The Saccharum genus comprises species with large and variable chromosome numbers, leading to challenges in genomic studies and breeding improvement. Cytogenetics, including classical and molecular approaches, has played a central role in deciphering the genome structure, classification, and evolution of the genus Saccharum. The application of fluorescence in situ hybridization using oligonucleotide probes significantly improved our understanding of the complex genomes of Saccharum species. This paper reviews the application and progress of cytogenetic techniques in Saccharum. Future applications of cytogenetics are discussed, as they could benefit both genomic studies and breeding of sugarcane as well as other plants with complex genomes.

Leaf, spike, stem, and root morphologies are key factors that determine crop growth, development, and productivity. Multiple genes that control these morphological traits have been identified in Arabidopsis, rice, maize, and other plant species. However, little is known about the genomic regions and genes associated with morphological traits in wheat. Here, we identified the ethyl methanesulfonate-derived mutant wheat line M133 that displays multiple morphological changes that include upward-curled leaves, paired spikelets, dwarfism, and delayed heading. Using bulked segregant RNA sequencing (BSR-seq) and a high-resolution genetic map, we identified TraesCS1D02G155200 (HB-D2) as a potential candidate gene. HB-D2 encodes a class III homeodomain-leucine zipper (HD-ZIP III) transcription factor, and the mutation was located in the miRNA165/166 complementary site, resulting in a resistant allele designated rHb-D2. The relative expression of rHb2 in the mutant plants was significantly higher (P<0.01) than in plants homozygous for the WT allele. Independent resistant mutations that disrupt the miRNA165/166 complementary sites in the A- (rHb-A2) and B-genome (rHb-B2) homoeologs showed similar phenotypic alterations, but the relative intensity of the effects was different. Transgenic plants expressing rHb-D2 gene driven by the maize UBIQUITIN (UBI) promoter showed similar phenotypes to the rHb-D2 mutant. These results confirmed that HB-D2 is the causal gene responsible for the mutant phenotypes. Finally, a survey of 1397 wheat accessions showed that the complementary sites for miRNA165/166 in all three HB2 homoeologs are highly conserved. Our results suggest that HB2 plays an important role in regulating growth and development in wheat.

The Ca²⁺/CaM signal transduction pathway helps plants adapt to environmental stress. However, our knowledge on the functional proteins of Ca²⁺/CaM pathway in peanut (Arachis hypogeae L.) remains limited. In the present study, a novel calmodulin 4 (CaM4)-binding protein S-adenosyl-methionine synthetase 1 (SAMS1) in peanut was identified using a yeast two-hybrid assay. Expression of AhSAMS1 was induced by Ca²⁺, ABA, and salt stress. To elucidate the function of AhSAMS1, physiological and phenotypic analyses were performed with wild-type and transgenic materials. Overexpression of AhSAMS1 increased spermidine and spermidine synthesis while decreased the contents of ethylene, thereby eliminating excessive reactive oxygen species (ROS) in transgenic lines under salt stress. AhSAMS1 reduced uptake of Na⁺ and leakage of K⁺ from mesophyll cells, and was less sensitive to salt stress during early seedling growth, in agreement with the induction of SOS and NHX genes Transcriptomics combined with epigenetic regulation uncovered relationships between differentially expressed genes and differentially methylated regions, which raised the salt tolerance and plants growth. Our findings support a model in which the role of AhSAMS1 in the ROS-dependent regulation of ion homeostasis was enhanced by Ca²⁺/CaM while AhSAMS1-induced methylation was regulated by CaM, thus providing a new strategy for increasing the tolerance of plants to salt stress.

Cotton (Gossypium spp.) yield is reduced by stress. In this study, high temperature (HT) suppressed the expression of the jasmonic acid (JA) biosynthesis gene allene oxide cyclase 2 (GhAOC2), reducing JA content and causing male sterility in the cotton HT-sensitive line H05. Anther sterility was reversed by exogenous application of methyl jasmonate (MeJA) to early buds. To elucidate the role of GhAOC2 in JA biosynthesis and identify its putative contribution to the anther response to HT, we created gene knockout cotton plants using the CRISPR/Cas9 system. Ghaoc2 mutant lines showed male-sterile flowers with reduced JA content in the anthers at the tetrad stage (TS), tapetum degradation stage (TDS), and anther dehiscence stage (ADS). Exogenous application of MeJA to early mutant buds (containing TS or TDS anthers) rescued the sterile pollen and indehiscent anther phenotypes, while ROS signals were reduced in ADS anthers. We propose that HT downregulates the expression of GhAOC2 in anthers, reducing JA biosynthesis and causing excessive ROS accumulation in anthers, leading to male sterility. These findings suggest exogenous JA application as a strategy for increasing male fertility in cotton under HT.

Cytokinins (CKs) function in plant development and during stress responses, but their role in drought tolerance in wheat is unknown. In the present study, 24 isopentenyltransferase (IPT) genes, encoding rate-limiting enzymes in CK biosynthesis were identified in the wheat genome. The chromosomal locations and structures of the genes, protein properties, and phylogenetic relationships were characterized. ATP/ADP TaIPT genes showed tissue-specific expression. TaIPT2, TaIPT7, and TaIPT8 expression was rapidly induced by 0.5-1 h drought treatments, which decreased to low levels after 2 h drought treatment, as did most other TaIPT genes. TaIPT8-5a/5b/5d triple mutants showed decreased levels of tZ-type CK under normal and drought conditions and reduced drought tolerance, which, however, did not manifest as phenotype alterations. By contrast, transgenic wheat plants with drought-induced TaIPT8 showed increased drought tolerance. Our study provides a foundation for further investigation of TaIPT genes and novel insights into the role of CKs in the drought response of wheat.

Alfalfa is the most widely cultivated perennial legume forage crop worldwide. Drought is one of the major environmental factors influencing alfalfa productivity. However, the molecular mechanisms underlying alfalfa responses to drought stress are still largely unknown. This study identified a drought-inducible gene of unknown function, designated as Medicago sativa DROUGHT-INDUCED UNKNOWN PROTEIN 1 (MsDIUP1). MsDIUP1 was localized to the nucleus, chloroplast, and plasma membranes. Overexpression of MsDIUP1 in Arabidopsis resulted in increased tolerance to drought, with higher seed germination, root length, fresh weight, and survival rate than in wild-type (WT) plants. Consistently, analysis of MsDIUP1 over-expression (OE) alfalfa plants revealed that MsDIUP1 also increased tolerance to drought stress, accompanied by physiological changes including reduced malondialdehyde (MDA) content and increased osmoprotectants accumulation (free proline and soluble sugar), relative to the WT. In contrast, disruption of MsDIUP1 expression by RNA interference (RNAi) in alfalfa resulted in a drought-hypersensitive phenotype, with a lower chlorophyll content, higher MDA content, and less osmoprotectants accumulation than that of the WT. Transcript profiling of alfalfa WT, OE, and RNAi plants during drought stress showed differential responses for genes involved in stress signaling, antioxidant defense, and osmotic adjustment. Taken together, these results reveal a positive role for MsDIUP1 in regulating drought tolerance.

The transport of proteins to and from the nucleus is necessary for many cellular processes and is one of the ways plants respond to developmental signals and environmental stresses. Nucleocytoplasmic trafficking of proteins is mediated by the nuclear transport receptor (NTR). Although NTR has been extensively studied in humans and Arabidopsis, it has rarely been identified and functionally characterized in rice. In this study, we identified exportin 1 in rice (OsXPO1) as a nuclear export receptor. OsXPO1 shares high protein identity with its functional homologs in Arabidopsis and other organisms. OsXPO1 localized to both the nucleus and the cytoplasm, directly interacted with the small GTPases OsRAN1 and OsRAN2 in the nucleus, and mediated their nuclear export. Loss-of-function osxpo1 mutations were lethal at the seedling stage. Suppression of OsXPO1 expression in RNA interference lines produced multifaceted developmental defects, including arrested growth, premature senescence, abnormal inflorescence, and brown and mouth-opened spikelets. Overexpression of OsXPO1 in rice reduced plant height and seed-setting rate, but increased plant tolerance in response to PEG-mimicked drought stress and salt stress. These results indicate that OsXPO1 is a nuclear export receptor and acts in regulating plant development and abiotic stress responses.

The jasmonic acid (JA) signaling pathway is involved in plant growth, development, and response to abiotic or biotic stresses. MYC2, a bHLH transcription factor, is a regulatory hub in the pathway. The function of ZmMYC7, a putative MYC2 ortholog, in jasmonate-signaled defense responses of maize has not been reported. In this study, we found that ZmMYC7 possesses JID, TAD, bHLH and Zip domains and essential characteristics of transcription factors: a nuclear location and transactivation activity. The ZmMYC7 mutants showed markedly increased sensitivity to Fusarium graminearum and Setosphaeria turcica. The expression levels of the defense-associated genes ZmPR1, ZmPR2, ZmPR3, ZmPR5, ZmPR6, and ZmPR7 in response to F. graminearum infection were downregulated in ZmMYC7 mutants, while ZmPR4 and ZmPR10 were up-regulated. ZmMYC7 interacted with members of the ZmJAZ family, including ZmJAZ8, ZmJAZ11, and ZmJAZ12. ZmMYC7 physically interacted with G-box cis-elements in the ZmERF147 promoter in vitro and transcriptional activation of ZmERF147 by ZmMYC7 was inhibited by ZmJAZ11 and ZmJAZ12. ZmERF147 mutants were more susceptible to F. graminearum infection than inbred line B73 with concomitant down-regulation of all defense-associated ZmPRs except ZmPR4. These findings indicate that ZmMYC7 functions in maize resistance to F. graminearum and sheds light on maize defense responses to pathogenic fungi via the JA signaling pathway.

The severity of Verticillium wilt on cotton caused by defoliating strains of Verticillium dahliae has gradually increased and threatens production worldwide. Identification of the molecular components of leaf defoliation may increase cotton tolerance to V. dahliae. Ethylene, a major player in plant physiological processes, is often associated with senescence and defoliation of plants. We investigated the cotton-V. dahliae interaction with a focus on the role of ethylene in defoliation and defense against V. dahliae. Cotton plants inoculated with V. dahliae isolate V991, a defoliating strain, accumulated more ethylene and showed increased disease symptoms than those inoculated with a non-defoliating strain. In cotton with a transiently silenced ethylene synthesis gene (GhACOs) and signaling gene (GhEINs) during cotton-V. dahliae interaction, ethylene produced was derived from cotton and more ethylene increased cotton susceptibility and defoliation rate. Overexpression of AtCTR1, a negative regulator in ethylene signaling, in cotton reduced sensitivity to ethylene and increased plant resistance to V. dahliae. Collectively, the results indicated precise regulation of ethylene synthesis or signaling pathways improve cotton resistant to Verticillium wilt.

Plants use a sophisticated immune system to perceive pathogen infection and activate immune responses in a tightly controlled manner. In barley, HvWRKY2 acts as a repressor in barley disease resistance to the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh). However, the molecular features of HvWRKY2 in its DNA-binding and repressor functions, as well as its target genes, are uncharacterized. We show that the W-box binding of HvWRKY2 requires an intact WRKY domain and an upstream sequence of~75 amino acids, and the HvWRKY2 W-box binding activity is linked to its repressor function in disease resistance. Chromatin immunoprecipitation (ChIP)-seq analysis identified HvCEBiP, a putative chitin receptor gene, as a target gene of HvWRKY2 in overexpressing transgenic barley plants. ChIP-qPCR and Electrophoretic Mobility Shift Assay (EMSA) verified the direct binding of HvWRKY2 to a W-box-containing sequence in the HvCEBiP promoter. HvCEBiP positively regulates resistance against Bgh in barley. Our findings suggest that HvWRKY2 represses barley basal immunity by directly targeting pathogen-associated molecular pattern (PAMP) recognition receptor genes, suggesting that HvCEBiP and likely chitin signaling function in barley PAMP-triggered immune responses to Bgh infection.

The overuse of nitrogen (N) fertilizer in fields has increased production costs and raised environmental concerns. Increasing the N use efficiency (NUE) of rice varieties is crucial for sustainable agriculture. Here we report the cloning and characterization of OsNPF3.1, a gene that controls rice NUE. An amino acid mutation in the OsNPF3.1 coding region caused different NUEs in wild and cultivated rice. OsNPF3.1, which is expressed mainly in the aerial parts of rice, also affects rice plant height, heading date, and thousand-grain weight. The OsNPF3.1 protein is located in the plasma membrane. When OsNPF3.1 was subjected to artificial selection, two naturally varying loci were associated with NUE, of which OsNPF3.1^Chr6_8741040 differed between indica and japonica rice. OsNPF3.1 can be used as a new target gene for breeding rice varieties with high NUE.

Nitrogen (N) is an essential plant growth nutrient whose coordinated distribution from source to sink organs is crucial for seed development and overall crop yield. We compared high and low N use efficiency (NUE) Brassica napus (rapeseed) genotypes. Metabonomics and transcriptomics revealed that leaf senescence induced by N deficiency promoted amino acid allocation from older to younger leaves in the high-NUE genotype at the vegetative growth stage. Efficient source to sink remobilization of amino acids elevated the numbers of branches and pods per plant under a N-deficiency treatment during the reproductive stage. A ¹⁵N tracer experiment confirmed that more amino acids were partitioned into seeds from the silique wall during the pod stage in the high-NUE genotype, owing mainly to variation in genes involved in organic N transport and metabolism. We suggest that the greater amino acid source-to-sink allocation efficiency during various growth stages in the high-NUE genotype resulted in higher yield and NUE under N deficiency. These findings support the hypothesis that strong amino acid remobilization in rapeseed leads to high yield, NUE, and harvest index.

Pea (Pisum sativum L.) is an annual cool-season legume crop. Owing to its role in sustainable agriculture as both a rotation and a cash crop, its global market is expanding and increased production is urgently needed. For both technical and regulatory reasons, neither conventional nor transgenic breeding techniques can keep pace with the demand for increased production. In answer to this challenge, CRISPR/Cas9 genome editing technology has been gaining traction in plant biology and crop breeding in recent years. However, there are currently no reports of the successful application of the CRISPR/Cas9 genome editing technology in pea. We developed a transient transformation system of hairy roots, mediated by Agrobacterium rhizogenes strain K599, to validate the efficiency of a CRISPR/Cas9 system. Further optimization resulted in an efficient vector, PsU6.3-tRNA-PsPDS3-en35S-PsCas9. We used this optimized CRISPR/Cas9 system to edit the pea phytoene desaturase (PsPDS) gene, causing albinism, by Agrobacterium-mediated genetic transformation. This is the first report of successful generation of gene-edited pea plants by this route.

ADP-glucose pyrophosphorylase (AGPase) influences cereal productivity. There are few reports on the function of cytosolic AGPase small subunit in bread wheat (TaAGPS). In the present study, TaAGPS was preferentially expressed in developing endosperm during grain-filling stages in bread wheat. TaAGPS allelic variations were characterized in 143 wheat accessions by PacBio RS II sequencing. Two haplotypes (TaAGPS-7A-TG and TaAGPS-7A-CT) of TaAGPS-7A were identified and corresponding functional markers were developed, whereas no variants of TaAGPS-7B and TaAGPS-7D were detected. TaAGPS-7A was associated with thousand-kernel weight (TKW) by haplotype-trait association analysis in two populations. Near-isogenic lines (NILs) with TaAGPS-7A-TG showed higher TKW and total kernel starch content than those with TaAGPS-7A-CT, owing to the higher AGPase activity of TaAGPS-7A-TG than TaAGPS-7A-CT both in vitro and in vivo. Overexpression of TaAGPS-7A-TG in bread wheat doubled the transcription levels of TaAGPS and increased AGPase activity by 55.7%, resulting in a 3.0-g higher TKW than in the wild type (WT). Knockdown of TaAGPS led to reduced expression of TaAGPS, AGPase activity, and TKW than in the WT. Thus, owing to the 218th amino acid change of Ser to Ala in TaAGPS-7A, the favorable haplotype TaAGPS-7A-TG showed higher AGPase activity, resulting in higher kernel starch content and grain weight. This finding could be applied to increasing starch content and grain weight in bread wheat.

Spike architecture is an indicative trait of grain yield in common wheat (Triticum aestivum). A segregating population was generated for mapping genes contributing to spike morphometric traits by crossing the two common wheat cultivars 'CItr 17600' with branching spikes and 'Yangmai 18' with normal spikes. A major quantitative trait locus for spike length was mapped to the Q5A region of chromosome 5A. Yangmai 18 carried a Q5Ab allele for short spikes, which harbored one SNP in the last intron, and a 1-bp InDel in the 720-bp fragment from the start codon, compared to Q5Aa in Chinese Spring. CItr 17600 harbored a q5Ab allele for long spikes, which has a 6-bp deletion compared to the reported q5Aa allele that was involved in the binding site of microRNA 172 (miR172). This 6-bp deletion in immediately upstream of this binding site was involved in changes of four amino acids. The natural q5A allele appeared to be rare in common wheat but frequent in tetraploid T. turgidum accessions with branching spikes. The CRISPR/Cas9 technology was used to edit the upstream region involving in the miR172 binding site in Yangmai 18 and identified two independent editing events, one with a 1-bp insertion in Q5A and the other with a 2-bp deletion in Q5D, resulting in several shapes of spikes in the transgenic progeny. In addition to the effects of natural q5A allele and the edited Q5A genes, this study indicated the regeneratability and transformability of Yangmai 18 as an elite cultivar. Altogether, this study provides insight into future modification and engineering of spike architecture in common wheat.

Gene resources associated with plant stature and flowering time are invaluable for maize breeding. In this study, using an F_2:3 population derived from a natural semi-dwarf mutant grmm and a normal inbred line Si 273, we identified a major pleiotropic QTL on the distal long arm of chromosome 1 (qPH1_dla), and found that qPH1_dla controlled plant height, flowering time, ear and yield traits. qPH1_dla was fine-mapped to a 16 kb interval containing ZmAMP1, which was annotated as a glutamate carboxypeptidase. Allelism tests using two independent allelic mutants confirmed that ZmAMP1 was the causal gene. Real-time quantitative PCR and genomic sequence analysis suggested that a nonsynonymous mutation at the 598th base of ZmAMP1 gene was the causal sequence variant for the dwarfism of grmm. This novel ZmAMP1 allele was named ZmAMP1_grmm. RNA sequencing using two pairs of near isogenic lines (NILs) showed that 84 up-regulated and 68 down-regulated genes in dwarf NILs were enriched in 15 metabolic pathways. Finally, introgression of ZmAMP1_grmm into Zhengdan 958 and Xianyu 335 generated two improved F₁ lines. In field tests, they were semi-dwarf, early-flowering, lodging-resistant, and high-yielding under high-density planting conditions, suggesting that ZmAMP1_grmm is a promising Green Revolution gene for maize hybrid breeding.

To extend the contemporary understanding into the grain yield heterosis of wheat, the current study investigated the contribution of deleterious alleles in shaping mid-parent heterosis (MPH). These alleles occur at low frequency in the genome and are often missed by automated genotyping platforms like SNP arrays. The deleterious alleles herein were detected using a quantitative measurement of evolutionary conservation based on the phylogeny of wheat and investigations were made to: (1) assess the benefit of including deleterious alleles into MPH prediction models and (2) understand the genetic underpinnings of deleterious SNPs for grain yield MPH using contrasting crosses viz. elite × elite (Exp. 1) and elite × plant genetic resources (PGR; Exp. 2). In our study, we found a lower allele frequency of moderately deleterious alleles in elites compared to PGRs. This highlights the role of purifying selection for the development of elite wheat cultivars. It was shown that deleterious alleles are informative for MPH prediction models: modelling their additive-by-additive effects in Exp. 1 and dominance as well as associated digenic epistatic effects in Exp. 2 significantly boosts prediction accuracies of MPH. Furthermore, heterotic- quantitative trait loci's underlying MPH was investigated and their properties were contrasted in the two crosses. Conclusively, it was proposed that incomplete dominance of deleterious alleles contributes to grain yield heterosis in elite crosses (Exp. 1).

“Breeding by design”? for pure lines may be achieved by construction of an additive QTL-allele matrix in a germplasm panel or breeding population, but this option is not available for hybrids, where both additive and dominance QTL-allele matrices must be constructed. In this study, a hybrid-QTL identification approach, designated PLSRGA, using partial least squares regression (PLSR) for model fitting integrated with a genetic algorithm (GA) for variable selection based on a multi-locus, multi-allele model is described for additive and dominance QTL-allele detection in a diallel hybrid population (DHP). The PLSRGA was shown by simulation experiments to be superior to single-marker analysis and was then used for QTL-allele identification in a soybean DPH yield experiment with eight parents. Twenty-eight main-effect QTL with 138 alleles and nine QTL×environment QTL with 46 alleles were identified, with respective contributions of 61.8% and 23.5% of phenotypic variation. Main-effect additive and dominance QTL-allele matrices were established as a compact form of the DHP genetic structure. The mechanism of heterosis superior-to-parents (or superior-to-parents heterosis, SPH) was explored and might be explained by a complementary locus-set composed of OD+ (showing positive over-dominance, most often), PD+ (showing positive partial-to-complete dominance, less often) and HA+ (showing positive homozygous additivity, occasionally) loci, depending on the parental materials. Any locus-type, whether OD+, PD+ and HA+, could be the best genotype of a locus. All hybrids showed various numbers of better or best genotypes at many but not necessarily all loci, indicating further SPH improvement. Based on the additive/dominance QTL-allele matrices, the best hybrid genotype was predicted, and a hybrid improvement approach is suggested. PLSRGA is powerful for hybrid QTL-allele detection and cross-SPH improvement.

Seed number per silique (SNPS) is one of seed yield components in rapeseed, but its genetic mechanism remains elusive. Here a double haploid (DH) population derived from a hybrid between female 6Q006 with 35-40 SNPS and male 6W26 with 10-15 SNPS was investigated for SNPS in the year 2017, 2018, 2019 and 2021, and genotyped with Brassica 60K Illumina Infinium SNP array. An overlapping major QTL (qSNPS.C09) explaining 51.50% of phenotypic variance on average was narrowed to a 0.90 Mb region from 44.87 Mb to 45.77 Mb on chromosome C09 by BSA-seq. Subsequently, two DEGs in this interval were detected between extreme individuals in DH and F₂ populations by transcriptome sequencing at 7 and 14 days after pollination siliques. Of which, BnaC09g45400D encoded an adenine phosphoribosyltransferase 5 (APT5) has a 48-bp InDel variation in the promoter of two parents. Candidate gene association analysis showed that this InDel variation was associated with SNPS in a nature population of rapeseed, where 54 accessions carrying the same haplotype as parent 6Q006 had higher SNPS than 103 accessions carrying the same haplotype as parent 6W26. Collectively, the findings are helpful for rapeseed molecular breeding of SNPS, and provide new insight into the genetic and molecular mechanism of SNPS in rapeseed.

Grain size is a key factor influencing grain yield and appearance quality in rice. We identified twelve quantitative trait loci (QTL) for grain length (GL), nine for grain width (GW), and nine for 1000-kernel weight (TKW) using GLU-SSSLs, which are single-segment substitution lines with Oryza glumaepatula as donor parent and Huajingxian 74 (HJX74) as recipient parent. Among the QTL, qGL1-2, qGL1-4, qGL9-2, qGW2-2, qGW9-1 and qTKW9-2 contributed to high grain yield. GL9 was identified as a candidate gene for qGL9-2 by map-based cloning and sequencing, and is a novel allele of GS9. The kernel of NIL-gl9 was slenderer and longer than that of HJX74, and the TKW and grain yield per plant of NIL-gl9 were higher than those of HJX74. The proportion of grain chalkiness of NIL-gl9 was much lower than that of HJX74. Thus, gl9 increased grain yield and appearance quality simultaneously. Three pyramid lines, NIL-gs3/gl9, NIL-GW7/gl9 and NIL-gw8/gl9, were developed and the kernel of each was longer than that of the corresponding recipient parent lines. The gl9 allele may be beneficial for breeding rice varieties with high grain yield and good appearance quality.

Variation in patterns of recombination in plant genomes provides information about species evolution, genetic diversity and crop improvement. We investigated meiotic crossovers generated in biparental segregating and reciprocal backcross populations of the allopolyploid genome of rapeseed (Brassica napus) (AACC, 2n= 38). A structured set of 1445 intercrossed lines was derived from two homozygous de novo genome-assembled parents that represented the major genetic clusters of semi-winter Chinese and winter European rapeseeds, and was used to increase QTL resolution and achieve genomic reciprocal introgression. A high-density genetic map constructed with 6161 genetic bins and anchored centromere regions was used to establish the pattern of recombination variation in each chromosome. Around 93% of the genome contained crossovers at a mean rate of 3.8 Cm Mb^-1, with the remaining 7% attributed to centromeres or low marker density. Recombination hotspots predominated in the A genome, including two-thirds of those associated with breeding introgression from B. rapa. Genetic background might affect recombination variation. Introgression of genetic diversity from European winter to Chinese semi-winter rapeseed showed an increase in crossover rate under the semi-winter environment. Evidence for an elevated recombination rate having historically contributed to selective trait improvement includes accumulation of favorable alleles for seed oil content on hotspots of chromosome A10. Conversely, strong artificial selection may affect recombination rate variation, as appears to be the case with a coldspot resulting from strong selection for glucosinolate alleles on A09. But the cold region would be promptly reactivated by crossing design indicated by the pedigree analysis. Knowledge of recombination hotspots and coldspots associated with QTL for 22 traits can guide selection strategies for introgression breeding between the two gene pools. These results and rich genomic resources broaden our understanding of recombination behavior in allopolyploids and may advance rapeseed genetic improvement.

Stalk strength increases resistance to stalk lodging, which causes maize (Zea mays L.) production losses worldwide. The genetic mechanisms regulating stalk strength remain unclear. In this study, three stalk strength-related traits (rind penetrometer resistance, stalk crushing strength, and stalk bending strength) and four plant architecture traits (plant height, ear height, stem diameter, stem length) were measured in three field trials. Substantial phenotypic variation was detected for these traits. A genome-wide association study (GWAS) was conducted using general and mixed linear models and 372,331 single-nucleotide polymorphisms (SNPs). A total of 94 quantitative trait loci including 241 SNPs were detected. By combining the GWAS data with public gene expression data, 56 candidate genes within 50 kb of the significant SNPs were identified, including genes encoding flavonol synthase (GRMZM2G069298, ZmFLS2), nitrate reductase (GRMZM5G878558, ZmNR2), glucose-1-phosphate adenylyltransferase (GRMZM2G027955), and laccase (GRMZM2G447271). Resequencing GRMZM2G069298 and GRMZM5G878558 in all tested lines revealed respectively 47 and 2 variants associated with RPR. Comparison of the RPR of the zmnr2 EMS mutant and the wild-type plant under high- and low-nitrogen conditions verified the GRMZM5G878558 function. These findings may be useful for clarifying the genetic basis of stalk strength. The identified candidate genes and variants may be useful for the genetic improvement of maize lodging resistance.

Wide hybridization is a strategy for broadening the genetic basis of wheat. Because an efficient method for inducing wheat-alien chromosome translocations will allow producing useful germplasm, it is desirable to discover new genes that induce chromosomal variation. In this study, chromosome 5P from A. cristatum was shown to induce many types of chromosomal structural variation in a common wheat background, including nonhomoeologous chromosome translocations, as revealed by genomic in situ hybridization, fluorescence in situ hybridization, and DNA marker analysis. Aberrant meiosis was associated with chromosomal structural variation, and aberrant meiotic behavior was observed in wheat-A. cristatum 5P monosomic and disomic addition lines, suggesting that the effect of chromosome 5P was independent of the number of chromosome 5P copies. Chromosome 5P disturbed homologous chromosome pairing at pachytene stage in a common wheat background, resulting in a high frequency of univalent formation and reduced crossing over. Thirteen genes involved in DNA repair or chromatin remodeling, including RAD52-like and MSH6 genes, were differentially expressed (upregulated) in wheat-A. cristatum 5P addition lines according to transcriptome analysis, implicating chromosome 5P in the process of meiotic double-strand break repair. These findings provide a new, efficient tool for inducing wheat–alien chromosome translocations and producing new germplasm.

Oligo probe staining is a low-cost and efficient chromosome identification technique. In this study, oligo genomic in situ hybridization (Oligo-GISH) technology was established in peanut. Peanut A and B subgenome-specific interspersed repeat (IR) oligo probe sets were developed based on clustering and electronic localization of tandem repeat sequences in the reference genome of Tifrunner. The Oligo-GISH kit was then used to perform staining of 15 Arachis species. The A-subgenome probe set stained the chromosomes of A- and E-genome Arachis species, the B-subgenome probe set stained those of B-, F-, K-, and E-genome species, and neither set stained those of H-genome species. These results indicate the relationships among the genomes of these Arachis species. The Oligo-GISH kit was also used for batch staining of the chromosomes of 389 seedlings from the irradiated M₁ generation, allowing 67 translocation and deletion lines to be identified. Subsequent Oligo-FISH karyotyping, FISH using single-copy probe libraries, and trait investigation identified seven homozygous chromosomal variants from the M₃ generation and suggested that there may be genes on chromosome 4B controlling seed number per pod. These findings demonstrate that the IR probe sets and method developed in this study can facilitate research on distant hybridization and genetic improvement in peanut.

Maize kernel moisture content (KMC) at harvest greatly affects mechanical harvesting, transport and storage. KMC is correlated with kernel dehydration rate (KDR) before and after physiological maturity. KMC and KDR are complex traits governed by multiple quantitative trait loci (QTL). Their genetic architecture is incompletely understood. We used a multiomics integration approach with an association panel to identify genes influencing KMC and KDR. A genome-wide association study using time-series KMC data from 7 to 70 days after pollination and their transformed KDR data revealed respectively 98 and 279 loci significantly associated with KMC and KDR. Time-series transcriptome and proteome datasets were generated to construct KMC correlation networks, from which respectively 3111 and 759 module genes and proteins were identified as highly associated with KMC. Integrating multiomics analysis, several promising candidate genes for KMC and KDR, including Zm00001d047799 and Zm00001d035920, were identified. Further mutant experiments showed that Zm00001d047799, a gene encoding heat shock 70 kDa protein 5, reduced KMC in the late stage of kernel development. Our study provides resources for the identification of candidate genes influencing maize KMC and KDR, shedding light on the genetic architecture of dynamic changes in maize KMC.

Lodging is a critical constraint to yield increase. There appear to be tradeoffs between yield formation and lodging resistance in maize. Hypothetically, it is feasible to reduce lodging risk as well as increase grain yield by optimizing dry-matter allocation to different organs under different environments. A three-year field experiment was conducted using four maize cultivars with differing lodging resistances and five growing environments in 2018-2020. Lodging-susceptible (LS) cultivars on average yielded more than lodging-resistant (LR) cultivars when lodging was not present. The yield components kernel number per ear (KN) and thousand-kernel weight (TKW) were both negatively correlated with lodging resistance traits (stalk bending strength, rind penetration strength, and dry matter weight per internode length). Before silking, the LR cultivar Lishou 1 (LS1) transported more assimilates to the basal stem, resulting in a thicker basal stem, which reduced dry matter allocation to the ear and in turn KN. The lower KN of LS1 was also due partly to the lower plant height (PH), which increased lodging resistance but limited plant dry matter production. In contrast, the LS cultivars Xianyu 335 (XY335) and Xundan 20 (XD20) produced and allocated more photoassimilates to ears, but limited dry matter allocation to stems. After silking, LS cultivars showed higher TKW than LR cultivars as a function of high photoassimilate productivity and high assimilate allocation to the ear. The higher lodging resistance of LS1 was due mainly to the greater assimilate allocation to stem after silking and lower PH and ear height (EH). High-yielding and high-LR traits of Fumin (FM985) were related to optimized EH and stem anatomical structure, higher leaf productivity, low assimilate demand for kernel formation, and assimilate partitioning to ear. A high pre-silking temperature accelerated stem extension but reduced stem dry matter accumulation and basal stem strength. Post-silking temperature influences lodging resistance and yield more than other environmental factors. These results will be useful in understanding the tradeoffs between KN, KW, and LR in maize and environmental influences on these tradeoffs.

A field experiment was performed to investigate the physiological mechanism of the simultaneous stresses of waterlogging and shading on leaf photosynthetic and senescence during three growth stages of summer maize. The responses of leaf gas exchange parameters and antioxidant enzyme activities of the summer maize hybrids Denghai 605 (DH605) to waterlogging (W), shading (S), and their combination (W+ S) for 6 days at the third leaf stage (V3), the sixth leaf stage (V6), and the tasseling stage (VT) were recorded. Shading, waterlogging, and their combination disturbed the activities of protective enzymes and increased the contents of H₂O₂ and O₂^-, accelerating leaf senescence and disordering photosynthetic characteristics. Under waterlogging, shading and their combination, leaf P_n, the photo-assimilates and grain yield was decreased. The greatest reduction for waterlogging and the combined stresses occurred at V3 and that for shading stress occurred at VT. The individual and combined stresses reduced the activities of protective enzymes and inhibited photosynthesis, reducing the accumulation of photosynthetic compounds and thereby yield. Waterlogging and the combined stresses at the V3 stage showed the greatest effect on leaf photosynthetic and senescence, followed by the V6 and VT stages. The greatest effect for shading stress occurred at VT, followed by the V6 and V3 stages, and the combined influence of shading and waterlogging was greater than that of either single stress.

Drought stress caused by insufficient irrigation or precipitation impairs agricultural production worldwide. In this study, a two-year field experiment was conducted to investigate the effect of coronatine (COR), a functional analog of jasmonic acid (JA), on maize drought resistance. The experiment included two water treatments (rainfed and irrigation), four COR concentrations (mock, 0 μmol L^-1; A1, 0.1 μmol L^-1; A2, 1 μmol L^-1; A3, 10 μmol L^-1) and two maize genotypes (Fumin 985 (FM985), a drought-resistant cultivar and Xianyu 335 (XY335), a drought-sensitive cultivar). Spraying 1 μmol L^-1 COR at seedling stage increased surface root density and size, including root dry matter by 12.6%, projected root area by 19.0%, average root density by 51.9%, and thus root bleeding sap by 28.2% under drought conditions. COR application also increased leaf area and SPAD values, a result attributed to improvement of the root system and increases in abscisic acid (ABA), JA, and salicylic acid (SA) contents. The improvement of leaves and roots laid the foundation for increasing plant height and dry matter accumulation. COR application reduced anthesis and silking interval, increasing kernel number per ear. COR treatment at 1 μmol L^-1 increased the yield of XY335 and FM985 by 7.9% and 11.0%, respectively. Correlation and path analysis showed that grain yields were correlated with root dry weight and projected root area, increasing maize drought resistance mainly via leaf area index and dry matter accumulation. Overall, COR increased maize drought resistance mainly by increasing root dry weight and root area, with 1 μmol L^-1 COR as an optimal concentration.

Abiotic stress such as high temperature at flowering is one of many conditions reducing yield of corn (Zea mays L.). Mixing corn cultivars with diverse functional traits increases within-crop diversity and provides a potential means of mitigating yield losses under stress conditions. We conducted a three-year field study to investigate the effects of cultivar mixtures on kernel setting rate, pollen sources, and yield. This study consisted of six treatments, including two high temperature-tolerant (HTT) monocrops of WK702 and DH701, two high temperature-sensitive (HTS) monocrops of DH605 and DH662, and two HTT-HTS mixtures of WK702-DH605 and DH701-DH662. The anthesis-silking interval (ASI) was 0.9-1.6 days shorter in mixtures than in monocrops. Kernel setting rate was increased in mixtures (86.4%-88.7%) compared with those in monocrops (74.7%-84.1%) as a result of synchrony and complementarity of pollination. Grain yields of the HTT-HTS mixtures increased by 13.3%-18.7%, equivalent to 1169 to 1605 kg ha⁻¹, in comparison with HTS corn monocrops. The results of SSR markers showed that cross-fertilization percentage in corn cultivar mixtures ranged from 29.3% to 47.8%, partially explaining yield improvement. Land equivalent ratio (LER) was 1.12 for corn mixtures and the partial land equivalent ratio (e.g., > 0.5) showed the complementary benefits in corn mixtures. The results indicated that mixing corn cultivars with diverse flowering and drought-tolerance traits increased yields via pollination synchrony.

The key to high-yielding peanut cultivation is the optimization of agricultural production practices. Regulating single-seed precise sowing (SSPS) density and paclobutrazol (P_bz) application concentration are effective practices that increase peanut yield by improving plant architecture, lodging resistance, and photosynthetic characteristics. Therefore, we conducted a two-factor field optimization experiment for the sowing density (D₁: 1.95 × 10⁵ plants ha⁻¹, D₂: 2.40 × 10⁵ plants ha⁻¹, D₃: 2.85 × 10⁵ plants ha⁻¹, and D₄: 3.30 × 10⁵ plants ha⁻¹) and P_bz application concentration (P₀: 0 mg L⁻¹ and P₁: 100 mg L⁻¹). The objective was to optimize agricultural production practices and provide a theoretical basis for high-yielding peanut cultivation by evaluating the effects of sowing density and P_bz application on plant architecture, lodging resistance, photosynthetic characteristics, and yield. The results showed that at the same P_bz application concentration, increasing sowing density increased lodging percentage and reduced leaf photosynthetic capacity. At the same sowing density, P_bz application reduced lodging percentage by decreasing plant height (PH), improving lignin biosynthesis-related enzyme activities, and enhancing stem puncture strength (SPS) and breaking strength (SBS). The paclobutrazol-induced alterations in plant architecture and lodging resistance improved light transmission at the middle and bottom leaf strata, resulting in the increase in relative chlorophyll content and net photosynthetic rate (P_n) of leaves. Furthermore, D₃P₁ treatment had the highest peanut yield among all treatments. In summary, the production strategy combining the sowing density of 2.85 × 10⁵ plants ha⁻¹ with the application of 100 mg L⁻¹ P_bz was found to be the optimal agricultural production practice for giving full play to production potential and achieving higher peanut yield.

A fast and efficient recognition method of transgenic lines will greatly improve detection efficiency and reduce cost. In this study, we successfully identified the transgenic soybean plants by the color. We isolated a GmW1 gene encoding a flavonoid 3′5′-hydroxylase from a soybean cultivar ZH42 (purple flower). We found that purple flowers occurred in the overexpression lines in the Jack and Williams 82 backgrounds (white flower). All plants with purple flowers were positive, and this trait seems stably inherited in the offspring. We have also obtained the editing plants, which were classified into three types according to the different flower colors appeared. We analyzed the phenotype and the homozygous types of the T₁ mutants. We also found that a correspondence between flower color and stem color. This study provides a visible color reporter on soybean transformation. It can be quickly and early to identify the transgenic soybean plants by stem color of seedlings, which substantially reduces the amount of labor and cost.

Yield losses of bread wheat due to crown rot can be more severe when drought conditions occur during the grain-filling period. Root architecture characteristics are important for soil exploration and below-ground resource acquisition and are essential for adaptation to water-limited environments. Traits such as root angle, length and density have been strongly associated with acquisition efficiency and contribute to yield stability of the crop. The impact of crown rot pathogens on wheat root architecture is poorly understood. We examined differences in root angle, length and number, as well as dry root weight of the crown rot-susceptible bread wheat cultivar, Livingston inoculated with one of two crown rot pathogens Fusarium culmorum or Fusarium pseudograminearum in a transparent-sided root observation chamber. Significant adverse impacts on plant health and growth were revealed by visual discolouration of the leaf sheaths; fresh and dry shoot weight; leaf area of the oldest and the youngest fully expanded leaf and leaf number. Values of most recorded root system measurements were reduced when inoculated with either F. culmorum or F. pseudograminearum. In contrast, root angle was increased in the presence of F. culmorum but was not significantly changed by F. pseudograminearum. The development of whiteheads and grain losses in bread wheat caused by crown rot have previously been associated with blockages of the vascular systems. The method employed here was able to identify differences in the pathogen impacts on roots, which were not detected using previous systems. This research indicates that in the presence of F. culmorum and F. pseudograminearum infection, not only reductions in the size and biomass of the shoot system but also changes in the length, biomass and architecture of the root system could play an important role in yield loss.