Abstract
BackgroundThis article describes the development of Multi-parent Advanced Generation Inter-Cross populations (MAGIC) in rice and discusses potential applications for mapping quantitative trait loci (QTLs) and for rice varietal development. We have developed 4 multi-parent populations: indica MAGIC (8 indica parents); MAGIC plus (8 indica parents with two additional rounds of 8-way F1 inter-crossing); japonica MAGIC (8 japonica parents); and Global MAGIC (16 parents – 8 indica and 8 japonica). The parents used in creating these populations are improved varieties with desirable traits for biotic and abiotic stress tolerance, yield, and grain quality. The purpose is to fine map QTLs for multiple traits and to directly and indirectly use the highly recombined lines in breeding programs. These MAGIC populations provide a useful germplasm resource with diverse allelic combinations to be exploited by the rice community.ResultsThe indica MAGIC population is the most advanced of the MAGIC populations developed thus far and comprises 1328 lines produced by single seed descent (SSD). At the S4 stage of SSD a subset (200 lines) of this population was genotyped using a genotyping-by-sequencing (GBS) approach and was phenotyped for multiple traits, including: blast and bacterial blight resistance, salinity and submergence tolerance, and grain quality. Genome-wide association mapping identified several known major genes and QTLs including Sub1 associated with submergence tolerance and Xa4 and xa5 associated with resistance to bacterial blight. Moreover, the genome-wide association study (GWAS) results also identified potentially novel loci associated with essential traits for rice improvement.ConclusionThe MAGIC populations serve a dual purpose: permanent mapping populations for precise QTL mapping and for direct and indirect use in variety development. Unlike a set of naturally diverse germplasm, this population is tailor-made for breeders with a combination of useful traits derived from multiple elite breeding lines. The MAGIC populations also present opportunities for studying the interactions of genome introgressions and chromosomal recombination.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-11) contains supplementary material, which is available to authorized users.
Highlights
This article describes the development of Multi-parent Advanced Generation Inter-Cross populations (MAGIC) in rice and discusses potential applications for mapping quantitative trait loci (QTLs) and for rice varietal development
Typical populations used for QTL mapping include F2, backcross (BC) or recombinant inbred (RI) populations derived from only two parents
Each population is comprised of 8 founder lines that include elite and modern varieties known to exhibit high yield potential, good grain quality, and tolerance to a range of biotic and abiotic stresses (Table 1)
Summary
This article describes the development of Multi-parent Advanced Generation Inter-Cross populations (MAGIC) in rice and discusses potential applications for mapping quantitative trait loci (QTLs) and for rice varietal development. The purpose is to fine map QTLs for multiple traits and to directly and indirectly use the highly recombined lines in breeding programs. These MAGIC populations provide a useful germplasm resource with diverse allelic combinations to be exploited by the rice community. Most of the varieties developed by breeders in self-pollinated crops like rice are based on single crosses between two parents. A multi-parent advanced generation intercross (MAGIC) strategy has been proposed to interrogate multiple alleles and to provide increased recombination and mapping resolution (Cavanagh et al 2008). Multi-parent populations are attractive for researchers due to the development of high-throughput SNP genotyping platforms and advances in statistical methods to analyze data from such populations
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