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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.


Frequency distribution of the introgression segments per each IL
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Fig1: Frequency distribution of the introgression segments per each IL

Mentions: A total of 241 introgressions, including 207 homozygous and 34 heterozygous segments, were detected on 12 chromosomes based on the genotypes of 133 SSR markers in 96 ILs (Additional file 1: Table S1). Each of the 96 ILs contained 0–7 homozygous and 0–3 heterozygous introgressions (Fig. 1). The ratio of homozygous to heterozygous introgression segments varied among the 12 rice chromosomes. Chromosome 8 was found to have the highest number of introgressions, while chromosome 5 revealed no introgression events. Ninety six ILs represented 66% of the O. rufipogon genome. The recurrent parent genome in ILs ranged from 86 to 99%, with a mean of 96%.Fig. 1


QTL Mapping of Grain Quality Traits Using Introgression Lines Carrying Oryza rufipogon Chromosome Segments in Japonica Rice
Frequency distribution of the introgression segments per each IL
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig1: Frequency distribution of the introgression segments per each IL
Mentions: A total of 241 introgressions, including 207 homozygous and 34 heterozygous segments, were detected on 12 chromosomes based on the genotypes of 133 SSR markers in 96 ILs (Additional file 1: Table S1). Each of the 96 ILs contained 0–7 homozygous and 0–3 heterozygous introgressions (Fig. 1). The ratio of homozygous to heterozygous introgression segments varied among the 12 rice chromosomes. Chromosome 8 was found to have the highest number of introgressions, while chromosome 5 revealed no introgression events. Ninety six ILs represented 66% of the O. rufipogon genome. The recurrent parent genome in ILs ranged from 86 to 99%, with a mean of 96%.Fig. 1

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.