Fine mapping and candidate gene analysis of the quantitative trait locus gw8.1 associated with grain length in rice.

A quantitative trait locus (QTL) gw8.1 was detected in the population derived from a cross between the elite japonica cultivar, 'Hwaseong' and Oryza rufipogon (IRGC 105491). Near isogenic lines (NILs) harboring the O. rufipogon segment on chromosome 8 showed increased grain length and weight compared to those of the recurrent parent, Hwaseong. This QTL was mapped to a 175.3-kb region containing 28 genes, of which four were considered as candidates based on the presence of mutations in their coding regions and as per the RNA expression pattern during the inflorescence stage. Leaves and panicles obtained from plants harvested 5 days after heading showed differences in gene expression between Hwaseong and gw8.1-NILs. Most genes were upregulated in O. rufipogon and gw8.1-NIL than in Hwaseong. Scanning electron microscopy analysis of the lemma inner epidermal cells indicated that cell length was higher in gw8.1 NIL than in Hwaseong, indicating that gw8.1 might regulate cell elongation. Among the candidate genes, LOC_Os08g34380 encoding a putative receptor-like kinase and LOC_Os08g34550 encoding putative RING-H2 finger protein were considered as possible candidates based on their functional similarity.

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

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.

High-density mapping of quantitative trait loci for grain-weight and spikelet number in rice.

BACKGROUND: High grain yield is one of the most important traits requiring improvement in rice breeding programs. Consequently, the genetic basis of spikelets per panicle (SPP) and grain weight (TGW) have received much research focus because of their importance in rice yield. RESULTS: In this study, IL28, which is a near isogenic line (NIL) developed by introgressing chromosomal segments of the cultivar 'Moroberekan' into the cultivar 'Ilpumbyeo', showed a significant increase in the number of spikelets per panicle (SPP) and 1,000-grain weight (TGW) compared to the recurrent parent, Ilpumbyeo. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo indicated that both qSPP6 and qTGW6 are located in the interval RM3430-RM20580. Following substitution mapping with 50 F3:4:5 lines, qSPP6 was mapped to a 429-kb interval between RM20521 and InDel-1, while qTGW6 was mapped to a 37.85-kb interval between InDel-1 and SNP--3 based on the japonica genome sequence. This result indicates that qSPP6 and qTGW6 are different genes. Yield trials with substitution lines indicated that lines harboring the homozygous Moroberekan segment at both the qSPP6 and qTGW6 region showed significantly higher grain yield than Ilpumbyeo. CONCLUSION: Because the Moroberekan alleles for SPP and TGW have been shown to be beneficial in the genetic background of Ilpumbyeo, both the qSPP6 and qTGW6 alleles might prove valuable in improving rice yields. Closely linked SSR markers are expected to facilitate the cloning of genes that underlie these QTLs, as well as with marker-assisted selection for variation in SPP and TGW in rice breeding programs.