Heat stress (HS) caused by rapidly warming climate has become a serious threat to global food security. Rice (Oryza sativa L.) is a staple food crop for over half of the world’s population, and its yield and quality are often reduced by HS. There is an urgent need for breeding heat-tolerant rice cultivars. Rice plants show various morphological and physiological symptoms under HS. Precise analysis of the symptoms (phenotyping) is essential for the selection of elite germplasm and the identification of thermotolerance genes. In response to HS, rice plants trigger a cascade of events and activate complex transcriptional regulatory networks. Protein homeostasis under HS is especially important for rice thermotolerance, which is affected by protein quality control, effective elimination of toxic proteins, and translational regulation. Although some agronomic and genetic approaches for improving heat tolerance have been adopted in rice, the molecular mechanisms underlying rice response to HS are still elusive, and success in engineering rice thermotolerance in breeding has been limited. In this review, we summarize HS-caused symptoms in rice and progress in heat-stress sensing and signal cascade research, and propose approaches for improving rice thermotolerance in future.

High temperature (HT) stress has become one of the most detrimental stresses in crop production among constantly changing environmental factors. Exploiting approaches to enhance crop thermotolerance would have great significance in assuaging adverse effects of HT stress on crop growth and development. As jasmonates (JAs) and brassinosteroids (BRs) are novel phytohormones and play important roles in responses to biotic and abiotic stresses and in a wide range of plant developmental processes, this paper reviewed the roles and mechanisms of JAs and BRs in mitigating HT stress, with focus on rice (Oryza sativa L.) subjected to HT stress during anthesis. It is demonstrated that JAs alleviate spikelet-opening impairment and BRs ameliorate pistil fertilization ability under HT stress during anthesis of rice, although there are controversial observations. Activating the defense system, enhancing osmotic regulation, protecting photosynthesis, and interacting with other phytohormones, especially with ethylene and abscisic acid, are main physiological mechanisms by which JAs or BRs attenuate HT stress to plants. Elevating levels of JAs or BRs in plants could be considered as an important approach to enhance crop thermotolerance through breeding new varieties. Using JAs or BRs as chemical regulators and adopting proper water and nitrogen management practices could reduce the harm of HT stress to rice. Further research is needed to elucidate the roles of JAs and BRs in different plant tissues in responses to HT stress under different genetic backgrounds and environments, reveal the molecular mechanism underlying JAs and BRs mediating HT stress, understand the cross-talk between phytohormones in modulating HT stress, and establish integrated crop management to minimize the hazard of HT stress in rice production.

Tillering contributes greatly to grain yield in wheat. Investigating the mechanisms of tillering provides a theoretical foundation and genetic resources for the molecular breeding of wheat. The regulation of tillering is a complex molecular process that involves a multitude of factors. Little is known about the molecular mechanisms in the wheat genome, although progress has been made in rice. Here we review the developmental characteristics of tillers and summarize current knowledge of the roles of endogenous and environmental factors in wheat tillering. We propose directions for future studies and advanced technologies to be used for gene identification and functional studies.

Mature chloroplasts, as the main sites of photosynthesis, are essential for seedling growth in higher plants. Loss of function of genes involved in chloroplast development changes plant phenotype. We obtained a YELLOW COTYLEDON (YCO) mutant in rapeseed (Brassica napus L.) using CRISPR-Cas9. Bn.YCO, a gene of unknown function, has two homologous copies (BnaA01.YCO and BnaC01.YCO) in B. napus. Homozygous mutation of these two homologs resulted in yellow cotyledons and chlorotic true leaves. Transmission electron microscopy revealed that the formation of thylakoid membranes was inhibited in yellow cotyledons. Sequence similarity search revealed that YCO was conserved in different species, and a subcellular location assay verified that Bn.YCO was located in the chloroplast. Bn.YCO was expressed in multiple tissues, most highly in cotyledons. Knockout of Bn.YCO blocked the transcription of plastid genes, especially those of photosystem genes transcribed by plastid-encoded polymerase. Transcriptome sequencing showed that the majority of genes involved in ribosome assembly and photosynthesis were down-regulated in Bn.yco mutants. These results suggested that loss of function of Bn.YCO affected plastid gene transcription, which influenced chloroplast biogenesis in rapeseed seedlings.

The C (Cys) 2H (His) 2-type transcription factor is one of the most important transcription factors in plants and plays a regulatory role in the physiological responses of rice to abiotic stresses. A novel rice C2H2-type zinc finger protein, abscisic acid (ABA)-drought-reactive oxygen species (ROS) 3 (OsADR3), was found to confer drought stress tolerance by enhancing antioxidant defense and regulating OsGPX1. Overexpression of OsADR3 in rice increased tolerance to drought stress by increasing ROS scavenging ability and ABA sensitivity. In contrast, CRISPR/Cas9-mediated knockout of osadr3 increased the sensitivity of rice to drought and oxidative stress. An exogenous ROS-scavenging reagent restored the drought-stress tolerance of osadr3-CRISPR plants. Global transcriptome analysis suggested that OsADR3 increased the expression of OsGPX1 under drought stress. Electrophoretic mobility shift, yeast one-hybrid, and dual-luciferase reporter assays revealed that OsADR3 modified the expression of OsGPX1 by directly binding to its promoter. Knockdown of OsGPX1 repressed ROS scavenging ability under drought stress in OsADR3-overexpression plants. These findings suggest that OsADR3 plays a positive regulatory role in drought-stress tolerance by inducing antioxidant defense and associated with the ABA signaling pathway in rice.

Chloroplasts are the center of plant life activities including photosynthesis, growth and development, and abiotic stress response. Chloroplast development and biogenesis in rice have been studied in detail, but how does abiotic stress affect chloroplasts is less studied. We obtained an albino mutant, alm1, whose chlorophyll content was greatly decreased. Transmission electron microscopy showed that chloroplast development in alm1 was blocked, especially in thylakoid-like structures, which could not form normally. The ALM1 gene encodes a chloroplast-localized superoxide dismutase. Full-length ALM1 successfully restored the non-albino phenotype, and in knockout lines, the albino phenotype reappeared. The ALM1 gene is expressed mainly in young leaves. alm1 plants died as a consequence of excessive reactive oxygen accumulation after the third-leaf stage. A series of biochemical assays verified that ALM1 interacted with the OsTrxz protein, which is one of the components of plastid-encoded RNA polymerase (PEP) complexes. A western blot experiment indicated that ALM1 played an important role in stabilizing OsTrxz in rice. An overexpression test of ALM1 revealed that ALM1 can increase drought resistance by removing excess reactive oxygen in rice seedlings. This study suggests that ALM1 not only participates in rice chloroplast biogenesis, but also increases rice stress resistance by scavenging excess reactive oxygen.

The breeding of herbicide-resistant wheat varieties has helped control weeds in wheat fields economically and effectively. Imidazolinone (IMI) herbicides are popular as they have low toxicity in mammals, are effective at small doses, and exhibit broad-spectrum herbicidal action in the field. Therefore, the isolation and genetic and molecular characterization of IMI-resistant wheat mutants will enhance weed management in wheat fields. In the present study, 352 IMI-resistant plants were isolated by genetic screening from a mutant pool prepared by EMS-based random mutagenesis. Cloning of the mutated genes from the IMI-resistant plants indicated that ten taals alleles had been isolated, and mutation in one of three TaALS homolog genes conferred IMI resistance, and such a mutation is a dominant trait. Further analysis showed that taals-d exhibited the greatest IMI resistance, whereas taals-b exhibited the weakest resistance to IMI among three homologous taals mutants. In terms of IMI resistance, the taals triple mutant was stronger than the taals double mutants, and the taals double mutants were stronger than the single mutants, indicating a dose-dependent effect of the TaALS mutation on IMI resistance in wheat. Biochemical analysis indicated that the mutation in TaALS increased the tolerance of TaALS to inhibition by IMI. Our work details the genetic and molecular characterization of als wheat mutants, provides a foundation for understanding IMI resistance and breeding wheat varieties with herbicide resistance, and indicates that genetic screening using a mutagenized pool is an effective and important means of breeding crops with additional desired agricultural traits.

Seed germination is the beginning of a new lifecycle, and involves many complex physiological and biochemical reactions including seed reserve mobilization in the endosperm and nutrient transport and reuse in the embryo. Although glutelin is a dominant storage protein in rice, its contribution to seed germination and its regulatory mechanisms are mostly unknown. Gibberellin (GA) and brassinosteroid (BR), two major growth-promoting phytohormones, also play positive roles in controlling seed germination. However, how GA and BR interact and coordinate seed germination and facilitate glutelin mobilization remains unclear. In the present study, biochemical and physiological analyses of seed germination indicated that both GA and BR promote seed germination and post-germination growth. Exogenous application of GA restored germination defects caused by BR deficiency or insensitivity. Proteomic and qRT-PCR results showed that the expression of several glutelin proteins and their encoding genes was induced by BR and GA in the embryo. Expression assays suggested that the increased accumulation of glutelin protein in the embryo was due to the accelerated degradation of glutelin by a cysteine proteinase (REP-1) in the endosperm. The breakdown of glutelin in the endosperm showed a strict positive correspondence with the length of the shoot. The GluA2 mutation led to reduced degradation rate of glutelin and defects in seed germination, and the promotion effect of GA on seed germination was weakened in the glua2 mutant. In vitro culture assay of rice embryos showed that glutelin mobilization functioned downstream of the GA and BR pathways to promote shoot elongation. These findings suggest a mechanism that mediates crosstalk between BR and GA in co-regulating rice seed germination and embryo growth.

Cotton (Gossypium spp.) is the most important natural textile fiber crop in the world. The ideal plant architecture of cotton is suitable for mechanical harvesting and productivity in modern agricultural production. However, cotton genes regulating plant development and architecture have not been fully identified. We identified a basic helix-loop-helix (bHLH) transcription factor, GhPAS1 (PAGODA1 SUPPRESSOR 1) in G. hirsutum (Upland cotton). GhPAS1 was located in the nucleus and showed a strong transcription activation effect. Tissue-specific expression patterns showed that GhPAS1 was highly expressed in floral organs, followed by high expression in early stages of ovule development and rapid fiber elongation. GhPAS1 overexpression in Arabidopsis and BRZ (brassinazole, BR biosynthesis inhibitor) treatment indicated that GhPAS1 positively regulates and responds to the BR (brassinosteroid) signaling pathway and promotes cell elongation. GhPAS1 overexpression in Arabidopsis mediated plant development in addition to increasing plant biomass. Virus-induced gene silencing of GhPAS1 indicated that down-regulation of GhPAS1 inhibited cotton growth and development, as plant height, fruit branch length, and boll size of silenced plants were lower than in control plants. Fiber length and seed yield were also lower in silenced plants. We conclude that GhPAS1, a bHLH transcription factor, regulates plant development and architecture in cotton. These findings may help breeders and researchers develop cotton cultivars with desirable agronomic characteristics.

Grain number per panicle (GNP) is a complex trait controlled by quantitative trait loci (QTL), directly determining grain yield in rice. Identifying GNP-associated QTL is desirable for increasing rice yield. A rice chromosome segment substitution line (CSSL), F771, which showed increased panicle length and GNP, was identified in a set of CSSLs derived from a cross between two indica cultivars, R498 (recipient) and WY11327 (donor). Genetic analysis showed that the panicle traits in F771 were semidominant and controlled by multiple QTL. Six QTL were consistently identified by QTL-seq analysis. Among them, the major QTL qPLN10 for panicle length and GNP was localized to a 121-kb interval between markers N802 and N909 on chromosome 10. Based on quantitative real-time PCR and sequence analysis, TAWAWA1 (TAW1), a known regulator of rice inflorescence architecture, was identified as the candidate gene for qPLN10. A near-isogenic line, NIL-TAW1, was developed to evaluate its effects. In comparison with the recurrent parent R498, NIL-TAW1 showed increased panicle length (14.0%), number of secondary branches (20.9%) and GNP (22.0%), and the final grain yield per plant of NIL-TAW1 was increased by 18.6%. Transgenic experiments showed that an appropriate expression level of TAW1 was necessary for panicle development. Haplotype analysis suggested that the favorable F771-type (Hap 13) of TAW1 was introduced from aus accessions and had great potential value in high-yield breeding both in indica and japonica varieties. Our results provide a promising genetic resource for rice grain yield improvement.

The ratoon stunting disease (RSD) of sugarcane, caused by the bacterium Leifsonia xyli subsp. xyli, is one of the major concerns to sugarcane production and breeding programs worldwide. Due to no obvious external symptoms, RSD cannot be easily detected by the growers, hence has reduced the world’s sugarcane production significantly. This study aimed to identify quantitative trait loci (QTL) associated with RSD resistance and to assist in the development of linked molecular markers for marker-assisted breeding to minimize the reduction in sugarcane yield by the RSD infection. A set of 146 individuals derived from a self-crossing of CP80-1827 were evaluated for RSD resistance in a mechanically duplicated inoculated field trial from 2014 to 2017 using tissue blot immunoassay. Leveraging the genetic data and the four years phenotyping data of CP80-1827 selfing population, linkage map construction and QTL analysis were conducted based on clonal F₁ and F₂ mapping population types with GACD V.1.2 and IciMapping V.3.3, respectively. A total of 23 QTL associated with RSD resistance were identified, which explained 6% to 13% of the phenotypic variation with the two types of software. A total of 82 disease resistance genes were identified by searching these 23 QTL regions on their corresponding regions on the Sorghum bicolor genome (44 genes), sugarcane R570 genome (20 genes), and S. spontaneum genome (18 genes), respectively. Compared with IciMapping V.3.3, GACD V.1.2 identified more major (6 vs. 3) and stable QTL (2 vs. 0), and more disease resistance genes (51 vs. 31), indicating GACD V.1.2 (clonal F₁ mapping type) is most likely to be more efficient than IciMapping (F₂ mapping type) for QTL analysis of a sefling population or clonal F₁ population in clonal species. The identified QTL controlling RSD resistance along with the associated SNP markers will assist sugarcane molecular breeding programs in combating this disease.

Soybeans specially the widely planted cultivars have been dramatically improved in agronomic performance and is well adapted to local planting environments after long-time domestication and breeding. Uncovering the unique genomic features of popular cultivars will help to understand how soybean genomes have been modified through breeding. We re-sequenced 134 soybean cultivars that were released and most widely planted over the last century in China. Phylogenetic analyses established that these cultivars comprise two geographically distinct sub-populations: Northeast China (NE) versus the Huang-Huai-Hai River Valley and South China (HS). A total of 309 selective regions were identified as being impacted by geographical origins. The HS sub-population exhibited higher genetic diversity and linkage disequilibrium decayed more rapidly compared to the NE sub-population. To study the association between phenotypic differences and geographical origins, we recorded the vegetative period under different growing conditions for two years, and found that clustering based on the phenotypic data was closely correlated with cultivar geographical origin. By iteratively calculating accumulated genetic diversity, we established a platform panel of cultivars and have proposed a novel breeding strategy named “Potalaization” for selecting and utilizing the platform cultivars that represent the most genetically diversity and the highest available agronomic performance as the “plateau” for accumulating elite loci and traits, breeding novel widely adapted cultivars, and upgrading breeding technology. In addition to providing new genomic information for the soybean research community, the “Potalaization” strategy that we devised will also be practical for integrating the conventional and molecular breeding programs of crops in the post-genomic era.

Drought priming is a promising approach to improve tolerance to further drought in wheat. The root apex plays important roles in drought however, its contribution to drought priming remains unknown. To provide mechanistic insights into this process, the transcriptomes and proteomes at three different zones along the root axis under drought stress were analyzed. Physiological assessment of root growth indicated that priming augmented roots growth in response to drought and also the levels of protective proline and glycine betaine. Scanning across the proximal to the distal zones of the root apex indicated increases the transcription of genes involved in primary and secondary metabolism. Conversely, genes related to translation, transcription, folding, sorting and degradation, replication and repair were increased in the apex compared to the proximal zone. A single drought episode suppressed their expression but prior drought priming served to maintain expression with recurrent drought stress. The differentially primed responses genes were mainly involved in the pathways related to plant hormone signaling, stress defense and cell wall modification. The prediction of regulatory hubs using Cytoscape implicated signaling components such as the ABA receptor PYL4 as influencing antioxidant status and the cell cycle. Based our integrative transcriptomic-proteomic assessments we present a model for drought priming protected plant hormone signaling transduction pathways to drive the cell cycle and cell wall loosening to confer beneficial effects on roots to counter the effects of drought. This model provides a theoretical basis for improvement of drought tolerance in wheat, via an increased understanding of drought priming induced drought tolerance.

Temperature of a plant organ constitutes an integrative index to its eco-physiological properties and status. However, little attempt has been made to dissect the combined effect of ecological and physiological factors on the surface temperature of a plant organ such as the rice spikelet. In this study, using a deactivated plant as reference, we developed a novel comparison method to dissect the environmental and physiological effects on temperature of rice spikelet. Three japonica rice cultivars with contrasting canopy features were used as testing materials. Temperatures of flag leaf, superior and inferior spikelets and their diurnal rhythm during grain filling stage were precisely measured by a hand-held infrared thermometer. The results showed that the variation of environmental conditions within a panicle was relatively minor, posing a limited influence on temperature difference between the superior and inferior spikelet. On the other hand, it was the intrinsic physiological properties that considerably affected the spatial variations of spikelet temperature within a panicle. Chemical analysis of sucrose and starch in grains and bracts indicated that the superior spikelet is more physiologically active at photosynthetic assimilation and starch biosynthesis. Interestingly, sugar in bracts exhibited a pattern of diurnal changes similar to the source leaf but different from the sink grain, confirming that bracts are source organs for grain filling. Our findings yield penetrating insight into the eco-physiological foundation of spikelet temperature, thus being helpful for the application of physiological approaches in crop breeding for cooler canopy.

Grain number per spikelet (GNS) is a key determinant of grain yield in wheat. A recombinant inbred line population comprising 300 lines was developed from a cross between a high GNS variety H461 and Chinese Spring from which the reference genome assembly of bread wheat was obtained. Both parents and the recombinant inbred lines were genotyped using the wheat 55K single nucleotide polymorphism (SNP) array. A high-density genetic map containing 21,197 SNPs was obtained. These markers covered each of the 21 chromosomes with a total linkage distance of 3792.71 cM. Locations of these markers in this linkage map were highly consistent with their physical locations in the genome assembly of Chinese Spring. The two parents and the whole RIL population were assessed for GNS in two consecutive years at two different locations. Based on multi-environment phenotype data and best liner unbiased prediction values, three quantitative trait loci (QTL) for GNS were identified. One of them located on chromosomes 2B and the other two on 2D. Phenotypic variation explained by these loci varied from 3.07% to 26.57%. One of these QTL, QGns.sicau-2D-2, was identified in each of all trials conducted. Based on the best linear unbiased prediction values, this locus explained 19.59%-26.57% of phenotypic variation. A KASP (Kompetitive Allele-Specific PCR) marker closely linked with this locus was generated and used to validate the effects of this locus in three different genetic backgrounds. The identified QTL and the KASP marker developed for it will be highly valuable in fine-mapping the locus and in exploiting it for marker-assisted selection in wheat breeding programs.

The MADS-box gene plays an important role in regulating plant growth and development. In this study, a SEP3-like MADS-box gene TaSEP3-1 was isolated from bread wheat. The expression patterns of the three homoeologs TaSEP3-A1, TaSEP3-B1, and TaSEP3-D1 were similar, and higher expression levels were detected in floral organs and developing kernels. TaSEP3-D1 was located in the nucleus and cytoplasm and possessed transactivation activity in yeast. Homoeolog sequence polymorphism analysis identified four, three, and four haplotypes of TaSEP3-A1, TaSEP3-B1, and TaSEP3-D1, respectively, and the haplotypes of TaSEP3-D1 had larger effects on agronomic traits than those of TaSEP3-A1 and TaSEP3-B1. D1_h4, significantly associated with heading date, plant height, and other yield-related traits, was the favored haplotype of TaSEP3-D1. Transgenic wheat genotypes overexpressing TaSEP3-D1 exhibited delayed heading and reduced plant height, indicating a role in regulating heading date and plant development. These results shed light on the role of TaSEP3-D1 in wheat plant development. The favored haplotype of TaSEP3-D1 can be applied in breeding to improve plant architecture and yield in wheat.

Oilseed rape (Brassica napus) with yellow flowers is an attractive ornamental landscape plant during the flowering period, and the development of different petal colors has become a breeding objective. Although yellowish flower color is a common variant observed in field-grown oilseed rape, the genetics behind this variation remains unclear. We obtained a yellowish-white flower (ywf) mutant from Zhongshuang 9 (ZS9) by ethyl methanesulfonate mutagenesis (EMS) treatment. Compared with ZS9, ywf exhibited a lower carotenoid content with a reduced and defective chromoplast ultrastructure in the petals. Genetic analysis revealed that the yellowish-white trait was controlled by a single recessive gene. Using bulked-segregant analysis sequencing (BSA-seq) and kompetitive allele-specific PCR (KASP), we performed map-based cloning of the ywf locus on chromosome A08 and found that ywf harbored a C-to-T substitution in the coding region, resulting in a premature translation termination. YWF, encoding phytoene desaturase 3 (PDS3), was highly expressed in oilseed rape petals and involved in carotenoid biosynthesis. Pathway enrichment analysis of the transcriptome profiles from ZS9 and ywf indicated the carotenoid biosynthesis pathway to be highly enriched. Further analyses of differentially expressed genes and carotenoid components revealed that the truncated BnaA08.PDS3 resulted in decreased carotenoid biosynthesis in the mutant. These results contribute to an understanding of the carotenoid biosynthesis pathway and manipulation of flower-color variation in B. napus.

Alfalfa (Medicago sativa L.) is the most widely cultivated perennial leguminous forage crop woldwide. MicroRNA156 (miR156) precursor genes from dicotyledonous species are reportedly useful for improving alfalfa plant architecture and abiotic stress resistance. However, there has been no report on whether a miR156 precursor gene from a monocotyledonous species functions in alfalfa. We introduced two tandem precursor genes of miR156, rice Osa-MIR156b and Osa-MIR156c (Osa-MIR156bc), into alfalfa. The expression of miR156 in the transgenic (TG) alfalfa was significantly elevated. Compared to wild-type plants, the TG plants overexpressing miR156 had more branches and leaves and showed improved salt and drought tolerance. Overexpression of miR156 slightly reduced plant height, but the biomass yield of TG plants grown in flowerpots was still increased. Forage quality of TG plants was markedly improved by reduction of acid detergent lignin (ADL) content and increase in crude protein content. The expression of the putative miR156 target genes MsSPL6, MsSPL12, and MsSPL13 in TG plants was repressed by miR156 overexpression, and that of all tested MsSPLs would be sharply increased under drought or salt stress. RNA sequencing revealed that overexpression of miR156 affected the expression of genes associated with abiotic stress resistance and plant development in multiple pathways. This first report of overexpression of monocot miR156 precursors in alfalfa sheds light on the function of miRNA156 precursors from the monocot species rice that could be used for genetic improvement of the dicot forage crop alfalfa.

Cassava, Manihot esculenta Crantz (Me), is a major dietary source of calories for over 700 million people in tropical regions. The production of cassava is constantly threatened by cassava bacterial blight (CBB), caused by Xanthomonas axonopodis pv. manihotis (Xam). The gene resources for CBB-resistant breeding of cassava are limited. In model plant species, ethylene response factors play important roles in response to pathogen infection. In this study, cassava ethylene response factors (MeERFs) were identified and characterized as the first step in studying their potential for CBB-resistant breeding of cassava. In the cassava genome 155 MeERFs were identified, of which 23 were induced by Xam infection. The promoter regions of 204 genes harbored GCC-box that had the potential to interact with MeERFs. Using 37 transcriptomes derived from Xam infection treatment, four gene co-expression modules for the MeERFs and GCC-box containing genes were constructed. Six MeERFs were associated with two GCC-box containing genes: transcription initiation factor TFIIE subunit beta (MeTFIIE), and histone-lysine N-methyltransferase ASHR1 (MeASHR1). Dual-luciferase reporter assays showed that MeERF10 and MeERF58 positively regulated MeTFIIE; MeERF137 negatively regulated MeTFIIE; MeERF10 and MeERF137 positively regulated MeASHR1; and MeERF35 negatively regulated MeASHR1. The four MeERFs may mediate pathogen response by regulating the expression of the two GCC-box containing genes.

Rice, a major staple, is the most salt-sensitive cereal. High salinity triggers several adaptive responses in rice to cope with osmotic and ionic stress at the physiological, cellular, and molecular levels. A major QTL for salinity tolerance, named Saltol, is present on chromosome 1 of Indian landraces such as Pokkali and Nona Bokra. The early proteomic and physiological responses to salinity in roots and shoots of FL478, an inbred rice line harboring the Saltol QTL, were characterized. Plantlets were cultured in hydroponic cultures with 100 mmol L⁻¹ NaCl and evaluated at 6, 24, and 48 h. At the physiological level, root length significantly increased at 48 h, whereas shoot length was reduced. The Na⁺/K⁺ ratio was maintained at lower levels in shoots than in roots, suggesting that roots play a protective role. More than 2000 proteins were detected in both tissues. Roots showed a faster and more coordinated proteomic response than shoots, evident after only 6 h of treatment. These responses showed clear correspondence with those of proteins involved in transcription and translation. Maintenance of mitochondrial activity and amino acid metabolism in roots, and activation of stress-responsive proteins such as dehydrins and PLAT in shoots, may play a key role during the response of the plant to salinity stress. Proteomic and physiological responses showed that roots respond in a more highly adaptive manner than shoots to salinity stress, suggesting that this tissue is critical to the tolerance observed in cultivars harboring Saltol.

Extensive exotic introgression could significantly enlarge the genetic distance of hybrid parental populations to promote strong heterosis. The goal of this study was to investigate whether genome-wide prediction can support pre-breeding in populations with exotic introgressions. We evaluated seed yield, seed yield related traits and seed quality traits of 363 hybrids of Brassica napus (AACC) derived from two parental populations divergent on massive exotic introgression of related species in three environments. The hybrids presented strong heterosis on seed yield, which was much higher than other investigated traits. Five genomic best linear unbiased prediction models considering the exotic introgression and different marker effects (additive, dominance, and epistatic effects) were constructed to test the prediction ability for different traits of the hybrids. The analysis showed that the trait complexity, exotic introgression, genetic relationship between the training set and testing set, training set size, and environments affected the prediction ability. The models with best prediction ability for different traits varied. However, relatively high prediction ability (e.g., 0.728 for seed yield) was also observed when the simplest models were used, excluding the effects of the special exotic introgression and epistasis effect by 5-fold cross validation, which would simplify the prediction for the trait with complex architecture for hybrids with exotic introgression. The results provide novel insights and strategies for genome-wide prediction of hybrids between genetically distinct parent groups with exotic introgressions.

Heterosis is an important biological phenomenon and widely applied in agriculture. Although many studies have been performed by using vegetative organs of F₁ hybrid plants, how heterosis (or hybrid vigor) is initiated and formed, particularly the underlying molecular mechanism, remain elusive. Hybrid contemporary seeds of rice indica varieties 9311 and PA64 were innovatively used and analysis of DNA methylome of embryo and endosperm at early developing stages revealed the globally decreased DNA methylation. Genes, especially those relate to hormones function and transcriptional regulation present non-additive methylation. Previously identified heterosis-related superior genes are non-additively methylated in early developing hybrid contemporary seeds, suggesting that key genes/loci responsible for heterosis are epigenetically modified even in early developing hybrid seeds and hypomethylation of hybrid seeds after cross-pollination finally result in the long-term transcriptional change of F₁ hybrid vegetative tissues after germination, demonstrating that altered DNA methylation in hybrid seeds is essential for initiation regulation and maintenance of heterosis exhibiting in F₁ hybrid plants. Notably, a large number of genes show non-additive methylation in the endosperm of reciprocal hybrids, suggesting that endosperm might also contribute to heterosis.

Straw incorporation is a global common practice to improve soil fertility and rice yield. However, the effect of straw incorporation on rice yield stability is still unknown, especially under high fertilization level conditions. Here, we reported the effect of straw returning on rice yield and yield stability under high fertilization levels in the rice-wheat system over nine years. The results showed that straw incorporation did not significantly affect the average rice yield of nine years. Straw incorporation reduced the coefficient of variation of rice yield by 25.8% and increased the sustainable yield index by 8.2%. The rice yield positively correlated with mean photosynthetically active radiation (PAR) of rice growth season and the effects of straw incorporation on rice yield depended on the PAR. Straw incorporation increased the rice yield by 5.4% in the low PAR years, whereas it did not affect the rice yield in the high PAR years. Long-term straw incorporation lowered soil bulk density but improved the soil organic matter, total N, available N, available P, and available K more strongly than straw removal. Our findings suggest that straw incorporation can increase rice yield stability through improving the resistance of rice plant growth to low PAR.

Barnyardgrass (Echinochloa spp.) is the most common noxious weed in rice paddies as it inhibits rice growth and reduces grain yield. To date, little information is available on above- and belowground-growth changes in rice due to neighboring barnyardgrass. This study aimed to investigate the changes in root traits and shoot growth of rice when it is grown with different kinds of barnyardgrass. Japonica rice plants (var. Nanjing 9108) were co-cultured with two varieties of Echinochloa crusgalli (L.) Beauv. (EP, var. mitis (pursh) Petern; EH, var. zelayensis (H.B.K.) Hitchc), and E. colonum (L.) Link (EL) in the field in 2017 and 2018. Four treatments included control (i.e., weed free rice plants) and co-cultures with each of three barnyardgrasses (EP, EH, and EL). The results revealed that EP, EH, and EL treatments significantly reduced rice grain yields by 30.6%-36.2%, 42.5%-46.5%, and 10.6%-14.3%, respectively. Shoot growth including shoot dry weight, leaf photosynthetic rate, zeatin (Z) and zeatin riboside (ZR) in grains, and activities of key enzymes involved in sucrose-to-starch conversion in grains and root traits, such as length density, root dry weight, total absorbing surface area, active absorption surface area, oxidation activity, and Z + ZR contents in roots were dramatically reduced during post-heading stages of rice when grown with the three kinds of barnyardgrass. Moreover, above-mentioned rice shoot growth indices were strongly and positively correlated with root traits. These results suggested the decrease in rice shoot growth and root traits during post-heading stages contributes to the reduction in the rice yield when it grows with barnyardgrass neighbors.

Two potential BRASSINAZOLE RESISTANT 1 (BZR1) homologs were downregulated by brassinosteroids (BRs) in Setaria italica roots. Functional analysis showed that BR regulates the dephosphorylation and nuclear localization of SiBZR1 and that SiBZR1 binds conserved BZR1-recognizing cis elements. In comparison with the wild type, SiBZR1-overexpressing S. italica seedlings were more sensitive to BR-inhibited primary root growth and drought stress, indicating that SiBZR1 is a positive regulator of BR signaling and a negative regulator of drought tolerance in S. italica. PLETHORA-LIKE 1 (SiPLT-L1) was found to be a direct target gene of SiBZR1 in S. italica roots. The expression of SiPLT-L1 was downregulated by SiBZR1. SiPLT-L1-overexpressing S. italica was less sensitive to BR-inhibited root growth and more tolerant to drought stress, possibly owing to the upregulation of drought-inducible Dehydrin-family genes.

Thaumatin-like protein (TLP) plays an important role in combating plant pathogen infection. Common root rot caused by Bipolaris sorokiniana and leaf rust caused by Puccinia triticina (Pt) are major fungal diseases in wheat. The disease responses of TaTLP1-overexpressing transgenic lines (TaTLP1-OE) were evaluated after inoculation with each pathogen. The TaTLP1-OE lines had no apparent differences in tiller number and 1000-kernel weight from the wild type Jinan Wheat No. 1 (JW1), whereas resistance to leaf rust and common root rot was improved, resulting from activated peroxidase and β-1,3-glucanase after B. sorokiniana infection, and reactive oxygen species-related genes were upregulated in TaTLP1-OE lines after Pt infection. These results indicated that stable expression of TaTLP1 increased resistance against both diseases.