Integrating genomics and mapping approaches to improve pearl millet productivity in drought prone regions of Africa and Asia

Lead Research Organisation: Aberystwyth University
Department Name: IBERS

Abstract

Declining water resources and unpredictable rainfall are serious threats to crop productivity throughout the world. Climate change scenarios indicate that water shortage and shortening of the effective growing season will be increasingly likely in sub-Saharan Africa and South Asia increasing the need for short-duration cereals such as pearl millet with enhanced drought tolerance. Although pearl millet is better adapted to water stress compared to other cereals, drought remains one of the most important factors in reducing yield and yield stability of this staple food grain crop of the world's poorest people. Improving pearl millet's tolerance to drought offers a sustainable route to alleviate poverty and food insecurity of pearl millet farmers in sub-Saharan Africa and South Asia. Efficient breeding for drought-prone environments, however, requires selection strategies that are sufficiently independent of the variation inherent in the natural environment to permit identification and use of true genetic differences. Molecular markers linked closely to traits such as pearl millet grain and stover yield during drought will provide increased reliability for selecting and breeding of these traits. The proposed research will conduct targeted genetic mapping of a genomic region on linkage group 2 known to be associated with a major drought tolerance QTL in pearl millet, in combination with precision phenotyping. A large population that is segregating only for the target drought tolerance QTL will be studied with the aim to delimit this QTL and identify closely-spaced markers. In addition, a large and diverse pearl millet germplasm panel will be used to identify additional favourable alleles/haplotypes associated with this QTL, using association genetic analysis. This association mapping is complementary to the targeted mapping approach and will identify more generic gene-based markers within the QTL. These markers would then be available for use in the transfer of this important drought tolerance QTL into a number of elite genetic backgrounds adapted to locations in Africa and Asia, using marker assisted back crossing, in collaboration with participating NARS scientists. Such material would be available as pre-breeding lines for future variety development in different parts of Africa and Asia, and involvement of NARS scientists in the process of this research, will ensure both training as well as the technology transfer. We will also explore potential physiological drought tolerance traits in near isogenic line pairs with and without the LG2 QTL to determine which traits relate to the field drought tolerance in this material. Such physiological information will help design new ideotypes of pearl millet (and other cereals) for drought-prone environments and enhance the understanding of the physiological mechanisms underlying this QTL. The direct beneficiaries of this project will be resource poor subsistence farmers in areas of Africa and Asia where pearl millet is the staple cereal and for whom food security is a very big issue. Marker-assisted breeding methods have the potential to dramatically improve the efficiency of breeding pearl millet hybrids that have improved drought tolerance together with local adaptation requirements combined with locally-preferred grain quality and improved yield attributes. The output of the proposed project will also provide a ground for map based cloning of drought tolerance gene(s) in future studies. While immediately applicable to pearl millet, generic knowledge and methodologies developed in this project will contribute to the global pool of knowledge in the important research area of drought tolerance and facilitate increased and sustainable crop production in water-limited environments globally.

Technical Summary

Pearl millet [Pennisetum glaucum (L.) R. Br.] is the staple cereal crop grown by subsistence farmers in the hottest, driest regions of sub-Saharan Africa and the Indian subcontinent where rain-fed crop production is possible. Unreliable and scant rainfall is the most important factor contributing to low grain and straw yields and poor yield stability of this crop. Efficient breeding for drought-prone environments requires selection strategies that are sufficiently independent of the variation inherent in the natural environments to permit identification and use of true genetic differences. The project will conduct targeted genetic mapping of a genomic region associated with a major drought tolerance QTL on LG 2 in pearl millet and identify closely-spaced gene-based markers associated with this QTL. An agronomically-elite near-isogenic population that segregates only for the genomic region associated with the drought tolerance QTL will be mapped with a wide range of novel markers identified using comparative mapping methods. In a complementary approach, association of these markers to the drought tolerance QTL will be tested by conducting association genetic analysis to identify more generic gene-based markers within the QTL. The tightly linked gene-based markers associated with the drought tolerance QTL thus identified will then be used to transfer this important QTL into a number of elite genetic backgrounds adapted to locations in Africa and Asia, using marker assisted back crossing. The near-isogenic lines developed will also be evaluated at various sites in Africa and Asia to confirm the effect of the QTL in a range of environments and to identify morpho-physiological traits associated with improved drought tolerance. Generic knowledge and methodologies developed in this project will contribute to the global pool of knowledge in this important research area and facilitate increased crop production in water-limited environments globally.

Publications

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? Deepmala Seghal, Leif Skot, Richa Singh, Rakesh Kumar Srivastava, Sankar Prasa (2009) PLoS ONE

 
Title Creating genetic markers to breed downy mildew and drought resistant pearl millet 
Description In collaboration with WREN Media, a popular article entitled "Creating genetic markers to breed downy mildew and drought resistant pearl millet" was prepared for publication in New Agriculturists. This article is also available at DFID R4D portal - http://www.dfid.gov.uk/r4d/caseStudies.asp?ArticleID=50751 
Type Of Art Creative Writing 
Year Produced 2011 
Impact no actual impacts realised to date 
URL http://www.dfid.gov.uk/r4d/caseStudies.asp?ArticleID=5075
 
Description The linkage group 2, having major drought tolerance (DT) QTL, was saturated with 24 new gene-based SNP and CISP markers, developed using in silico approaches (Sehgal et al. 2012). Of these, 18 markers mapped in the DT-QTL region. In addition to LG2, other linkage groups have also been saturated with gene-based markers (Sehgal et al. 2012). Key discoveries have been:
_ The DT-QTL has been fine mapped to a 3 cM interval.
- its effects on grain yiled under drought conditions further validated.
- Novel genetic resources e.g. pearl millet inbred germplasm association panel (PMiGAP)) that was developed in the project is now proving as a permanent resource to identify additonal genetic variations of pearl millet traits by scientists across the globe.
Exploitation Route Some of the crosses developed in the project are in the pipelines for turning into released cultivars for farmers in India and sub Saharn Africa. They also can be used as donors in breeding other useful traits in pearl millet. Currently the research outcomes are exploited through links with ICRISAT and Indian pearl millet research programmes who are using genetic materials, crosses and linked molecular markers in their breeding programmes. All genetic materials, crosses, and linked markers developed during the project are easily accessible to them and these organisation are free to exploit them in their breeding programmes.

Further, the project findings have enabled us winning of a new project at Aberystwyth University funded by the Innovate UK (previously known by name Technology Strategy Board; TSB) and industrial partners Unilever and Hindustan Lever Ltd to develop benefits of pearl millet for people suffering from diabetes.. The genetic and genomic resources developed during the projects are also being used in training research students and in developing further research products
Sectors Agriculture, Food and Drink,Environment

URL https://www.aber.ac.uk/en/research/excellence/impact/pearl-millet/
 
Description The findings of my project are now routinely being used in developing pearl millet varieties for use by farmers in India and in sub Saharan Africa. The resources we developed in this project (for example, Pearl millet inbred germplasm association panel (PMiGAP)) are also being used in identifying further genetic variations for traits by IBERS, ICRISAT and partners across the globe.
First Year Of Impact 2010
Sector Agriculture, Food and Drink
Impact Types Cultural,Societal,Economic

 
Description BBSRC doctoral training award
Amount £147,755 (GBP)
Funding ID BB/M502728/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2014 
End 09/2018
 
Description BBSRC-DFID
Amount £742,106 (GBP)
Funding ID BB/F004133/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2008 
End 12/2012
 
Description TSB
Amount £499,990 (GBP)
Funding ID 131788 
Organisation Innovate UK 
Sector Public
Country United Kingdom
Start 01/2015 
End 06/2016
 
Description Under this funding, two PhD students from CCSHAU were trained in the area of marker development, genotyping, phenotyping and analysis of genetic and phenotypic data.
Amount £31,500 (GBP)
Funding ID BB/H53166X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2010 
End 06/2012
 
Title Genetic resources for improving efficiency of breeding in pearl millet 
Description Near isogenic lines of pearl millet bred with drought tolerance and downy mildew resistance QTLs, pearl millet ibred germplasm association panel (PMiGAP), Marker assisted selection method in pearl millet 
Type Of Material Technology assay or reagent 
Provided To Others? Yes  
Impact New varieties developed using these genetic resources and tools are in the pipeline which when available will be made available for farmers to use 
 
Description Collaboration between ICRISATand IBERS 
Organisation Chaudhary Charan Singh Haryana Agricultural University
Country India 
Sector Academic/University 
PI Contribution Collaboration was made between CCSHAU and IBERS. Under this collaboration, two PhD students registered at CCSHAU were trained at IBERS w.e.f. June 13, 2011 ? June 15, 2012. One of the PhD students explored synteny of pearl millet DT-QTL region on LG2 across grasses including rice, sorghum and ryegrass and conducted expression analysis of candidate genes in DT-QTL region by semi-quantitative RT PCR. The other PhD student is working on MAS for downy mildew for which mapped SSR markers in downy mildew (DM) QTL regions on LGs 1 and 4, using cross ICMP 451 x HBL11, for use in transferring DM-QTLs into HBL11. Both students have been imparted training on development of molecular markers including gene-based markers, genotyping using different gel systems including PAGE and by fluorescent labelling, scoring on gels and by using different computer programs like GENEMAPPER, genetic mapping using JOINMAP, MAPMAKER, MAPMAKER QTL, THREADMAPPER etc.
Collaborator Contribution field phenotyping, generating of new crosses and genetic resources
Impact Generation of Near osgenic lines Generation of PMiGAP
Start Year 2011
 
Description Partnership between NARS institutes of India and IBERS 
Organisation Chaudhary Charan Singh Haryana Agricultural University
Country India 
Sector Academic/University 
PI Contribution 1. Seeds of DT-QTL NILs (ICMR 1029, ICMR 1031, ICMR 1040, ICMR 1046, ICMR 2042 and ICMR 2044) were provided to NARS partners (CSSRI) to test them under a range of salinity and alkalinity conditions. It was found that DT-QTL provided added advantage under salinity and alkalinity conditions. The results were published in a peer reviewed journal Molecular Breeding with one of the NARS partners as lead author (Sharma et al. 2011). Based on these results, DT-QTL on LG2 has become a major target for
Collaborator Contribution Sandwich students did part of their research degree course work and thesis work there at the partner organisation
Impact Two sandwich students completed their PhD degree under this partenership Joint Research Paper
Start Year 2008
 
Description iCASE studentship 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC)
Country United Kingdom 
Sector Public 
PI Contribution A PhD studentship training is underway
Collaborator Contribution Funding for the training
Impact underway
Start Year 2014
 
Description iCASE studentship 
Organisation Unilever
Country United Kingdom 
Sector Private 
PI Contribution A PhD studentship training is underway
Collaborator Contribution Funding for the training
Impact underway
Start Year 2014
 
Title New pyramided lines having QTLs of drought tolernace and downy mildew developed and made available to reserachers in India and SSA 
Description Seeds of 162 recombinant individuals from within the high resolution cross were provided to Indian collaborators for multilocational trials (in Bawal, Jamnagar, Mandore and Patancheru) which identified following five pyramided lines having QTLs of drought tolerance (LG2) and downy mildew (LGs 1 and 4) (Fig. 1) a. (ICMR01029-7xICMR01004-7)-2-2041-B b. (ICMR01029-7xICMR01004-7)-2-1288-B c. (ICMR01029-7xICMR01004-7)-2-2034-B d. (ICMR01029-7xICMR01004-7)-2-1621-B e. (ICMR01029-7xICMR01004-7)-2 
Type Of Technology New Material/Compound 
Year Produced 2012 
Impact No actual Impacts realised to date 
 
Description Foster capacity building of the NARS breeding programme 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Three NARS scientists from India and Ghana were invited at IBERS and/or ICRISAT for training in practical aspects of DNA extraction, marker development, genotyping, phenotyping and analysis of genetic and phenotypic data. Two were trained at IBERS w.e.f. May 7 - July 1, 2010. One attended a CEG training course course on "Application of Molecular Markers in Crop Improvement" held on 7-19 November, 2010 at ICRISAT, Hyderabad, India. Besides routine molecular biology techniques and software prog

Researchers and students could know how the concept of MAS works and being used in practical pearl millet breeding programmes
Year(s) Of Engagement Activity 2009,2010,2011,2012,2013