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QTL Mapping of Grain Quality Traits Using Introgression Lines Carrying Oryza rufipogon Chromosome Segments in Japonica Rice

View Article: PubMed Central - PubMed

ABSTRACT

Background: Improved eating quality is a major breeding target in japonica rice due to market demand. Consequently, quantitative trait loci (QTL) for glossiness of cooked rice and amylose content associated with eating quality have received much research focus because of their importance in rice quality.

Results: In this study, QTL associated with 12 grain quality traits were identified using 96 introgression lines (IL) of rice developed from an interspecific cross between the Korean elite O. sativa japonica cultivar ‘Hwaseong’ and O. rufipogon over 7 years. QTL analyses indicated that QTL qDTH6 for heading date, detected on chromosome 6 is associated with variance in grain traits. Most QTLs detected in this study clustered near the qDTH6 locus on chromosome 6, suggesting the effect of qDTH6. O. rufipogon alleles negatively affected grain quality traits except for a few QTLs, including qGCR9 for glossiness of cooked rice on chromosome 9. To characterize the effect of the O. rufipogon locus harboring qGCR9, four lines with a single but different O. rufipogon segment near qGCR9 were compared to Hwaseong. Three lines (O. rufipopgon ILs) having O. rufipogon segment between RM242 and RM245 in common showed higher glossiness of cooked rice than Hwaseong and the other line (Hwaseong IL), indicating that qGCR9 is located in the 3.4-Mb region between RM242 and RM245. Higher glossiness of cooked rice conferred by the O. rufipogon allele might be associated with protein content considering that three lines had lower protein content than Hwaseong (P < 0.1). These three O. rufipogon ILs showed higher yield than Hwaseong and Hwaseong IL due to increase in spikelets per panicle and grain weight indicating the linkage of qGCR9 and yield component QTLs.

Conclusion: The qGCR9 locus is of particular interest because of its independence from other undesirable grain quality traits in O. rufipogon. SSR markers linked to qGCR9 can be used to develop high-quality japonica lines and offer a starting point for map-based cloning of genes underlying this trait. To our knowledge, this is the first report to map a beneficial QTL for glossiness of cooked rice from a wild rice, O. rufipogon.

Electronic supplementary material: The online version of this article (doi:10.1186/s12284-016-0135-0) contains supplementary material, which is available to authorized users.

No MeSH data available.


Graphical representation of four ILs and a map of the target region for glossiness of cooked rice QTL, qGCR9 on chromosome 9. White and black portions of the graph are homozygous Hwaseong and homozygous O. rufipogon, respectively. The table to the right of the graphical genotypes indicates mean values of traits. Years were treated as replications. & P1: Hwaseong, P2: O. rufipogon. 1)PC protein content, AC amylose content, HR head rice ratio, CR chalky rice ratio, GCR glossiness of cooked rice, DTH days to heading. 2)Numbers followed by the same letter in each column are not significantly different based on Duncan’s multiple range test. A, B: ranked by Duncan test at P < 0.05. a, b: ranked by Duncan test at P < 0.1
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Fig5: Graphical representation of four ILs and a map of the target region for glossiness of cooked rice QTL, qGCR9 on chromosome 9. White and black portions of the graph are homozygous Hwaseong and homozygous O. rufipogon, respectively. The table to the right of the graphical genotypes indicates mean values of traits. Years were treated as replications. & P1: Hwaseong, P2: O. rufipogon. 1)PC protein content, AC amylose content, HR head rice ratio, CR chalky rice ratio, GCR glossiness of cooked rice, DTH days to heading. 2)Numbers followed by the same letter in each column are not significantly different based on Duncan’s multiple range test. A, B: ranked by Duncan test at P < 0.05. a, b: ranked by Duncan test at P < 0.1

Mentions: qGCR9 improved the glossiness of cooked rice in the Hwaseong cultivar background (Table 3). To characterize and further define the location of qGCR9, four lines with a single O. rufipogon segment near qGCR9 on chromosome 9 were selected and screened with additional SSR markers (Fig. 5). Of the four ILs, three ILs, CR71, CR81, and CR82 with significantly higher values of glossiness of cooked rice than the control Hwaseong, shared the O. rufipogon segment between RM242 and RM245 in common, whereas CR73 with the O. rufipogon segment between RM321 and RM6491 showed no difference in the glossiness of cooked rice with Hwaseong. These results suggest that the 3.4-Mb O. rufipogon segment between RM242 and RM245 is associated with an increase in glossiness of cooked rice. Although CR20 and CR56 possssed an O. rufipogon segment near qGCR9, they were not included in the analysis because they had O. rufipogon segments in Hwaseong background. No significance difference in the glossiness of cooked rice between CR20 (66.1) and Hwaseong (66.1 and 69.0), and CR56 and Hwaseong (68.9 and 69.0) was observed and these two lines will be useful to further narrow down the candidate region. The protein content values of these three lines were lower than Hwaseong (P < 0.1) indicating that protein content might be associated with the variation of GCR; however, no difference in amylose content, head rice ratio, days to heading or chalky rice ratio was observed. Four ILs, with different O. rufipogon DNA segments in the target region were used for yield trials together with Hwaseong over 7 years. The yield trials were conducted using a completely randomized block design with two replications (Table 5). Three lines, CR71, CR81, and CR82 performed better than Hwaseong in spikelets per panicle and grain yield. However, no difference was observed for grain shape traits of rough and brown rice, grain length, width, thickness, and weight. Results showed that the average grain yield per plant of three lines CR71, CR81, and CR82 were 3.4–10.6% and 5.6–13.0% higher than that of CR73 and Hwaseong, respectively. The difference in grain yield per plant was significant (P ≤ 0.05) between three ILs (CR71, CR81, and CR82) and CR73 and Hwaseong, but there was no significant difference between CR73 and Hwaseong (Fig. 5). Same results were obtained for spikelets per panicle. No difference was observed in ripening ratio and panicle number (data not shown). These results indicate that the yield increase in three lines, CR71, CR81, and CR82 is mainly due to an increase in spikelets per panicle.Fig. 5


QTL Mapping of Grain Quality Traits Using Introgression Lines Carrying Oryza rufipogon Chromosome Segments in Japonica Rice
Graphical representation of four ILs and a map of the target region for glossiness of cooked rice QTL, qGCR9 on chromosome 9. White and black portions of the graph are homozygous Hwaseong and homozygous O. rufipogon, respectively. The table to the right of the graphical genotypes indicates mean values of traits. Years were treated as replications. & P1: Hwaseong, P2: O. rufipogon. 1)PC protein content, AC amylose content, HR head rice ratio, CR chalky rice ratio, GCR glossiness of cooked rice, DTH days to heading. 2)Numbers followed by the same letter in each column are not significantly different based on Duncan’s multiple range test. A, B: ranked by Duncan test at P < 0.05. a, b: ranked by Duncan test at P < 0.1
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121107&req=5

Fig5: Graphical representation of four ILs and a map of the target region for glossiness of cooked rice QTL, qGCR9 on chromosome 9. White and black portions of the graph are homozygous Hwaseong and homozygous O. rufipogon, respectively. The table to the right of the graphical genotypes indicates mean values of traits. Years were treated as replications. & P1: Hwaseong, P2: O. rufipogon. 1)PC protein content, AC amylose content, HR head rice ratio, CR chalky rice ratio, GCR glossiness of cooked rice, DTH days to heading. 2)Numbers followed by the same letter in each column are not significantly different based on Duncan’s multiple range test. A, B: ranked by Duncan test at P < 0.05. a, b: ranked by Duncan test at P < 0.1
Mentions: qGCR9 improved the glossiness of cooked rice in the Hwaseong cultivar background (Table 3). To characterize and further define the location of qGCR9, four lines with a single O. rufipogon segment near qGCR9 on chromosome 9 were selected and screened with additional SSR markers (Fig. 5). Of the four ILs, three ILs, CR71, CR81, and CR82 with significantly higher values of glossiness of cooked rice than the control Hwaseong, shared the O. rufipogon segment between RM242 and RM245 in common, whereas CR73 with the O. rufipogon segment between RM321 and RM6491 showed no difference in the glossiness of cooked rice with Hwaseong. These results suggest that the 3.4-Mb O. rufipogon segment between RM242 and RM245 is associated with an increase in glossiness of cooked rice. Although CR20 and CR56 possssed an O. rufipogon segment near qGCR9, they were not included in the analysis because they had O. rufipogon segments in Hwaseong background. No significance difference in the glossiness of cooked rice between CR20 (66.1) and Hwaseong (66.1 and 69.0), and CR56 and Hwaseong (68.9 and 69.0) was observed and these two lines will be useful to further narrow down the candidate region. The protein content values of these three lines were lower than Hwaseong (P < 0.1) indicating that protein content might be associated with the variation of GCR; however, no difference in amylose content, head rice ratio, days to heading or chalky rice ratio was observed. Four ILs, with different O. rufipogon DNA segments in the target region were used for yield trials together with Hwaseong over 7 years. The yield trials were conducted using a completely randomized block design with two replications (Table 5). Three lines, CR71, CR81, and CR82 performed better than Hwaseong in spikelets per panicle and grain yield. However, no difference was observed for grain shape traits of rough and brown rice, grain length, width, thickness, and weight. Results showed that the average grain yield per plant of three lines CR71, CR81, and CR82 were 3.4–10.6% and 5.6–13.0% higher than that of CR73 and Hwaseong, respectively. The difference in grain yield per plant was significant (P ≤ 0.05) between three ILs (CR71, CR81, and CR82) and CR73 and Hwaseong, but there was no significant difference between CR73 and Hwaseong (Fig. 5). Same results were obtained for spikelets per panicle. No difference was observed in ripening ratio and panicle number (data not shown). These results indicate that the yield increase in three lines, CR71, CR81, and CR82 is mainly due to an increase in spikelets per panicle.Fig. 5

View Article: PubMed Central - PubMed

ABSTRACT

Background: Improved eating quality is a major breeding target in japonica rice due to market demand. Consequently, quantitative trait loci (QTL) for glossiness of cooked rice and amylose content associated with eating quality have received much research focus because of their importance in rice quality.

Results: In this study, QTL associated with 12 grain quality traits were identified using 96 introgression lines (IL) of rice developed from an interspecific cross between the Korean elite O. sativa japonica cultivar &lsquo;Hwaseong&rsquo; and O. rufipogon over 7 years. QTL analyses indicated that QTL qDTH6 for heading date, detected on chromosome 6 is associated with variance in grain traits. Most QTLs detected in this study clustered near the qDTH6 locus on chromosome 6, suggesting the effect of qDTH6. O. rufipogon alleles negatively affected grain quality traits except for a few QTLs, including qGCR9 for glossiness of cooked rice on chromosome 9. To characterize the effect of the O. rufipogon locus harboring qGCR9, four lines with a single but different O. rufipogon segment near qGCR9 were compared to Hwaseong. Three lines (O. rufipopgon ILs) having O. rufipogon segment between RM242 and RM245 in common showed higher glossiness of cooked rice than Hwaseong and the other line (Hwaseong IL), indicating that qGCR9 is located in the 3.4-Mb region between RM242 and RM245. Higher glossiness of cooked rice conferred by the O. rufipogon allele might be associated with protein content considering that three lines had lower protein content than Hwaseong (P&thinsp;&lt;&thinsp;0.1). These three O. rufipogon ILs showed higher yield than Hwaseong and Hwaseong IL due to increase in spikelets per panicle and grain weight indicating the linkage of qGCR9 and yield component QTLs.

Conclusion: The qGCR9 locus is of particular interest because of its independence from other undesirable grain quality traits in O. rufipogon. SSR markers linked to qGCR9 can be used to develop high-quality japonica lines and offer a starting point for map-based cloning of genes underlying this trait. To our knowledge, this is the first report to map a beneficial QTL for glossiness of cooked rice from a wild rice, O. rufipogon.

Electronic supplementary material: The online version of this article (doi:10.1186/s12284-016-0135-0) contains supplementary material, which is available to authorized users.

No MeSH data available.