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A major quantitative trait locus for increasing cadmium-specific concentration in rice grain is located on the short arm of chromosome 7.

ABSTRACT: Large phenotypic variations in the cadmium (Cd) concentration of rice grains and shoots have been observed. However, the genetic control of Cd accumulation remains poorly understood. Quantitative trait loci (QTLs) determining the grain Cd concentration of rice grown in a Cd-polluted paddy field were identified. Using a mapping population consisting of 85 backcross inbred lines derived from a cross between the low-Cd-accumulating cultivar Sasanishiki (japonica) and high-Cd-accumulating cultivar Habataki (indica), two QTLs for increasing grain Cd concentration were found on chromosomes 2 and 7. A major-effect QTL, qGCd7 (QTL for grain Cd on chromosome 7), was detected on the short arm of chromosome 7. It accounted for 35.5% of all phenotypic variance in backcross inbred lines. qGCd7 was not genetically related to any QTLs for concentrations of essential trace metals (Cu, Fe, Mn, and Zn) or those for agronomic traits such as heading date, suggesting that this QTL is specific to Cd. Furthermore, the existence of qGCd7 was confirmed using chromosome segment substitution lines (CSSLs) and an F(2) population from a cross between the target CSSL and Sasanishiki grown in a Cd-polluted paddy soil. To our knowledge, qGCd7 is a novel QTL with major effects for increasing grain Cd concentrations.

SUBMITTER: Ishikawa S

PROVIDER: S-EPMC2814118 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature

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A major quantitative trait locus for increasing cadmium-specific concentration in rice grain is located on the short arm of chromosome 7.

Ishikawa Satoru S Abe Tadashi T Kuramata Masato M Yamaguchi Masayuki M Ando Tsuyu T Yamamoto Toshio T Yano Masahiro M

Journal of experimental botany 20091218 3

Large phenotypic variations in the cadmium (Cd) concentration of rice grains and shoots have been observed. However, the genetic control of Cd accumulation remains poorly understood. Quantitative trait loci (QTLs) determining the grain Cd concentration of rice grown in a Cd-polluted paddy field were identified. Using a mapping population consisting of 85 backcross inbred lines derived from a cross between the low-Cd-accumulating cultivar Sasanishiki (japonica) and high-Cd-accumulating cultivar H ...[more]

PMID: 20022924

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Project description:Background:Thousand grain weight is a key component of grain yield in rice, and a trait closely related to grain length (GL) and grain width (GW) that are important traits for grain quality. Causal genes for 16 quantitative trait loci (QTL) affecting these traits have been cloned, but more QTL remain to be characterized for establishing a genetic regulating network. A QTL controlling grain size in rice, qGS10, was previously mapped in the interval RM6100-RM228 on chromosome 10. This study aimed to delimitate this QTL to a more precise location. Method:A total of 12 populations were used. The ZC9 population comprised 203 S 1:2 families derived from a residual heterozygous (RH) plant in the F 9 generation of the indica rice cross Teqing (TQ)/IRBB52, segregating the upper region of RM6100-RM228 and three more regions on chromosomes 1, 9, and 11. The Ti52-1 population comprised 171 S 1 plants derived from one RH plant in F 7 of TQ/IRBB52, segregating a single interval that was in the lower portion of RM6100-RM228. The other ten populations were all derived from Ti52-1, including five S 1 populations with sequential segregating regions covering the target region and five near isogenic line (NIL) populations maintaining the same segregating pattern. QTL analysis for 1,000-grain weight, GL, and GW was performed using QTL IciMapping and SAS procedure GLM. Result:Three QTL were separated in the original qGS10 region. The qGL10.1 was located in the upper region RM6704-RM3773, shown to affect GL only. The qGS10.1 was located within a 207.1-kb interval flanked by InDel markers Te20811 and Te21018, having a stable and relatively high effect on all the three traits analyzed. The qGS10.2 was located within a 1.2-Mb interval flanked by simple sequence repeat markers RM3123 and RM6673. This QTL also affected all the three traits but the effect was inconsistent across different experiments. QTL for grain size were also detected in all the other three segregating regions. Conclusion:Three QTL for grain size that were tightly linked on the long arm of chromosome 10 of rice were separated using NIL populations with sequential segregating regions. One of them, qGS10.1, had a stable and relatively high effect on grain weight, GL, and GW, providing a good candidate for gene cloning. Another QTL, qGS10.2, had a significant effect on all the three traits but the effect was inconsistent across different experiments, providing an example of genotype-by-environmental interaction.

Project description:BackgroundBacterial grain rot (BGR), caused by the bacterial pathogen Burkholderia glumae, is a destructive disease of rice. Because BGR tends to be highly affected by environmental conditions such as temperature and humidity, it is difficult to evaluate BGR resistance of diverse cultivars with different heading dates by using field inoculation. Molecular tagging of genes involved in BGR is an important objective for rice breeding.ResultsIn this study, we mapped a quantitative trait locus (QTL) for BGR resistance by a modified cut-panicle inoculation method. First, we assessed the levels of BGR resistance in 84 cultivars by a standard cut-panicle inoculation technique, in which panicles are harvested and inoculated in the laboratory under controlled conditions. For the genetic analysis, we selected two cultivars: Kele, a resistant traditional lowland cultivar (indica) that originated in India, and Hitomebore, a susceptible modern lowland cultivar (temperate japonica) from Japan. Second, by comparing the susceptibility of Kele and Hitomebore spikelets before and up to 3 days after anthesis, we found a dramatic decline in susceptibility at 1 day after anthesis in Kele but not in Hitomebore. Thus, we applied a modified method by inoculating spikelets at 1 day after anthesis for further analysis. To search for QTLs associated with BGR resistance, we measured the ratio of diseased spikelets (RDS, an index reflecting both quantity and severity of infection) and the ratio of diseased spikelet area (RDSA) in 110 backcrossed inbred lines (BILs) derived from a cross between Kele and Hitomebore. One major QTL associated with both RDS and RDSA was detected on the long arm of chromosome 1. This QTL explained 25.7% and 12.1% of the total phenotypic variance in RDS and RDSA in the BILs, respectively, and the Kele allele increased BGR resistance.ConclusionsWe mapped a major QTL for BGR resistance on the long arm of chromosome 1. These results clearly demonstrated that genetic analysis of BGR resistance in rice can be effectively performed and that this trait could be a target of marker-assisted selection in rice breeding programs.

Project description:Background:Grain weight is a grain yield component, which is an integrated index of grain length, width and thickness. They are controlled by a large number of quantitative trait loci (QTLs). Besides major QTLs, minor QTLs play an essential role. In our previous studies, QTL analysis for grain length and width was performed using a recombinant inbred line population derived from rice cross TQ/IRBB lines. Two major QTLs were detected, which were located in proximity to GS3 and GW5 that have been cloned. In the present study, QTLs for grain weight and shape were identified using rice populations that were homozygous at GS3 and GW5. Method:Nine populations derived from the indica rice cross TQ/IRBB52 were used. An F10:11population named W1, consisting of 250 families and covering 16 segregating regions, was developed from one residual heterozygote (RH) in the F7generation of Teqing/IRBB52. Three near isogenic line (NIL)-F2 populations, ZH1, ZH2 and ZH3 that comprised 205, 239 and 234 plants, respectively, were derived from three RHs in F10:11. They segregated the target QTL region in an isogenic background. Two NIL populations, HY2 and HY3, were respectively produced from homozygous progeny of the ZH2 and ZH3 populations. Three other NIL-F2 populations, Z1, Z2 and Z3, were established using three RHs having smaller heterozygous segments. QTL analysis for 1000-grain weight (TGW), grain length (GL), grain width (GW), and length/width ratio (LWR) was conducted using QTL IciMapping and SAS procedure with GLM model. Result:A total of 27 QTLs distributed on 12 chromosomes were identified. One QTL cluster, qTGW2/qGL2/qGW2 located in the terminal region of chromosome 2, were selected for further analysis. Two linked QTLs were separated in region Tw31911-RM266. qGL2 was located in Tw31911-Tw32437 and mainly controlled GL and GW. The effects were larger on GL than on GW and the allelic directions were opposite. qTGW2 was located in Tw35293-RM266 and affected TGW, GL and GW with the same allelic direction. Finally, qTGW2 was delimited within a 103-kb region flanked by Tw35293 and Tw35395. Conclusion:qTGW2 with significant effects on TGW, GL and GW was validated and fine-mapped using NIL and NIL-F2 populations. These results provide a basis for map-based cloning of qTGW2 and utilization of qTGW2 in the breeding of high-yielding rice varieties.

Dataset Information

A major quantitative trait locus for increasing cadmium-specific concentration in rice grain is located on the short arm of chromosome 7.

Publications

A major quantitative trait locus for increasing cadmium-specific concentration in rice grain is located on the short arm of chromosome 7.

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