Relative Germination Index Research Articles

Sweet corn association panel and genome-wide association analysis reveal loci for chilling-tolerant germination

Sweet corn is highly susceptible to the deleterious effects of low temperatures during the initial stages of growth and development. Employing a 56K chip, high-throughput single-nucleotide polymorphism (SNP) sequencing was conducted on 100 sweet corn inbred lines. Subsequently, six germination indicators—germination rate, germination index, germination time, relative germination rate, relative germination index, and relative germination time—were utilized for genome-wide association analysis. Candidate genes were identified via comparative analysis of homologous genes in Arabidopsis and rice, and their functions were validated using quantitative real-time polymerase chain reaction (qRT-PCR). The results revealed 35,430 high-quality SNPs, 16 of which were significantly correlated. Within 50 kb upstream and downstream of the identified SNPs, 46 associated genes were identified, of which six were confirmed as candidate genes. Their expression patterns indicated that Zm11ΒHSDL5 and Zm2OGO likely play negative and positive regulatory roles, respectively, in the low-temperature germination of sweet corn. Thus, we determined that these two genes are responsible for regulating the low-temperature germination of sweet corn. This study contributes valuable theoretical support for improving sweet corn breeding and may aid in the creation of specific germplasm resources geared toward enhancing low-temperature tolerance in sweet corn.

GWAS reveals novel loci and identifies a pentatricopeptide repeat-containing protein (CsPPR) that improves low temperature germination in cucumber.

Low temperatures (LTs) negatively affect the percentage and rate of cucumber (Cucumis sativus L.) seed germination, which has deleterious effects on yield. Here, a genome-wide association study (GWAS) was used to identify the genetic loci underlying low temperature germination (LTG) in 151 cucumber accessions that represented seven diverse ecotypes. Over two years, phenotypic data for LTG i.e., relative germination rate (RGR), relative germination energy (RGE), relative germination index (RGI) and relative radical length (RRL), were collected in two environments, and 17 of the 151 accessions were found to be highly cold tolerant using cluster analysis. A total of 1,522,847 significantly associated single-nucleotide polymorphism (SNP) were identified, and seven loci associated with LTG, on four chromosomes, were detected: gLTG1.1, gLTG1.2, gLTG1.3, gLTG4.1, gLTG5.1, gLTG5.2, and gLTG6.1 after resequencing of the accessions. Of the seven loci, three, i.e., gLTG1.2, gLTG4.1, and gLTG5.2, showed strong signals that were consistent over two years using the four germination indices, and are thus strong and stable for LTG. Eight candidate genes associated with abiotic stress were identified, and three of them were potentially causal to LTG: CsaV3_1G044080 (a pentatricopeptide repeat-containing protein) for gLTG1.2, CsaV3_4G013480 (a RING-type E3 ubiquitin transferase) for gLTG4.1, and CsaV3_5G029350 (a serine/threonine-protein kinase) for gLTG5.2. The function for CsPPR (CsaV3_1G044080) in regulating LTG was confirmed, as Arabidopsis lines ectopically expressing CsPPR showed higher germination and survival rates at 4°C compared to the wild-type, which preliminarily illustrates that CsPPR positively regulates cucumber cold tolerance at the germination stage. This study will provide insights into cucumber LT-tolerance mechanisms and further promote cucumber breeding development.

Genome‐wide association analysis of chilling‐tolerant germination in a new maize association mapping panel

AbstractMaize is a crop that is highly susceptible to the negative effects of low temperature. Low temperature can delay seed germination and cause a decrease in seed vigor, which seriously affects seedling emergence and yield. In this study, 190 maize accessions (inbred lines) with strong germination potential at normal temperature (25°C) were selected from more than 500 accessions to construct a new association mapping panel to further investigate germination under chilling stress (5°C). We re‐sequenced the genomes of the 190 diverse accessions and obtained 4,886,919 high‐quality SNPs. We then used this data to analyze population structure, perform principal components analysis, and construct a phylogenetic tree of the new maize panel. The relative germination rate (RGR) and relative germination index (RGI) are two traits that are significantly related to chilling‐tolerant germination. Genome‐wide association analysis showed that RGR and RGI shared a major QTL, and they also shared the top SNP. There were a total of 26 significant SNPs in common. These SNPs hit directly or indirectly within 37 candidate genes. Among these 37 gene candidates, eight are homologs of genes previously reported to be related to both germination and low‐temperature stress, and another 12 genes related to low‐temperature stress or other abiotic stresses such as drought, salinity, oxidative, and high light stress. In addition, RGR and RGI had another 15 and 26 significant SNPs, respectively, which were associated with 17 and 92 candidate genes, respectively. Further qRT‐PCR analysis using 26 chilling‐tolerant and 22 chilling‐sensitive accessions implied that Zm00001eb272370, Zm00001eb272390, and Zm00001eb272400 associated with the top SNP, may play different roles during cold‐germination. Thus, our study not only established a new association mapping panel suitable for investigation of germination at low temperature but also provided valuable genetic resources for future studies to improve chilling‐tolerant maize varieties.

Identification of Candidate Genes for Salt Tolerance at the Germination Stage in Japonica Rice by Genome-Wide Association Analysis

Rice salt tolerance at the germination stage directly affects the germination rate and seedling establishment of rice directly seeded in saline soils, which in turn affects yield. In this study, we determined the relative germination potential (RGP) and relative germination index (RGI) under 200 mM salt stress and control conditions using 295 japonica rice accessions. Statistical analysis showed extensive phenotypic variations under salt stress conditions. Twenty-one varieties with an RGP ≥ 80% and an RGI ≥ 80% were screened. Based on genotypic data including, 788,396 single-nucleotide polymorphisms (SNPs), 40 quantitative trait loci (QTL) were localized on rice chromosomes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, and 12, which were shown to be significantly associated with rice salt tolerance at the germination stage, including 20 for RGP and 20 for RGI, using genome-wide association analysis. Six QTL with ≥ 3 consecutive significant SNP loci and localized in the same LD interval were selected for further analysis. Four rice genes (LOC_Os01g04920, LOC_Os10g38350, LOC_Os10g38470, and LOC_Os10g38489) were selected as important candidates for salt tolerance based on haplotype analysis and functional annotation. The findings could facilitate the development of valuable rice varieties for direct seeding in salinized soil and improve japonica rice salt tolerance at the germination stage through molecular breeding.

Genome-Wide Association Study Reveals a Genetic Mechanism of Salt Tolerance Germinability in Rice (Oryza sativa L.).

Salt stress is one of the factors that limits rice production, and an important task for researchers is to cultivate rice with strong salt tolerance. In this study, 211 rice accessions were used to determine salt tolerance germinability (STG) indices and conduct a genome-wide association study (GWAS) using 36,727 SNPs. The relative germination energy (RGE), relative germination index (RGI), relative vigor index (RVI), relative mean germination time (RMGT), relative shoot length (RSL), and relative root length (RRL) were used to determine the STG indices in rice. A total of 43 QTLs, including 15 for the RGE, 6 for the RGI, 7 for the RVI, 3 for the RMGT, 1 for the RSL, and 11 for the RRL, were identified on nine chromosome regions under 60 and 100 mM NaCl conditions. For these STG-related QTLs, 18 QTLs were co-localized with previous studies, and some characterized salt-tolerance genes, such as OsCOIN, OsHsp17.0, and OsDREB2A, are located in these QTL candidates. Among the 25 novel QTLs, qRGE60-1-2 co-localized with qRGI60-1-1 on chromosome 1, and qRGE60-3-1 and qRVI60-3-1 co-localized on chromosome 3. According to the RNA-seq database, 16 genes, including nine for qRGE60-1-2 (qRGI60-1-1) and seven for qRGE60-3-1 (qRVI60-3-1), were found to show significant differences in their expression levels between the control and salt treatments. Furthermore, the expression patterns of these differentially expressed genes were analyzed, and nine genes (five for qRGE60-1-2 and four for qRGE60-3-1) were highly expressed in embryos at the germination stage. Haplotype analysis of these nine genes showed that the rice varieties with elite haplotypes in the LOC_Os03g13560, LOC_Os03g13840, and LOC_Os03g14180 genes had high STG. GWAS validated the known genes underlying salt tolerance and identified novel loci that could enrich the current gene pool related to salt tolerance. The resources with high STG and significant loci identified in this study are potentially useful in breeding for salt tolerance.

Efficacy of Trichoderma harzianum against Fusarium oxysporum and Rhizoctonia solani on bean and tomato plants

Experiments were conducted in the laboratory, greenhouse, and field at the Papua New Guinea University of Technology (PNGUT) to assess the efficacy of Trichoderma harzianum against Rhizoctonia solani and Fusarium oxysporum. The dual culture of T. harzianum with R. solani and F. oxysporum isolated from the diseased bean and tomato plants under laboratory conditions showed 60.1% and 63.3%, and 54.9% and 61.6% growth reduction for R. solani and F. oxysporum, respectively. In greenhouse fungal inoculation experiments, bean and tomato plants showed relative germination index ranging from 0.56 to 1, 0.83 to 1, and disease reduction ranging from 64.8 to 96.1, and 20.3 to 83.7%, respectively. Field experiments involved tests with T. harzianum against one pathogenic fungus or against a combination of both R. solani and F. oxysporum, applied simultaneously as the pathogenic fungi or five days before application of pathogenic fungi. The results for bean and tomato plants showed relative germination index ranging from 0.42 to 0.94, and 0.63 to 0.94, and disease reduction recorded at 63.8 to 96.1%, and 11.3 to 63.9%, respectively. The outcomes of this study will form the basis for further investigation into the potential routine use of Trichoderma spp. as biological control agents against soil-borne pathogens in PNG.

Effects of Some Heavy Metals on Germination and Seedling Growth of Sorghum

Heavy metal contamination in soils can adversely affect seed germination and seedling growth of most plants. This research was conducted to determine the effects of different doses (0, 100, 200, 400 and 800 mg L-1) of Ni (nickel), Cd (cadmium), Pb (lead), Cr (chromium) and Hg (mercury) on seed germination and seedling growth of sorghum. The study was conducted in laboratory conditions at the Agricultural Faculty of Akdeniz University in 2017. Sorghum cv. N48×Early Sumac was used as the plant material. In the research, germination rate (GR), relative germination index (RGI), mean germination time (MGT), relative vigor index (RVI), relative root length (RRL), relative shoot length (RSL), root fresh weight (RFW) and shoot fresh weight (SFW) were measured during germination and seedling growth to determine the effects of heavy metals. The results showed that both germination and seedling growth properties were adversely affected by heavy metals. In addition, while the negative effect of cadmium on germination properties was limited, it had serious negative effects on seedling characteristics of sorghum. Increasing heavy metal doses adversely affected all investigated properties. In conclusion, all heavy metals including Hg and Cd had negative effect on germination and seedling growth of sorghum in the study.

Evaluation of pre-harvest sprouting resistance of wheat varieties from different ecological regions

The pre-harvest sprouting (PHS) resistance of 137 wheat varieties from different regions was evaluated and the relative germination index (RGI) was calculated. The relationships between PHS and grain quality traits, amylase activity and related gene expression level of these varieties were analyzed. The results showed that wheat varieties from the middle and lower reaches of Yangtze River Valley winter wheat region had the lowest RGI value and the highest ratio of resistant pre-harvest sprouting wheat varieties, followed by the varieties from the upper reach of Yangtze River Valley winter wheat region and from the Yellow and Huai River Valley. Red-grain wheat had lower RGI than white-grain wheat. RGI was positively correlated with seed length, seed width, and spikelet number, but not correlated with other grain traits (panicle type, ear color, ear length, and spikelet density, grain per spike and 1000-grain weight). RGI was negatively associated with the test weight, dough development time, and flour yield, but not with other quality indices (protein content, wet gluten content, water absorption, stability time, sedimentation, extension area, extensibility and max resistance). Amylase activity of different varieties increased with seed imbibition time. RGI was positively associated with α-amylase activity after germinating for 24-72 hours. The cluster analysis results of resistant varieties were consistent with the PHS resistance evaluation after 48 hours. RGI was positively associated with the related gene expression with seed imbibition time.

Screening of Chilli ( Capsicum annum L.) Genotypes for Drought Tolerant at Seedling Emergence Stage

Forty seven chilli (Capsicum annum L.) genotypes were evaluated for their genetic potential to drought tolerant at germination stage using 12.5% polyethylene (PEG, MW6000). Relative germination energy (RGE), relative germination rate (RGR), relative germination index (RGI), relative vitality index (RVI) and their relative PEG injury rate were computed to identify the most tolerant genotypes on germination stage. Significant differences were observed among the genotypes, treatments and their interactions for evaluated traits suggesting a great amount of variability for drought tolerant in chilli. Based on aggregated score of RGE, RGR, RGI and RVI parameters BD-10906, BD-10912, BD-10911, BD-10916 and BD-10913 were the top five genotypes, whereas BD-10902, RT-20, AM-29, BD-10893 and BD-10930 lowermost five genotypes in the rank of drought tolerant which is an indication of their tolerant and susceptible to drought stress. The lowest relative PEG injury rate was observed in tolerant genotypes, contrary the highest rate was recorded in susceptible genotypes. Dendrogram using Agglomerative Clustering Method grouped the 47 genotypes into four different clusters at the 0.668 co-phenetic correlation coefficient. Drought tolerant chilli genotypes grouped in cluster I, while the susceptible genotypes clustered together in group III and IV and a number of moderate tolerant genotypes gathered in cluster II. Consequently the maximum mean values of tested parameters viz. RGR (91.30), RGE (30.43), RGI (40.58) and RVI (54.10) were observed in clusters I. Positive and significant correlation values were observed between the tolerant indications parameters. RGI showed comparatively strong and positive correlation with all tested parameters. Thus, tolerant and susceptible genotypes will be progressed for further tolerant study in seedling stage.

Screening of Tomato Inbred-Lines for Drought Tolerance at Germination and Seedling Stage

This investigation was carried out to screen 45 tomatoes inbred-lines’ response to drought at germination and seedling stage. These inbred-lines which were collected from different countries were screened with osmotic concentration of 12.5% polyethylene glycol 6000 while their respective control treatments were treated using distilled water for twelve days at germination stage. Relative germination energy, relative germination rate, relative germination index, relative vitality index and the relative PEG injury rate were computed to identify the most tolerant inbred-lines on germination stage. Inbred-lines TTI1103B-2, A0911, Roma, L12, and TTD210B were found to be the most tolerant. While inbred-lines L9, TTI1109B-1-2-1, A4, B6 and A7 were the most sensitive to drought. Moreover, analysis of variance revealed significant differences among the inbred-lines studied. The experiment was repeated for confirmation and the result was similar. An additional study was conducted on 30 days old seedlings to observe their water stress response at their seedling stage. A total of 30 inbred-lines, 10 inbred-lines each from tolerant, moderate and sensitive; were selected based on the results found at germination stage. After proper watering for 30 days, watering was stopped for the following 10 days. After that, the dead and alive was counted. The seedlings were then re-watered for the following one week and those recovered from dead were counted again. Finally, the dead percentage and recovery percentage was computed as an indicator of water stress tolerance. And the result was very similar to the experiment done on germination stage.

Low-temperature tolerance of pepper at germination stage and its evaluation method

以108个辣椒品种为试材, 测定了低温(18 ℃)下种子的相对发芽势、相对发芽率、相对胚根长、相对发芽指数和相对活力指数, 并采用极点排序法对辣椒不同品种的耐低温性进行综合评价。结果表明: 辣椒 不同品种种子萌芽期的耐低温性不同, 相对发芽率、相对发芽指数、相对胚根长和相对活力指数4项指标在不同品种间差异达显著水平(<i>P</i><0.05)。选用上述4个指标, 采用极点排序法计算得到各品种的综合评价得分, 根据综合评价得分将108个辣椒品种分为10个耐低温品种, 9个低温敏感品种, 其余为中度耐低温品种。辣椒种子相对发芽势、相对胚根长与综合评价得分的相关性达到显著水平; 相对发芽率、相对发芽指数、相对活力指数与综合评价得分的相关性达极显著水平, 且相对活力指数与综合评价得分的相关性最高(<i>r</i>=0.899 9)。通过测定低温下辣椒品种萌芽期相关性状指标, 采用极点排序法可对辣椒种子萌芽期耐低温性进行快速、准确的评价。

Mapping of QTLs Underlying Tolerance to Alkali at Germination and Early Seedling Stages in Rice

A double haploid (DH) population including 120 lines derived from a cross between indica rice (Oryza sativa L.) TN1 and japonica rice CJ06 was used to detect quantitative trait loci (QTLs) for 10-trait relative values of alkali damage at germination period and early seedling stage under 0.15% Na2CO3 stress. Correlation analyses showed that alkali damage rate in germination period (ADG) had significant positive correlation with relative germination energy (RGE), relative germination rate (RGR) and relative germination index (RGI), and alkali damage rate at early seedling stage (ADS) had significantly correlation with relative seedling height (RSH), relative root length (RRL), relative root number (RRN) and relative seedling dry weight (RDW). ADG and ADS can be used as evaluation indexes of alkaline tolerance in rice. By using QTLNetwork 2.0 software, 14 additive QTLs and 13 epistatic QTLs controlling the tolerance to alkali were mapped. Two main effect QTLs were detected in same region, RM251–RM3280, on chromosome 3, and three main effect QTLs were mapped between RM3286 and RM1279 on chromosome 7. Epistasis analysis showed that some epistatic loci, like RM1–RM1195, RM1358–RM290, RM1279–RM505, and RM1246–RM519 on chromosome 1, 2, 7, and 12 respectively were important under alkali stress, included two or more epistatic QTLs, indicating that the QTLs displayed their effects through different ways of interaction. Among the key loci under alkali stress one may be pleiotropic or some closely linked each other. Comparing QTLs with those found in other researches, some alkali resistance QTLs were likely to be in the same region with some salt resistance QTLs. A presume was made that QTLs in this articlemight include two types, one for resistance to ions (K+ or Na+) stress and other for resisttance to high pH stress, the latter may play an important role for tolerance to alkali. Many rice varieties have different resistance QTLs for alkali stress; we can pyramid them through marker-assistant selection to breed varieties suitable to growth in saline-alkalized land.

Mapping of QTL Underlying Tolerance to Alkali at Germination and Early Seedling Stages in Rice

To detect quantitative trait loci (QTLs) associated with tolerance to alkali damage, 120 double haploid (DH) lines derived from the cross between TN1 ( Oryza sativa L. subsp. indica) and Chunjiang 06 ( O. sativa L. subsp. japonica) were used as mapping population. The seeds were treated with 0.15% Na 2CO 3 (alkali stress) and distilled water (control) and 10 traits were determined as indicators for alkali damage at germination and early seedling stages. The alkali damage rate in germination stage (ADG) positively correlated ( P < 0.05) with the relative germination energy (RGE), relative germination rate (RGR), and relative germination index (RGI); and the alkali damage rate at early seedling stage (ADS) had significantly correlation with relative seedling height (RSH), relative root length (RRL), relative root number (RRN), and relative seedling dry weight (RDW). ADG and ADS could be used as indicators for alkaline tolerance in rice. Using QTLNetwork2.0 software, 14 additive QTLs and 13 pairs of epistatic QTLs controlling the tolerance to alkali were mapped. Two main-effect QTLs were detected in the region of RM251– RM3280 on chromosome 3, and 3 main-effect QTLs were mapped between RM3286 and RM1279 on chromosome 7. Epistatic loci, such as RM1– RM1195, RM1358– RM290, RM1279– RM505, and RM1246– RM519 on chromosomes 1, 2, 7, and 12, respectively, were important under alkali stress. The key loci under alkali stress may be pleiotropic or closely linked to each other. Some alkali resistance QTLs were likely to be in the same regions with salt resistance QTLs reported earlier. The QTLs detected in this study might be 2 types corresponding to resistances to ions (K + or Na +) stress and high pH stress, respectively, and the latter probably plays an important role in the tolerance to alkali in rice.

Genetic analysis on aging-resistant in rice seed

Relative germination percentage, relative germination rate, and relative germination index were studied using P1, P2, and 350 lines of a RIL population from the japonica rice (Oryza sativa L. japonica) cross of Bing 8979/C Bao. By means of mixed major gene plus polygene inheritance models, genetic analysis showed that relative germination percentage, relative germination rate, and relative germination index were controlled by two major genes plus polygenes. Both major genes and polygenes showed additive-epistatic effects. The additive effects were larger than epistatic effects in the two major genes. The heritability of major genes was larger than that of polygenes in all the three traits, indicating that the three traits investigated in the present study were mainly governed by major genes.