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5th NGGIBCI - 2015
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3rd NGS Workshop - 2012
2nd NGS Workshop - 2010
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2nd MAS Workshop- 2010
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2nd National Workshop on Marker-Assisted Selection for Crop Improvement
(27-29 October 2010) ICRISAT, Patancheru, A.P, India




List of participants

ICRISAT in collaboration with Department of Biotechnology, Government of India and Generation Challenge Program (GCP – a programme of the CGIAR) has hosted the "2nd National Workshop on Marker-Assisted Selection (MAS) for Crop Improvement" during 27-29 October 2010, at ICRISAT Campus, Greater Hyderabad, India. The objective of this workshop was to create awareness among the crop breeding community in India about the latest developments in the field of marker assisted selection (MAS). For achieving this goal, the academic programme of the workshop also included presentations and discussions in the related fields of genomics, quantitative genetics and bioinformatics, that were relevant to a full discussion on MAS for crop improvement. The PIs/ Co- PIs/Collaborators of ongoing projects funded under the Accelerated Crop Improvement Programme (ACIP) of DBT and the senior scientists involved in evaluation and monitoring of these molecular breeding projects will participate in this workshop. Some senior scientists and experts both from India and abroad also joined as special invitees to deliberate on this important subject.

The development of DNA (or molecular) markers and their use has already made a major impact on the way we conduct research in the field of plant genetics and also on the selection strategies we use in plant breeding. During the last two decades, both interval mapping and association mapping have been successfully used to identify marker-trait associations (MTA) for a variety of traits in all major crops to facilitate the use of marker genotyping as a substitute for cumbersome phenotypic selection, particularly for the traits that are difficult to score visually. Techniques have also been developed to undertake 'background selection' to reconstitute the genome of recurrent parent after transfer of a desirable gene through backcross method of plant breeding. The marker assisted selection (MAS) has thus reached a stage, when it is already being used as an integral component of conventional plant breeding, leading in several crops to the development of improved cultivars/hybrids that are being grown by the farmers in different parts of the world. The techniques involved in MAS are also evolving further to make MAS cost-effective and to further accelerate the process of plant breeding. For instance, in addition to the routine marker-aided backcrossing (MABC), marker-assisted recurrent selection (MARS) and genome wide slection (GWS) are the two new approaches that are now being practiced to improve the efficiency and effectiveness of MAS. DNA sequencing-based genotyping has also emerged as a new approach due to the emerging new generation sequencing (NGS) technologies that would reduce the cost of whole genome sequencing by several orders.

It is thus obvious that recent advances in the areas of DNA sequencing, genotyping, bioinformatics and statistical genetics/genomics offer immense opportunities for the use of modern genetics for gene/QTL discovery and allele mining, thus transforming crop breeding approaches. A number of phenomics and molecular breeding platforms have also been developed to bring precision in working out marker-trait associations and their use for MAS. Therefore, plant breeders are at a threshold for a major transformation in the methods they use in conventional plant breeding; they need to equip themselves for using these modern genomics tools in their breeding programmes. The workshop has been planned to bring the leading scientists in the area of modern genomics and those involved in molecular breeding both from India and abroad. The deliberations and brainstorming sessions of this workshop should hopefully empower molecular breeding community in using modern genomics and breeding methodologies for crop improvement.

With an objective to share the experience and views of experts in the area of molecular breeding, we are providing the presentations made at this workshop. While these presentations are made freely available to everyone, you are requested to seek permission of the respective presenter/speaker, in case you may be required to use some of slides/figures, etc. and a proper citation (In: 2nd National Workshop on Marker-Assisted Selection for Crop Improvement, 27-29 October 2010, ICRISAT, Hyderabad, AP, India) should be given

For any further information please contact Rajeev K Varshney or KDV Prasad.

Technical Sessions and Presentations

Day 1, Wednesday, 27 October 2010

Session I: Inaugural Session

Keynote Address

Genomics-assisted crop improvement: Hope or hype?

Roberto Tuberosa

Uni Bologna, Italy

Session II: Genomics Platform

(Co-Chairs: Roberto Tuberosa & Rajeev Varshney)

Plant molecular breeding based on next generation sequencing (NGS)

Gengyun Zhang

Beijing Genomics Institute, China

Genotyping technologies in plant breeding; from application in MAS into high-throughput genomic selection capability

Richard Hodgson

Illumina Inc. Asia Pacific, Singapore

Developing 384-plex SNP marker sets for breeding and genetics applications in rice

Mike Thomson

IRRI, The Philippines

Selecting traits using SNPs as markers in oil palm to improve productivity

Rajinder Singh

Malaysian Palm Oil Board


Brain-storming I

High-throughput sequencing and genotyping

Facilitators:  Rajeev Varshney, ICRISAT  & NK Singh, NRCPB

Day 2, Thursday, 28 October 2010

Session III: Modern Approaches, Decision Support &

Analytical Tools

(Co-Chairs: PK Gupta & Oscar Riera-Lizarazu)

Population-specific research needs to launch genomic selection

Jean-Luc Jannink,

USDA/ARS and Cornell Uni, USA

Computational complexities in NGS data analysis and the way forward

Asoke Talukder, Geschickten Solutions, Bangalore

SNP discovery from amphidiploid species and transferability across the Brassicaceae

Jacqueline Batley

Uni Queensland, Australia

A data visualization and decision support system for marker-assisted backcrossing programs

Trushar Shah

ICRISAT, Hyderabad

Session IV: Molecular Breeding: Opportunities and

Challenges in Major Crops

(Co-Chairs: EA Siddiq & Tom Hash)

Molecular marker-assisted breeding for stress tolerance and nutritional quality improvement in maize

BM Prasanna


Molecular breeding in wheat: Opportunities and challenges

PK Gupta

CCSU, Meerut

Molecular breeding in rice: Opportunities and challenges

NK Singh

NRCPB, New Delhi

Molecular breeding in sorghum: Opportunities and challenges

Tom Hash, ICRISAT, Hyderabad


Session V: Molecular Breeding: Opportunities and Challenges

in Orphan and Vegetable Crops

(Co-Chairs: HS Gupta & HS Dhaliwal)

Genetics and genomics resources for enhancing conventional breeding in pearl millet

Rattan Yadav, IGER, UK

Molecular breeding in vegetable crops: Opportunities and challenges

P Kadirvel, AVRDC-The World Vegetable Center, Taiwan

Molecular breeding in legume crops: Opportunities and challenges

Rajeev Varshney

ICRISAT, Hyderabad

Day 3, Friday, 29 October 2010

Session VI: Molecular Breeding: Opportunities

and Challenges in Oilseed Crops

(Co-Chairs: RP Sharma & PM Gaur)

Molecular breeding in brassica: Opportunities and challenges

T Mohapatra, NRCPB, New Delhi

Molecular breeding in oilseed crops: Opportunities and challenges

V Dinesh Kumar, DOR, Hyderabad

Molecular breeding in cotton: Opportunities and challenges

Vijay N Waghmare, CICR, Nagpur

Brain-storming II

Molecular Breeding in India

Facilitators:  PK Gupta, CCSU Meerut & Oscar Riera-Lizarazu, ICRISAT

Concluding Session

(Co-Chair: RR Sinha & DA Hoisington)

Report-Brain-storming I

Rajeev Varshney,

ICRISAT, Hyderabad

Report-Brain-storming II

PK Gupta, CCSU, Meerut

Summary of the workshop

PK Gupta, CCSU, Meerut

Remarks from DBT

RR Sinha, DBT, New Delhi

Remarks from ICRISAT

Dave Hoisington

ICRISAT, Hyderabad

Vote of thanks

Rajeev Varshney

ICRISAT, Hyderabad

Please contact : Dr Rajeev Varshney, Director-Center of Excellence in Genomics, ICRISAT, Patancheru, 502 324, India;
Office: +91 40 3071 3305; Email : r.k.varshney@cgiar.org
Center of Excellence in Genomics. 2008