| In recent years, with the rapid development of economy in our country, the labor cost of the traditional planting cultivation mode had been greatly increased. For the low cost and simple operation, the direct-seeded rice is widely used. The successful direct-seeded rice requires high seed vigor, which can improve higher germination rate and uniformity in the field. Therefore, raising rice seed vigor is an important part of the study of crop genetics and breeding. In this study, QTL mapping of seed vigor was carried out during mature period, the germination, and seedling stages in rice. And the main effect QTL of a salt-tolerant at seed germination wad fine mapped. The main results were as follows:A rice population of recombinant inbred lines (RILs) was used to determine the genetic characteristics of seed dormancy (SD) at 4 (early),5 (middle) and 6 (late) weeks after heading stages. Dynamic analysis showed that the indica IR28 variety tended to have deeper dormancy than the japonica Daguandao at the middle and late development stages. The level of SD decreased with the process of seed development. The significant interaction between heading date (HD) and SD occurred only in those seeds collected at the early development stage. A total of nine additive quantitative trait loci (QTLs) and eight epistatic QTLs for SD were identified at three seed development stages. Of them, one additive and four epistatic QTLs were identified for the early stage, six additive and one epistatic QTL for the middle stage and two additive and three epistatic QTLs for the late stage. The phenotypic variation explained by each additive and epistatic QTL ranged from 5.8 to 30.6% and from 3.8 to 13.1%, respectively. Compared with the additive QTLs, epistatic interactions were much more important for SD at the early and late development stages. Two major additive QTLs, qSD3.1 and qSD4.1, were identified; each QTL could explain more than 20% of the total phenotypic variance and each dormancy-enhancing allele could decrease the germination percentage by about 10%. By comparing the chromosomal positions of theseadditive QTLs with those previously identified, five additive QTLs, qSD1.2, qSD2.1, qSD3.2, qSD4.1 and qSD9.1, might represent novel genes. One QTLidentified here, qHD 1, and nine QTLs identified in previous studies for HD were co-located with our QTLs for SD, which indicated that the significant correlation between SD and HD might be due to the linkage of QTLs for SD and HD. Four RILs with deep dormancy at development stages but non-dormancy after post-ripening under different germination conditions were selected. Using the selected RILs, three cross combinations of SD for the development of RILpopulations were predicted. The selected RILs and the identified QTLs might be applicable for the improvement of pre-harvest sprouting tolerance by markerassisted selection in rice.Seed vigor is an important characteristic of seed quality. In this study,276 indica rice varieties derived from 18 global regions in the world were used to carry out association mapping for seed vigor at germination and seedling stages under normal, salt and drought conditions. Genome-wide association mapping using information from 159 simple sequence repeat (SSR) markers and using general linear model (Q, GLM) and mixed linear model (Q+K, MLM) were performed to identify the marker loci/QTLs underlying the naturally occurring variations of seed vigor including germination percentage (GP), germination index (GI) and seedling survival (SS) under three conditions in rice. The genotyping demonstrated that the average polymorphic information content (PIC) value of varieties is 0.4262 and these varieties could be divided into two main cluster groups. There were significant variety differences in seed vigor at germination and seedling stages under three conditions among the indica rice collections. Correlation analysis indicated that there were positively significant relationships in GP and GI among normal, salt and drought conditions, while no significant relationship between seed germination and seedling growth under stress condition; few varieties were salt and drought tolerant at both germination and seedling stages. The GLM detected a total of 167 marker-trait associations involving 50 SSR markers under three conditions, while 79 marker-trait associations involving 29 SSR markers identified by MLM. Of them,78 marker-trait associations involving 29 SSR markers were detected by both methods; thus a total of 46 QTLs were identified for there traits under three conditions including 22,14 and 10 QTLs for GP, GI and SS, respectively. Comparing three conditions, the identification of co-localized QTLs occurred in 15 markers regions, among them 1 for normal and drought condition,14 for drought and salt conditions, and none for three conditions. The co-localized QTLs for seed germination and seedling growth were detected in only one region under drought condition. By comparing the chromosomal positions of these QTLs with those previously identified,23 QTLs involving 14 SSR markers might represent novel genes. According to the estimates for the allelic effects of the detected QTL, the best four cross combinations of each trait for the development of RIL populations were predicted. The selected varieties and the identified QTLs might be applicable to improve rice seed vigor by the marker-assisted selection approach.The pervious study showed that a Japonica variety Jiucaiqing from taihu basin was high salt-tolerant variety. By comparing seed vigor between Jiucaiqing and IR26 (moderate salt sensitive indica variety) under the different levels of salt stress (0-400 mM NaCl), the results showed that IR26 has higher seed vigor under low salt stress (0-200 mM NaCl), but seed vigor of Jiucaiqing have significantly higher than that of IR26 under high salt stress (250-250 mM NaCl). At the same time, Jiucaiqing was used as the donor, and ER26 as receptor, chromosome segment substitution lines (CSSLs) and BC3F2 population were build to carry out QTL mapping of seed vigor under salt stress. The results showed that QTL qGR3.1, qGR3.2, qGB.1 and qGI3.2 of the seed vigor traits, located on RM3372 and RM15456, were detected by CSSLs population under 275 mM NaCl stress. Only one QTL, qGRl controlling seed germination rate under 350 mM NaCl stress, was detected on RM5389-RM5759 interval of chromosome 1. Moreover, a QTL qGR3.2 of controling seed germination rate, were detected using 9322 and 9324 BC3F2 populations under 275 mM NaCl stress, in which the ranges of LOD values, the additive effect and contribution rate were 1.96-5.27,6.68-12.46 and 6.47%-12.16%, respectively. Comparing physical position of detected QTLs between CSSL and BC3F2 population, we found that qGR3.2 was mapped at the same position interval. By fine mapping, qGR3.2 was mapped on the CJPS30-CJPS14 interval further, which was about 74.8 Kb. As bioinformation analysis shown, seven candidate genes (LOC_Os03g43580 LOC_Os03g43590 LOC_Os03g43610, LOC_Os03g43620, LOC_Os03g43650 LOC_Os03g43660 LOC_Os03g43670) were predicted, which could be used for further research. |
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