Plant Molecular Biology Reporter

, Volume 29, Issue 3, pp 663–680 | Cite as

Meta-analysis of Yield QTLs Derived from Inter-specific Crosses of Rice Reveals Consensus Regions and Candidate Genes

  • B. P. Mallikarjuna Swamy
  • Neelamraju Sarla


Several reports on mapping and introgression of quantitative trait loci (QTLs) for yield and related traits from wild species showed their importance in yield improvement. The aim of this study was to locate common major effect, consistent and precise yield QTLs across the wild species of rice by applying genome-wide QTL meta-analysis for their use in marker-aided selection (MAS) and candidate gene identification. Seventy-six yield QTLs reported in 11 studies involving inter-specific crosses were projected on a consensus map consisting of 699 markers. The integration of 11 maps resulted in a consensuses map of 1,676 cM. The number of markers ranged from 32 on chromosome 12 to 96 on chromosome 1. The order of markers between consensus map and original map was generally consistent. Meta-analysis of 68 yield QTLs resulted in 23 independent meta-QTLs on ten different chromosomes. Eight meta-QTLs were less than 1.3 Mb. The smallest confidence interval of a meta-QTL (MQTL) was 179.6 kb. Four MQTLs were around 500 kb and two of these correspond to a reasonably small genetic distance 4.6 and 5.2 cM, respectively, and suitable for MAS. MQTL8.2 was 326-kb long with a 35-cM interval indicating it was in a recombination hot spot and suitable for fine mapping. Our results demonstrate the narrowing down of initial yield QTLs by Meta-analysis and thus enabling short listing of QTLs worthy of MAS or fine mapping. The candidate genes shortlisted are useful in validating their function either by loss of function or over expression.


Meta-analysis Oryza sativa Wild species Yield Marker-assisted selection Candidate genes 



BPMS thanks UGC–CSIR for Senior Research Fellowship. NS thanks Department of Biotechnology, Government of India for financial support to the Network Project on Functional Genomics of rice at DRR. We thank the Director of DRR for constant support and encouragement.

Supplementary material

11105_2010_274_MOESM1_ESM.doc (166 kb)
Table 1 (DOC 166 kb)


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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  1. 1.Biotechnology, Directorate of Rice ResearchHyderabadIndia
  2. 2.Plant Breeding, Genetics and Biotechnology DivisionInternational Rice Research InstituteMetro ManilaPhilippines

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