Dynamic quantitative trait locus analysis of seed vigor at three maturity stages in rice.

Seed vigor is an important characteristic of seed quality. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of seed vigor, including the germination potential, germination rate, germination index and time for 50% of germination, at 4 (early), 5 (middle) and 6 weeks (late) after heading in two years. A total of 24 additive and 9 epistatic quantitative trait loci (QTL) for seed vigor were identified using QTL Cartographer and QTLNetwork program respectively in 2012; while 32 simple sequence repeat (SSR) markers associated with seed vigor were detected using bulked segregant analysis (BSA) in 2013. The additive, epistatic and QTL × development interaction effects regulated the dry maturity developmental process to improve seed vigor in rice. The phenotypic variation explained by each additive, epistatic QTL and QTL × development interaction ranged from 5.86 to 40.67%, 4.64 to 11.28% and 0.01 to 1.17%, respectively. The QTLs were rarely co-localized among the different maturity stages; more QTLs were expressed at the early maturity stage followed by the late and middle stages. Twenty additive QTLs were stably expressed in two years which might play important roles in establishment of seed vigor in different environments. By comparing chromosomal positions of these stably expressed additive QTLs with those previously identified, the regions of QTL for seed vigor are likely to coincide with QTL for grain size, low temperature germinability and seed dormancy; while 5 additive QTL might represent novel genes. Using four selected RILs, three cross combinations of seed vigor for the development of RIL populations were predicted; 19 elite alleles could be pyramided by each combination.

Identification of QTLs with additive, epistatic and QTL × development interaction effects for seed dormancy in rice.

Seed dormancy (SD) is an important agronomic trait affecting crop yield and quality. In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of SD at the early (4 weeks after heading), middle (5 weeks after heading) and late (6 weeks after heading) development stages. The level of SD decreased with the process of seed development, and the SD was significantly affected by the heading date (HD) and temperature at the early and middle development stages. A total of eight additive quantitative trait loci (QTLs) for SD were identified at three development stages, and more QTLs were expressed at the early and late development stages. Among them, four, one and three additive QTLs were identified at the early, middle and late development stages, respectively. Epistatic QTLs and QTL-by-development interactions were detected by the joint analysis of multi-development phenotypic values, and one additive and two epistatic QTLs were identified. The phenotypic variation of SD explained by each additive, epistatic QTL and QTL × development interaction ranged from 8.0 to 13.5 %, 0.7 to 3.9 % and 1.3 to 2.8 %, respectively. One major QTL qSD7.1 for SD was tightly linked to the major QTL qHD7.4 for HD, which might be applied to reveal the relationship of SD and HD. By comparing chromosomal positions of these additive QTLs with those previously identified, five additive QTLs qSD1.1, qSD2.1, qSD2.2, qSD4.1 and qSD4.2 might represent novel genes. The best three cross combinations for the development of RIL populations were predicted to improve SD. The selected RILs and the identified QTLs might be applicable to improve the rice pre-harvest sprouting tolerance by the marker-assisted selection approach.

Dynamic quantitative trait loci analysis of seed reserve utilization during three germination stages in rice.

In this study, one rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of seed reserve utilization during the early (day 6), middle (day 10) and late (day 14) germination stages. The seedling dry weight (SDW) and weight of the mobilized seed reserve (WMSR) were increased, while the seed reserve utilization efficiency (SRUE) decreased, during the process of seed germination. The SDW and WMSR were affected by the seed weight, while the SRUE was not affected by the seed weight. A total of twenty unconditional and twenty-one conditional additive QTLs and eight epistatic QTLs were identified at three germination stages, and the more QTLs were expressed at the late germination stage. Among them, twelve additive and three epistatic QTLs for SDW, eight additive and three epistatic QTLs for WMSR and thirteen additive and two epistatic QTLs for SRUE were identified, respectively. The phenotypic variation explained by each additive QTL, epistatic QTL and QTL × development interaction ranged from 6.10 to 23.91%, 1.79 to 6.88% and 0.22 to 2.86%, respectively. Two major additive QTLs qWMSR7.1 and qSRUE4.3 were identified, and each QTL could explain more than 20% of the total phenotypic variance. By comparing the chromosomal positions of these additive QTLs with those previously identified, eleven QTLs might represent novel genes. The best four cross combinations of each trait for the development of RIL populations were selected. The selected RILs and the identified QTLs might be applicable to improve rice seed reserve utilization by the marker-assisted selection approach.

QTL analysis of Na+ and K+ concentrations in roots and shoots under different levels of NaCl stress in rice (Oryza sativa L.).

The key to plant survival under NaCl salt stress is maintaining a low Na(+) level or Na(+)/K(+) ratio in the cells. A population of recombinant inbred lines (RILs, F(2:9)) derived from a cross between the salt-tolerant japonica rice variety Jiucaiqing and the salt-sensitive indica variety IR26, was used to determine Na(+) and K(+) concentrations in the roots and shoots under three different NaCl stress conditions (0, 100 and 120 mM NaCl). A total of nine additive QTLs were identified by QTL Cartographer program using single-environment phenotypic values, whereas eight additive QTLs were identified by QTL IciMapping program. Among these additive QTLs, five were identified by both programs. Epistatic QTLs and QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values, and one additive QTL and nine epistatic QTLs were identified. There were three epistatic QTLs identified for Na(+) in roots (RNC), three additive QTLs and two epistatic QTLs identified for Na(+) in shoots (SNC), four additive QTLs identified for K(+) in roots (RKC), four additive QTLs and three epistatic QTLs identified for K(+) in shoots (SKC) and one additive QTL and one epistatic QTL for salt tolerance rating (STR). The phenotypic variation explained by each additive, epistatic QTL and QTL×environment interaction ranged from 8.5 to 18.9%, 0.5 to 5.3% and 0.7 to 7.5%, respectively. By comparing the chromosomal positions of these additive QTLs with those previously identified, five additive QTLs, qSNC9, qSKC1, qSKC9, qRKC4 and qSTR7, might represent novel salt tolerance loci. The identification of salt tolerance in selected RILs showed that a major QTL qSNC11 played a significant role in rice salt tolerance, and could be used to improve salt tolerance of commercial rice varieties with marker-assisted selection (MAS) approach.