Dong-Min Kim

Mapping QTLs for salt tolerance in an introgression line population between Japonica cultivars in rice

QTL analysis of physiological traits related to salt tolerance was carried out using 117 BC3F5 lines derived from a cross between “Ilpumbyeo” as a recurrent parent and “Moroberekan” as a donor parent. The 117 introgression lines with the parents were evaluated for five traits; dry weight, fresh weight, leaf area, seedling height, and survival rate under control and salinity conditions (55 mM) at the seedling stage. To identify QTLs related to salt tolerance, 125 SSR markers showing polymorphisms between the parents were genotyped for the 117 BC3F5 lines. A total of eight QTLs were detected on chromosomes 1, 6, and 7. These include two QTLs on chromosomes 6 and 7 for reduction rate of dry weight (R2 = 10.2∼13.6%), three QTLs on chromosomes 1, 6, and 7 for reduction rate of fresh weight (R2 = 10.9∼13.9 %), two QTLs on chromosomes 1 and 7 for reduction rate of leaf area (R2 = 12.1%), and one QTL on chromosome 7 for reduction rate of seedling height (R2 = 10.5%). The Moroberekan alleles contributed the positive effect at these eight QTL loci. Although the parents, Ilpumbyeo and Moroberekan, were not salt tolerant as the salt tolerant check variety, Pokkali, some lines displayed a similar level of tolerance as Pokkali. The effect of the QTL on chromosome 7 was further confirmed by evaluating four lines containing the target QTL for fresh and dry weight, turgid weight, and relative water content (RWC). Significant differences between each line and Ilpumbyeo were detected for dry and fresh weight, and RWC values, and these results seem to indicate the beneficial effect of the Moroberekam alleles for salt tolerance. A set of introgression lines are being developed containing only few chromosomal segments from Moroberekan in the Ilpumbyeo background. These would be useful in developing salt tolerant lines in the breeding program.

QTL mapping reveals a tight linkage between QTLs for grain weight and panicle spikelet number in rice

BackgroundA number of QTL studies reported that one genomic region was associated with several traits, indicating linkage and/or pleiotropic effects. The question of pleiotropy versus tight linkage in these studies should be solved using a large-size population combined with high-density mapping. For example, if each of the 2 parents has a TGW-increasing or SPP-increasing QTL that is tightly linked, complementary combination of the 2 beneficial QTLs by using molecular markers could produce higher yields compared to the 2 parents. However, a pleiotropic QTL with opposite effects on the SPP and 1,000-grain weight (TGW) is complicated and challenging in terms of its application to rice improvement.ResultsIn this study, using a series of BC5F4 nearly isogenic lines (NILs) that were derived from a cross between the Korean japonica cultivar Hwayeongbyeo and Oryza rufipogon, we demonstrated that 2 QTLs, qSPP5 for spikelets per panicle (SPP) and qTGW5 for grain weight (TGW), are tightly linked on chromosome 5. Alleles from the O. rufipogon parent increased the SPP and decreased TGW in the Hwayeongbyeo background. qSPP5 was located within a 803-kb interval between the simple sequence repeat (SSR) markers INDEL3 and RM18076. Based on the map position, qTGW 5 seemed to be the same gene as qSW5, which controls grain morphology. The additive effect of the O. rufipogon allele at qSPP5 was 10–15 SPP, and 33.0% of the phenotypic variance could be explained by the segregation of the SSR marker RM18058. Yield trials with BC5F4 NILs showed that lines that contained a homozygous O. rufipogon introgression at the qSPP5 region out-yielded sibling NILs that contained Hwayeongbyeo DNA by 15.3% and out-yielded the Hwayeongbyeo parent by 7.3%.ConclusionBased on the finding that the O. rufipogon allele for the SPP was beneficial in the japonica and indica cultivar backgrounds, the qSPP5 allele could be valuable for improving rice yields. In addition, the NIL populations and molecular markers are useful for cloning qSPP5.

Mapping quantitative trait loci for awnness and yield component traits in isogenic lines derived from an Oryza sativa/O. rufipogon cross.

An advanced backcross line, HR9118, was produced from a single plant of BC2F3 families derived from a cross between Oryza rufipogon Griff. (IRGC 105491) as a donor parent and the O. sativa subsp. japonica cv. Hwaseongbyeo as a recurrent parent. Although HR9118 resembled Hwaseongbyeo, several traits were different from those of Hwasoengbyeo, including days to heading, plant height, and awn. These differences between Hwasongbyeo and HR9118 could be attributed to introgressed O. rufipogon chromosome segments into HR9118. Introgression analysis using 460 SSR markers revealed that three O. rufipogon-specific chromosome segments were detected in HR9118 genome. F2:3 populations derived from the cross between Hwaseongbyo and HR9118, consisting of 340 F2 plants and 137 F3 lines, were used to map and characterize QTLs for 12 traits. QTL analysis identified a total of 17 QTLs in the F2:3 populations. Of these, seven QTLs were shared by the F2 and F3 populations, whereas the other ten QTLs were identified only in the F3 population. In seven (41.2%) QTLs identified in this study, the O. rufipogon-derived alleles contributed desirable agronomic effects despite the overall undesirable characteristics of the wild phenotype. Each of three O. rufipogon introgressed segments contained multiple QTLs, indicating linkage and/or pleotropic effects. A cluster of eight QTLs was detected on chromosome 8 including a major QTL for awn. Substitution mapping using F2 population indicated that awn8 was located within an interval between two SSR makers RM23326 and RM23356 which are 590 kb apart. SSR markers tightly linked to QTLs for yield components detected in this study will facilitate cloning of the gene underlying this QTL as well as marker-assisted selection for variation in grain weight in an applied breeding program.

QTL mapping of cold tolerance at the seedling stage using introgression lines derived from an intersubspecific cross in rice.

Low-temperature stress is an important factor controlling the growth and development of rice (Oryza sativa L.) in temperate region. In this study, a molecular linkage map consisting of 136 SSR markers was employed to identify QTL associated with cold tolerance at the seedling stage. 80 recombinant inbred lines (RILs) from an intersubspecific cross between Milyang23 (O. sativa ssp. Indica) and Hapcheonaengmi3, a japonica weedy rice and the parents were evaluated for leaf discoloration and SAPD value of seedlings. Rice plants were grown for 15 days in the low-temperature condition (13/20°C day/night) and the control condition (25/20°C day/night) in the growth chamber. The degree of leaf discoloration showed a highly significant correlation with the SPAD value in the low-temperature plot (r = -0.708, P < 0.0001). A total of four QTLs for SPAD were identified and the phenotypic variance explained by each QTL ranged from 5.4 to 16.0%. Two QTLs detected in the control condition were located on chromosomes 2 and 5, respectively. Two QTL on chromosomes 1 and 4 were detected at the low-temperature condition and Hapcheonaengmi3 alleles increased the SPAD values at these loci. Substitution mapping was conducted to delimit the position of qSPA-4 using introgression lines derived from the same cross. Results indicated that qSPA-4 was located in a 810-Kb region flanked by RM16333 and RM16368. The results indicated that Hapcheonaengmi3 contains QTL alleles that are likely to improve cold tolerance of Indica rice.

Analysis of QTL Interaction for Grain Weight using Near Isogenic Lines in Rice

Grain weight (GW) is one of the most important targets for grain yield in rice breeding. In previous studies, two quantitative trait loci (QTLs) for grain weight, tgw2 and gw8.1, were identified using progeny derived from crosses between the japonica cultivar Hwaseong and Oryza grandiglumis, and between Hwaseong and O. rufipogon (IRGC 105491), respectively. The wild alleles increased GW at two loci. An F2 population (186 plants) was developed by crossing two near isogenic lines (NILs) harboring tgw2 and gw8.1 to test their interaction. Simple sequence repeat (SSR) markers tightly linked to the two QTLs were used to check the genotype of the F2 population. Based on the genotype at the two loci, tgw2 and gw8.1, the F2 plants were classified into 9 groups with a combination of three genotypes at each of the two loci. Two-way ANOVA revealed no interaction between the 2 QTLs in the F2 population. The 1,000 grain weight (TGW) of homozygous plants with wild alleles at the two loci was significantly higher than that of plants with a single QTL in the F2 and F3 lines. These results indicate that two QTLs act additively, in distinct or complementary pathways, to control grain weight. Based on these results, it is desirable to pyramid the two QTLs into a single line, since the double-QTL line displayed further increase of TGW in the Hwaseong background.

A New High-yielding Rice Variety ‘Hwaweon 7’ with Lodging Tolerance

‘Hwaweon 7’ was developed from a cross between the African upland cultivar, ‘Moroberekan’ and ‘Ilpumbyeo’ based on marker-aided backcross selection. The recurrent parent, Ilpumbyeo is a high grain quality cultivar with medium to late maturity. Hwaweon 7 is nearly isogenic to Ilpumbyeo except a small Moroberekan introgressed segment on chromosome 6 harboring genes related with spikelets per panicle and internode diameter. The preliminary and replicated yield trial was conducted at Chungnam National University and Chungcheongnamdo Agricultural Research & Extension (CARES), Yesan in 2010 and 2011. The local adaptability test was carried out by the National Seed Management Office (NSMO) in 2012 and 2013. This cultivar was registered to NSMO with a cultivar designated as “Hwaweon7”. This cultivar averaged 80cm in culm length and has a medium growth duration. Milled rice of “Hwaweon7” is translucent and the grain quality traits are comparable to those of the recurrent parent. The average yield potential of Hwaweon 7 in grain was about 6.48 MT/ha at the ordinary fertilizer level for two years about 5.1% higher than that of Ilpumbyeo due to increase in spikelets per panicle. This variety is tolerant to lodging and the tolerance is due to the APO1 gene controlling the base internode diameter on chromosome 6 introgressed from the donor parent, Moroberekan. The Apo1 gene would be useful in enhancing resistance to lodging in rice breeding program.

Validation of QTLs associated with spikelets per panicle and grain weight in rice

In this study, a near-isogenic line (BC 4 F 10 ) CR572 developed by introgressing a chromosomal segment from Oryza rufipogon (accession no. 105491) into the Oryza sativa subsp. japonica cv. Hwaseong was found to exhibit a significant increase in the number of spikelets per panicle (SPP) and grain weight compared with the recurrent parent Hwaseong. Quantitative trait locus (QTL) analysis in F 2 generation derived from the cross between CR572 and Hwaseong revealed that two QTLs, qSPP1 and qTGW1 , were linked to a simple sequence repeat marker, RM283, on chromosome 1. The additive effect of the O. rufipogon allele at qSPP1 was 13 SPP, and 21.6% of the phenotypic variance was explained by the segregation of RM283. The qTGW1 QTL explained 19.1% of the phenotypic variance for grain weight. Substitution mapping was carried out with five F 3 lines derived from F 2 plants having informative recombination breakpoints within the target region. Substitution mapping indicated the linkage of qSPP1 and qTGW1 . The grain yield of CR572 was 18.2 and 15.8% higher than that of Hwaseong at two locations, respectively, mainly due to the increase in 1000-grain weight and SPP. These results are very useful for QTL cluster transfer by molecular marker-assisted selection in rice breeding programmes and for QTL gene cloning by map-based cloning.