Rice Lines Research Articles

Physiological and transcriptomic analysis of OsLHCB3 knockdown lines in rice.

The online version contains supplementary material available at 10.1007/s11032-023-01387-z.

Assessment of Multiple Tolerance Indices to Identify Rice Lines Suitable for the Aerobic System of Cultivation

Climate resilience is the most concentrated subject in the current scenario for rice improvement. The aerobic system of rice cultivation involving direct seeding with need-based irrigation in non-puddled soil is gaining ground with respect to a current scenario of water scarcity. The selection of lines suitable and stable under aerobic along with irrigated conditions without any yield penalty is one of the focus areas of the breeding programme for resource use efficiency. In the present study, we have screened a panel of 118 rice lines under aerobic i.e. limited water conditions and irrigated conditions at ARS Dhadesugur Karnataka to identify ideal selection indices viz. STI, TOL, SSI, YSI, YR, YI, PYR, MP and GMP for selecting the best high-yielding and stable lines under both rice cultivation methods. The deployment of selection indices here only pertains to finding the differences in yield per plant under aerobic and irrigated conditions. According to the results of multivariate analysis (correlation and PCA), STI, YI, MP and GMP exhibited a strong correlation with YP and YS. Therefore, they appear to be the most effective stress indices for the selection of lines with good yield potential under water-limited and irrigated conditions. These indices serve as valuable selection criteria for the identification of aerobic-tolerant cultivars from both water-limited and normal conditions. These indices identified lines, DB 5 (Swarna × Oryza nivara (IRGC 81848)) and NPK-40 (Swarna × Oryza nivara (IRGC81832)) wild introgression lines. GNV-14-96-1 (BPT-5204 × Nerica line) Advanced breeding line. JBB 631-1 ((Swarna*2/ IRGC 4105) (RP 5405-JBB-631-1-1-1-1-1-1)) Tropical japonica × indica introgression line. KR-209 (Wazuhophek × ISM) and KR-262 (Wazuhophek × ISM) recombinant introgression lines. TI-36 and TI-124 Ethyl Methane Sulfonate (EMS) mutants of BPT-5204. WB-10 (Langphou) and WB-16 (Phouoibi) North-Eastern Landraces were promising for both environments. These lines are suitable because of low grain yield loss under aerobic conditions and can be further considered for cultivation.

Creating high-resistant starch rice by simultaneous editing of SS3a and SS3b.

Creating high-resistant starch rice by simultaneous editing of SS3a and SS3b.

Panicle branching of nutritious rice based on good agricultural practices

Panicle branching is one of the characters that can distinguish one rice cultivar from another. Agricultural practices determined the performance of panicle branching. The trial aimed to study the differences among ten rice lines based on panicle branching characters cultivated based on good farming practices. Seven pure lines and three varieties were planted as genetic material in 4 replications. The trial was conducted in Bandung in 2020 at an altitude was 460 m asl. The characters observed were panicle length, main axis length, number of total grain per panicle, number of primary branches, number of secondary branches, primary branch length, secondary branch length, and number of secondary branches primary branch. All the panicle branching characters showed different among genetical material planted. The longest panicle was found in IR 105730-B-79-1-4-SKI-1-8, but the longest main axis length was found in Inpari IR Nutrizinc, local variety and IR 105730-B-79-1-4-SKI-1-8. The genotype of IR 105734-B-64-1-1-SKI-1-SG-11 showed had the most grains number (223.28), and the genotype of IR 105730-B-79-1-4-SKI-1-8 was not different with IR 105734-B-64-1-1-SKI-1-SG-11. In the other characters, the genotype of IR 105730-B-79-1-4-SKI-1-8 was relatively showed a good performance, especially in primary branch length, secondary branch length, and number of secondary branches primary branch.

Purification of local upland rice seeds based on morphological characteristics

This research is directed to overcome the problem of upland rice seeds that are no longer pure, because they have been mixed with other types of rice seeds, which can result in a decrease in the quality or nature of superior upland rice which is already favorable by the community. Seed purification is needed to restore the purity of the seeds of superior local upland rice lines. Another target of this research is to produce basic seeds of pure local upland rice lines (without mixture), which are needed for further breeding programs, or for the purpose of releasing varieties, as well as for production purposes for consumption. This study aims to select and detect the same/uniform morphological characteristics of local upland rice in each seed lot and to find out which seed lots show high uniformity. The experiment used a Randomized Block Design (RBD) consisting of 20 seed lots as treatment and each seed lot was made into a so-called “grid” (replication) of 3 grids. This research was conducted at the Field Laboratory, Experimental Garden II, Faculty of Agriculture, Halu Oleo University. Observational data were analyzed with variance and qualitative characters were converted to binary data and analyzed by the NTSYS program. If there is a significant effect, then proceed with the Scott Knott group test (α = 0.05). The results showed a very significant effect on the variables of flowering age, productive tillers and flag leaf angle, and no significant effect on the variables of plant height, number of leaves, number of tillers, harvest age, panicle length, flag leaf area, total grain per panicle and percentage of grain. per panicle.

Novel Salinity-Tolerant Third-Generation Hybrid Rice Developed via CRISPR/Cas9-Mediated Gene Editing.

Climate change has caused high salinity in many fields, particularly in the mud flats in coastal regions. The resulting salinity has become one of the most significant abiotic stresses affecting the world's rice crop productivity. Developing elite cultivars with novel salinity-tolerance traits is regarded as the most cost-effective and environmentally friendly approach for utilizing saline-alkali land. To develop a highly efficient green strategy and create novel rice germplasms for salt-tolerant rice breeding, this study aimed to improve rice salinity tolerance by combining targeted CRISPR/Cas9-mediated editing of the OsRR22 gene with heterosis utilization. The novel alleles of the genic male-sterility (GMS) and elite restorer line (733Srr22-T1447-1 and HZrr22-T1349-3) produced 110 and 1 bp deletions at the third exon of OsRR22 and conferred a high level of salinity tolerance. Homozygous transgene-free progeny were identified via segregation in the T2 generation, with osrr22 showing similar agronomic performance to wild-type (733S and HZ). Furthermore, these two osrr22 lines were used to develop a new promising third-generation hybrid rice line with novel salinity tolerance. Overall, the results demonstrate that combining CRISPR/Cas9 targeted gene editing with the "third-generation hybrid rice system" approach allows for the efficient development of novel hybrid rice varieties that exhibit a high level of salinity tolerance, thereby ensuring improved cultivar stability and enhanced rice productivity.

Pathogenicity and Genetic Variations in Magnaporthe oryzae Isolates from One Rice Variety Planting in Paddy and Upland Fields

Rice is the most important crop for worldwide consumers. The water utilization of rice planting is more than 50% of agricultural water in China, and it is necessary to breed water-saving and drought-resistant rice. The rice variety Dianheyou 615 can be planted in the paddy and upland fields, which satisfies rice production farmers in mountainous regions of Yunnan. We aimed to explore the variations in Magnaporthe oryzae isolates collected from Dianheyou 615 planted in paddy or upland fields. Through pathogenicity tests, we found that most isolates had the highest pathogenicities, but there were no significant differences between the paddy and upland isolates. By a combination of monogenetic and elite rice lines, with a further resistance assessment, the monogenetic lines with Pi9, Diantun 506, and Lvhan 1 displayed better resistances. Moreover, we re-sequenced 15 isolates to explore their genetic variations. Our results showed that the source of the upland isolates may have been the offspring of the paddy isolates, but there were many genes with specifically found SNPs in two populations that would develop subdivisions after long-time planting. Overall, we compared the pathogenicities and genetic variations in blast isolates from the planting of Dianheyou 615 in paddy and upland fields, which provided references for the influence of the planting environment on population subdivisions.

G×E analysis to Identify the Stable High-yielding Rice Lines among a Set of Selected Germplasm Panel

Rice lines need to be grown and evaluated for yield under different agro-ecological locations to identify stable and high-yielding lines for deployment in breeding programs. With this aim, a set of rice germplasm was evaluated for G×E in four different environments (E1-Dadesuguru-Wet 2020, E2-ICAR–IIRR-Dry 2019, E3-ICAR–IIRR-Wet 2020, E4-ICAR–IIRR-Dry 2020). The experimental trial was laid out in a randomized complete block (RCB) design with three replications at each location for 118 rice lines. Data on yield per plant was analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI) and Genotype, and Genotype × Environment Interaction (GGE) models. The combined analysis of variance (ANOVA) manifested significant variations for tested genotypes, locations, years, genotype × year, and genotype × location interactions revealing the influence of environmental factors on yield traits. All four environments showed discrimination power, whereas E2 and E3 were found as the representative environment as they fall near the Average-Environment axis (AEA). The AMMI biplot PC1 contributed 79.20% variability and PC2 contributed 15.18% variability. From the GGE biplot analysis, the rice lines Phouren, JBB-631-1, and JBB-1325 were found to be the best and most stable. The rice lines Phouren, PUP-229, and TI-112 were stable in the first sub-group Dhadesugur-Wet 2020 (E1). The rice lines Langphou, and NPK-45 were stable in the second sub-group ICAR-IIRR-Wet 2020 (E3). Environment ICAR-IIRR-Dry 2019 (E2) was the third subgroup and the rice lines Moirangphou-Yenthik and TI-3 topped for the same. The ICAR IIRR-Dry 2020 (E4) environment formed the fourth subgroup where Phouren-Amubi, TI-128 and JBB-1325 topped the season. In conclusion, this study revealed that G × E interactions are significant for yield variation, and its AMMI and biplots analysis are efficient tools for visualizing the response of genotypes to different locations.

Registration of RU9601099 short‐grain rice germplasm

AbstractThe University of Arkansas System Division of Agriculture Arkansas Agricultural Experiment Station released the germplasm of a short‐grain rice (Oryza sativa L.) known by its experimental designation RU9601099 (Reg. no. GP‐150, PI 701904). The line originated from the cross ‘Koshihikari’/’Mars’ (cross no. 900625), made at the Rice Research and Extension Center, Stuttgart, AR, in 1990. The RU9601099 line has an average yield of 7698 kg ha−1, excellent milling yield of 62/71 (% head rice/% total rice), and greater straw strength than either of its parents. The RU9601099 line provides a high‐yielding, lodging resistant, Japanese‐quality short‐grain rice line that is agronomically adapted to Arkansas growing conditions. These characteristics make this line beneficial for mid‐South producers to market rice to Japan.

Morpho-physiological characterization and metabolic profiling of rice lines for immunity to counter Helminthosporiumoryzae

Heliminthosporium oryzae is a necrotrophic fungal pathogen that effect rice crops grown on millions of hectares. We evaluated nine newly establishing rice lines and one local variety for resistance against H. oryzae. Significant (P ≤ 0.05) differences in response to pathogen attack were recorded in all rice lines. Maximum disease resistance was recorded in Kharamana under pathogen attack as compared to uninfected plants. A comparison of decline in shoot length revealed that Kharamana and Sakh experienced minimum lost (9.21%, 17.23%) in shoot length respectively against control while Binicol exhibited highest reduction (35.04%) in shoot length due to H. oryzae attack. Post-infection observations of shoot fresh weight revealed 63% decline in Binicol and declared it as the most susceptible rice line. Sakh, Kharamana and Gervex exhibited minimum fresh weight decrease (19.86%, 19.24% and 17.64% respectively) as compared to other lines under pathogen attack. Maximum chlorophyll-a contents were recorded in Kharamana under control and post pathogen attackconditions. Following the inoculation of H. oryzae, SOD was increased up to 35% and 23% in Kharamana and Sakh. However, minimum POD activity was recorded in Gervex followed by Swarnalata, Kaosen and C-13 in non-inoculated and pathogen-inoculated plants. Significant decrease in ascorbic acid contents (73.7% and 70.8%) was observed in Gervex and Binicol that later contributed in their susceptibility to H. oryzae attack. Pathogen attack caused Significant (P ≤ 0.05) changes in secondary metabolites in all rice lines but minimum total flavonoids, anthocyanin and lignin were observed in Binicol in uninfected plants and attested its susceptibility to pathogen. In post-pathogen attack conditions, Kharamana showed best resistance against pathogen by exhibiting a significantly high and maximum value of morpho-physiological, and biochemical attributes. Our findings suggest that tested resistant lines can be further explored for multiple traits including molecular regulation of defense responses to breed immunity in rice varieties.

Mapping and validation of quantitative trait loci associated with dorsal aleurone thickness in rice (Oryza sativa)

Mapping of QTLs for dorsal aleurone thickness (DAT) was performed using chromosome segment substitution lines in rice. Three QTLs, qDAT3.1, qDAT3.2, and qDAT7.1, were detected in multiple environments. As a specified endosperm cell type, the aleurone has an abundance of various nutrients. Increasing the number of aleurone layers is a practicable way of developing highly nutritious cereals. Identifying genes that can increase aleurone thickness is useful for the breeding of aleurone traits to improve the nutritional and health values of rice. Here, we found that iodine staining could efficiently distinguish the aleurone layers, which revealed great variation of the aleurone thickness in rice, especially at the dorsal side of the seed. Therefore, we used a population of chromosome segmental substitution lines (CSSLs) derived from Koshihikari and Nona Bokra for quantitative trait locus (QTL) analysis of the dorsal aleurone thickness (DAT). Three QTLs, qDAT3.1, qDAT3.2, and qDAT7.1, were detected in multiple seasons. Among these, qDAT3.2 colocalizes with Hd6 and Hd16, two QTLs previously identified to regulate the heading date of Koshihikari, explaining the negative correlation between the DAT and days to heading (DTH) in rice. We also provide evidence that early-heading ensures the filling of rice seed under a relatively high temperature to promote aleurone thickening. qDAT7.1, the most stable QTL expressed in different environments, functions independently from heading date. Although Nona Bokra has a lower DAT, its qDAT7.1 allele significantly increased DAT in rice, which was further validated using two near-isogenic lines (NILs). These findings pave the way for further gene cloning of aleurone-related QTLs and may aid the development of highly nutritious rice.

Mapping of QTLs for Brown Rice Traits Based on Chromosome Segment Substitution Line in Rice (Oryza sativa L.)

Brown rice traits are critical to both grain yield and quality. In the present study, the chromosome segment substitution lines (CSSLs) population derived from a cross between japonica Koshihikari and indica Nona Bokra was used to analyze the brown rice length (BRL), brown rice width (BRW), length–width ratio of brown rice (BLWR), brown rice thickness (BRT), brown rice perimeter (BRP), brown rice area (BRA), thousand-grain weight of brown rice (BRGW), brown rice ratio (BRR), taste value of brown rice (BTV), and water content of brown rice (BWC). Correlations analysis showed that most of the brown rice traits had significant correlations with each other, except for BRR, BTV, and BWC. A total of sixty-one QTLs for these traits were identified under three environments, which mapped to chromosomes 1, 2, 3, 5, 6, 7, 8, 10, 11, and 12, with the LOD ranging from 2.52 to 16.68 and accounting for 2.60 to 25.38% of the total phenotypic variations. Moreover, thirty pairs of epistatic interactions for BRL, BRW, BLWR, BRP, and BRA were estimated and distributed on all chromosomes except 10. These findings will provide a further understanding of the genetic basis of brown rice traits and facilitate the genetic improvement of rice yield and quality through breeding.

CRISPR-Cas9-mediated editing of the OsHPPD 3′ UTR confers enhanced resistance to HPPD-inhibiting herbicides in rice

This study reports the creation of herbicide-resistant rice lines via CRISPR-Cas9-mediated editing of the 3' UTR of OsHPPD. Resistance index calculations revealed that two resistant lines, TS8-2#-10 and TS8-8#-6, exhibited 4.8-fold and 3.7-fold greater resistance to HPPD-inhibiting herbicides compared with the wild type, YG3012.

Maintenance of Methyl-Esterified Pectin Level in Pollen Mother-Cell Stages Is Required for Microspore Development.

Pectin modification and degradation are vital for plant development, although the underlying mechanisms are still not well understood. Furthermore, reports on the function of pectin in early pollen development are limited. We generated OsPME-FOX rice lines with little methyl-esterified pectin even in the early-pollen mother-cell stage due to overexpression of the gene encoding pectin-methylesterase. Overexpression of OsPME1 in rice increased the activity of PME, which decreased the degree of pectin methyl esterification in the cell wall. OsPME1-FOX grew normally and showed abnormal phenotypes in anther and pollen development, especially in terms of the pollen mother-cell stage. In addition, we examined modifications of cell-wall polysaccharides at the cellular level using antibodies against polysaccharides. Immunohistochemical staining using LM19 and LM20 showed that methyl-esterified pectin distribution and the pectin contents in pollen mother-cell wall decreased in OsPME1-FOX compared with the wild type. Thus, the maintenance of methyl-esterified pectin plays a role in degrading and maintaining the pollen mother-cell wall during microspore development.

Life history and life table parameters of the rice weevil, Sitophilus oryzae L. (Coleoptera: Curculionidae) fed on 10 rice cultivars and lines in Iran

The rice weevil, Sitophilus oryzae L. (Coleoptera: Curculionidae), is one of the most destructive pests of stored cereal grains globally. We evaluated the resistance of different rice cultivars (Anam, Gilar, Hashemi, Keshvari, Rash, and Tisa) and lines (8608, MN-7, TH-1, and TH-2) using life history and life table parameters of S. oryzae at 28 ± 1 °C, 70 ± 5% relative humidity, and complete darkness. The immature survival of S. oryzae ranged from 37% on Rash to 82% on Hashemi. The developmental times on tested rice cultivars and lines were significantly shortest on Hashemi (35.39 days) and longest on Rash (45.20 days). The fecundity (number of eggs laid per reproductive day) of S. oryzae reared on Hashemi (318.16 eggs) was about 2.5-fold higher than that on Rash (127.40 eggs). The highest intrinsic rate of increase (rm) was in S. oryzae reared on Hashemi (0.076 day−1), and the lowest was on Rash (0.043 day−1). The grain weight loss varied from 11.31% on Rash to 40.54% on Hashemi. Significant negative correlations were recorded between the starch, protein, and total phenolics content of tested grains and fecundity, rm, net reproductive rate (R0), and finite rate of increase (λ) of S. oryzae. Owing to slow development, poor fecundity, low grain weight loss, and low rm value of S. oryzae on cultivar Rash, it was more unsuitable diet than the other cultivars and lines for population growth of this weevil. Resistant rice cultivar(s) could be used in a manner consistent with other controlling methods for integrated management of S. oryzae.

Transcriptomic and methylomic analyses provide insights into the molecular mechanism and prediction of heterosis in rice.

Heterosis has been widely used in multiple crops. However, the molecular mechanism and prediction of heterosis remains elusive. We generated five F1 hybrids [four showing better-parent heterosis (BPH) and one showing mid-parent heterosis], and performed the transcriptomic and methylomic analyses to identify the candidate genes for BPH and explore the molecular mechanism of heterosis and the potential predictors for heterosis. Transcriptomic results showed that most of the differentially expressed genes shared in the four better-parent hybrids were significantly enriched into the terms of molecular function, and the additive and dominant effects played crucial roles for BPH. DNA methylation level, especially in CG context, significantly and positively correlated with grain yield per plant. The ratios of differentially methylated regions in CG context in exons to transcription start sites between the parents exhibited significantly negative correlation with the heterosis levels of their hybrids, as was further confirmed in 24 pairwise comparisons of other rice lines, implying that this ratio could be a feasible predictor for heterosis level, and this ratio of less than 5 between parents in early growth stages might be a critical index for judging that their F1 hybrids would show BPH. Additionally, we identified some important genes showing differential expression and methylation, such as OsDCL2, Pi5, DTH2, DTH8, Hd1 and GLW7 in the four better-parent hybrids as the candidate genes for BPH. Our findings helped shed more light on the molecular mechanism and heterosis prediction.

Whole-genome analysis of recombinant inbred rice lines reveals a quantitative trait locus on chromosome 3 with genotype-by-environment interaction effects.

Elucidating genotype-by-environment (GxE) interactions is fundamental for understanding the interplay between genetic and environmental factors that shape complex traits in crops. GxE interactions are of practical importance, as they determine the performance of cultivars grown in different environments, prompting the need for an efficient approach for evaluating GxE interactions. Here, we describe a method for GxE detection that involves comparing linear mixed models. This method successfully detected GxE interactions in rice (Oryza sativa) recombinant inbred lines grown at three locations. We identified a quantitative trait locus (QTL) on chromosome 3 that was associated with heading date, grain number, and leaf length. The effect of this QTL on plant growth-related traits varied with environmental conditions, indicating the presence of GxE interactions. Therefore, our method enables a powerful GxE detection pipeline that should facilitate the production of high-yielding crops in a given environment.

Molecular and phenotypic markers for pyramiding multiple traits in rice

Abstract Gene pyramiding has been developed for effective resistant genes, such as bacterial blight resistance genes. However, in this report, pyramiding for multiple traits is presented. We evaluated 28 pyramided rice lines derived from 7 hybridizations of valuable parents for high yield potential, early maturity, aroma, high grain quality, and resistance to brown planthopper using both simple-sequence repeat markers and phenotypic markers. Pyramided rice genotypes were evaluated with RM282 molecular marker linked to GW3 gene associated with grain weight, RM259 (number of panicles), RM3600 (length of panicles), RM3701 (short panicles), RM19414 (Hd3), RM7601 (Hd2), RM190, and SSIIa (waxy), IFAP and ESP (aroma), RM586 (Bph3 and Bph4), and RM8213 (Qpbh4 and Bph17(t)). Eight genotypes (i.e., #9, #15, #16, #22, #25, #26, #27, and #28) were confirmed to have desired genes associated with multiple important traits based on molecular markers and morpho-agronomic traits. A strong correlation was found between RM19414 and heading date, between specific markers for aroma and sensory test. Meanwhile, a weak correlation was found between RM259 with panicle number, RM586, and RM8213 with trichome density. As presented in this study, gene pyramiding promises a new hope to combine multiple traits in rice breeding. Promising rice lines will be incorporated in the multiple traits breeding program.

Characterization and fine-mapping of a new Asian rice selfish genetic locus S58 in Asian-African rice hybrids.

We identified and fine-mapped S58, a selfish genetic locus from Asian rice that confers hybrid male sterility in crosses between Asian and African cultivated rice, and found a natural neutral allele in Asian rice lines that will be useful for overcoming S58-mediated hybrid sterility. Hybrids between Asian cultivated rice (Oryza sativa L.) and African cultivated rice (Oryza glaberrima Steud) display severe hybrid sterility (HS), hindering the utilization of strong heterosis in hybrids between these species. Several African rice selfish loci causing HS in Asian-African cultivated rice hybrids have been identified, but few such Asian rice selfish loci have been found. In this study, we identified an Asian rice selfish locus, S58, which causes hybrid male sterility (HMS) in hybrids between the Asian rice variety 02428 and the African rice line CG14. Genetic analysis confirmed that S58 causes a transmission advantage for the Asian rice S58 allele in the hybrid offspring. Genetic mapping with near-isogenic lines and DNA markers delimited S58 to 186 kb and 131 kb regions of chromosome 1 in 02428 and CG14, respectively, and revealed complex genomic structural variation over these mapped regions. Gene annotation analysis and expression profiling analyses identified eight anther-expressed candidate genes potentially responsible for S58-mediated HMS. Comparative genomic analysis determined that some Asian cultivated rice varieties harbor a 140 kb fragment deletion in this region. Hybrid compatibility analysis showed that this large deletion allele in some Asian cultivated rice varieties can serve as a natural neutral allele, S58-n, that can overcome S58-mediated interspecific HMS. Our study demonstrates that this selfish genetic element from Asian rice is important for HMS between Asian and African cultivated rice, broadening our understanding of interspecific HS. This study also provides an effective strategy for overcoming HS in future interspecific rice breeding.

Growth, nutrient uptake and transcriptome profiling of rice seedlings in response to mixed provision of ammonium- and nitrate-nitrogen

Nitrogen (N) is a principal macronutrient and plays a paramount role in mineral nutrition of rice plants. Mixed provision of ammonium- and nitrate-nitrogen (MPAN) at a moderate level could enhance N uptake and translocation and promote growth of rice, but current understanding of their molecular mechanisms is still insufficient. Two rice lines of W6827 and GH751, with contrasting ability of N uptake, were subjected to four levels of MPAN (NH4+/NO3− = 100:0, 75:25, 50:50, 25:75) in hydroponic experiments. In terms of plant height, growth rate and shoot biomass, growth of GH751 tended to increase firstly and then decrease with enhancement in NO3−-N ratio. It attained maximal level under 75:25 MPAN, with an 8.3% increase in shoot biomass. In general, W6827 was comparatively less responsive to MPAN. For GH751, the uptake rate of N, phosphor (P) and potassium (K) under 75:25 MPAN was enhanced by 21.1%, 20.8% and 16.1% in comparison with that of control (100:0 MPAN). Meanwhile, the translocation coefficient and content in shoots of N, P and K were all increased significantly. In contrast to transcriptomic profile under control, 288 differentially expressed genes (DEGs) were detected to be up-regulated and 179 DEGs down-regulated in transcription under 75:25 MPAN. Gene Ontology analysis revealed that some DEGs were up-regulated under 75:25 MPAN and they code for proteins mainly located in membrane and integral component of membrane and involved in metal ion binding, oxidoreductase activity and other biological processes. KEGG pathway enrichment analysis indicated that DEGs related to nitrogen metabolism, carbon fixation in photosynthetic organisms, photosynthesis, starch and sucrose metabolism, and zeatin biosynthesis were up- or down-regulated in transcription under 75:25 MPAN, and they are responsible for improved nutrient uptake and translocation and enhanced growth of seedlings.