Confirmation of Novel Quantitative Trait Loci for Seed Dormancy at Different Ripening Stages in Rice

Seed dormancy contributes resistance to pre-harvest sprouting. Effects on respective quantitative trait loci （QTLs） for dormancy should be assessed by using fresh seeds before germinability altered through storage. We investigated QTLs related to seed dormancy using backcross inbred lines derived from a cross between Nipponbare and Kasalath. Four putative QTLs for seed dormancy were detected immediately after harvest using composite interval mapping. These putative QTLs were mapped near C1488 on chromosome 3 （qSD-3.1）, R2171 on chromosome 6 （qSD-6.1）, R1245 on chromosome 7 （qSD-7.1） and C488 on chromosome 10 （qSD-IO.1）. Kasalath alleles promoted dormancy for qSD-3.1, qSD-6.1 and qSD-7.1, and the respective proportions of phenotypic variation explained by each QTL were 12.9%, 9.3% and 8.1%. We evaluated the seed dormancy harvested at different ripening stages during seed development using chromosome segment substitution lines （CSSLs） to confirm gene effects. The germination rates of CSSL27 and CSSL28 substituted with the region including qSD-6.1 were significantly lower than those of Nipponbare and other CSSLs at the late ripening stage. Therefore, qSD-6.1 is considered the most effective novel QTL for pre-harvest sprouting resistance among the QTLs detected in this study.

Characterization of QTL for unique agronomic traits of new-plant-type rice varieties using introgression lines of IR64

To enhance the yield potential of an elite indica rice cultivar,an introgression(BC_3-derived) line of IR64,YTH288,was developed using a new-plant-type cultivar,IR66215-44-2-3,as a donor parent.YTH288 has agronomically valuable characteristics such as large panicles,few unproductive tillers,and large leaves inherited from NPT.To identify the genetic basis of these traits,we used 167 F_2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits:days to heading(DTH),culm length(CL),flag leaf length(FLL),flag leaf width(FLW),and filled spikelet number per panicle(FSN).Six putative QTL were detected:four on chromosome4(for CL,FLL,FLW,and FSN) and two on chromosome 2(for DTH and FLL).All QTL with the IR66215-44-2-3 allele,except that for FLL on chromosome 2,had positive effects on each trait.To confirm the effects of these putative QTL,we developed NILs with the IR64 genetic background by marker-assisted selection.We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes2 and 4.Additionally,four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropic To enhance the yield potential of an elite indica rice cultivar, an introgression(BC3-derived) line of IR64, YTH288, was developed using a new-plant-type cultivar,IR66215-44-2-3, as a donor parent. YTH288 has agronomically valuable characteristics such as large panicles, few unproductive tillers, and large leaves inherited from NPT.To identify the genetic basis of these traits, we used 167 F2 plants derived from a cross between IR64 and YTH288 to conduct QTL analysis for five agronomic traits: days to heading(DTH), culm length(CL), flag leaf length(FLL), flag leaf width(FLW), and filled spikelet number per panicle(FSN). Six putative QTL were detected: four on chromosome4(for CL, FLL, FLW, and FSN) and two on chromosome 2(for DTH and FLL). All QTL with the IR66215-44-2-3 allele, except that for FLL on chromosome 2, had positive effects on each trait. To confirm the effects of these putative QTL, we developed NILs with the IR64 genetic background by marker-assisted selection. We observed significant differences in several agronomic traits between IR64 and NILs that carried these QTL on chromosomes2 and 4. Additionally, four IR64-NILs carrying chromosomal segments derived from different NPT varieties on the long arm of chromosome 4 exhibited similar pleiotropiceffects for unique agronomic traits. These NILs can be used as research materials for studying each trait and as breeding materials for yield improvement of indica rice cultivars.