Magnesium (Mg) affects various critical physiological and biochemical processes in higher plants, and its deficiency impedes plant growth and development. Although potassium (K)-induced Mg deficiency in agricultural production is widespread, the specific relationship of K with Mg and especially its competitive nature is poorly understood. This review summarizes current knowledge on the interactions between K and Mg with respect to their root uptake, root-to-shoot translocation and distribution in plants. Their synergistic effects on certain physiological functions are also described. The antagonistic effect of K on Mg is stronger than that of Mg on K in root absorption and transport within plants, indicating that the balanced use of K and Mg fertilizers is necessary for sustaining high plant-available Mg and alleviating K-induced Mg deficiency, especially in plant species with high K demand or in high-available-K soil. The relationship between Mg and K in plant tissues may be antagonistic or synergistic depending on plant species, cell type, leaf age, source- and sink organs. There are synergistic effects of K and Mg on photosynthesis, carbohydrate transport and allocation, nitrogen metabolism, and turgor regulation. Definition of optimal K/Mg ratios for soils and plant tissues is desirable for maintaining proper nutritional status in plants, leading to a physiological state supporting crop production. Future research should concentrate on identifying the physiological and molecular mechanisms underlying the interactions between K and Mg in a given physiological function.

Over the last few decades, waterlogging stress has increasingly threatened global cotton production. Waterlogging results in reduced soil oxygen, impairing the growth and development of this valuable crop and often resulting in severe yield loss or crop failure. However, as cotton has an indeterminate growth habit, it is able to adapt to waterlogging stress by activating three mechanisms: the escape, quiescence, and self-regulating compensation mechanisms. The escape mechanism includes accelerated growth, formation of adventitious roots, and production of aerenchyma. The quiescence mechanism involves reduced biomass accumulation and energy dissipation via physiological, biochemical, and molecular events. The self-regulation compensation mechanism allows plants to exploit their indeterminate growth habit and compensatory growth ability by accelerating growth and development following relief from waterlogging stress. We review how the growth and development of cotton is impaired by waterlogging, focusing on the three strategies associated with tolerance and adaptation to the stress. We discuss agronomic measures and prospects for mitigating the adverse effects of waterlogging stress.

Carbon isotope composition (δ¹³C) of a plant organ is an inherent signature reflecting its physiological property, and thus is used as an integrative index in crop breeding. It is also a non-intrusive method for quantifying the relative contribution of different source organs to grain filling in cereals. Using the samples collected from two-year field and pot experiments with two nitrogen (N) fertilization treatments, we investigated the temporal and spatial variations of δ¹³C in source organs of leaf, sheath, internode, and bracts, and in sink organ grain. Constitutive nature of δ¹³C was uncovered, with an order of leaf (−27.84‰) < grain (−27.82‰) < sheath (−27.24‰) < bracts (−26.81‰) < internode (−25.67‰). For different positions of individual organs within the plant, δ¹³C of the leaf and sheath presented a diminishing trend from the top (flag leaf and its sheath) to the bottom (the last leaf in reverse order and its sheath). No obvious pattern was found for the internode. For temporal variations, δ¹³C of the leaf and sheath had a peak (the most negative) at 10 days after anthesis (DAA), whereas that of the bracts showed a marked increase at the time point of anthesis, implying a transformation from sink to source organ. By comparing the δ¹³C in its natural abundance in the water-soluble fractions of the sheath, internode, and bracts with the δ¹³C in mature grains, the relative contribution of these organs to grain filling was assessed. With reference to the leaf, the internode accounted for as high as 32.64% and 42.56% at 10 DAA and 20 DAA, respectively. Meanwhile, bracts presented a larger contribution than the internode, with superior bracts being higher than inferior bracts. In addition, N topdressing reduced the contribution of the internode and bracts. Our findings clearly proved the actual significance of non-foliar organs of the internode and bracts for rice yield formation, thus extending our basic knowledge of source and sink relations.

Endosperm as the storage organ of starch and protein in cereal crops largely determines grain yield and quality. Despite the fact that several pentatricopeptide repeat (PPR) proteins required for endosperm development have been identified in rice, the molecular mechanisms of many P-type PPR proteins in endosperm development remains unclear. Here, we isolated a rice floury endosperm mutant ppr5 that developed small starch grains and an abnormal aleurone layer, accompanied by decreased starch, protein, and amylose contents. Map-based cloning combined with a complementation test demonstrated that PPR5 encodes a P-type PPR protein that is localized to the mitochondria. The mutation in PPR5 caused reduced splicing efficiency of mitochondrial NADH dehydrogenase 4 (nad4) gene intron 3 and reduced complex I assembly and activity. Loss of PPR5 function greatly up-regulated expression of alternative oxidases (AOXs), reduced ATP production, and affected mitochondrial morphology. We demonstrate that PPR5, as a P-type PPR protein, is required for mitochondrial function and endosperm development by controlling the cis-splicing of mitochondrial nad4 intron 3.

Seed dormancy of cultivated rice was largely weakened during the progress of domestication. Correct timing and uniformity of seed germination are important for rapid seedling establishment and high-yield production. In the present study, we found that the heading-date gene Ghd7 acted as a negative regulator of germination. A mutant of ghd7 showed low sensitivity to exogenous ABA treatment during seed germination. Further investigation revealed reduced accumulation of ABA in mature ghd7 seeds as a consequence of dampened expression of OsNCED genes. Moreover, elevated GA₃ level was detected in seeds of ghd7 mutant during imbibition course, which was attributed to the induction of genes responsible for the synthesis pathways of bioactive GAs. Thus, Ghd7 inhibits seed germination by increasing the ABA/GA₃ ratio. Besides revealing pleiotropic effects of Ghd7, our results indicate its role in linking seed germination to growth-phase transition in rice, which would enrich the theoretical basis for future breeding practices.

Weeds and weedy rice plague commercial rice fields in many countries. Developing herbicide-tolerance rice is the most efficient strategy to control weed proliferation. CRISPR/Cas9-mediated gene editing, which generates small InDels and nucleotide substitutions at and around target sites using error-prone non-homologous end joining DNA repairing, has been widely adopted for generation of novel crop germplasm with a wide range of genetic variation in important agronomic traits. We created a novel herbicide-tolerance allele in rice by targeting the acetolactate synthase (OsALS) gene using CRISPR/Cas9-mediated gene editing. The novel allele (G628W) arose from a G-to-T transversion at position 1882 of OsALS and conferred a high level of herbicide tolerance. Transgene-free progeny carrying homozygous G628W allele were identified and showed agronomic performance similar to that of wild-type plants, suggesting that the G628W allele is a valuable resource for developing elite rice varieties with strong herbicide tolerance. To promote use of the G628W allele and to accelerate introgression and/or pyramiding of the G628W allele with other elite alleles, we developed a DNA marker for the G628W allele that accurately and robustly distinguished homozygous from heterozygous segregants. Our result further demonstrates the feasibility of CRISPR/Cas9-mediated gene editing in creating novel genetic variation for crop breeding.

Fiber length is one of the most important quality parameters of cotton fibers. Transcriptomic analyses of developing cotton fibers have identified genes preferentially expressing in fiber elongation stage, but few have been functionally characterized. Here, on the basis of confirmation of the preferential expression profile of GhAlaRP (Gh_A09G1166 and Gh_D09G1172), an alanine rich protein gene, in the rapid elongating fibers, we investigated the role of GhAlaRP in fiber development by generating transgenic cottons with an increased or decreased expression level of GhAlaRP. Our results showed that the fiber length was consistently significantly shorter in both the GhAlaRP-RNAi lines and the alarp mutant generated by genome editing than in the control YZ-1. GhAlaRP was localized on plasma membrane, nucleus and endoplasmic reticulum. The yeast two-hybrid assay and bimolecular fluorescence complementation assay showed that GhAlaRP co-expresses and interacts with GhAnnexin (Gh_D11G2184) and GhEXPA (Gh_A10G2323) that are involved in fiber elongation. Down-regulation of GhAlaRP co-suppressed the expression levels of GhAnnexin and GhEXPA. These results suggest a role of GhAlaRP in regulation of cotton fiber elongation, which could be achieved by regulating the functions of GhAnnexin and GhEXPA.

Fusarium ear rot (FER) is a destructive maize fungal disease worldwide. In this study, three tropical maize populations consisting of 874 inbred lines were used to perform genome-wide association study (GWAS) and genomic prediction (GP) analyses of FER resistance. Broad phenotypic variation and high heritability for FER were observed, although it was highly influenced by large genotype-by-environment interactions. In the 874 inbred lines, GWAS with general linear model (GLM) identified 3034 single-nucleotide polymorphisms (SNPs) significantly associated with FER resistance at the P-value threshold of 1 × 10⁻⁵, the average phenotypic variation explained (PVE) by these associations was 3% with a range from 2.33% to 6.92%, and 49 of these associations had PVE values greater than 5%. The GWAS analysis with mixed linear model (MLM) identified 19 significantly associated SNPs at the P-value threshold of 1 × 10⁻⁴, the average PVE of these associations was 1.60% with a range from 1.39% to 2.04%. Within each of the three populations, the number of significantly associated SNPs identified by GLM and MLM ranged from 25 to 41, and from 5 to 22, respectively. Overlapping SNP associations across populations were rare. A few stable genomic regions conferring FER resistance were identified, which located in bins 3.04/05, 7.02/04, 9.00/01, 9.04, 9.06/07, and 10.03/04. The genomic regions in bins 9.00/01 and 9.04 are new. GP produced moderate accuracies with genome-wide markers, and relatively high accuracies with SNP associations detected from GWAS. Moderate prediction accuracies were observed when the training and validation sets were closely related. These results implied that FER resistance in maize is controlled by minor QTL with small effects, and highly influenced by the genetic background of the populations studied. Genomic selection (GS) by incorporating SNP associations detected from GWAS is a promising tool for improving FER resistance in maize.

Gray leaf spot (GLS) caused by Cercospora zeae-maydis and C. zeina is an extremely devastating leaf disease that limits maize production annually. The use of GLS-resistant maize hybrids is the most cost-effective approach for reducing losses. Resistance to GLS is quantitatively inherited in maize (Zea mays L.) and further sources of resistance remain to be analyzed. Here, we detected qRgls1.06, a major quantitative trait locus for GLS resistance in bin 1.06 that explained approximately 55% of the phenotype variance. Fine mapping over 2 consecutive years localized qRgls1.06 to a 2.38-Mb region. Homozygous qRgls1.06^WGR/WGR plants in DZ01 background displayed higher GLS resistance and 100-grain weight than DZ01 plants. The GLS responses of several susceptible elite inbred lines were improved by the introduction of qRgls1.06 by marker-assisted backcrossing. Our findings extend the understanding of the genetic basis of resistance to GLS and provide a set of resistant germplasm for genetic improvement of resistance to GLS in maize.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most economically destructive pathogens. The soybean line Zhongpin03-5373 (ZP), which combines resistance genes from several donors, is highly resistant to SCN race 3 (SCN3). In our previous study, two QTL (rhg1 and GmSNAP11) were identified in a population of recombinant inbred lines derived from a cross between ZP and the susceptible parent Zhonghuang 13. The two QTL explained around one-third of the resistance, suggesting the presence of further QTL contributing to SCN resistance. In the present study, we used an improved version of the genetic map comprising the previously applied 1062 molecular markers and 47 newly developed InDel (insertion-deletion) markers. The improved map revealed a novel locus contributing to SCN3 resistance: qSCN3-1, flanked by InDel marker InDel1-7 and SNP marker Map-0047, explained 4.55% of the phenotypic variance for resistance to SCN3 and was not involved in digenic epistatic interaction with rhg1 and GmSNAP11. Haplotypes of Map-0047_CAPS (a CAPS marker developed for Map-0047) and InDel1-7 were significantly associated with SCN3 resistance in a panel of 209 resistant and susceptible accessions. Using further allele-combination analysis for three functional markers representing three cloned resistance genes (rhg1, Rhg4, and GmSNAP11) and two markers flanking qSCN3-1, we found that adding the resistance allele of qSCN3-1 greatly increased soybean resistance to SCN, even in diverse genetic backgrounds. The qSCN3-1 locus will be useful for marker-assisted polygene pyramid breeding and should be targeted for the future identification of candidate genes.

Early seedling vigor (ESV) is a major breeding target in rice, especially under direct seeding. To identify quantitative trait locus (QTL) affecting ESV, a recombinant inbred line population derived from a cross between 02428 and YZX, two cultivars differing in vigor during early seedling growth, was used for QTL analysis. Nine traits associated with ESV were examined using a high-density map. Of 16 additive loci identified, three were detected in two generations and thus considered stable. Four epistatic interactions were detected, one of which was repeated in two generations. Further analysis of the pyramiding effect of the three stable QTL showed that the phenotypic value could be effectively improved with an increasing number of QTL. These results were combined with results from our previous QTL analysis of the germination index. The lines G58 and G182 combined all the favourable alleles of all three stable QTL for ESV and three QTL for germination speed. These two lines showed rapid germination and strong ESV. A total of 37 candidate differentially expressed genes were obtained from the regions of the three stable QTL by analysis of the dynamic transcriptomic expression profile during the seedling growth period of the two parents. The QTL are targets for ESV breeding and the candidate genes await functional validation. This study provides a theoretical basis and a genetic resource for the breeding of direct-seeded rice.

Flowering time is an indicator of adaptation in maize and a key trait for selection in breeding. The genetic basis of flowering time in maize, especially in response to plant density, remains unclear. The objective of this study was to identify maize quantitative trait loci (QTL) associated with flowering time-related traits that are stably expressed under several plant densities and show additive effects that vary with plant density. Three hundred recombinant inbred lines (RIL) derived from a cross between Ye 478 and Qi 319, together with their parents, were planted at three plant densities (90,000, 120,000, and 150,000 plants ha⁻¹) in four environments. The five traits investigated were days to tasseling (DTT), days to silking (DTS), days to pollen shed (DTP), interval between anthesis and silking (ASI), and interval between tasseling and anthesis (TAI). A high-resolution bin map was used for QTL mapping. In the RIL population, the DTT, DTS, and DTP values increased with plant density, whereas the ASI and TAI values showed negligible response to plant density. A total of 72 QTL were identified for flowering time-related traits, including 15 stably expressed across environments. Maize flowering time under different densities seems to be regulated by complex pathways rather than by several major genes or an independent pathway. The effects of some stable QTL, especially qDTT8-1 and qDTT10-4, varied with plant density. Fine mapping and cloning of these QTL will shed light on the mechanism of flowering time and assist in breeding early-maturing maize inbred lines and hybrids.

Previously we identified a major cotton fiber strength QTL (qFS-c7-1) on chromosome A07 using a multi-parent advanced generation intercross (MAGIC) population. To assess the stability and transferability of this QTL and its utility in cotton breeding, we made ten new populations. These populations were developed from crosses between MAGIC recombinant inbred lines, or between cotton cultivars that are different from the MAGIC parents. A total of 2801 F₂ plants were grown and their fiber quality traits were measured. We also selected a subset of F₃ seeds from two populations, and grew F₃ progeny plots to further evaluate the stability of this QTL. Our results showed that the peak of qFS-c7-1 is at 70-72 Mb region. This QTL had a major effect on fiber strength explaining 21.9% phenotypic variance. Its effect on other fiber quality attributes such as micronaire, short fiber content, length and uniformity varied between populations, and no effect on fiber elongation was observed. The QTL effects were stable in the populations analyzed, and in different generations of the same population. The SSR and SNP markers near and within the QTL peak reported herein will assist selecting superior fiber quality traits in breeding, with a recommendation that the parental cotton lines should be analyzed using the seven DNA markers within the QTL peak before fully implementing marker assisted selection in a cotton breeding program.

Mepiquat chloride (MC) priming alleviates the effects of salt stress during seed germination in cotton (Gossypium hirsutum L.), but the mechanisms underlying its effects are unknown. We found that MC priming increases salt tolerance, as evidenced by marked increases in seed vigor and germination rates, and alleviated salt toxicity by reducing Cl⁻ accumulation in germinating seeds. Consistently, electrophysiological experiments revealed that the seeds with MC priming displayed superior Cl⁻ exclusion ability in the root apex. These beneficial effects of MC priming were abolished by the abscisic acid (ABA)-synthesis blocker fluridone under salt stress. MC priming induced an early response to acclimatization and stress, as indicated by rapidly increasing ABA content during initial exposure to salt stress. Transcriptome analyses revealed that MC priming induced an array of differentially expressed genes (DEGs) in germinating seeds. The most noticeable changes in germinating seeds were MC priming-induced increases in the expression of DEGs encoding components of ABA biosynthesis, ABA catabolism, and ABA signaling pathways under salt stress. MC priming also increased the expression of some DEGs encoding Cl⁻ ion transporters (e.g. CCC, SLAC1/SLAH1/SLAH3, CLC, and ALMT9) in germinating seeds. These results indicate that MC priming-induced ABA contributes to Cl⁻ homeostasis in tissues and acts as a positive regulator of salt tolerance via regulation of Cl⁻ transporters (particularly CCC and SLAC1/SLAH1/SLAH3). Taken together, these findings shed light on the molecular mechanism underlying MC-mediated tolerance to salt stress during seed germination.

Dominant early heading (DEH) in rice (Oryza sativa L.) is of interest in both breeding and genetics. The genetic mechanisms underlying DEH have remained largely unclear. We have developed a near-isogenic DEH line without yield drag named DEH_229 by sister-line backcross (BC) breeding with MH63, a restorer, as the genetic background. We conducted a pilot genetic investigation under both short-day (SD) and long-day (LD) conditions. The DEH line harbored only 1.06% variation in the genome sequence relative to MH63. The variants were distributed throughout the genome. Using QTL mapping by sequencing (QTL-seq) on an F₂ population derived from a cross of MH63 × DEH_229, 57 loci were detected under the SD condition. Joint mapping employing a genome-wide association study with accessions from the 3000 rice genome sequencing project (3K-RG), reduced the number of QTL by 43.9%. Using Rice Functional Genomics & Breeding (RFGB) database, the number of SNP cluster regions within the QTL regions reduced by 27.3%. Further comparison of the genome variation between DEH_229 and MH63 in addition to gene annotation information revealed a new DEH allele of DTH3 with multiple variable sites as a possible major factor underlying the early-heading phenotype of DEH_229. An InDel marker, ZMEH_1, was designed based on the variation between DEH_229 and MH63 within this region. It accounted for 86.0% of heading date variation under both SD and LD conditions in 109 randomly chosen progeny derived from extreme lines of the MH63 × DEH_229 population. This study reveals the genetic complexity of DEH in the near-isogenic line and may provide useful material and marker information for plant molecular breeding.

Excessive use of nitrogen fertilizer and high planting density reduce grain weight in wheat. However, the effects of high nitrogen and planting density on the filling of grain located in different positions of the wheat spikelet are unknown. A two-year field experiment was conducted to investigate this question and the underlying mechanisms with respect to hormone and carbohydrate activity. Both high nitrogen application and planting density significantly increased spike density, while reducing kernel number per spike and 1000-kernel weight. However, the effects of high nitrogen and high plant density on kernel number per spike and 1000-kernel weight were different. The inhibitory effect of high nitrogen application and high planting density on kernel number per spike was achieved mainly by a reduction in kernel number per spikelet in the top and bottom spikelets. However, the decrease in 1000-kernel weight was contributed mainly by the reduced weight of grain in the middle spikelets. The grain-filling rate of inferior grain in the middle spikelets was significantly decreased under high nitrogen input and high planting density conditions, particularly during the early and middle grain-filling periods, leading to the suppression of grain filling and consequent decrease in grain weight. This effect resulted mainly from inhibited sucrose transport to and starch accumulation in inferior grain in the middle spikelets via reduction of the abscisic acid/ethylene ratio. This mechanism may explain how high nitrogen application and high planting density inhibit the grain filling of inferior wheat grain.

New indica and japonica hybrid rice cultivars, such as the Yongyou series, provide farmers with very high yield potential. However, information on their canopy light capture and solar radiation use efficiency in the late season is limited. Field experiments were performed to compare the radiation-use parameters of four rice types: indica rice (IR), inbred japonica rice (IJR), hybrid japonica rice (HJR), and hybrid indica/japonica rice (HIJR), from 2016 to 2018 during the late season in Hangzhou, China. The grain yield, aboveground biomass, intercepted solar radiation (SI), and radiation-use efficiency (RUE) of the HIJR were on average respectively 13.4%-53.4%, 14.3%-30.6%, 7.6%-21.4%, and 8.2%-14.9% higher than those of the HJR, IJR, and IR. The leaf area index (LAI) of the HIJR was 18.2%-57.0% greater than that of the IJR and HJR at four growth stages, resulting in respectively 17.8%-38.5% and 10.7%-42.8% greater canopy light interception rates (LIR) and amount of intercepted solar radiation during the vegetative stage. The prolonged grain-filling stage also led to respectively 33.9%-52.6% and 30.5%-51.4% increases in amounts of incident and intercepted radiation for the HIJR relative to the IR during grain filling. These results indicate that the SI superiority of the HIJR was caused by canopy closure as rapid as that of the IR during the vegetative stage (greater LAI and canopy LIR during the growing season) and a grain-filling stage as long as that of the HJR. For grain-filling stage, differences in leaf P_n between HIJR, IR, and IJR were not significant, suggesting that the greater RUE of the HIJR (12.7%-52.8% higher) than that of the other rice types resulted from improved canopy architecture after flowering (FL). Principal components analysis (PCA) revealed that the superiority of the HIJR in terms of solar radiation use resulted from the greater canopy light capture capability of IR and the prolonged growth period (especially during grain filling) of japonica rice in the late growing season.

Reserve starch of cereal crop accounts for about 70% of grain endosperm and acts as an important human carbohydrate resource worldwide. Wheat reserve starch is synthesized by enzymatic machinery in endosperm cells. To identify genes involved in starch biosynthesis, we constructed 30 RNA-Seq libraries of 10 endosperm-development periods and performed expression and localization analyses. Of 166 endosperm-expressed homologs of starch biosynthesis-related genes, 74 showed expression correlated with reserve starch accumulation, including 26 with expected subcellular distribution and higher expression than their isoforms. The key proteins SUS3, UGP1, cAGPase, and Bt1-3 formed the main metabolic pathway and contributed the major substrates for starch processing in amyloplasts. Important isoforms, key pathway proteins, and the main carbon flux toward starch formation in the reserve starch biosynthesis pathway were identified. Based on a co-expression analysis, a library of 425 transcription factors was produced to screen for common regulators. TaMYB44 had features of transcription factors and bound to TaSUT1, TaSSIIIa, TaBEIIa, TaISA1, and TaBEIIb promoters in yeast, suggesting that the gene is a pathway regulator. This study sheds light on understanding the mechanism of reserve starch biosynthesis and will be helpful for increasing starch content in wheat endosperm via biotechnological strategies.

Wheat-rye T1BL·1RS translocation lines are widely used, especially in China, but their processing quality is generally poor. An interfering expression vector targeting the ω-secalin genes was constructed with the 1Bx7 seed-specific promoter. Biolistic-mediated genetic transformation of the wheat cultivar KN199 carrying the T1BL·1RS translocation generated 10 transgenic lines. Two representative transgenic lines, 8-2 and 13-7, were selected for analysis. Compared with the control, the two transformants showed an up to 4.5-fold decrease in total ω-secalins and various levels of decrease in ω-gliadins, γ-gliadins, and low-molecular-weight glutenins. A decrease in high molecular weight (HMW) glutenin 1Bx7 was detected only in 8-2, owing possibly to promoter methylation. Increased levels of α-gliadins were observed in both transformants, but increased levels of HMW glutenins were observed only in 13-7. Line 13-7 showed increases in gluten index, Zeleny sedimentation value, stabilization time, and maximum resistance. Its bread volume was 849.6 mL, an 11.9% increase over that of the control. Line 8-2 showed decreases in these parameters, but its total cake-making quality score was 88, an 17.3% increase over that of the control. The study demonstrates that the same RNAi construct may produce different effects on wheat processing quality and highlights the influence of the vector promoter in RNA interference.

Nitrogen (N), phosphorus (P), and potassium (K) are important for plant growth and development. MicroRNAs (miRNAs) play important roles in regulating plant response to nutrient (N, P, and K) deficiencies. Several miRNAs have been identified under nutrient deficiency conditions in many plant species. However, the manner in which miRNAs regulate the interaction between NPK signaling pathways under multiple nutrient deficiency remains largely unknown. We systematically compared and identified microRNAs involved in both single and triple NPK nutrient deficiency responses. We identified 32 shoot and 17 root miRNAs differentially expressed under potassium deficiency. Several NP starvation-associated miRNAs including miR169s and miR399s, were also regulated by K deficiency. Several identified miRNAs including miR5565c, miR5564, and miR1432 have not previously been associated with respectively N, P, and K deficiency (−N, −P, and −K). Expression correlation analysis between miRNAs and their predicted targets showed that miR169, miR172, and miR160 displayed expression trends exactly opposite to those of their corresponding predicted targets. Of 550 predicted novel miRNAs, novel_mir_42 was upregulated in shoots under −K but was downregulated under −N and −P. The effects of combined NPK starvation were not a simple addition of the individual stresses on sorghum seedlings. The identified common and specific differentially expressed miRNAs were observed under single and combined NPK deficiencies. These findings will help to further elucidate the functions of microRNAs and their interactions under multiple nutrient deficiency.

Heterosis is a well-known phenomenon widely applied in agriculture. Recent studies have suggested that differential gene and protein expression between hybrids and their parents play important roles in heterosis. Alternative splicing (AS) is an essential posttranscriptional mechanism that can greatly affect the transcriptome and proteome diversity in plants. However, genome-wide AS divergence in hybrids compared to their parents and its potential contribution to heterosis have not been comprehensively investigated. We report the direct profiling of the AS landscape using RNA sequencing data from immature ears of the maize hybrid ZD808 and its parents NG5 and CL11. Our results revealed a large number of significant differential AS (DAS) events in ZD808 relative to its parents, which can be further classified into parental-dominant and novel DAS patterns. Parental-dominant, especially NG5-dominant, events were prevalent in the hybrid, accounting for 42% of all analyzed DAS events. Functional enrichment analysis revealed that the NG5-dominant AS events were involved mainly in regulating the expression of genes associated with carbon/nitrogen metabolism and cell division processes and contributed greatly to maize ear heterosis. Among ZD808, CL11, and NG5, 32.5% of DAS contained or lacked binding sites of at least one annotated maize microRNA (miRNA) and may be involved in miRNA-mediated posttranscriptional regulation. Cis regulation was the predominant contributor to AS variation and participates in many important biological processes associated with immature ear development. This study provides a comprehensive view of genome-wide alternative splicing variation in a maize hybrid.

As the main byproduct of cotton fiber, the cotton seed yields about 1.6 times that of fiber, with its oil rich in unsaturated fatty acids, mainly linoleic acid. It is desirable for breeders to increase the oil content of cottonseed without affecting the yield and quality of cotton fiber. In this study, a seed-specific promoter- (alpha-globulin gene promoter-) driven GhDGAT1 overexpression vector (P_αGlob-GhDGAT1) was constructed and used to transform an upland cotton line YZ1 (Gossypium hirsutum). Overexpression of the cotton gene GhDGAT1 in cotton seeds increased its total oil content from 4.7% to 13.9% in different transgenic lines and different generations. With the increase of oil content, the composition and contents of the main fatty acids in cotton seed also changed, as reflected by the contents of the main saturated fatty acids and unsaturated oleic acid. GhDGAT1 could be used to increase oil content and improve oil composition in cottonseed.