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

Abstract

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

Pleiotropic Effects of Rice Florigen Gene RFT1 on the Amino Acid Content of Unmilled Rice

“…In the present study, replacement of the ZS97 allele of RFT1 with the MY46 and ZH11 alleles resulted in increasing the contents of most amino acids ( Supplementary Table S2; Tables 3-5). Obviously, the effects of RFT1 on HD and AAC have opposite allelic directions, which is in accordance with the opposite allelic directions between QTLs for HD and PC located on the short arm of chromosome 6 (Wada et al, 2006;Yun et al, 2016).…”

“…Utilization of the pleiotropic effects of heading-date genes on AAC and PC could help to meet the diverse requirements of protein for human consumption. High contents of protein and amino acids are favorable for enhancing the nutritional value, but unfavorable for eating quality (Martin and Fitzgerald, 2002;Kwon et al, 2011;Yun et al, 2016) and undesirable for some uses such as wine-making (Yoshida et al, 2002) and certain types of diet . Alleles for promoting HD and increasing AAC could be selected for developing rice varieties with high nutritional values; and alleles for delaying heading and reducing AAC may be applied for developing high-yielding varieties with good eating quality.…”

“…In rice, the short arm of chromosome 6 is a region harboring multiple genes that play critical roles in the regulation of heading date (HD), including Hd1, Hd3a, RFT1, and Hd17/Hd3b (Hori et al, 2016). In a number of segregating populations that derived from intra-subspecies or inter-species crosses, negative correlation between HD and PC was observed (Wada et al, 2006;Kwon et al, 2011;Yun et al, 2016), which could be partially ascribed to a QTL region on the short arm of chromosome 6 that affected both HD and PC with opposite allelic directions (Wada et al, 2006;Yun et al, 2016). These results suggest that one or more heading-date genes located in this region may have pleiotropic effects on the contents of proteins and amino acids.…”

Validation of a QTL for Grain Size and Weight Using an Introgression Line from a Cross Between Oryza Sativa and Oryza Minuta

“…Transfer and utilization useful genes from wild rice into cultivated varieties are effective and aim to improve grain yield, quality, and crop genetic diversity (Brar and Khush 1997;Xie et al 2008;Yun et al 2016;Qi et al 2017). However, efforts to improve rice grain traits of modern cultivars using O. minuta as donor parents are limited.…”

“…However, low crossability and limited recombination between unrelated genomes limit the transfer QTLs from Oryza minuta to cultivars. Following the availability of advanced backcross quantitative trait loci (AB-QTL) approach proposed by Tanksley and Nelson (1996), several studies have been reported to identify the QTLs controlling yield and quality-related traits and to simultaneously transfer them from wild to cultivated species (Xiao et al 1998;Thomson et al 2003;Yoon et al 2006;Tian et al 2006;Mallikarjuna Swamy et al 2012;Yun et al 2016). However, few attempts have been made to identify and capture yield-related QTLs from Oryza minuta into cultivars.…”