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QTL Analysis for Grain Quality Properties in a Japonica Rice Combination

Jong-Sik Lee1, W.G. Ha1, J.K. Chang1, K.L. Ryu1, Jun Hyeon Cho1, You-Chun Song1, Oh-Kyung Kwon1, S.J. Yang1, H.Y. Kim2 and H. S. Suh3

1 National Yeongnam Agricultural Research Institute, NICS, RDA, Milyang www://nyaes@rda.go.kr Email :leejsyr@rda.go.kr
2
International Rice Research Institute, Email mailto:h.kim@cgiar.org 3Yeoungnam University, Email hssuh@yeungnam.ac.kr

Abstract

The objective of this study was to identify QTLs associated with the chemical traits and palatability of cooked rice in japonica rice recombination. The population used in this study consisted of 179 F7~8 recombinant inbred lines (RILs) derived from a japonica rice cross between Ilpumbyeo with an excellent eating quality and YR15965Acp33 with a poor eating quality through method a single-seed descendent. The high palatability of Ilpumbyeo was mainly originated a high palatability Japanese variety, Koshihikari. YR15965Acp33 was derived from a combination between temperate japonica variety, Hwayeongbyeo, and sub-tropical japonica, Shennung 89-366. The 179 RILs and their parents were cultivated at three locations, namely: Sangju (mid-mountainous area), Yeongdeog (coastal area) and Milyang (plain area) in 2000 and 2002. To obtain the putative QTLs associated with amylose content, protein content, and Mg/K equivalent ratio, Toyo taste meter value (TTV) were analysed. In the chemical traits, four QTLs For amylose content were detected in two environments and located in the same on chromosomes 2 and 12, respectively. All of the QTLs for protein and Mg/K were not detected in any more two environments. Eighteen QTLs for TTV were detected on six out of twelve chromosomes. The QTLs on chromosomes 1, 6, 7, and 12 were detected in more than two environments and located in the same or similar loci. The QTLs associated with on chromosome 12 were detected in all environments tested. Two RILs showing significant transgressive segregation for TTV should be useful as a good breeding material for eating quality.

Media summary

One hundred and twenty seven (12.3%) markers from a total of 1,038 showed polymorphic band using SSR marker in between two japonica parents. For TTV, QTLs associated with on chromosome 12 were detected in all environments.

Key Words

Rice, Grain quality, Chemical trait, QTL, Eating quality

Introduction

The preferences of grain quality properties may vary from one ethnic group or geographical region to another, and may vary from one country to another country (Juliano et al. 1964, Lee 2003). Korean people like japonica rice because it is more sticky and soft than most indica in cooked rice. Nowadays, rice breeding for grain quality is the most important objective in Korea. Particularly, improving taste and grain appearance are key points for a rice breeding program. In this study, QTL analysis using SSRs markers for eating quality was applied using 179 RILs populations derived from the cross between a japonica, Ilpumbyeo, and a japonica, YR15965Acp33.

Methods

The 179 RILs and their parents were cultivated at three locations, namely: Sangju (mid-mountainous area), Yeongdeog (coastal area) and Milyang (plain area) in 2000 and 2002. Amylose content, protein content, Mg/K equivalent ratio and Toyo taste meter value (TTV) were investigated. TTV was determined using Toyo taste meter (model: MA-90B) in accordance with operation manual (TRCM Co.). The panel test (sensory evaluation) was conducted by 15~20 well- trained panelists according to standard method of NYARI. The linkage map was constructed with 127 simple sequence repeats (SSRs) markers using the Mapmaker program version 2.0(Lander et al. 1987, McCouch et al. 2002). The analysis of QTL was done using both single point and interval-mapping analysis using the software qGENE version 3.06 for Macintosh (Nelson 1997).

Results

Figure 1. Distribution of amylose, protein content, Mg/K equivalent, and Toyo taste meter value (TTV) in the RIL population. E 1 : Milyang (’00), E2 : Yeongdeog (’00), E3 : Sangju (’00), E4 : Milyang (’02), E5 : Yeongdeog (’02).

Figure 2. QTL linkage map for TTV and chemical properties using SSR markers in 179 RILs derived from the cross of Ilpumbyeo and YR15065Acp33. Arrows indicated the pleiotropic and/or tight linkage effects between TTV and chemical properties. Putative QTLs identified for TTV was used the composite interval mapping method with a LOD threshold of 1.5. Putative QTLs identified for chemical properties was used the composite interval mapping method with a LOD threshold of 2.0. E 1 : Milyang (’00), E2 : Yeongdeog (’00), E3 : Sangju (’00), E4 : Milyang (’02), E5 : Yeongdeog (’02).

Conclusion

To elucidate the usefulness of Toyo taste meter for indirect evaluation for eating quality of cooked rice, the relationship between the sensory test parameters and Toyo taste meter value (TTV) was studied. Correlation coefficients between the sensory evaluation parameters and the TTV in three years exhibited high positive correlation(r=0.81**~0.89**, n=27~47) with the palatability score of cooked rice. In the previous studies, Japanese researchers reported that correlation coefficients between sensory test and TTV exhibited high positive correlation with the palatability score of cooked rice (Nagasawa et al. 1994, Azuma et al. 1994, Hoshi et al. 1995). Therefore, eating quality of cooked rice was measured by the TTV instead of palatability score because sensory test needed much time and effortwith well-trainedpanelists.

In respect to chemical traits, six QTLs for amylose content, five QTLs for protein, and six QTLs for Mg/K equivalent ratio were detected in five environments. For amylose content, four QTLs were detected in two environments and located on the same on chromosomes 2 and 12, respectively. All of the QTLs for protein and Mg/K ratio were not detected in any more two environments.

Eighteen QTLs for TTV with a LOD threshold of 1.5 were detected on six out of twelve chromosomes. However, the QTLs on chromosomes 7 and 12 were not confirmed using the empirical LOD threshold of 2.0. The phenotypic variation explained (R2%) by each QTL for TTV ranged from 2.7 to 10.0%. These QTLs on chromosomes 1, 6, and 12increased the TTV from Ilpumbyeo alleles. The QTLs associated with on chromosome 12 were detected in all environments tested.

A total of eight loci with pleiotropic effects and/or tight linkage were observed in this study. In the chemical traits associated with TTV, three loci within the genomic RM3360 (qMg/K-1-1), RM594 (qPC-1 and qMg/K-1-2) and RM5389 (qMg/K-1-3) on chromosome 1 were simultaneously influenced by the Mg/K equivalent ratio and protein content. One locus within the genomic RM7552 (qPC-6) on chromosome 6 was simultaneously influenced by the protein content. Two loci within the genomic OSR20 (qAC-12-1), and RM270 (qPC-12) on chromosome 12 were simultaneously influenced by the amylose content and protein content.

As results, the study suggest that 1) TTV is controlled by the four loci on chromosomes 1, 6, 7, and 12, is affected mostly as minor QTLs. Particularly, the amylose and protein content are not related with QTLs for TTV on chromosome 6 (wx locus). The QTLs for TTV are detected on chromosome 12 in all environments. It is necessary to clarify the characterization of the QTLs detected on chromosome 6, 12 and the mechanism of cooked rice taste, based on the development of isogenic lines for the QTLs detected by marker assisted selection. 2) The Ilpumbyeo for TTV have favorable alleles for fourteen out of eighteen QTLs. 3) Two RILs showing significant transgressive segregation for TTV should be useful as a good breeding material for eating quality. In this study, QTLs detected for improving chemical traits and TTV will help for improving the eating quality in japonica rice breeding.

References

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