, 213:37 | Cite as

Identification of quantitative trait loci for panicle length and yield related traits under different water and P application conditions in tropical region in rice (Oryza sativa L.)

  • Ian Paul Navea
  • Maria Stefanie Dwiyanti
  • Jonghwa Park
  • Backki Kim
  • Sangbum Lee
  • Xing Huang
  • Hee-Jong Koh
  • Joong Hyoun Chin


Climate change is projected to have a serious impact on the yield potential of rice in tropical as well as in temperate countries. It is therefore essential to develop rice varieties which are climate change ready and with stable yield when grown under low inputs of irrigation water and fertilizer. In this study, the effects of the shift from temperate to tropical environment as well as the different levels of water regime-phosphorus application were evaluated using a set of temperate recombinant inbred lines (RILs) derived from a cross between Dasanbyeo (Tongil-type indica) and TR22183 (temperate japonica). Here, we have identified genetic mechanisms for yield stability mainly by observing the panicle length in the RILs and the parental lines. TR22183 grown in the Philippines showed no reduction in panicle length whereas the Dasanbyeo exhibited a considerable reduction in panicle length when grown in the Philippines compared to those grown in Korea. In the RILs, a total of 18 QTLs for panicle length were identified across 12 chromosomes except in chromosomes 6 and 7. There were six interesting panicle length QTLs, qPL1.4, qPL2.1, qPL2.2, qPL4.1, qPL9.2, and qPL11.2 on chromosomes 1, 2, 4, 9, and 11 respectively. They were clustered together with other yield-related QTLs such as spikelet number and grain number in two different years. Except for qPL2.1, all the beneficial alleles originated from TR22183. The panicle length QTLs were identified across different water-P treatments. Interestingly, qPL1.4, qPL2.1, qPL4.1, and qPL11.2 were constantly detected in the low-input tropical condition. No QTL for panicle length was identified in the parallel experiment conducted under temperate conditions in Korea suggesting that the QTLs identified in tropical conditions could be useful in breeding programs to develop rice varieties that have stable yield potential under a warming temperate climate.


Climate change Phosphorus Panicle length Yield QTL EpQTL SNP 



This study was supported by a Grant from the Next-Generation BioGreen 21 Program (No. PJ01102401) of the Rural Development Administration, Korea. We would like to thank IRRI GSL and the MBAST staff of the International Rice Research Institute and Dr. Hong-Ryul Kim of Seoul National University in Korea. We also would like to thank Mr. Karl Jensen Victorio and Quedahm Chin for editing the manuscript thoroughly.

Supplementary material

10681_2016_1822_MOESM1_ESM.tif (1.8 mb)
Supplementary Fig. 1. Phenotypic distribution of panicle length of DT-RILs under four water-P conditions in Philippines (Exp12 and Exp14). DS: Dasanbyeo parental phenotype, TR: TR22183 parental phenotype, RF_0P: rainfed, no P application, IR_0P: irrigated, no P application, RF_60P: rainfed, normal P application, IR_60P: irrigated, normal P application (TIFF 1855 kb)
10681_2016_1822_MOESM2_ESM.tif (2 mb)
Supplementary Fig. 2. Agro-meteorological data of the experiments conducted under tropical conditions (TIFF 2018 kb)
10681_2016_1822_MOESM3_ESM.tif (11.5 mb)
Supplementary Fig. 3. M-QTLs and EpQTLs identified in this study (TIFF 11800 kb)
10681_2016_1822_MOESM4_ESM.tif (1.5 mb)
Supplementary Fig. 4. Comparison in panicle length of DT-RILs with different combinations of allele types in qPL2.1 and qPL9.2. DS: Dasanbyeo allele, TR: TR22183 allele, RF: rainfed condition, IR: irrigation condition, 0P: no P application, 60P: normal P application (TIFF 1513 kb)
10681_2016_1822_MOESM5_ESM.pdf (56 kb)
Supplementary Table 1. Distribution of agronomic traits in DT-RILs and parental lines in different P-water treatments in tropical conditions (PDF 57 kb)
10681_2016_1822_MOESM6_ESM.pdf (34 kb)
Supplementary Table 2. Correlation of panicle length to other yield-related traits (PDF 35 kb)
10681_2016_1822_MOESM7_ESM.pdf (57 kb)
Supplementary Table 3. Soil nature and property from the experiment conducted in tropical conditions (PDF 58 kb)
10681_2016_1822_MOESM8_ESM.pdf (59 kb)
Supplementary Table 4. Analysis of variance table using GLM analysis on P and water effect on panicle length (PDF 60 kb)
10681_2016_1822_MOESM9_ESM.pdf (124 kb)
Supplementary Table 5. Panicle length EpQTLs identified in this study (PDF 125 kb)
10681_2016_1822_MOESM10_ESM.pdf (44 kb)
Supplementary Table 6. Differential QTLs identified in different P-water treatments in the tropics (PDF 44 kb)
10681_2016_1822_MOESM11_ESM.pdf (73 kb)
Supplementary Table 7. Total PVE (%) of each trait under different P-water treatments (PDF 73 kb)
10681_2016_1822_MOESM12_ESM.pdf (168 kb)
Supplementary Table 8. QTLs identified in this study co-located with previously published QTLs (PDF 169 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2017

Authors and Affiliations

  1. 1.Plant Breeding, Genetics, and Biotechnology DivisionInternational Rice Research InstituteLos BanosPhilippines
  2. 2.Division of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life SciencesSeoul National UniversitySeoulKorea
  3. 3.Graduate School of Integrated BioindustrySejong UniversitySeoulKorea

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