To address the global demand for rapeseed while considering farmers' profit, we face the challenges of making a quantum leap in seed yield and, at the same time, reducing yield loss due to biotic and abiotic stresses. We also face the challenge of efficiently applying new transformative biotechnology tools such as gene editing and breeding by genome design to increase rapeseed productivity and profitability. In this Perspective, we review advances in research on the physiological and genetic bases of both stress factors-affected yield stability and seed yield potential, focusing on source-sink relationships and allocation of photosynthetic assimilates to vegetative growth and seed development. We propose research directions and highlight the role of plant architecture in the relative contributions of the root system, leaves, and pods to seed yield. We call for de novo design of new rapeseed crops. We review trait variation in existing germplasm and biotechnologies available for crop design. Finally, we discuss opportunities to apply fundamental knowledge and key germplasm to rapeseed production and propose an ideotype for de novo design of future rapeseed cultivars.

Chloroplasts are essential for plant growth and development, as they play a key role in photosynthesis. The chloroplast biogenesis process is complex and its regulatory mechanism remains elusive. We characterized a spontaneous Brassica napus (rapeseed) mutant, ytg, that showed a delayed greening phenotype in all green organs and retarded growth. We identified BnaA02.YTG1 encoding a chloroplast-localized tetratricopeptide repeat protein widely expressed in rapeseed tissues. We speculated that the ytg phenotype was caused by the deletion of BnaA02.YTG1 based on sequence comparison of 4608 (with normal green leaves, isolated from the elite Chinese rapeseed cultivar ZS11) and ytg combined with transcriptome data and CRISPR/Cas9 gene editing results. The homologous gene (BnaC02.YTG1) restored the phenotype of the mutant. BnaA02.YTG1 interacted with MORF2, MORF8, and OZ1. RNA editing of the ndhD-2, ndhF-290, petL-5, and ndhG-50 plastid transcripts was affected in ytg. These findings suggested that BnaA02.YTG1 participates in RNA editing events. We predicted 29 RNA editing sites in the chloroplast of Brassica napus by comparison with the Arabidopsis chloroplast genome. We conclude that BnaA02.YTG1 affects the posttranscriptional regulation of plastid gene expression and suggest that a tetratricopeptide repeat protein is involved in the chloroplast RNA editing in rapeseed.

The release of mitochondrial genome sequences provides the basis for characterizing interspecific and intraspecific variation in Brassica mitochondrial genomes. However, few B. juncea (mustard) mitochondrial genomes have been published. We assembled the mitochondrial genomes of three B. juncea subspecies and compared them with previously published genomes. The genomes were phylogenetically classified into A, B, C, and Bna clades. Two variant sites, a transversion (C â†' A) at nt 79,573 and a 31-bp copy-number variation between nts 65,564 and 65,596, were identified. Based on these variant sites, mitotype-specific sequence markers were developed to characterize the variation among worldwide 558 B. juncea accessions. Three mitochondrial genome types (mitotypes MT1-MT3) were identified. In terms of geographical distribution, MT1 and MT2 accessions were distributed mainly to the north and MT3 to the south of 34°N. Root mustards carried only MT1, leaf and stem mustards carried mainly MT3, and seed mustards carried all three mitotypes, implying that the mitotypes underwent selection during B. juncea domestication. A new form of oil mustard evolved by hybridization between two gene pools in southwest China.

Silique length influences seed yield in oilseed rape. It shows extensive variation in germplasm resources, and identifying the underlying genes and regulatory mechanisms would advance breeding for the trait. In the present study, a genome-wide association study (GWAS) using 331 core accessions planted in 10 environments revealed 13 loci associated with silique length on chromosomes A01, A04, A07, A09, and C03, explaining 6.2%-19.2% of phenotypic variance. Physiological analysis showed that silique length variation was attributable to differences in silique growth rate and/or duration before four weeks after flowering, with levels of endogenous phytohormones (auxin, ethylene, and GA24, GA12, and GA44) playing an important role. Cytological analysis showed that silique length variation was due mainly to differences in cell number followed by cell size. Transcriptomic analysis of two pools of silique walls with opposite length extremes revealed 3248 differentially expressed genes (DEGs). These DEGs were enriched in several pathways (such as cell wall, cell division, and hormone metabolism) associated with cell proliferation and expansion and silique development. Integrating GWAS, RNA-seq, and functional annotation results revealed 15 candidate genes for the major associated locus qSL.A09-3. Of these, BnaA9.ARF18 and BnaA9.CYP78A9 were validated by haplotype analysis followed by candidate gene association. Sequence variation in the coding region of BnaA9.ARF18 and expression of BnaA9.CYP78A9 in silique walls were strongly associated with silique length. Our results provide an explanation for the natural variation of silique length in oilseed rape germplasm and offer useful information for its improvement.

Rapeseed (Brassica napus) supplies about half of the vegetable oil in China. Increasing oil production and searching for genes that control oil content in the crop are research goals. In our previous studies, four major QTL for oil content located on A08, A09, C03 and C06 in the KenC-8 × N53-2 (KN DH) mapping population were detected. The parental lines were resequenced to identify structural variations and candidate genes affecting oil content in these four major QTL regions. Insertion-deletion (InDel) markers were developed and used to narrow the regions. Differentially expressed genes located in the regions were investigated. GO and KEGG analysis showed that several genes were associated with lipid metabolism. Several transcription factors with higher expression in N53-2 than in KenC-8 were identified. These results shed light on the genetic control of oil content and may be helpful for the development of high-oil-content cultivars.

Pod shattering causes severe yield loss in rapeseed (Brassica napus L.) under modern agricultural practice. Identification of highly shatter-resistant germplasm is desirable for the development of rapeseed cultivars for mechanical harvesting. In the present study, an elite line OR88 with strong shatter resistance and a lignified-layer bridge (LLB) structure was identified. The LLB structure was unique to OR88 and co-segregated with high pod-shatter resistance. The LLB structure is differentiated at stage 12 of gynoecium development without any gynoecium defects. Genetic analysis showed that LLB is controlled by a single recessive gene. By BSA-Seq and map-based cloning, the resistance gene location was delimited to a 0.688Â Mb region on chromosome C09. Transcriptome analysis suggested BnTCP8.C09 as the gene responsible for LLB. The expression of BnTCP.C09 was strongly downregulated in OR88, suppressing cell proliferation in the pod valve margin. KASP markers linked to the candidate gene were developed. This pod shatter-resistant line could be used in rapeseed breeding programs by direct transfer of the gene with the assistance of the DNA markers.

Brassica crops, which are of worldwide importance, provide various oil, vegetable and ornamental products, as well as feedstocks for animal husbandry and biofuel industry. Cinnamoyl-CoA reductase (CCR) is the entry point to the lignin pathway and a crucial locus in manipulation of associated traits, but CCR-associated metabolism and traits in Brassica crops have remained largely unstudied except in Arabidopsis thaliana. We report the identification of 16 CCR genes from Brassica napus and its parental species B. rapa and B. oleracea. The BnCCR1 and BnCCR2 subfamilies displayed divergent organ-specificity and participation in the yellow-seed trait. Their functions were dissected via overexpression of representative paralogs in B. napus. BnCCR1 was expressed preferentially in G- and H-lignin biosynthesis and vascular development, while BnCCR2 was expressed in S-lignin biosynthesis and interfascicular fiber development. BnCCR1 showed stronger effects on lignification-related development, lodging resistance, phenylpropanoid flux control, and seed coat pigmentation, whereas BnCCR2 showed a stronger effect on sinapate biosynthesis. BnCCR1 upregulation delayed bolting and flowering time, while BnCCR2 upregulation weakened the leaf vascular system in consequence of suppressed G-lignin accumulation. BnCCR1 and BnCCR2 were closely but almost oppositely linked with glucosinolate metabolism via inter-pathway crosstalk. We conclude that BnCCR1 and BnCCR2 subfamilies offer great but differing potential for manipulating traits associated with phenylpropanoids and glucosinolates. This study reveals the CCR1-CCR2 divergence in Brassicaceae and offers a resource for rapeseed breeding for lodging resistance, yellow-seed traits, and glucosinolate traits.

Sclerotinia sclerotiorum is generally considered one of the most economically damaging pathogens in oilseed rape (Brassica napus). Breeding for Sclerotinia resistance is challenging, as no immune germplasm available in B. napus. It is desirable to develop new breeding strategies. In the present study, host-induced gene silencing (HIGS), developed based on RNA interference (RNAi), was applied to protect B. napus from S. sclerotiorum infection. Three pathogenicity genes, the endo-polygalacturonase gene (SsPG1), cellobiohydrolase gene (SsCBH), and oxaloacetate acetylhydrolase gene (SsOAH1), were chosen as HIGS targets. Co-incubation of synthesized double-stranded RNAs (dsRNAs) with S. sclerotiorum in liquid medium significantly reduced the transcript levels of the target genes. Application to plant surfaces of dsRNA targeting the three genes conferred effective protection against S. sclerotiorum. Stable transgenic B. napus plants expressing small interfering RNAs with sequence identity to SsPG1, SsCBH, and SsOAH1 were generated. HIGS transgenic B. napus prevented the expression of S. sclerotiorum target genes, slowed pathogenicity-factor accumulation, impeded fungal growth, and suppressed appressorium formation, thereby conferring resistance to S. sclerotiorum. Simultaneous silencing of SsPG1, SsCBH, and SsOAH1 by stable expression of a chimeric hairpin RNAi construct in B. napus led to enhanced protection phenotypes (with disease lesion size reduced by 36.8%-43.7%). We conclude that HIGS of pathogenic-factor genes of S. sclerotiorum is a promising strategy for controlling Sclerotinia rot in oilseed rape.

A narrow genetic base has hindered improvement of Brassica juncea (A^jA^jB^jB^j). In this study, large-scale genomic components were introduced from diploid ancestor species into modern B. juncea using a digenomic hexaploid strategy. The hexaploids A^jA^jA^rA^rB^jB^j and A^jA^jB^jB^jBⁿBⁿ were first developed from B. juncea × B. rapa (A^rA^r) and B. juncea × B. nigra (BⁿBⁿ), and then crossed with dozens of B. nigra and B. rapa, respectively. Both types of hexaploid showed high pollen fertility and moderate seed set throughout the S₁ to S₃ generations, and could be crossed with diploid progenitor species under field conditions, in particular for the combination of A^jA^jB^jB^jBⁿBⁿ × B. rapa. Thirty A^jA^rBⁿB^j-type and 31 A^jA^rBⁿB^j-type B. juncea resources were generated, of which the A^jA^rBⁿB^j type showed higher fertility. Of these new-type B. juncea resources, 97 individual plants were genotyped with 42 simple sequence repeat markers, together with 16 current B. juncea accessions and 30 hexaploid plants. Based on 180 polymorphic loci, the new-type B. juncea resources and current B. juncea were separated clearly into distinct groups, with large genetic distance between the new-type B. juncea resources and current B. juncea. Our study provides a novel approach to introducing large-scale genomic components from diploid ancestor species into B. juncea.

Biological yield indicates the potential for increasing yield. Leaf carbon metabolism plays an important role in the biomass accumulation of rapeseed (Brassica napus L.). Field experiments with the hybrid HZ62 (with a conventional plant architecture) grown in 2016-2017, and HZ62 and accession 1301 (with a compact plant architecture) grown in 2017-2018 were conducted to characterize the physiological and proteomic responses of leaf photosynthetic carbon metabolism to density and row spacing configurations. The densities were set at 15×10⁴ ha^-1 (D1), 30×10⁴ ha^-1 (D2), and 45×10⁴ ha^-1 (D3) (main plot), with row spacings of 15 cm (R15), 25 cm (R25), and 35 cm (R35) (subplot). Individual and plant population biomass accumulation was greatest at R25, R15, and R15 for D1, D2, and D3, respectively, for both genotypes. In comparison with D1R25, the individual aboveground biomass of HZ62 decreased by 60.2%, whereas the population biomass increased by 31.9%, and the individual biomass of genotype 1301 decreased by 54.0% and the population biomass increased by 53.9% at D3R15. Leaf carbon metabolic enzymes varied between genotypes at flowering stage. In contrast to D1R25, at D3R15 the activities of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and sucrose phosphate synthase (SPS) and the contents of starch, sucrose and soluble sugars in leaves were significantly decreased in HZ62 and increased in genotype 1301. The activities of fructose-1,6-bisphosphatase (FBPase) decreased, in consistency with the abundance of fructose-bisphosphate aldolase in HZ62. In contrast, sucrose synthase (SuSy) activity appeared to decrease in both genotypes, but a significant increase in abundance of a protein with sucrose synthase was found in the 1301 genotype by proteomic analysis. With increased density and reduced row spacing, the expression of most key proteins involved in carbon metabolism was elevated, and enzyme activity and carbon assimilate content were increased in 1301, whereas HZ62 showed the opposite trend, indicating that the compact plant type can accumulate more population biomass with denser planting.

Coleorhiza hairs are hairlike structures in seeds of the grass family (Poaceae). The molecular mechanisms underlying its formation are largely unknown, study on this topic will expand our understanding of the effects of water status on germination during rice (Oryza sativa L.) direct seeding. Seeds of Nipponbare were treated under two water conditions: in one, half of the seed surface was immersed in water and the other half was embryo side in air (EIA), and in the other, the whole seed was covered by water (CBW). Coleorhiza hairs formed only in EIA samples. Transcriptomics was used to identify the gene regulation during coleorhiza hair formation in EIA (vs. CBW) embryos and endosperm. Embryos displayed more transcriptome modulation even though smaller in size than the endosperm. Differentially expressed genes (DEGs) were enriched in both primary and secondary metabolism and showed changes in abscisic acid, auxin, jasmonic acid, and salicylic acid signatures. Metabolites enrichment data were positively correlated with gene expression changes in the affected metabolic functional pathways. The presence of shorter coleorhiza hairs in an OsRHL1 (Os06g0184000, a coleorhiza hair formation regulation candidate gene) knockout mutant suggested that root hair-associated DEGs share molecular regulators that control the formation of coleorhiza hairs.

Rice caryopses are enclosed by outer glumes. The size and dimension of the outer glume are the main determinants of caryopsis size. However, it is unclear whether caryopsis development is completely dependent on the size of the glume, or whether it can grow and expand autonomously despite the constraint of glume enclosure. We report the identification of a mutant line that produces normal-sized glumes with smaller mature caryopses that do not fill the entire glume cavity. The caryopsis phenotype in the pex1 mutant is caused by a reduction in cell size. OsPEX1, a leucine-rich repeat extensin gene, was highly expressed in the developing caryopsis. Overexpression of OsPEX1 driven by a constitutive promoter recapitulated the mutant phenotype, showing that the small-caryopsis phenotype is caused by overexpression of the OsPEX1 gene. Free amino acids, including several essential amino acids, and crude protein were increased in pex1 relative to the wild type, endowing pex1 with improved nutritional quality. Our results suggest that caryopsis development can be genetically uncoupled from maternally controlled glume development and that OsPEX1 might be a new resource for improving nutritional quality of rice cultivars.

The LGS1 (Large grain size 1) gene, also known as GS2/GL2/OsGRF4, is involved in regulating grain size and quality in rice, but the mechanism governing grain size has not been elucidated. We performed transcriptomic, proteomic, and phosphoproteomic analyses of young rice panicles in Samba (a wild-type cultivar with extra-small grain) and NIL-LGS1 (a nearly isogenic line of LGS1 with large grain in the Samba genetic background) at three developmental stages (4-6) to identify internal dynamic functional networks determining grain size that are mediated by LGS1. Differentially expressed proteins formed seven highly functionally correlated clusters. The concordant regulation of multiple functional clusters may be key features of the development of grain length in rice. In stage 5, 16 and 24 phosphorylated proteins were significantly up-regulated and down-regulated, and dynamic phosphorylation events may play accessory roles in determining rice grain size by participating in protein-protein interaction networks. Transcriptomic analysis in stage 5 showed that differentially expressed alternative splicing events and dynamic gene regulatory networks based on 39 transcription factors and their highly correlated target genes might contribute to rice grain development. Integrative multilevel omics analysis suggested that the regulatory network at the transcriptional and posttranscriptional levels could be directly manifested at the translational level, and this analysis also suggested a regulatory mechanism, regulation of protein translation levels, in the biological process that extends from transcript to protein to the development of grain. Functional analysis suggested that biological processes including MAPK signaling, calcium signaling, cell proliferation, cell wall, energy metabolism, hormone pathway, and ubiquitin-proteasome pathway might be involved in LGS1-mediated regulation of grain length. Thus, LGS1-mediated regulation of grain size is affected by dynamic transcriptional, posttranscriptional, translational and posttranslational changes.

Interaction between the embryo and endosperm affects seed development, an essential process in yield formation in crops such as rice. Signals that mediate communication between embryo and endosperm are largely unknown. We used the notched-belly (NB) mutant with impaired communication between embryo and endosperm to investigate the effect of the embryo on developmental staging of the endosperm and signaling pathways in the embryo that regulate endosperm development. Hierachical clustering of mRNA datasets from embryo and endosperm samples collected during development in NB and a wild type showed a delaying effect of the embryo on the developmental transition of the endosperm by extension of the middle stage. K-means clustering further identified coexpression modules of gene sets specific to embryo and endosperm development. Combined gene expression and biochemical analysis showed that T6P-SnRK1, gibberellin and auxin signaling by the embryo regulate endosperm developmental transition. We propose a new seed developmental staging system for rice and identify the most detailed signature of rice grain formation to date. These will direct genetic strategies for rice yield improvement.

Genetic recombination produces new allelic combinations, thereby introducing variation for domestication. Allopolyploidization has increased the evolutionary potential of hexaploid common wheat by conferring the advantages of heterosis and gene redundancy, but whether a relationship exists between allopolyploidization and genetic recombination is currently unknown. To study the impact of allopolyploidization on genetic recombination in the ancestral D genome of wheat, we generated new synthetic hexaploid wheats by crossing tetraploid Triticum turgidum with multiple diploid Aegilops tauschii accessions, with subsequent chromosome doubling, to simulate the evolutionary hexaploidization process. Using the DArT-Seq approach, we determined the genotypes of two new synthetic hexaploid wheats with their parents, F₂ plants in a diploid population (2x, D₁D₁ × D₂D₂) and its new synthetic hexaploid wheat-derived population (6x, AABBD₁D₁ × AABBD₂D₂). About 11% of detected SNP loci spanning the D genome of Ae. tauschii were eliminated after allohexaploidization, and the degree of segregation distortion was increased in their hexaploid offspring from the F₂ generation. Based on codominant genotypes, the mean genetic interval length and recombination frequency between pairs of adjacent and linked SNPs on D genome of the hexaploid F₂ population were 2.3 fold greater than those in the diploid F₂ population, and the recombination frequency of Ae. tauschii was increased by their hexaploidization with T. turgidum. In conclusion, allopolyploidization increases genetic recombination of the ancestral diploid D genome of wheat, and DNA elimination and increased segregation distortion also occur after allopolyploidization. Increased genetic recombination could have produced more new allelic combinations subject to natural or artificial selection, helping wheat to spread rapidly to become a major global crop and thereby accelerating the evolution of wheat via hexaploidization.

Salinity causes a detrimental impact on plant growth, particularly when the stress occurs during germination and early development stages. Barley is one of the most salt-tolerant crops; previously we mapped two quantitative trait loci (QTL) for salinity tolerance during germination on the short arm of chromosome 2H using a CM72/Gairdner doubled haploid (DH) population. Here, we narrowed down the major QTL to a region of 0.341 or 0.439Â Mb containing 9 or 24 candidate genes belonging to 6 or 20 functional gene families according to barley reference genomes v1 and v3 respectively, using two DH populations of CM72/Gairdner and Skiff/CM72, F₂ and F₃ generations of CM72/Gairdner/*Spartacus CL. Two Receptor-like kinase 4 (RLPK4) v1 or Receptor-like kinase (RLK) v3 could be the candidates for enhanced germination under salinity stress because of their upregulated expression in salt-tolerant variety CM72. Besides, several insertion/deletion polymorphisms were identified within the 3rd exon of the genes between CM72 and Gairdner. The sequence variations resulted in shifted functional protein domains, which may be associated with differences in salinity tolerance. Two molecular markers were designed for selecting the locus with receptor-like protein kinase 4, and one was inside HORVU2Hr1G111760.1 or HORVU.MOREX.r3.2HG0202810.1. The diagnostic markers will allow for pyramiding of 2H locus in barley varieties and facilitate genetic improvement for saline soils. Further, validation of the genes to elucidate the mechanisms involved in enhancing salinity tolerance at germination and designing RLPK4 specific markers is proposed. For this publication, all the analysis was based on barley reference genome of 2017 (v1), and it was used throughout for consistence. However, the positions of the markers and genes identified were updated according to new genome (v3) for reference.

Black point disease caused by Bipolaris sorokiniana is a problem in wheat production worldwide. We aimed to identify major quantitative trait loci (QTL) for resistance to black point and develop molecular markers for marker-assisted selection (MAS). A recombinant inbred line (RIL) population derived from a cross between Wanyuanbai 1 (susceptible) and SN4143 (resistant) was evaluated for black point response at three locations during two years under artificial inoculation with B. sorokiniana, providing data for six environments. Thirty resistant and 30 susceptible RILs were selected to form resistant and susceptible bulks, respectively, that were genotyped by the wheat 660K SNP array; 685 single-nucleotide polymorphisms (SNPs) were identified, among which 385 (56.2%) and 115 (16.8%) were located on chromosomes 4A and 2B, respectively. Bulked segregant RNA-Seq analysis identified candidate regions on chromosomes 4A (4.60-40.28Â Mb) and 5A (1.22-48.47Â Mb). Genetic linkage maps were constructed for chromosomes 2B, 4A, and 5A using 59 polymorphic dCAPS and SSR markers. Finally, two QTL, designated QBB.hau-4A and QBB.hau-5A, were detected on chromosomes 4A and 5A, respectively. The resistance allele of QBB.hau-4A was derived from SN4143, and that of QBB.hau-5A came from Wanyuanbai 1. QBB.hau-4A with a large and consistent effect (15.1%) is likely to be a new locus for black point resistance. The markers linked to QBB.hau-4A and QBB.hau-5A have potential application in MAS-based breeding.

The Hessian fly (HF, Mayetiola destructor) is one of the destructive pests of wheat (Triticum aestivum L.) worldwide. Resistant cultivars can effectively minimize wheat damage due to this insect pest. To identify new quantitative trait loci (QTL) for HF resistance, a population of recombinant inbred lines (RILs) was developed from a cross between the HF-resistant wheat cultivar ‘Chokwang' and susceptible wheat ‘Ning 7840', and phenotyped for responses to HF attack. A linkage map was constructed using 1147 single nucleotide polymorphism (SNP) markers generated from genotyping-by-sequencing (GBS). One major QTL, QHf.hwwg-6BS, for HF-resistance was identified on chromosome arm 6BS, which explained up to 84.0% of the phenotypic variation and was contributed by Chokwang. Two RILs showed recombination in the candidate interval of QHf.hwwg-6BS, which delimited QHf.hwwg-6BS to a 4.75 Mb physical interval between 6,028,601 bp and 10,779,424 bp on chromosome arm 6BS of IWGSC Chinese Spring reference genome RefSeq v2.0. Seven GBS-SNPs in the candidate interval were converted into Kompetitive allele specific polymerase chain reaction (KASP) markers. Two of them, KASP-6B112698 and KASP-6B7901215, were validated in a U.S. winter wheat panel. KASP-6B112698 was nearly diagnostic, thus can be used to screen QHf.hwwg-6BS and pyramid it with other resistance genes in breeding programs.

The development and deployment of diverse resistance sources in new wheat cultivars underpin the durable control of stripe rust. In the present study, two loci for adult plant resistance (APR), QYrSM155.1 and QYrSM155.2, were identified in the Chinese wheat breeding line Shaanmai 155. QYrSM155.1 was mapped to a 3.0-cM interval between the single-nucleotide polymorphism (SNP) markers AX-109583610 and AX-110907562 on chromosome arm 2BL. QYrSM155.2 was mapped to a 2.1-cM interval flanked by the SNP markers AX-110378556 and AX-86173526 on chromosome arm 7AS. A genome-wide association study was used to identify markers associated with APR in a panel of 411 spring wheat lines. Thirteen and 11 SNPs were significantly associated with QYrSM155.1 and QYrSM155.2, respectively, corresponding to physical intervals of 653.75-655.52Â Mb on 2BL and 81.63-83.93Â Mb on 7AS. To characterize the haplotype variation and the distribution of these QTL, haplotype analysis was performed based on these SNPs in an independent panel of 1101 worldwide wheat accessions. Three major haplotypes (2B_h1, 2B_h2, and 2B_h3) for QYrSM155.1 and four major haplotypes (7A_h1, 7A_h2, 7A_h3, and 7A_h4) for QYrSM155.2 were identified. Accessions individually harboring QYrSM155.1_h1 and QYrSM155.2_h1 haplotypes and their combination displayed resistance. Additional assays of 1306 current Chinese cultivars and breeding lines using markers flanking QYrSM155.1 and QYrSM155.2 indicated that the resistance haplotypes of the two QTL were present in respectively 1.45% and 14.16% of lines. Increasing resistance haplotype frequencies at these two loci using marker-assisted selection should benefit wheat production in China.

The emergence and spread of wheat blast caused by fungal pathogen Magnaporthe oryzae pathotype Triticum is a threat to global wheat production. The resistance level and genetic loci for blast resistance in Chinese germplasm remain unknown. A panel of 266 bread wheat accessions from China, CIMMYT-Mexico and other countries was screened for head blast resistance under 12 field experiments in Bolivia and Bangladesh. Subsequently, a genome-wide association study was performed to understand the genetic basis of wheat blast resistance. The average blast index of all the accessions was 53.7% ± 12.7%, and 10 accessions including Chinese accessions Yumai 10 and Yu 02321 showed moderate to high levels of blast resistance, accounting for only 3.8% in the panel. Fifty-eight significant SNPs clustered in a 28.9 Mb interval on the 2AS/2NS translocation region, explaining phenotypic variation between 10.0% and 35.0%. The frequency of the 2AS/2NS translocation in the Chinese accessions was as low as 4.5%. These results indicated that the 2NS fragment was the only major locus conferring resistance to wheat blast in this panel, and the resistant and moderately resistant lines identified could be deployed in breeding.

Soybean mosaic virus (SMV) is a member of the genus Potyvirus that extensively impairs global soybean production. The full-length coding sequence of the MADS-box transcription factor GmCAL was cloned from the SMV-resistant soybean cultivar Kefeng 1. SMV-induced expression analysis indicated that GmCAL responded quickly to SMV-SC8 infection in Kefeng 1 but not in NN1138-2. GmCAL was expressed at high levels in flowers and pods but at lower levels in leaves. The gene was localized to the nucleus by subcellular localization assay. Virus-induced gene silencing did not increase the accumulation of SMV in GmCAL-silenced Kefeng 1 plants (with silencing efficiency ∼ 80%) after SC8 inoculation. GmCAL-silencing plants still conferred resistance to SC8 that might be owing to incomplete silencing of genes with lower expression. SMV content decreased significantly in GmCAL-overexpressing NN1138-2 plants after SMV-SC3, SMV-SC7, and SMV-SC8 inoculation in comparison with a vector control, showing that overexpression of GmCAL conferred broad-spectrum resistance to multiple SMV strains. These results confirm that GmCAL, a key regulator but not a specific SC8 resistance gene (Rsc8), is a positive regulatory transcription factor involved in soybean resistance to SMV.

Peanut (Arachis hypogea L.) bacterial wilt (BW) is a devastating disease caused by Ralstonia solanacearum that results in severe yield and quality losses. Plant defensins are short cysteine-rich peptides with antimicrobial activity. The role of defensin genes (AhDef) in peanut is unclear. A genome-wide investigation of AhDef genes was undertaken, and 12 identified AhDef genes were classified into two groups containing the gamma-thionin domain formed by four disulfide pairs: Cys1-Cys8, Cys2-Cys5, Cys3-Cys6, and Cys4-Cys7. In silico analysis revealed that AhDef genes showed highly conserved architectural features and contained cis-elements associated with phytohormone signaling and defense responses. A highly resistant cultivar, H108 (R) and a susceptible accession, H107 (S) were tested by R. solanacearum inoculation. H108 (R) showed fewer symptoms than H107 (S) owing to inhibition of bacterial reproduction and spread in the vascular bundles of roots and stems. In a transcriptomic expression profile, AhDef genes, particularly AhDef1.6 and AhDef2.2, were up-regulated in H108 (R) compared with H107 (S) under R. solanacearum infection and phytohormone treatment. Subcellular localization showed that the AhDef1.6 and AhDef2.2 proteins were both expressed specifically on the plasma membrane. Overexpression of protein fusion AhDef2.2-YFP in Nicotiana benthamiana and peanut leaves increased resistance to R. solanacearum, suggesting its role in response to BW infection. AhDef2.2 may be valuable for peanut resistance breeding.

Peanut is a major oilseed and food legume. Shelling percentage (SP), closely associated with seed yield, is a trait whose improvement is a major goal of peanut breeding. In this study, a mapping population (Xuhua 13 × Zhonghua 6) was used to map quantitative trait loci (QTL) controlling SP in four environments. Two stable major QTL for SP were mapped on both SSR- and SNP-based genetic maps. qSPA07.1 on chromosome A07 explained up to 31.7% of phenotypic variation, and qSPA08.2 on chromosome A08 explained up to 10.8%. Favorable alleles of qSPA07.1 and qSPA08.2 were derived from the female and male parents, respectively. Eight recombinant inbred lines (RILs) carrying both favorable alleles showed superiority in SP over the two parents in all environmental trials. A combination of the two favorable alleles using the linked markers was verified to increase SP by ∼5% in the RIL population and by ∼3% SP in diverse peanut cultivars. qSPA07.1 and qSPA08.2 were delimited to respectively a 0.73-Mb interval harboring 96 genes and a 3.93-Mb interval harboring 238 genes. Respectively five and eight genes with high expression in pods, including enzymes and transcription factors, were assigned as candidate genes for qSPA07.1 and qSPA08.2. These consistent major QTL provide an opportunity for fine mapping of genes controlling SP, and the linked markers may be useful for genetic improvement of SP in peanut.

Drought is one of the primary abiotic stress factors affecting the yield, growth, and development of soybeans. In extreme cases, drought can reduce yield by more than 50%. The seedling stage is an important determinant of soybean growth: the number and vigor of seedlings will affect growth and yield at harvest. Therefore, it is important to study the drought resistance of soybean seedlings. In this study, a recombinant inbred line (RIL) population comprising 234 F_6:10 lines (derived from Zhonghuang 35 × Jindou 21) and a panel of 259 soybean accessions was subjected to drought conditions to identify the effects on phenotypic traits under these conditions. Using a genetic map constructed by single nucleotide polymorphism (SNPs) markers, 18 quantitative trait loci (QTL) on 7 soybean chromosomes were identified in two environments. This included 9 QTL clusters identified in the RIL population. Fifty-three QTL were identified in 19 soybean chromosomes by genome-wide association analysis (GWAS) in the panel of accessions, including 69 significant SNPs (-log₁₀ (P) ≥ 3.97). A combination of the two populations revealed that two SNPs (-log₁₀ (P) ≥ 3.0) fell within two of the QTL (qPH7-4 and qPH7-6) confidence intervals. We not only re-located several previously reported drought-resistance genes in soybean and other crops but also identified several non-synonymous stress-related mutation site differences between the two parents, involving Glyma.07g093000, Glyma.07g093200, Glyma.07g094100 and Glyma.07g094200. One previously unreported new gene related to drought stress, Glyma.07g094200, was found by regional association analysis. The significant SNP CHR7-17619 (G/T) was within an exon of the Glyma.07g094200 gene. In the RIL population, the DSP value of the "T"? allele of CHR7-17619 was significantly (P ＜ 0.05) larger than the "G"? allele in different environments. The results of our study lay the groundwork for cloning and molecular marker-assisted selection of drought-resistance genes in soybeans at the seedling stage.

Low temperature in early spring impairs wheat growth and grain yield. However, little is known about the cytological and molecular mechanisms underlying low temperature regulation of wheat spike development. Microstructure observation and transcriptome sequencing of wheat spikes under low temperature were conducted. Low temperature slowed spike development, reduced the yield-component parameters of wheat spikes at the harvest stage, delayed the formation of lateral spikelets and tissue development, and induced the early differentiation of terminal spikelets. Low temperature increased the content of abscisic acid and caused the upregulation of genes in the abscisic acid signaling pathway, including those encoding PP2Cs, SnRK2s, and bZIP transcription factors. Low temperature also induced the upregulation of 33 cold-responsive genes involved in wheat response to low-temperature stress and regulation of abscisic acid biosynthesis and metabolism of other substances. The wheat spike adapted to cold conditions by changing the expression levels of genes involved in spike morphogenesis, including the transcription-factor genes MADS6, ERF4, ERF78, WOX6, and NAC48. These findings suggest that low temperature in early spring delays wheat spike development by increasing abscisic acid content or affecting the expression of genes involved in morphogenesis.

Planting maize at high densities leads to early leaf senescence, and the resulting reduction in the number of lower leaves affects the plant's root function and lowers its grain yield. However, the nature of the process by which lower leaf senescence affects biomass accumulation and grain yield formation in maize is not clear. This study aimed to shed light on how these factors are related by investigating the effects of the plant growth regulator 6-benzyladenine (6-BA) on the senescence of lower leaves of maize plants. In two maize cultivars planted at densities of 67,500 (low density, LD) and 90,000 (high density, HD) plants ha^-1, plants treated with 6-BA maintained a high green leaf area index (LAI) longer than control (CK) plants, enabling them to maintain a higher photosynthetic rate for a longer period of time and produce more biomass before reaching physiological maturity. Spraying the lower leaves of maize plants with a 6-BA solution increased the distribution of ¹³C-photosynthates to their roots, lower leaves and bracts, a result that can be ascribed to a decreased retention of ¹³C-photosynthates in the stem and grain. In both seasons of the experiment, maize plants treated with 6-BA accumulated more N in grain and maintained a higher N content in roots and leaves, especially in lower leaves, than CK. Increased C assimilation in the lower leaves may explain why N uptake in plants subjected to the 6-BA treatment exceeded that in CK plants and why both photosynthesis rate and dry matter accumulation were maintained throughout grain filling. Our results suggest that a suitable distribution of C and N in leaves post-silking may maintain plant root function, increase N use efficiency, maximize the duration of high LAI, and increase grain yield.

The moisture-conserving effect of straw mulch-based no-tillage (SMNT) is expected to increase fertile spikes and grain yield in environments with rainfall less than 200 mm. However, the mechanisms underlying the positive effect of SMNT on wheat tillering are not fully elucidated. A split-plot experiment was designed to investigate the combined effects of SMNT and cultivars on tillering of dryland wheat grown under both dry and favorable climates. Application of SMNT to a cultivar with 1-2 tillers exploited both tillering and kernel-number plasticity, increasing the mean grain yield by 20.5%. This increase was attributed primarily to an increased first-tiller emergence rate resulting from increased N uptake, leaf N content, and N remobilization from tillers to their grain. The second and third tillers, as transient sinks, contributed to the tiller survival rate, which depends on tiller leaf number. The increased total N uptake by SMNT also increased the dry mass yield of tillers and the C:N ratio, reducing the asymmetric competition between main stem and tillers. Owing to these beneficial effects, reduced mitogen-activated protein kinase (MAPK) and abscisic acid signals were observed under SMNT, whereas indole-3-acetic acid (IAA) signals and genes involved in DNA replication and mismatch repair were increased. These signals activated three critical transcription factors (the calmodulin-binding transcription activator, GRAS domain, and cysteine-2/histidine-2 family) and further increased rapid drought response and tiller maintenance after stem extension. Phenylpropanoid biosynthesis, sphingolipid biosynthesis, and galactose metabolism were most relevant to increased tillering under SMNT because of their critical role in drought response and lignin biosynthesis. Our results suggest that straw mulch-based no-tillage activates rapid drought response and improved wheat tillering by coordinating root N uptake, N remobilization, and asymmetric competition between main stem and tillers.

Straw strip mulching (SM) is a new mulching technology. From 2012 to 2018, SM's effects on soil moisture and temperature and production performances were compared with other mulching practices, using three treatments: full-cover plastic mulch (PM), no mulch with wheat sown in rows as the control (CK), and SM with 50% to 59% of the field area mulched. Compared with CK, on average over six growing seasons, SM and PM increased grain yield by 27.0% and 21.7%, straw yield by 21.6% and 22.6%, kernels ha⁻¹ by 26.6% and 19.0%, net income by 29.8% and −25.0%, soil temperature at 5 cm by −1.5 °C and 0.2 °C from overwintering to maturity, and soil water storage at 0-200 cm by 25 and 22 mm, respectively. The increase in soil moisture in SM and PM was greater in the early period (overwintering to jointing) than in the later period (booting to maturity) and at 0 to 120 cm than at 120-200 cm in the early period. Although the mean evapotranspiration of whole growth period across six seasons was similar among treatments, SM and PM increased water consumption during the key formation period of yield components after overwintering by 16 and 32 mm, respectively, while reducing it before overwintering. Compared with CK, SM and PM had the effects of warming during overwintering and cooling after jointing. By increasing water consumption after overwintering and ratio of transpiration to evapotranspiration and providing favorable soil temperature for multiple growth stages and more sufficient soil moisture, SM and PM promoted vegetative growth and increased kernels ha⁻¹, the main mechanisms by which SM and PM increased grain yield relative to CK. Relative to PM, SM is a more economically beneficial and environment-friendly technology for dryland wheat production.

Increasing plant density can increase cereal crop yields. However, the physiological and anatomical mechanisms of grain yield increase at high plant densities in maize-based intercropping systems are not well understood. A two-year field experiment was conducted in 2018 and 2019 to investigate grain yield, photosynthetic characteristics, stomatal traits, and leaf anatomy of maize plants in an intercropping system with high plant densities. Two cropping patterns (monocropping and intercropping) and three plant densities (D1, 78,000 plants ha^-1; D2, 103,500 plants ha^-1; D3, 129,000 plants ha^-1) were arranged in a randomized block design. Increasing maize plant density significantly increased maize yield, and intercropping gave a significant yield advantage over monocropping under the same plant density. Intercropping combined with high plant density increased the leaf area and SPAD value of maize, increasing the photosynthesis rates after the harvest of pea. At the twelfth leaf stage, the stomatal density and stomatal area of intercrops combined with medium plant density increased by respectively 10.5% and 18.4% relative to their values for the corresponding density of monocrops. Although leaf thickness of maize was reduced by increasing plant density, the chloroplast number and grana lamella number were higher in intercropping than in monocropping under different plant densities. These positive changes in leaf anatomy resulted in increased photosynthesis, suggesting a physiological basis for the increase in grain yield.

The relationship between parental genetic differences and the quality and yield of japonica hybrid rice strongly influences japonica hybrid rice breeding. In this study, 137 parental lines of japonica hybrid rice were genotyped using 8K rice SNP-Chips to characterize their genetic diversity, population structure, and indica-genotype proportion. The genetic diversity of total parental lines averaged 0.264, with values of 0.287 for restorer lines and 0.148 for the sterile lines. The introduction of indica lineage increased the genetic diversity of restorer lines relative to that of sterile lines. By model-based population structure analysis, the 137 lines were divided into 14 groups. According to the grouping results, eight restorer lines and five sterile lines were selected from different groups for cross breeding, yielding 40 japonica hybrid rice combinations (F₁). Investigation of the yield and quality of these combinations showed that high-yield combinations could be obtained by increasing parental genetic distance to 0.8-0.9, a result accomplished largely by the introduction of indica genomic components of restorer lines. To further improve grain quality, the genetic distance between parents should be reduced to 0.4-0.5, suggesting an indica-genotype proportion of 30%-40% for restorer lines. This study may provide a reference for breeding of japonica hybrid rice.

Rye (Secale cereale genome RR), a close relative of common wheat, possesses valuable resistance genes for wheat improvement. Due to the co-evolution of pathogen virulence and host resistance, some resistance genes derived from rye have lost effectiveness. Development and identification of new, effective resistance genes from rye is thus required. In the current study, wheat-rye line WR56 was produced through distant hybridization, embryo rescue culture, chromosome doubling and backcrossing. WR56 was then proved to be a wheat-rye 2RL ditelosomic addition line using GISH (genomic in situ hybridization), mc-FISH (multicolor fluorescence in situ hybridization), ND-FISH (non-denaturing FISH), mc-GISH (multicolor GISH) and rye chromosome arm-specific marker analysis. WR56 exhibited a high level of adult plant resistance to powdery mildew caused by Blumeria graminis f. sp. tritici (Bgt). This resistance was carried by the added 2RL telosomes and presumed to be different from Pm7 which is also located on chromosome arm 2RL but confers resistance at the seedling and adult stages. WR56 will be a promising bridging parent for transfer of the resistance to a more stable wheat breeding line. A newly developed 2RL-specific KASP (kompetitive allele specific PCR) marker should expedite that work.