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Salt–alkaline stress is one of the most stressful occurrences, causing negative effects on plant development and agricultural yield. Identifying and utilizing genes that affect alkaline tolerance is an excellent approach to accelerate breeding processes and meet the needs for remediating saline–alkaline soil. Here, we employed a mapping population of 176 recombinant inbred lines (RILs) produced from a cross between alkali-tolerant Longdao5 and alkali-sensitive Zhongyouzao8 to identify the quantitative trait loci (QTLs) determining alkali tolerance at the seedling stage. For the evaluation of alkali tolerance, the recovered seedling's average alkali tolerance index (ATI), root number (RN), root length (RL), seedling dry weight (SW), root dry weight (RW), and seedling height (SH) were assessed, together with their relative alkaline damage rate. Under alkaline stress, the ATI was substantially negative connected with the root number, seedling height, seedling dry weight, and root dry weight; however, it was considerably positive correlated with the relative alkaline damage rate of the root number and root dry weight. A total of 13 QTLs for the root number, root length, seedling height, seedling dry weight, root dry weight, and alkali tolerance index under alkaline stress were identified, which were distributed across chromosomes 1, 2, 3, 4, 5, 7, and 8. All of these QTLs formed two QTL clusters for alkali tolerance on chromosome 5 and chromosome 7, designated AT5 and AT7, respectively. Nine QTLs were identified for the relative alkaline damage rate of the root number, root length, seedling height, seedling dry weight, and root dry weight under alkali stress. These QTLs were located on chromosome 2, 4, 6, 7, 8, 9, and 12. In conclusion, these findings further strengthen our knowledge about rice's genetic mechanisms for alkaline tolerance. This research offers clues to accelerate breeding programs for new alkaline-tolerance rice varieties. [ABSTRACT FROM AUTHOR]

A full structural equation model (SEM) typically consists of both a measurement model (describing relationships between latent variables and observed scale items) and a structural model (describing relationships among latent variables). However, often researchers are primarily interested in testing hypotheses related to the structural model while treating the measurement model as a necessary but not primary focus of the overall model. In this case, researchers often wish to isolate and just evaluate the fit of the structural model. In our research, we examine a two-stage approach that can compute the chi-square statistic and fit indices for evaluating only the fit of the structural model in a full SEM. We call these the structural chi-square statistic and structural fit indices. For structural fit indices, we focused on the root mean square error of approximation (RMSEA), comparative fit index (CFI), and standardized root mean square residual (SRMR). We developed several new versions of the structural chi-square statistic, structural fit indices, and confidence intervals (CIs) of the structural fit indices. Through a simulation study, we demonstrated that several versions of our newly developed structural chi-square statistic yielded the nominal Type-I error rate; and the same versions of the structural fit indices exhibited low bias and their corresponding CIs had high coverage rates. Therefore, we recommend researchers use these versions of the structural chi-square test of fit alongside the structural fit indices when evaluating the fit of the structural model. [ABSTRACT FROM AUTHOR]

Zhang and Savalei proposed an alternative scale format to the Likert format, called the Expanded format. In this format, response options are presented in complete sentences, which can reduce acquiescence bias and method effects. The goal of the current study was to compare the psychometric properties of the Rosenberg Self-Esteem Scale (RSES) in the Expanded format and in two other alternative formats, relative to several versions of the traditional Likert format. We conducted two studies to compare the psychometric properties of the RSES across the different formats. We found that compared with the Likert format, the alternative formats tend to have a unidimensional factor structure, less response inconsistency, and comparable validity. In addition, we found that the Expanded format resulted in the best factor structure among the three alternative formats. Researchers should consider the Expanded format, especially when creating short psychological scales such as the RSES. [ABSTRACT FROM AUTHOR]

Normal theory full-information maximum likelihood (FIML) is a common estimation technique for incomplete data in structural equation modeling (SEM). However, it is not commonly known that approximate fit indices (AFIs) can be distorted, relative to their complete data counterparts, when FIML is used to handle missing data. In this article, we show that two most popular AFIs, the root-mean-square error of approximation (RMSEA) and the comparative fit index (CFI) often approach different population values under FIML estimation when missing data are present. By deriving the FIML fit function for incomplete data and showing that it is different from the usual maximum likelihood (ML) fit function for complete data, we provide a mathematical explanation for this phenomenon. We also present several analytic examples as well as the results of two large sample simulation studies to illustrate how AFIs change with missing data. [ABSTRACT FROM AUTHOR]

Presents the calculation of the contribution of intraionic electric-dipole transitions between the 3d[sup8] and 3d[sup7] 4p configurations of nickel ions doped in barium ferrites to the Faraday effect. Theory and calculation; Calculation of Zeeman splitting of crystal electric field-split levels; Values of diagonal matrix elements.

Reverse worded (RW) items are often used to reduce or eliminate acquiescence bias, but there is a rising concern about their harmful effects on the covariance structure of the scale. Therefore, results obtained via traditional covariance analyses may be distorted. This study examined the effect of the RW items on the factor structure of the abbreviated 18-item Need for Cognition (NFC) scale using confirmatory factor analysis. We modified the scale to create three revised versions, varying from no RW items to all RW items. We also manipulated the type of the RW items (polar opposite vs. negated). To each of the four scales, we fit four previously developed models. The four models included a 1-factor model, a 2-factor model distinguishing between positively worded (PW) items and RW items, and two 2-factor models, each with one substantive factor and one method factor. Results showed that the number and type of the RW items affected the factor structure of the NFC scale. Consistent with previous research findings, for the original NFC scale, which contains both PW and RW items, the 1-factor model did not have good fit. In contrast, for the revised scales that had no RW items or all RW items, the 1-factor model had reasonably good fit. In addition, for the scale with polar opposite and negated RW items, the factor model with a method factor among the polar opposite items had considerably better fit than the 1-factor model. [ABSTRACT FROM AUTHOR]

Many psychological scales written in the Likert format include reverse worded (RW) items in order to control acquiescence bias. However, studies have shown that RW items often contaminate the factor structure of the scale by creating one or more method factors. The present study examines an alternative scale format, called the Expanded format, which replaces each response option in the Likert scale with a full sentence. We hypothesized that this format would result in a cleaner factor structure as compared with the Likert format. We tested this hypothesis on three popular psychological scales: the Rosenberg Self-Esteem scale, the Conscientiousness subscale of the Big Five Inventory, and the Beck Depression Inventory II. Scales in both formats showed comparable reliabilities. However, scales in the Expanded format had better (i.e., lower and more theoretically defensible) dimensionalities than scales in the Likert format, as assessed by both exploratory factor analyses and confirmatory factor analyses. We encourage further study and wider use of the Expanded format, particularly when a scale’s dimensionality is of theoretical interest. [ABSTRACT FROM AUTHOR]

Bootstrapping approximate fit indexes in structural equation modeling (SEM) is of great importance because most fit indexes do not have tractable analytic distributions. Model-based bootstrap, which has been proposed to obtain the distribution of the model chi-square statistic under the null hypothesis (Bollen & Stine, 1992), is not theoretically appropriate for obtaining confidence intervals (CIs) for fit indexes because it assumes the null is exactly true. On the other hand, naive bootstrap is not expected to work well for those fit indexes that are based on the chi-square statistic, such as the root mean square error of approximation (RMSEA) and the comparative fit index (CFI), because sample noncentrality is a biased estimate of the population noncentrality. In this article we argue that a recently proposed bootstrap approach due to Yuan, Hayashi, and Yanagihara (YHY; 2007) is ideal for bootstrapping fit indexes that are based on the chi-square. This method transforms the data so that the “parent” population has the population noncentrality parameter equal to the estimated noncentrality in the original sample. We conducted a simulation study to evaluate the performance of the YHY bootstrap and the naive bootstrap for 4 indexes: RMSEA, CFI, goodness-of-fit index (GFI), and standardized root mean square residual (SRMR). We found that for RMSEA and CFI, the CIs under the YHY bootstrap had relatively good coverage rates for all conditions, whereas the CIs under the naive bootstrap had very low coverage rates when the fitted model had large degrees of freedom. However, for GFI and SRMR, the CIs under both bootstrap methods had poor coverage rates in most conditions. [ABSTRACT FROM AUTHOR]

The chlorophyll content is one of the most important traits selected by breeders, and it is controlled by quantitative trait loci (QTLs) derived from natural variations in rice. We analyzed the QTL controlling chlorophyll content by using 94 RILs derived from a cross between 2 japonica rice cultivars, Lijiangxintuanheigu (LTH) and Shennong265 (SN265). Twenty-two QTLs controlling chlorophyll content at tillering stage, heading stage, and maturity stage were detected, respectively. Among them, Rice cv. LTH had a positive allele only at 1 locus (qCTH4) on chromosome 4. Further analysis indicated that the genetic effect of qCTH4 was the net effects within the period from tillering to heading. The QTL qCTH4 controlling chlorophyll content from tillering to heading locates between RM255 and RM349 on chromosome 4 with a LOD score 19.41, and the QTL qCTH4 explains 61.42% of phenotypic variation. In order to eliminate the influence of other QTLs, 1 single residual heterozygous plant, RH-qCTH4, was selected based on the genotypes of 114 Simple Sequence Repeat (SSR) markers. Using the segregating population derived from RH-qCTH4 by self-crossing, this region was narrowed down to an interval between RM3276 and RM17494 in an approximately 771kb target region. These results are useful for map-based cloning of qCTH4 and for marker-assisted selection of high photosynthetic efficiency variety. [ABSTRACT FROM PUBLISHER]

Abstract: A theoretical investigation on the anisotropic magnetic property and Faraday rotation in Er3Ga5O12 (ErGaG) is presented. With particular consideration of the anisotropy of the exchange interaction between rare-earth ions (Er3+), the magnetization, based on the quantum theory, in ErGaG under high magnetic field (HMF) is calculated. Theoretical calculations show that the appropriate choice of the crystal field (CF) parameters is of great importance. A novel three-level model is presented, and in terms of this model the Faraday rotation under HMF is calculated. In addition, it is demonstrated that the Faraday rotation () depends not only on the magnetization (M) but also on the magnetic field (He ). The theory is in good agreement with the experiment. [Copyright &y& Elsevier]

Tillage practices are of critical importance in maintaining soil quality on cropland and for food production, with rice cultivation representing a significant portion of the world's food production and greenhouse gas (GHG) emissions. While numerous studies have examined the effects of reduced and no-tillage on soil GHG emissions and rice yields, the impact of adopting a rotational approach to tillage practices on the rice cultivation cycle remains uncertain. In this study, we conducted a four-year (2017–2020) field experiment in a single rice-growing area in Northeast China with the aim of investigating the effects of different tillage practices on GHG emissions from paddy fields and rice yields under full straw return conditions. We set up three experimental treatments: rotary tillage, plowing, and rotational tillage (i.e., a combination of one year of plowing and one year of rotary tillage). The results showed that averaged across all treatments, average methane (CH4, 302.6 ± 51.1 kg ha−1) and nitrous oxide (N2O, 0.86 ± 0.361 kg ha−1) emissions and rice yield (9.0 ± 0.9 t ha−1) did not exhibit significant inter-annual variability during the entire experimental period and were comparable to the average for the region. The ranking of GHG emissions during the rice-growing season was as follows: rotary tillage > plowing > rotational tillage. Across the experimental period, CH4 and N2O emissions were 9.1% and 8.5% lower in the plowing treatment and 21.2% and 13.1% lower in the rotational tillage treatment compared to the rotary tillage treatment. During the experimental period, there was no significant effect of tillage treatments on rice yield. This reduction in emissions may be attributed to changes in soil penetration resistance. In the rotational and plowing treatments, soil penetration resistance was in a range more adapted to rice growth and GHG emissions reduction compared to the rotary tillage treatment. The yield-scale GHG emission intensity was reduced by 12.7% and 26.1% in the plowing and rotational tillage treatments, respectively, in comparison to the rotary tillage treatment. This suggests that rotational tillage is a management practice that can achieve greenhouse gas emission reductions in paddy fields and stabilize or possibly increase rice yields. Consequently, the results demonstrated that a rotational alternation of multiple tillage practices is a synergistic strategy for achieving low carbon and high yield in rice in the cold rice-growing region of Northeast China. [ABSTRACT FROM AUTHOR]

The article focuses on the handling of missing data and it's effect on full-information maximum likelihood estimation (FIML) values in structural equation modeling.

Chloroplasts are essential sites for plant photosynthesis, and the biogenesis of the photosynthetic complexes involves the interaction of nuclear genes and chloroplast genes. In this study, we identified a rice pale green leaf mutant, crs2. The crs2 mutant showed different degrees of low chlorophyll phenotypes at different growth stages, especially at the seedling stage. Fine mapping and DNA sequencing of crs2 revealed a single nucleotide substitution (G4120A) in the eighth exons of CRS2, causing a G-to-R mutation of the 229th amino acid of CRS2 (G229R). The results of complementation experiments confirmed that this single-base mutation in crs2 is responsible for the phenotype of the crs2 mutant. CRS2 encodes a chloroplast RNA splicing 2 protein localized in the chloroplast. Western blot results revealed an abnormality in the abundance of the photosynthesis-related protein in crs2. However, the mutation of CRS2 leads to the enhancement of antioxidant enzyme activity, which could reduce ROS levels. Meanwhile, with the release of Rubisco activity, the photosynthetic performance of crs2 was improved. In summary, the G229R mutation in CRS2 causes chloroplast protein abnormalities and affects photosystem performance in rice; the above findings facilitate the elucidation of the physiological mechanism of chloroplast proteins affecting photosynthesis. [ABSTRACT FROM AUTHOR]

Rice breeders are now developing new varieties with semi-high or even high plant height to further increase the grain yield, and the problem of lodging has re-appeared. We identified a major quantitative trait locus (QTL), qSCM4, for resistance to lodging by using an F2 segregant population and a recombinant self-incompatible line population from the cross between Shennong265 (SN265) and Lijiangxintuanheigu (LTH) after multiple years and multiple environments. Then, the residual heterozygous derived segregant population which consisted of 1781 individual plants, and the BC3F2 segregant population which consisted of 3216 individual plants, were used to shorten the physical interval of qSCM4 to 58.5 kb including 11 genes. DNA sequencing revealed the most likely candidate gene for qSCM4 was Os04g0615000, which encoded a functional protein with structural domains of serine and cysteine. There were 13 DNA sequence changes in LTH compared to SN265 in this gene, including a fragment deletion, two base changes in the 3′ UTR region, six base changes in the exons, and four base changes in the introns. A near-isogenic line carrying qSCM4 showed that it improved the lodging resistance through increasing stem thickness by 25.3% and increasing stem folding resistance by 20.3%. Furthermore, it was also discovered that qSCM4 enhanced the primary branch per panicle by 16.7%, secondary branch by per panicle 9.9%, and grain number per panicle by 14.7%. All the above results will give us a valuable genetic resource for concurrently boosting culm strength and lodging resistance, and they will also provide a basis for further research on the lodging resistance mechanism of rice. [ABSTRACT FROM AUTHOR]

Climate change has increased the trend in the intensity of global extreme weather events, including chilling. Nitrogen is one of the most essential nutrients for rice growth and development. Chilling will limit the uptake and translocation of nitrogen and the formation of grain protein in rice plants. The experiment conducted in the climate chamber with chilling stress applied at the grain filling stage revealed different effects on protein concentration in aboveground organs and caused asymmetry in grain protein contents (GPC) and grain protein yield (GPY). Chilling stress applied during the grain filling stage reduced the accumulation rate of rice grain protein by inhibiting the nitrogen uptake and the translocation from vegetative organs to grains, which resulted in a 35 % decrease in grain nitrogen accumulation and a 92 % increase in vegetative organs during grain filling. Consequently, the average nitrogen harvest index is reduced by 12 %. Nitrogen accumulation was severely affected when cooling degree days (CDD) ≥ 70 °C days. As the chilling intensity increased, the decrease of GPY was more significant than that of GPC. Moreover, we improved the grain temperature-nitrogen uptake function under chilling stress based on the relationship between CDD and the reduction in rice grains. By comparing the improved function and the modules in the existing crop model using the datasets from open field and artificial control experiments, we demonstrated that the current research on quantifying rice nitrogen uptake at extreme temperature stress needed further improvement. The effects of environmental stress on grain nitrogen accumulation are complex. Future studies should pay more attention to the ability of extreme temperature stress to affect nitrogen accumulation in various rice organs. • Chilling during grain filling extends the duration, reduces nitrogen uptake, and retains more protein in rice organs. • Mild chilling during grain filling increase GPC but reduce GPY. Prolonged chilling decrease both GPC and GPY, with a greater reduction in GPY. • Multi-year data was used to compare crop models under chilling stress, developing a function to quantify CDD's effect on grain nitrogen uptake. [ABSTRACT FROM AUTHOR]

The hereditary basis and identification of novel genes of heading date have significant implications for japonica rice improvement in northeast China, especially in Heilongjiang province. A re‐sequenced recombinant inbred line (RIL) population derived from the cross between Lijiangxintuanheigu (LTH) and Shennong 265 (SN265) was used to detect the genetic basis for the RIL in 2017 and 2018. Fourteen heading date quantitative trait loci (QTLs), including nine in 2017 and thirteen in 2018, were detected with a linkage map containing 2,818 bin markers. They were distributed on chromosomes 3, 4, 6 and 9–11 with 9.34%–25.26% phenotypic variations. The QTLs qHD3a, qHD4a, qHD4b, qHD4c, qHD9b, qHD10, qHD11c and qHD11d were identified in both years. The qTRS1, qTRS3a (qHD3a), qTRS3b (qHD3b) and qTRS9 (qHD9a) alleles from LTH and the qTRS4 allele from SN265 were identified by controlling the temperature responsiveness in the RIL population. The explained phenotypic variation in these five QTLs varied from 14.52% to 26.31%. In order to accurately determine the difference in heading date under different temperature conditions, the RILs and two parents were grown in a phytotron. Four QTLs controlling temperature responsiveness were identified on chromosomes 3, 6 and 9, including qTRS3a (qHD3a), qTRS3b (qHD3b), qTRS6 and qTRS9 (qHD9a). In a different environment, qTRS3a (qHD3a), qTRS3b (qHD3b) and qTRS9 (qHD9a) were detected. A comparison of chromosomal locations between the QTLs detected in this study and heading date genes previously cloned indicated that DTH3, Hd16, RFL, HAF1, Ehd2 and RBS1 might be candidate genes for them. The four major heading date genes (Hd1, Ghd7, Ghd7.1 and Ghd8) affecting ecogeographical adaptation were sequenced between SN265 and LTH. SN265 carried a functional Hd1 haplotype, a weak functional Ghd7 haplotype, a weak functional Ghd7.1 haplotype and a weak functional Ghd8 haplotype. LTH also carried functional Hd1 haplotype, a weak functional Ghd7 haplotype, a non‐functional Ghd7.1 haplotype and a non‐functional Ghd8 haplotype. The combinations of the Hd1, Ghd7, Ghd7.1 and Ghd8 alleles in SN265 and LTH largely defined their short heading date under long‐day conditions. The selection of heading date gene combinations with functional Hd1 alleles and non‐functional alleles or weak functional alleles of Ghd7, Ghd7.1 and Ghd8 would be an effective way to improve japonica rice with proper heading days in Northeast China. The novel QTLs detected in this study could also become a valuable source for designing the appropriate heading date in Northeast China japonica rice. [ABSTRACT FROM AUTHOR]

Water regime and nitrogen (N) fertilizer are two important factors impacting greenhouse gases (GHG) emission from paddy field, whereas their effects have not been well studied in cold region. In this study, we conducted a two-year field experiment to study the impacts of water regime and N fertilizer on rice yields and GHG emissions in Harbin, China, a cold region located in high latitudes. Our results showed that intermittent irrigation significantly decreased methane (CH 4 ) emission compared with continuous flooding, however, the decrement was far lower than the global average level. The N 2 O emissions were very small when flooded but peaked at the beginning of the disappearance of floodwater. The N fertilizer treatments increased CH 4 emissions at low level (75 kg N/ha). But both CH 4 and N 2 O emissions were uninfluenced at the levels of 150 kg N/ha and 225 kg N/ha. Rice yields increased under intermittent irrigation and were highest at the level of 150 kg N/ha. From our results, we recommended that the intermittent irrigation and 150 kg N/ha as the ideal water regime-nitrogen fertilizer incorporation for this area to achieve low GHG emissions without impacting rice yields. [ABSTRACT FROM AUTHOR]

Japonica rice mainly distributes in north of China, which accounts for more than half of the total japonica rice cultivated area of China. High yield, good grain quality and early heading date were the main breeding traits and commercial property in this region. We performed re-sequencing and genome wide variation analysis of one typical northern japonica rice variety Longdao24 and its parents (Longdao5 and Jigeng83) using the Illumina sequencing technology. 53.17 G clean bases were generated and more than 96.8% of the reads were mapped to the genomic reference sequence. An overall average effective depth of 43.67 × coverage was achieved. We identified 420,475 SNPs, 95,624 InDels, and 14,112 SVs in Longdao24 genome with the genomic sequence of the japonica cultivar Nipponbare as reference. We identified 361,117 SNPs and 81,488 InDels between Longdao24 genome and Longdao5 genome. We also detected 428,908 SNPs and 97,209 InDels between Longdao24 genome and Jigeng83 genome. Twenty-two yield related genes, twenty-two grain quality related genes and thirty-nine heading date genes were analyzed in Longdao24. The alleles of Gn1a, EP3, SCM2, Wx, ALK, OsLF and Hd17 came from the female parent Longdao5. The other alleles of qGW8, SSIVa, SBE3, SSIIIb, SSIIc, DTH2, Ehd3 and OsMADS56 came from the male parent Jigeng83. These results will help us to research the genetics basis of yield, grain quality and early heading date in northern rice of China. [ABSTRACT FROM AUTHOR]

Grain numbers is one of the determinations for rice yield and directly associated with spikelet numbers per panicle and its normal development. Lots of genes responsible for spikelet numbers and spikelet early development have been identified, but the molecular information about the spikelet development at later development is still limited. Here, we isolated a rice spikelet abnormal development mutant, which shows degenerated spikelet at the top panicle and named aborted top spikelet mutant 1( Ats1). The spikelets derived from the middle and bottom branches per panicle of Ats1 show normal development with those of wild type. However, a large number of branches and spikelets with arrested development were often observed only on apex panicle. The abnormality did not appear until the stage In8 when rachises elongate rapidly and reproductive organs get mature, based on observations through SEM analysis. The aborted spikelet could develop the complete floral organs with a pair of rudimentary glume, a pair of empty glume, two lodicule, six stamens and one carpel. But all these floral organs did not develop maturity. Genetic analysis on two F2 populations indicated that the Ats1 was controlled by a single dominant gene. By using bulked segregant analysis of F2 population developed from Ats1 crossing with Songjing6, ATS1 was mapped on chromosome 8 between RM3819 and RM5556. Then, the fine mapping was performed with 1078 F2 population developed from Ats1 and IR36. The ATS1 locus was finely mapped in an 85.7 kb region between RM22448 and STS8-2 with 8 genes according to the rice annotation project database. Sequence analysis of the candidate genes within the delimited region of the Ats1 and Akihikari showed two-nucleotide changes, including single-nucleotide substitutions corresponding to an amino acid substitution from asparagine to lysine acid in exons 3 and a 1-bp deletion resulting in a premature stop codon in exon 22 at the candidate gene, LOC_Os08g06480. A cleaved amplified polymorphic sequence ( CAPS) marker, CAPS-ats1, was developed from the 1-bp deletion site. The complete cosegregation of the CAPS genotypes with the matching phenotypes were observed in the F2 populations. This suggested that Os08g06480 is most likely the ATS1 gene. These results will provide more information for better understanding of the molecular mechanism governing top spikelet abortion within a short developmental period. [ABSTRACT FROM AUTHOR]

Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned DEP1 gene. Among the LTG QTLs, qLTG3 and qLTG7b were also located at relatively small genetic intervals that define two known LTG genes, qLTG3-1 and OsSAP16. Sequencing comparisons between the two parents demonstrated that LTH possesses qLTG3-1 and OsSAP16 genes, and SN-265 owns the DEP1 gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for qLTG6 at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, LOC_Os06g01320 was identified as the most possible candidate gene for qLTG6, which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties. [ABSTRACT FROM AUTHOR]