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Open Access Highly Accessed Research article

QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.)

Balram Marathi12*, Smriti Guleria2, Trilochan Mohapatra3, Rajender Parsad4, Nagarajan Mariappan5, Vinod Kunnummal Kurungara5, Salwandir Singh Atwal6, Kumble Vinod Prabhu2, Nagendra Kumar Singh7 and Ashok Kumar Singh2

Author Affiliations

1 International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines

2 Indian Agricultural Research Institute, New Delhi, 110012, India

3 Central Rice Research Institute, Cuttak, 753006, India

4 Indian Agricultural Statistical Research Institute, New Delhi, 110012, India

5 Regional Station, Indian Agricultural Research Institute, Aduthurai, 612101, India

6 Regional Station, Indian Agricultural Research Institute, Karnal, 132001, India

7 National Research Centre on Plant Biotechnology, New Delhi, 110012, India

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BMC Plant Biology 2012, 12:137  doi:10.1186/1471-2229-12-137

Published: 9 August 2012

Abstract

Background

Rice is staple food for more than half of the world’s population including two billion Asians, who obtain 60-70% of their energy intake from rice and its derivatives. To meet the growing demand from human population, rice varieties with higher yield potential and greater yield stability need to be developed. The favourable alleles for yield and yield contributing traits are distributed among two subspecies i.e., indica and japonica of cultivated rice (Oryza sativa L.). Identification of novel favourable alleles in indica/japonica will pave way to marker-assisted mobilization of these alleles in to a genetic background to break genetic barriers to yield.

Results

A new plant type (NPT) based mapping population of 310 recombinant inbred lines (RILs) was used to map novel genomic regions and QTL hotspots influencing yield and eleven yield component traits. We identified major quantitative trait loci (QTLs) for days to 50% flowering (R2 = 25%, LOD = 14.3), panicles per plant (R2 = 19%, LOD = 9.74), flag leaf length (R2 = 22%, LOD = 3.05), flag leaf width (R2 = 53%, LOD = 46.5), spikelets per panicle (R2 = 16%, LOD = 13.8), filled grains per panicle (R2 = 22%, LOD = 15.3), percent spikelet sterility (R2 = 18%, LOD = 14.24), thousand grain weight (R2 = 25%, LOD = 12.9) and spikelet setting density (R2 = 23%, LOD = 15) expressing over two or more locations by using composite interval mapping. The phenotypic variation (R2) ranged from 8 to 53% for eleven QTLs expressing across all three locations. 19 novel QTLs were contributed by the NPT parent, Pusa1266. 15 QTL hotpots on eight chromosomes were identified for the correlated traits. Six epistatic QTLs effecting five traits at two locations were identified. A marker interval (RM3276-RM5709) on chromosome 4 harboring major QTLs for four traits was identified.

Conclusions

The present study reveals that favourable alleles for yield and yield contributing traits were distributed among two subspecies of rice and QTLs were co-localized in different genomic regions. QTL hotspots will be useful for understanding the common genetic control mechanism of the co-localized traits and selection for beneficial allele at these loci will result in a cumulative increase in yield due to the integrative positive effect of various QTLs. The information generated in the present study will be useful to fine map and to identify the genes underlying major robust QTLs and to transfer all favourable QTLs to one genetic background to break genetic barriers to yield for sustained food security.