Download MAGIC Rice: production, characterization, and its use in breeding

MAGIC Rice: production, characterization, and its use in breeding networks
Hei Leung*, Nonoy Bandillo, Pauline Andrea Muyco, Chitra Raghavan, Anna Sevilla, Irish Lobina, Shalabh Dixit, Michael Thomson, Ramil Mauleon, Arvind Kumar,
Rakesh Kumar Singh, Glenn Gregorio and Edilberto Redoña
Background
 MAGIC stands for ‘multi-parent advanced generation intercrosses’. It was first
introduced by Mott et al. (2000, PNAS USA 97:12649-12654) in animals as an
improvement over the advanced intercrossing (AIC) method.
 It is a powerful method to increase the precision of genetic markers linked to the
quantitative trait loci (QTL) for fine-mapping of multiple QTLs for multiple traits in the
same population.
 Advanced intercrossed lines (AILs) are generated by randomly and sequentially
intercrossing a population initially originating from crosses between pairs of inbred
‘founder lines’. These intercrossed lines are then cycled through multiple generations of
random mating.
 Each generation reduces the extent of linkage disequilibrium (LD), thus allowing QTL
to be mapped more accurately. Lines derived from early generations can be used for
QTL detection and coarse mapping, while those derived from later generations will only
detect marker-trait associations if markers are located very close to the QTL.
 The goal of this project is to develop two MAGIC populations of at least 2,000 inbred
lines in rice, Oryza sativa L., one each for indica and japonica subspecies, that will be
used for localizing QTL for multiple traits to regions of 3 centiMorgans (cM) or less.
Germplasm/variety Varietal type Origin
Crossing scheme for MAGIC populations
Agronomic relevance
Asia-Indica group
Fedearroz 50
Indica
Colombia
Popular variety in several countries;
with stay green/delayed senescence
& quality traits; disease tolerance;
progenitor of many breeding lines
Blast-resistant; high-yielding; in the
pedigrees of many varieties in south
China
High-yielding and most popular
variety of the Philippines
High-yielding variety in NPT II
background
Shan-Huang Zhan-2
(SHZ-2)
Indica
China
IRRI 123 (PSBRc82)
Indica
IRRI
IR77186-122-2-2-3
(PSBRc 158)
Indica / tropical
japonica
background
Indica
IRRI
IR77298-14-1-2-10
IR4630-22-2-5-1-3
Indica
IRRI
IR45427-2B-2-2B-1-1
Indica
IRRI
Sambha Mahsuri + Sub1
Indica
IRRI
Germplasm/variety
IRRI
Drought-tolerant in lowlands with
IR64 background and tungroresistant
Good plant type; salt-tolerant at
seedling and reproductive stages;
Fe toxicity-tolerant
Mega variety with wide compatibility;
good grain quality; submergencetolerant
Varietal type
Origin
Agronomic Relevance
CSR 30
Basmati group
India
Cypress
Tropical japonica
USA
IAC 165
Tropical japonica
Jinbubyeo
Inia Tacuari
Temperate
japonica
Glaberrima blood
in indica
background
Cross between
tropical japonica
and indica
Tropical japonica
Latin
America
Korea
Sodicity-tolerant; Basmati-type
aromatic grain
High-yielding with good grain
quality; cold-tolerant
Aerobic rice adaptation
Colombia XXI
Tropical japonica
Asia–Japonica group
WAB 56-125
IR73571-3B-11-3-K2
WARDA
IRRIKorea
project
Uruguay
High-yielding; cold-tolerant (an E.
African problem)
NERICA background (O.
glaberrima); heat-tolerant and
early flowering
Tongil type; salinity-tolerant
Use and distribution of MAGIC lines for genetic evaluation and breeding.
Genotyping, phenotyping and field performance data will be collected, analyzed and
displayed for use by Community of Practice in individual breeding programs.
With earliness, wide adaptation, &
good grain quality
Colombia High-yielding; delayed senescence
Current Activities – MAGIC indica
Genotyping and Phenotyping
Biotic– blast, bacterial blight
Abiotic- submergence, drought, salt tolerance and tolerance to iron toxicity
Trait-specific SNP marker using Fluidigm system
Genotyping by Sequencing
Single seed descent (SSD) – creating Advanced Intercross Lines AILs
Mapping and identification of QTLs
Populations, stages and size
Preliminary screening for drought tolerance n MAGIC indica S4 plants (SSD) –
RM324 (DTY2.1), RM551 (DTY4.3). E is IR77298-14-1-2-10 (Founder line)
Transmission of traits/QTL markers in random S4 lines
(indica MAGIC)
Rapid Generation Advancement
(90 days sowing to harvest)
Preliminary screening of MAGIC indica S4 plants –
against Blast disease at the IRRI blast nursery
SHZ-2
IR77298-14-1-2-10
IR45427-2B-2-2B-1-1
IRRI BLAST NURSERY
Plant Breeding, Genetics and Biotechnology Division
International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
Telephone: +63 (2) 580-5600 ext. 2341/2288; Fax: +63 (2) 580-5699
E-mail: [email protected]
10 hours light 14 hours
darkness - 30 days after
trans planting.
Outputs
 Providing solutions to a range of production constraints particularly
stress tolerance) in the target countries through the use of advanced
MAGIC lines.
 An assessment and understanding of the potential of enhanced
recombination in generating novel diversity.
 Broadening of germplasm adaptation in multiple environments.
 Novel traits precisely tagged by molecular markers, which can be
deployed in selection.
 An integrated genotype and phenotype data set from multiple
environments, providing a resource to enable breeding selection.
 Beyond trait mapping, the highly recombined MAGIC populations
may be used directly as source materials for the extraction and
development of breeding lines and varieties adapted to different
environments in Asia and Africa.
 These populations will be distributed freely for use in research by
the International Network for Genetic Evaluation of Rice or INGER
(http://www.seeds.irri.org/inger/)
GCP Project G4008.01: Population
development through multi-parent advanced
generation inter-crosses (MAGIC) among
diverse genotypes to facilitate gene discovery
for various traits in rice