: Phosphorus efficiency in rice – Press release and Blogpost | Indonesia | Back story – how it all began
Updates on: aluminium tolerance (maize) | sorghum work in Kenya (newspaper article)
Genomic Products

Maize facts & figures
(IBP website)
Information & genomics
(IBP website)

Rice facts & figures
(IBP website)
Information & genomics
(IBP website)

Sorghum facts & figures
(IBP website)
Information & genomics
(IBP website)

Agricultural Genomics Network (AGN)

hosted on the IBP website, with a discussion forum on LinkedIn

Main objectives:

Develop a community to discuss advances in genomics and provide critical appraisal of genomic technologies, tools and approaches
Develop a portal that will present the information on tools, resources developed by GCP or available in the public domain either by hosting some of them, or by providing links to other existing databases and portals, and
Broker access to economically priced large scale sequencing, construction of variety of (BAC, cDNA, fosmid) libraries, physical mapping, sequencing and re-sequencing, etc, provided by third-party service providers.

Products

Please remember to 'shop' for genomic resources through our Product Catalogue

Comparative genomics - Agricultural genomics network

2011-10-27T19:52:56-05:00

With an objective of making genetic research and breeding applications cost-effective by enhancing adoption of modern genomic technologies, GCP is exploring possible initiation of the Agricultural Genomics Network (AGN) as a part of the Integrated Breeding Platform (IBP). AGN is expected to have the following three main components:

Develop a community to discuss advances in genomics and provide critical appraisal of genomic technologies, tools and approaches
Develop a portal that will present the information on tools, resources developed by GCP or available in the public domain either by hosting some of them, or by providing links to other existing databases and portals, and
Broker access to economically priced large scale sequencing, construction of variety of (BAC, cDNA, fosmid) libraries, physical mapping, sequencing and re-sequencing, etc, provided by third-party service providers (eg. BGI, JCVI, NCGR).

Comparative genomics – Aluminium tolerance and phosphorus efficiency – Rice

2011-10-27T19:43:22-05:00

Improved rice cultivars for Asian problem soils: Pyramiding of major genes/QTLs for tolerance to phosphorus deficiency and aluminium toxicity (G7010.03.04)

Target country	Indonesia
Lead institute	International Rice Research Institute (IRRI)
Partners	Japan International Research Center for Agricultural Sciences (JIRCAS) Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA, Agricultural Research Corporation), Brazil Cornell University/United States Department of Agriculture–Agricultural Research Services (USDA–ARS)

In Asia, about 60 percent of rainfed rice is grown on soils that are affected by multiple stresses. These typically include phosphorus (P) deficiency as well as acidity, salinity, aluminium (Al) toxicity and drought. The development of rice cultivars with multiple stress tolerance is therefore considered an important breeding goal.

This project seeks to develop breeding lines with multiple tolerance through pyramiding of individual QTLs, starting with combined tolerance of P deficiency and Al toxicity. This is particularly relevant in order to fully benefit from Pup1 gene because the tolerance mechanism conferred by Pup1, high relative root growth, would be compromised if cultivars were sensitive to Al toxicity since excess Al severely inhibits root growth and thereby water and nutrient uptake.

P deficiency and Al toxicity are soil-related stresses that typically coincide on acid soils that are very common in the humid tropics. The Pup1 locus has shown its potential in partly overcoming the negative effects of P deficiency. Introgression of Pup1 into widely grown upland and irrigated rice varieties following the marker-assisted backcrossing approach that was successfully applied for submergence tolerance is near completion and the first field experiments were conducted in Indonesia. This project will continue and complete these activities within the commissioned project G4008.41 (Application and validation of the major QTL phosphate uptake 1 [Pup1]), which ended in December 2009. This will ensure that the developed breeding lines and Pup1 marker technology are handed over to country partners in Asia and Africa for testing and development of local Pup1 varieties. –

Objectives

Map Al-tolerance loci in populations developed from highly Al-tolerant Indonesian upland varieties.
Develop rice breeding lines with tolerance of P deficiency, drought, and Al toxicity through pyramiding of major target QTLs.
Disseminate seeds to country partners and assist them in the implementation of screening protocols and marker technology.
Enable Pup1 cloning in sorghum and maize by providing gene-specific markers and conduct screenings.

Facts and figures on rice (IBP webiste)

Comparative genomics - Aluminium tolerance and Phosphorus efficiency - Maize

2011-10-27T19:22:59-05:00

Marker-assisted backcrossing for improving phosphorus-use efficiency and tolerance to aluminium toxicity via Pup1 and Alt_SB genes in maize (G7010.03.05)

Target country	Kenya
Lead institute	Moi University/Kenya Agricultural Research Institute (KARI)
Partners	Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA, Agricultural Research Corporation), Brazil Japan International Research Center for Agricultural Sciences (JIRCAS) International Rice Research Institute (IRRI) United States Department of Agriculture–Agricultural Research Services (USDA–ARS) Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT; the International Maize and Wheat Improvement Center)

Phosphorus (P) deficiency and aluminium (Al) toxicity are two of the most important constraints responsible for low maize productivity on acid soils worldwide, and particularly in Africa where because of resource limitations low input agriculture is the norm

This project will use molecular breeding approaches as well as conventional breeding to speed up development of maize varieties adapted to the acid soils of Africa. The research proposed here is closely connected to the other two maize projects on comparative genomics, and should result in significant improvements in maize yields on acid soils in Kenya and other African countries, as well as in Brazil.

Objectives

Screening of Kenyan maize germplasm for Al tolerance in nutrient solution, for ZmMATE gene expression, and for P efficiency in the field
Development of maize topcrosses for assessing yield performance under acid soil conditions in Kenya
Evaluation of Kenyan maize topcrosses, synthetics and hybrids for Al tolerance and P efficiency in the field
Marker-assisted selection for genes/QTLs to improve Al tolerance and P-use efficiency in locally adapted maize germplasm
Develop mapping populations using the highly aluminium-tolerant Kenyan sources, 203B, K4 and/or CON 5
Training and capacity building

Comparative Genomics – Phosphorus efficiency – Sorghum

2011-10-27T19:14:44-05:00

Improving phosphorus efficiency in sorghum by the identification and validation of sorghum homologues for Pup1, a major QTL underlying phosphorus uptake in rice, and identification of other P efficiency QTLs (G7010.03.06)

Target countries	Kenya, Niger
Lead institute	Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA, Agricultural Research Corporation), Brazil
Partners	Cornell University/United States Department of Agriculture–Agricultural Research Services (USDA–ARS) Institut national de la recherche agronomique du Niger (INRAN)Japan International Research Center for Agricultural Sciences (JIRCAS) Moi University/Kenya Agricultural Research Institute (KARI)

Low productivity due to soil constraints and a lack of properly adapted crop cultivars is a serious problem in many parts of Africa, where sorghum is a staple food supporting millions of the rural poor. Pup1 is a major QTL located on rice chromosome 12 that underlies phosphorus (P) efficiency and has the potential to increase P acquisition efficiency in other cereals. Research findings from a long-term collaboration between IRRI and JIRCAS has resulted in the fine-mapping of the Pup1 locus to a ~150 Kb region on chr 12, and 2–4 high-quality Pup1 candidate genes have been identified.

Taking advantage of the complete sequence of the sorghum genome, this project seeks establish a framework based on comparative genomics to identify sorghum Pup1 homologues and will validate their role as bona fide genes underlying tolerance to P deficiency. The project further aims to lay the foundation for a molecular breeding programme targeting marginal soils in Niger and Kenya and other areas of Sub-Saharan Africa to improve food security and farmer income.

Objectives

The overall objective is to identify genes related to tolerance to P deficiency in sorghum, with a focus on Pup1 homologs in sorghum and the sorghum Al tolerance gene, AltSB, which will be transferred to the Sorghum Molecular Breeding (SorghumMB) project for deployment into breeding programmes. Specific objectives are:

Identify homologs of rice Pup1 that are associated with traits related to P-deficiency tolerance in sorghum and also clarify the role of the Alt_SB gene in tolerance to low P.
Validate genes associated with P deficiency tolerance in sorghum.

Comparative genomics - Phosphorus efficiency - Maize

2011-10-27T19:07:49-05:00

Cloning, characterisation and validation of Pup1/P efficiency in maize (G7010.03.01)

Target country	Kenya
Lead institute	Cornell University/United States Department of Agriculture–Agricultural Research Services (USDA–ARS)
Partners	Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA, Agricultural Research Corporation), Brazil Japan International Research Center for Agricultural Sciences (JIRCAS) International Rice Research Institute (IRRI) Kenya: Moi University; Kenya Agricultural Research Institute (KARI)

The interdisciplinary team involving the institutes above is working on the successful implementation of the identification and characterisation of genes associate with maize phosphorus (P) efficiency (tolerance to low phosphorus. Bioinformatics is being used to identify homologues of the rice Pup-1 gene in maize and a set of markers for these genes will be developed. Field phenotyping will be conducted in Kenya and Brazil.

Objectives

Pup1 gene candidate identification in maize
QTL/gene mapping for P use efficiency in maize
Inheritance studies on maize root architecture under high and low P
Validation of maize Pup1 candidate genes and if necessary novel P-efficiency QTLs (if maize Pup1 homologues are not functional in P efficiency)

Comparative Genomics – Aluminium tolerance and phosphorus efficiency – Sorghum

2011-10-25T03:25:13-05:00

Establishing a molecular breeding programme based on the aluminium tolerance gene Alt_SB and the P efficiency QTL, Pup1, for increasing sorghum production in sub-Saharan Africa (G7010.03.03)

Target countries	Kenya, Niger
Lead institute	International Crops Research Institute for the Semi-Arid Tropics
Partners	Institut national de la recherche agronomique du Niger (INRAN) Kenya : Moi University, Kenya Agricultural Research Institute (KARI) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA, Agricultural Research Corporation), Brazil Cornell University/United States Department of Agriculture–Agricultural Research Services (USDA–ARS)

In Africa, a combination of soil constraints and a lack of adapted crop cultivars are clearly two of the most important factors responsible for low grain yield. Low productivity is a serious problem in many parts of Africa where sorghum is a staple food supporting millions of the rural poor. This project will attempt to validate homologs of the major rice P uptake QTL, Pup1, functioining as P deficiency tolerance genes in sorghum, and investigate a similar role for the major Al tolerance gene, AltSB. If successful, we will develop molecular markers for Pup1 validated homologues for marker-assisted selection for P deficiency tolerance in sorghum. We are also developing and validating gene-specific markers for Alt_SB within other GCP projects. The project implements a molecular breeding programme targeting Niger and Kenya using random mating ms3 populations (RMPs) for the eventual development of improved varieties and breeding materials with Al tolerance and improved performance under low P stress. These two target traits largely underlie adaptation to acid soil and low-phosphorus conditions. This project will build upon the progress achieved in the GCP commissioned project, ‘Assessment of the breeding value of superior haplotypes for Alt_SB, a major Al-tolerance gene in sorghum: linking upstream genomics to acid soil breeding in Niger and Mali (ALTFIELD).’ The results will be validated in Kenya and Niger as well as at EMBRAPA Maize and Sorghum (EMBRAPA MS) using S1 and S2 selected progenies from RMPs in phenotyping sites specifically developed for this purpose.

Overall goal:

develop the capacity and necessary tools in African institutions for stacking desirable genes in the development of elite multiple trait cultivars and to develop breeding materials that show superior performance in soils where Al toxicity and low P availability can cause serious reductions in productivity.

Objectives

Development of adequate elite random mating ms3 populations (RMPs) segregating for both Al tolerance and P acquisition efficiency and the generation of half-sib/full-sib and S1 progenies for marker assisted selection for Alt_SB and Pup1.
Development of marker-assisted selection (MAS) protocols for Alt_SB and Pup1* and their application in half-sib, full-sib, and S1 progeny derived from the RMPs.
Field validation of S2 progenies with superior Alt_SB or Pup1 alleles, and progeny where Alt_SB and Pup1 have been pyramided
Generate through marker-assisted backcrossing locally adapted breeding lines (at least one per partner country) which combine a favourable Alt_SB allele with 1–3 closely linked morphological markers (ie, awning, and possibly ms3, and in Niger or Kenya the red Pericarp colour is also an option)
Development of human resources and minimal infrastructure for executing MAS recurrent selection and marker assisted backcrossing.

Comparative genomics - Capacity building

2011-06-04T16:28:32-05:00

Comparative Genomics - Capacity Building

Comparative genomics - Aluminium tolerance - Rice

2011-06-04T16:27:39-05:00

Cloning, characterisation and validation of Alt_SB/Al tolerance in rice (G7009.07)

Target country	Indonesia
Lead institute	Cornell University/United States Department of Agriculture–Agricultural Research Services (USDA–ARS)
Partner	Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development (ICABIOGRAD)

A primary limitation to crop production on acid soils, which make up as much as 50 percent of the world’s arable lands, is aluminium (Al) toxicity. On acid soils, Al toxicity results in rapid damage and growth inhibition of root systems, which leads to significant yield reductions due to inhibited uptake of water and nutrients.

Rice is the most Al-tolerant cereal, yet Al toxicity is still a major limitation to rice production in both rainfed lowlands and uplands.

In this project we are taking advantage of the recently cloned sorghum Al-tolerance gene that is a member of the MATE family of organic solute transporters, to identify rice homologues that are candidate tolerance genes. In rice, a computational analysis of the MATE family was conducted which identified five MATE genes that are co-localised with previously identified Al-tolerance QTLs. They are now being tested as candidate Al-tolerance genes using T-DNA rice knockout lines.

Should these homologues not be functional in rice, complementary approaches are already in place.

Objectives

Characterise T-DNA knockouts for candidate Alt_SB MATE homologues in rice for physiological function and involvement in Al tolerance and quantification of the role of these candidate MATE genes in rice Al tolerance.
Fine-map and/or clone the gene(s) underlying the novel major Al resistance QTLs previously identified on rice chr 12.
Complete the whole genome mapping for rice Al tolerance using the OryzaSNP II chip (44k SNP chip)
Initiate development of Al tolerance NILs based on identified QTLs and also newly mapped loci from whole-genome association mapping to quantify the contribution of individual loci to Al tolerance and as a resource for breeding for rice Al tolerance.

Comparative genomics - Aluminium tolerance - Maize

2011-06-04T16:27:08-05:00

Cloning, characterisation and validation of Alt_SB/Al tolerance in maize (G7010.03.02)

Target country	Kenya
Lead institute	Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA, Agricultural Research Corporation), Brazil
Partners	Cornell University/United States Department of Agriculture–Agricultural Research Services (USDA–ARS) Kenya: Moi University; Kenya Agricultural Research Institute (KARI

Over 50% of the world’s potentially arable lands consist of acid soils, where aluminium (Al) toxicity is the primary factor limiting maize yield, one of the world’s most important food crop. This problem is particularly acute inlow-input agricultural systems, which encompasses a large portion of the farmers in Sub-Saharan Africa, as well as smallscale farmers in other developing regions.

Aluminium tolerance is a quantitatively inherited trait in maize, a crop that displays considerable variation for this trait, as well a highly complex genome organisation.

Taking advantage of the aluminium (Al) tolerance gene cloned in sorghum (Alt_SB), as well as findings from recent GCP-supported research in maize where two major Al tolerance QTLs were co-localised with AltSB homologues (ZmMATE genes), we seek to characterise and validate functional ZmMATE genes or QTLs conferring superior Al tolerance in maize.

This strategy is premised on project genetic resources already available as near-isogenic lines for both QTLs, segregating populations and crosses between Brazilian sources of Al tolerance and Kenyan-adapted germplasm. This structured germplasm, as well as newly developed crosses, are being subjected to molecular, physiological and field evaluations in order to accomplish the functional validation of candidate genes or QTLs for improving Al tolerance in different tropical maize germplasm.

This work involves collaborators with a long history of successful partnership on maize and sorghum Al tolerance.

The research findings from this project will both greatly increase our understanding of the molecular and genetic basis for cereal Al tolerance, and – more importantly – will provide the basic materials for molecular breeding programmes focusing on improving maize production and stability on acid soils in Africa and other developing regions.

Objectives

1.    Validation of functional ZmMATE genes or Al-tolerance QTLs in the maize Brazilian crosses
2.    Development and screening of molecular markers for ZmMATE genes or Al tolerance QTLs studies
3.    Validation of ZmMATE genes or Al tolerance QTLs in a panel of Kenyan and Brazilian maize lines

Generation Challenge Programme >> Research Themes >> Capacity building

Comparative Genomics InfoCentre

Comparative genomics - Agricultural genomics network

Comparative genomics – Aluminium tolerance and phosphorus efficiency – Rice

Improved rice cultivars for Asian problem soils: Pyramiding of major genes/QTLs for tolerance to phosphorus deficiency and aluminium toxicity (G7010.03.04)

Objectives

Comparative genomics - Aluminium tolerance and Phosphorus efficiency - Maize

Marker-assisted backcrossing for improving phosphorus-use efficiency and tolerance to aluminium toxicity via Pup1 and AltSB genes in maize (G7010.03.05)

Objectives

Comparative Genomics – Phosphorus efficiency – Sorghum

Improving phosphorus efficiency in sorghum by the identification and validation of sorghum homologues for Pup1, a major QTL underlying phosphorus uptake in rice, and identification of other P efficiency QTLs (G7010.03.06)

Objectives

Comparative genomics - Phosphorus efficiency - Maize

Cloning, characterisation and validation of Pup1/P efficiency in maize (G7010.03.01)

Objectives

Comparative Genomics – Aluminium tolerance and phosphorus efficiency – Sorghum

Establishing a molecular breeding programme based on the aluminium tolerance gene AltSB and the P efficiency QTL, Pup1, for increasing sorghum production in sub-Saharan Africa (G7010.03.03)

Overall goal:

Objectives

Comparative genomics - Capacity building

Comparative genomics - Aluminium tolerance - Rice

Cloning, characterisation and validation of AltSB/Al tolerance in rice (G7009.07)

Objectives

Comparative genomics - Aluminium tolerance - Maize

Cloning, characterisation and validation of AltSB/Al tolerance in maize (G7010.03.02)

Objectives

Marker-assisted backcrossing for improving phosphorus-use efficiency and tolerance to aluminium toxicity via Pup1 and Alt_SB genes in maize (G7010.03.05)

Establishing a molecular breeding programme based on the aluminium tolerance gene Alt_SB and the P efficiency QTL, Pup1, for increasing sorghum production in sub-Saharan Africa (G7010.03.03)

Cloning, characterisation and validation of Alt_SB/Al tolerance in rice (G7009.07)

Cloning, characterisation and validation of Alt_SB/Al tolerance in maize (G7010.03.02)