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Seed germination is a complex trait determined by both quantitative trait loci (QTLs) and environmental factors and also their interactions. In this study, we mapped one major QTLqSE3 for seed germination and seedling establishment under salinity stress in rice. To understand the molecular basis of this QTL, we isolated qSE3 by map-based cloning and found that it encodes a K + transporter gene, OsHAK21. The expression of qSE3 was significantly upregulated by salinity stress in germinating seeds. Physiological analysis suggested that qSE3 significantly increased K + and Na + uptake in germinating seeds under salinity stress, resulting in increased abscisic acid (ABA) biosynthesis and activated ABA signaling responses. Furthermore, qSE3 significantly decreased the H 2 O 2 level in germinating seeds under salinity stress. All of these seed physiological changes modulated by qSE3 might contribute to seed germination and seedling establishment under salinity stress. Based on analysis of single-nucleotide polymorphism data of rice accessions, we identified a HAP3 haplotype of qSE3 that was positively correlated with seed germination under salinity stress. This study provides important insights into the roles of qSE3 in seed germination and seedling establishment under salinity stress and facilitates the practical use of qSE3 in rice breeding., (© 2018 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.)

Heikezijing, a japonica rice landrace from the Taihu region of China, exhibited broad-spectrum resistance to more than 300 isolates of the blast pathogen (Magnaporthe oryzae). In our previous research, we fine mapped a broad-spectrum resistance gene, Pi-hk1, in chromosome 11. In this research, 2010-9(G1), one of the predominant races of blast in the Taihu Lake region of China, was inoculated into 162 recombinant inbred lines (RIL) and two parents, Heikezijing and Suyunuo, for mapping the resistance-blast quantitative trait loci (QTL). Three QTL (Lsqtl4-1, Lsqtl9-1, and Lsqtl11-1) associated with lesion scores were detected on chromosomes 4, 9, and 11 and two QTL (Lnqtl1-1 and Lnqtl9-1) associated with average lesion numbers were detected on chromosomes 1 and 9. The QTL Lsqtl9-1 conferring race-specific resistance to 2010-9(G1) at seedling stages showed logarithm of the odds scores of 9.10 and phenotypic variance of 46.19% and might be a major QTL, named Pi-hk2. The line RIL84 with Pi-hk2 derived from a cross between Heikezijing and Suyunuo was selected as Pi-hk2 gene donor for developing fine mapping populations. According to the resistance evaluation of recombinants of three generations (BC 1 F 2 , BC 1 F 3 , and BC 1 F 4 ), Pi-hk2 was finally mapped to a 143-kb region between ILP-19 and RM24048, and 18 candidate genes were predicted, including genes that encode pleiotropic drug resistance protein 4 (n = 2), WRKY74 (n = 1), cytochrome b5-like heme/steroid-binding domain containing protein (n = 1), protein kinase (n = 1), and ankyrin repeat family protein (n = 1). These results provide essential information for cloning of Pi-hk2 and its potential utility in breeding resistant rice cultivars by marker-assisted selection.

Easy shattering reduces yield from grain loss during rice ( L.) harvest. We characterized a nonshattering rice landrace Jiucaiqing from Taihu Lake valley in China. The breaking tensile strength (BTS; grams force, gf) of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering at 0, 7, 14, 21, 28, and 35 d after heading (DAH). The BTS of Jiucaiqing did not significantly decrease with increasing DAH, maintaining a level of 152.2 to 195.9 gf, while that of IR26 decreased greatly during 0 to 14 DAH and finally stabilized at ∼100 gf. Then the chromosome segment substitution lines (CSSLs) and near isogenic lines (NILs) of Jiucaiqing in IR26 background were developed for quantitative trait loci (QTL) mapping. Four putative QTL (, , , and ) for shattering were detected, and the was confirmed on chromosome 1. We further mapped to a 98.4-kb region, which contains 14 genes. Os01g62920 was considered to be a strong candidate for , which colocated with . Further quantitative real-time polymerase chain reaction (PCR) analyses confirmed that the QTL can significantly decrease the expression of shattering related genes (, , , , and ) especially at the middle development stage at 10 and 15 cm panicle length, which causes rice shattering decrease. The elite allele and the NIL with desirable agronomic traits identified in this study could be useful for rice breeding., (Copyright © 2016 Crop Science Society of America.)

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.

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.

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.

Salt tolerance of rice (Oryza sativa L.) at the seedling stage is one of the major determinants of its stable establishment in saline soil. One population of recombinant inbred lines (RILs, F (2:9)) derived from a cross between the salt-tolerant variety Jiucaiqing and the salt-sensitive variety IR26 was used to determine the genetic mechanism of four salt tolerance indices, seedling height (SH), dry shoot weight (DSW), dry root weight (DRW) and Na/K ratios (Na/K) in roots after 10 days in three salt concentrations (0.0, 0.5 and 0.7 % NaCl). The main effect QTLs (M-QTLs) and epistatic QTLs (E-QTLs) were detected by QTL IciMapping program using single environment phenotypic values. Eleven M-QTLs and 11 E-QTLs were identified for the salt tolerance indices. There were six M-QTLs and two E-QTLs identified for SH, three M-QTLs and five E-QTLs identified for DSW, two M-QTLs and one E-QTL identified for DRW, and three E-QTLs identified for Na/K. The phenotypic variation explained by each M-QTL and E-QTL ranged from 7.8 to 23.9 % and 13.3 to 73.7 %, respectively. The QTL-by-environment interactions were detected by QTLNetwork program in the joint analyses of multi-environment phenotypic values. Six M-QTLs and five E-QTLs were identified. The phenotypic variation explained by each QTL and QTL × environment interaction ranged from 0.95 to 6.90 % and 0.02 to 0.50 %, respectively. By comparing chromosomal positions of these M-QTLs with those previously identified, five M-QTLs qSH1.3, qSH12.1, qSH12.2, qDSW12.1 and qDRW11 might represent novel salt tolerance genes. Five selected RILs with high salt tolerance had six to eight positive alleles of the M-QTLs, indicating that pyramiding by marker-assisted selection (MAS) of M-QTLs can be applied in rice salt tolerance breeding programs.

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.

Rice blast is one of the most devastating diseases affecting rice production worldwide. One japonica landrace, Heikezijing, from the Taihu Lake area in China, has been reported to be highly resistant to most of the rice blast isolates collected from China and Japan. To effectively dissect the inheritance of its resistance, a population of recombinant inbred lines (RILs) (F(2:8)) was constructed from a cross between Heikezijing and Suyunuo, a blast-susceptible cultivar. Nineteen blast isolates from China and Japan were inoculated into 166 RILs and their parents, and 22 quantitative trait loci (QTLs) conferring resistance to these isolates were identified and mapped onto rice chromosomes 1, 7, 9, 11, and 12. Most of the QTLs conferred race-specific resistance to blast. Some QTLs, such as qtl11-5-5, conferred resistance to two or more isolates. One blast-resistant gene cluster, including qtl11-2-2, qtl11-3-1, qtl11-4-1, qtl11-5-5, qtl11-6-1, qtl11-7-5, qtl11-8-2, qtl11-9-2, qtl11-10-4, and qtl11-11-1, was found on the long arm of chromosome 11 in the japonica landrace. These loci offered effective resistance toward as many as 17 isolates, including 16 isolates from seven Chinese race groups and 1 isolate from Japan. The results from this study suggest that the Heikezijing landrace involves a number of genes that are associated with broad-spectrum resistance to rice blast.