Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding

Abstract

Background: 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. 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.

Results: The 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.

Conclusion: The 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.

Figure 1

Crossing schemes to produce four multi-parent advanced generation inter-cross (MAGIC) populations: a) Development of the indica MAGIC population. The same scheme was used for the development of the japonica MAGIC population b) Development of the MAGIC plus and global MAGIC populations. The global population includes eight indica and eight japonica founder lines, which carry QTLs conferring tolerance of biotic and abiotic stresses. A, B, C, D, E, F, G and H – represent the 8 indica parents; I, J, K, L, M, N, O and P – represent the 8 japonica parents; Gen- generation; SSDM – single seed descent method ,S – selfing.

Figure 2

Cladogram (neighbor joining) of the 200 S4 indica MAGIC lines and 8 founders using 634 SNP marker sites (no missing calls or heterozygous sites).

Figure 3

Blast disease - Manhattan plot (MLM) showing GWA and highlighting significant associations near previously detected QTLs on chromosomes 2, 3, 9 and 10; x axis – position on chromosomes 1 to 12; y-axis (-) Log p-value of markers; solid line – p < 0.0001.

Figure 4

Bacterial blight - Manhattan plots (MLM) showing GWA to bacterial blight strains (a) PXO61, (b) PXO341, (c) PXO86, and (d) PXO99. Note the high level of association with SNPs on chromosome 11 (figures a and b) pointing to Xa4 and xa5 on chromosome 5 (figure c). GWAS detects both Xa4 and xa5 (figure d) in response to PXO99. x axis – position on chromosomes 1 to 12; y-axis (-) Log p-value of markers; solid line – p < 0.0001.

Figure 5

Abiotic stress - Manhattan plots (MLM) showing GWA to (a) salt tolerance and (b) submergence. Note the association on chromosome 1 - Saltol to salt tolerance and detection of the SUB1 locus on chromosome 9 in response to submergence. x axis – position on chromosomes 1 to 12; y-axis (-) Log p-value of markers; solid line – p < 0.0001.

Figure 6

Grain quality - Manhattan plots (MLM) showing GWA for (a) amylose content – waxy chromosome 6 (b) grain length GS3 on chromosome 3 (c) grain width GB* QTL for grain breadth Ref. Redoña and Mackill (1998) on chromosomes 7 and (d) gelatinization temperature SSIIa Chromosome 6. x axis – position on chromosomes 1 to 12; y-axis (-) Log p-value of markers; solid line – p < 0.0001.