In flowering plants, the inflorescence meristem (IM) provides founder cells to form successive floral meristems, which are precursors of fruits and seeds. The activity and developmental progression of IM are thus critical for yield production in seed crops. In some cereals, such as rice (Oryza sativa) and maize (Zea mays), the size of undifferentiated IM, which is located at the inflorescence apex, is positively associated with yield traits such as spikelet number. However, the relationship between IM size and yield-related spike traits remains unknown in the Triticeae tribe. Here we report that IM size has a negative correlation with yield traits in barley (Hordeum vulgare). Three FASCIATED EAR (FEA) orthologs, HvFEA2, HvFEA3, and HvFEA4, regulate IM size and spike morphogenesis and ultimately affect yield traits. Three HvFEAs genes are highly expressed in developing spikes, and all three loss-of-function mutants exhibit enlarged IM size, shortened spikes, and reduced spikelet number, which may lead to reduced grain yield. Natural variations identified in HvFEAs indicate selection events during barley domestication. We further reveal that HvFEA4, as a transcription factor, potentially targets multiple pathways during reproductive development, including transcriptional control, phytohormone signaling, and redox status. The roles of barley FEA genes in limiting IM size and promoting spikelet formation suggest the potential of increasing yield by manipulating IM activity.

MicroRNAs (miRNAs) are important regulatory elements involved in the regulation of various plant developmental and physiological processes by blocking the expression of target genes. MiR156 and miR529 are two combinatorial regulators, which cooperatively target the SQUAMOSA PROMOTER BINDING-LIKE (SPL) family genes. However, there has been no report about the functional conservation and divergence of miR156 and miR529 during plant development to date. In this study, the biological function and relationship of miR156, miR529 and their target OsSPL14 in rice were explored. Overexpression of miR156e or miR529a (miR156e-OE and miR529a-OE) increased the grain size and tiller number but decreased the plant height and panicle length, while an opposite phenotype was observed for their target mimicry (miR156-MIMIC and miR529a-MIMIC) transgenic plants. Stem-loop RT-PCR results revealed ubiquitous expression of miR156 in roots, axillary buds and leaves, while miR529 was preferentially expressed in the panicle. Accordingly, OsSPL14 could be preferentially and precisely cleaved by miR529a in young panicle but by miR156 in vegetative tissues. Transgenic plants generated by the target immune strategy exhibited obvious growth defects upon the blocking of miR156 and/or miR529 function in rice, confirming that both miR156 and miR529 play important roles in controlling rice growth and development. Moreover, the miR156/miR529-OsSPL14 module negatively controlled grain size by regulating the genes associated with grain size and cell cycling, and controlled plant height through a more complicated mechanism. Taken together, our results demonstrate that miR156 and miR529 respectively function dominantly in the vegetative stage and reproductive stage to control rice growth and development by regulating the accumulation of OsSPL14. These findings facilitate a better understanding of the functional conservation and divergence of miR156 and miR529 family in the miRNA combinatorial regulatory network of plants.

Flowering time is a key agronomic trait that directly affect the adaptation and yield of soybean. After whole genome duplications, about 75% of genes being represented by multiple copies in soybean. There are four TERMINAL FLOWER 1 (TFL1) genes in soybean, and the TFL1b (Dt1) has been characterized as the determinant of stem growth habit. The function of other TFL1 homologs in soybean is still unclear. Here, we generated knockout mutants by CRISPR/Cas9 genome editing technology and found that the tfl1c/tfl1d double mutants flowered significantly earlier than wild-type plants. We investigated that TFL1c and TFL1d could physically interact with the bZIP transcription factor FDc1 and bind to the promoter of APETALA1a (AP1a). RNA-seq and qRT-PCR analyses indicated that TFL1c and TFL1d repressed the expressions of the four AP1 homologs and delayed the flowering time in soybean. The two genes play important roles in the regulation of flowering time in soybean and mainly act as the flowering inhibitors under long-day conditions. Our results identify novel components in the flowering-time regulation network of soybean and will be invaluable for molecular breeding of improved soybean yield.

Plant architecture is a target of crop improvement. The soybean mutant ideal type 1 (it1) displays a pleiotropic phenotype characterized by compact plant architecture, reduced plant height, shortened petioles, wrinkled leaves, and indented seeds. Genetic analysis revealed that the pleiotropic phenotype was controlled by an incomplete dominant gene. We characterized the cellular phenotypes of it1 and positionally cloned the it1 locus. Detailed morphogenetic analysis of the it1 mutant revealed an excess of xylem cells and expanded phloem, and polygonal pavement cells. Positional cloning showed that the phenotype was caused by a G-to-A mutation in the second exon of the α-tubulin gene (Glyma.05G157300). The mutation altered microtubule arrangement in pavement cells, changing their morphology. Overexpression of Gmit1 resulted in an it1-like phenotype and polygonal pavement cells and microtubules of overexpressors were parallel or slightly inclined. Five suppressor mutants able to suppress the phenotype of it1 were obtained by EMS mutagenesis in the it1 background. All these mutants carried an additional mutation in the it1 gene. These results suggest that the pleiotropic phenotype of it1 is caused by the mutation in the α-tubulin gene.

Plants are capable of regulating their shoot architecture in response to diverse internal and external environments. The circadian clock is an adaptive mechanism that integrates information from internal and ambient conditions to help plants cope with recurring environmental fluctuations. Despite the current understanding of plant circadian clock and genetic framework underlying plant shoot architecture, the intricate connection between these two adaptive mechanisms remains largely unclear. In this study, we elucidated how the core clock gene LUX ARRHYTHMO (LUX) regulates shoot architecture in the model legume plant Medicago truncatula. We show that mtlux mutant displays increased main stem height, reduced lateral shoot length, and decreased the number of lateral branches and biomass yield. Gene expression analysis revealed that MtLUX regulated shoot architecture by repressing the expression of strigolactone receptor MtD14 and MtTB1/MtTCP1A, a TCP gene that functions centrally in modulating shoot architecture. In vivo and in vitro experiments showed that MtLUX directly binds to a cis-element in the promoter of MtTB1/MtTCP1A, suggesting that MtLUX regulates branching by rhythmically suppressing MtTB1/MtTCP1A. This work demonstrates the regulatory effect of the circadian clock on shoot architecture, offering a new understanding underlying the genetic basis towards the flexibility of plant shoot architecture.

Because plant mechanical strength influences plant growth and development, the regulatory mechanisms underlying cell-wall synthesis deserve investigation. Rice mutants are useful for such research. We have identified a novel brittle culm 25 (bc25) mutant with reduced growth and partial sterility. BC25 encodes an UDP-glucuronic acid decarboxylase involved in cellulose synthesis and belongs to the UXS family. A single-nucleotide mutation in BC25 accounts for its altered cell morphology and cell-wall composition. Transmission electron microscopy analysis showed that the thickness of the secondary cell wall was reduced in bc25. Monosaccharide analysis revealed significant increases in content of rhamnose and arabinose but not of other monosaccharides, indicating that BC25 was involved in xylose synthesis with some level of functional redundancy. Enzymatic assays suggested that BC25 functions with high activity to interconvert UDP-glucuronic acid (UDP-GlcA) and UDP-xylose. GUS staining showed that BC25 was ubiquitously expressed with higher expression in culm, root and sheath, in agreement with that shown by quantitative real-time (qRT)-PCR. RNA-seq further suggested that BC25 is involved in sugar metabolism. We conclude that BC25 strongly influences rice cell wall formation.

The genetic pathways of rice seedling growth have a major impact on seedling emergence from soil and development. In this study, we identified a new bHLH transcription factor, BEAR1, from rice RNAi mutant library. Both the BEAR1-RNAi and bear1 CRISPR mutants had accelerated seedling growth. Histological section of leaves showed accelerated development of lacuna and vascular bundles in bear1 mutant. GUS staining revealed that BEAR1 was highly expressed in coleoptiles and leaves at seedling stage. Expression analysis of gibberellin (GA) biosynthesis and metabolic genes and content determination of active GAs indicated that the expression of GA biosynthesis genes, especially OsKS4 and OsCPS2, were upregulated and the GAs content were significantly increased in bear1, which correlated with the seedling phenotype of bear1 mutant. Molecular and biochemical assays revealed that BEAR1 directly binds to the promoter of OsKS4, thereby repressing its expression. Haplotypes analysis showed clear differentiation in indica and japonica rice varieties, and a strong correlation with seedling height. These findings provide novel insights into the regulation of seedling growth in rice.

The leaf is the main organ for rapeseed photosynthesis, and its morphology influences photosynthetic efficiency and supports increased planting density and yield. However, the molecular regulatory mechanism of leaf morphology in Brassica napus is poorly understood, restricting progress in breeding for the trait. We describe a novel dominant mutation, curly leaf 1 (cl1), which confers uneven dorsal-ventral axis development, irregular cellular structure and influenced gravitropic response in the seedling stage. The CL1 locus was mapped to a 1.573-Mb interval on chromosome A05 using simple sequence repeat (SSR) markers, and co-segregated with the phenotype of plants in the curly F₂ population. A substitution (P62S) was identified in the highly conserved degron motif (GWSPV) of the IAA2 protein in the cl1 mutant, and the P62S substitution impaired the interaction between IAA2 and TIR1 in the presence of auxin, influencing auxin signaling. The P62S substitution-induced curly leaf phenotype was verified by ectopic expression of BnaA05.iaa2 in Arabidopsis and B. napus. Our findings explain the function of IAA2 in rapeseed, providing a foundation for future investigation of auxin signaling and the mechanisms underlying leaf development in B. napus.

Using naturally colored cotton (NCC) can eliminate dyeing, printing and industrial processing, and reduce sewage discharge and energy consumption. Proanthocyanidins (PAs), the primary coloration components in brown fibers, are polyphenols formed by oligomers or polymers of flavan-3-ol units derived from anthocyanidins. Three essential structural genes for flavanone and flavonoid hydroxylation encoding flavanone-3-hydroxylase (F3H), flavonoid 3′-hydroxylase (F3′H) and flavonoid 3′5′-hydroxylase (F3′5′H) are initially committed in the flavonoid biosynthesis pathway to produce common precursors. The three genes were all expressed predominantly in developing fibers of NCCs, and their expression patterns varied temporally and spatially among NCC varieties. In GhF3Hi, GhF3′Hi and GhF3′5′Hi silenced lines of NCC varieties XC20 and ZX1, the expression level of the three genes decreased in developing cotton fiber, negatively correlated with anthocyanidin content and fiber color depth. Fiber color depth and type in RNAi lines changed with endogenous gene silencing efficiency and expression pattern,the three hydroxylase genes functioned in fiber color formation. GhF3H showed functional differentiation among NCC varieties and GhF3′H acted in the accumulation of anthocyanin in fiber. Compared with GhF3′H, GhF3′5′H was expressed more highly in brown fiber with a longer duration of expression and caused lighter color of fibers in GhF3′5′H silenced lines. These three genes regulating fiber color depth and type could be used to improve these traits by genetic manipulation.

Cotton fiber is a raw material for the global textile industry and fiber quality is essential to its industrial application. Carotenoids are plant secondary metabolites that may serve as dietary components, regulate light harvesting, and scavenge reactive oxygen species. Although carotenoids accumulate predominantly in rapidly elongating cotton fibers, their roles in cotton fiber development remain poorly understood. In this study, a fiber-specific promoter proSCFP was applied to drive the expression of GhOR1^Del, a positive regulator of carotenoid accumulation, to upregulate the carotenoid level in cotton fiber in planta. Fiber length, strength, and fineness were increased in proSCFP:GhOR1^Del transgenic cotton and abscisic acid (ABA) and ethylene contents were increased in elongating fibers. The ABA downstream regulator GhbZIP27a stimulated the expression of the ethylene synthase gene GhACO3 by binding to its promoter, suggesting that ABA promoted fiber elongation by increasing ethylene production. These findings suggest the involvement of carotenoids and ABA signaling in promoting cotton fiber elongation and provide a strategy for improving cotton fiber quality.

Nitrogen (N) fertilization is necessary for obtaining high rice yield. But excessive N fertilizer reduces rice plant N efficiency and causes negative effects such as environmental pollution. In this study, we assembled key genes involved in different nodes of N pathways to boost nitrate and ammonium uptake and assimilation, and to strengthen amino acid utilization to increase grain yield and nitrogen use efficiency (NUE) in rice. The combinations OsNPF8.9a × OsNR2, OsAMT1;2 × OsGS1;2 × OsAS1, and OsGS2 × OsAS2 × OsANT3 optimized nitrate assimilation, ammonium conversion, and N reutilization, respectively. In co-overexpressing rice lines obtained by co-transformation, the tiller number, biomass, and grain yield per plant of the OsAMT1;2 × OsGS1;2 × OsAS1-overexpressing line exceeded those of wild-type ZH11, the OsNPF8.9a × OsNR2 × OsGS1;2 × OsAS1-overexpressing line, and the OsGS2 × OsAS2 × OsANT3-overexpressing line. The glutamine synthase activity, free amino acids, and nitrogen utilization efficiency (NUtE) of the OsAMT1;2 × OsGS1;2 × OsAS1-overexpressing line exceeded those of ZH11 and other lines that combined key genes. N influx efficiency was increased in the OsAMT1;2 × OsGS1;2 × OsAS1-overexpressing line and OsNPF8.9a × OsNR2 × OsGS1;2 × OsAS1-overexpressing line under a low ammonium and a low nitrate treatment, respectively. We propose that combining overexpression of OsAMT1;2, OsGS1;2, and OsAS1 is a promising breeding strategy for systematically increasing rice grain yield and NUE by focusing on key nodes in the N pathway.

Single nucleotide polymorphism (SNP) genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants. In this study, a high-quality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide, which was then tested extensively in 192 representative rice samples. Printed on the GeneTitan chips of Affymetrix Axiom each containing 56,606 SNP markers, the Rice3K56 array has a high genotyping reliability (99.6%), high and uniform genome coverage (an average of 6.7-kb between adjacent SNPs), abundant polymorphic information and easy automation, compared with previously developed rice SNP arrays. When applied in rice varietal differentiation, population diversity analysis, gene mapping of 13 complex traits by a genome-wide association study analysis (GWAS), and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations, these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding.

The Chinese wheat landrace Kaixianluohanmai (KL) expresses the ph-like phenotype. A major QTL, QPh.sicau-3A (syn. phKL), responsible for this effect has been mapped to chromosome arm 3AL. This study presents some characteristics of homoeologous pairing and recombination induced by phKL. In KL haploids, the level of homoeologous pairing was elevated relative to Ph1 Chinese Spring (CS) haploids. There was a clear preference for A-D pairing and less frequent for A-B and B-D, reflecting the higher levels of affinity between genomes A and D in wheat. The characteristics of pairing were affected by temperature and magnesium ion supplementation. The suitability of phKL for chromosome engineering was tested on three pairs of homoeologues: 2S^v-2B, 2S^v-2D, and 2RL-2BL. The recombination rates were 1.68%, 0.17%, and 0%, respectively. The phKL locus in KL induced a moderate level of homoeologous chromosome pairing and recombination when the Ph1 locus of wheat was present, both in wheat haploids and hexaploids. The Ph1-imposed criteria for chromosome pairing and crossing over were relaxed to some degree, permitting homoeologous crossing over but only between closely related chromosomes; there was no crossing over between more differentiated chromosomes. Therefore, the phKL system (QPh.sicau-3A) can be a useful tool in chromosome engineering of wheat to transfer genes from closely related species with the benefit of reduced genomic chaos generated by the ph1b mutation.

Wheat awns contribute to photosynthesis and grain production. In this study, an F₂ population and F_2:3 families from a cross between the awned line 7D12 and the Chinese awnless variety Shiyou 20 (SY20) were used to identify loci associated with awn length. Bulked-segregant RNA sequencing and linkage mapping identified a single dominant locus in a 0.3 cM interval on chromosome 5AL. Five genes were in the interval, including the recently cloned awn inhibitor B1. Although a single copy of the B1 gene was detected in 7D12, SY20 carried five copies of the gene. Increased copy number of B1 in SY20 enhanced gene expression. Based on sequence variation among the promoter regions of five B1 gene copies in SY20, two dominant markers were developed and found to cosegregate with B1 in a population of 931 wheat accessions. All 77 awnless accessions harbored sequence variations in the B1 promoter regions similar to those of SY20 and thus carried multiple copies of the gene, whereas 15 randomly selected awned wheats carried only one copy. These results suggest that an increase in copy number of the B1 gene is associated with inhibition of awn length.

Soybean is the primary source of plant protein for humans. Owing to the indigestibility of the raffinose family of oligosaccharides (RFO), raffinose and stachyose are considered anti-nutritive factors in soybean seeds. Low-RFO soybean cultivars are generated by mutagenesis of RFO biosynthesis genes, but the carbohydrate profiles invite further modification to lower RFOs. This study employed a pooled multiplex genome editing approach to target four seed-specifically expressed genes mediating RFO biosynthesis, encoding three raffinose synthases (RS2, RS3, and RS4) and one stachyose synthase. In T₁ progeny, rs2/rs3 and rs4/sts homozygous double mutants and a rs2/rs3/rs4/sts quadruple mutant (rfo-4m) were characterized. The rs2/rs3 mutant showed reduced raffinose and stachyose contents, but the rs4/sts mutant showed only reduced stachyose in seeds. The RFO contents in the rfo-4m mutant were almost eliminated. Metabolomic analysis showed that the mutation of four RFO biosynthesis genes led to a shift of metabolic profile in the seeds, including the accumulation of several oligosaccharides-related metabolites. These mutants could contribute to precision breeding of soybean cultivars for soy food production.

A biparental soybean population of 364 recombinant inbred lines (RILs) derived from Zhongdou 41 × ZYD 02.878 was used to identify quantitative trait loci (QTL) associated with hundred-seed weight (100-SW), pod length (PL), and pod width (PW). 100-SW, PL, and PW showed moderate correlations among one another, and 100-SW was correlated most strongly with PW (0.64-0.74). Respectively 74, 70, 75 and 19 QTL accounting for 38.7%-78.8% of total phenotypic variance were identified by inclusive composite interval mapping, restricted two-stage multi-locus genome-wide association analysis, 3 variance-component multi-locus random-SNP-effect mixed linear model analysis, and conditional genome-wide association analysis. Of these QTL, 189 were novel, and 24 were detected by multiple methods. Six loci were associated with 100-SW, PL, and PW and may be pleiotropic loci. A total of 284 candidate genes were identified in colocalizing QTL regions, including the verified gene Seed thickness 1 (ST1). Eleven genes with functions involved in pectin biosynthesis, phytohormone, ubiquitin-protein, and photosynthesis pathways were prioritized by examining single nucleotide polymorphism (SNP) variation, calculating genetic differentiation index, and inquiring gene expression. The prediction accuracies of genomic selection (GS) for 100-SW, PL, and PW based on single trait-associated markers reached 0.82, 0.76, and 0.86 respectively, but selection index (SI)-assisted GS strategy did not increase GS efficiency and inclusion of trait-associated markers as fixed effects reduced prediction accuracy. These results shed light on the genetic basis of 100-SW, PL, and PW and provide GS models for these traits with potential application in breeding programs.

Seed weight is a component of seed yield in rapeseed (Brassica napus L.). Although quantitative trait loci (QTL) for seed weight have been reported in rapeseed, only a few causal quantitative trait genes (QTGs) have been identified, resulting in a limitation in understanding of seed weight regulation. We constructed a gene coexpression network at the early seed developmental stage using transcripts of 20,408 genes in QTL intervals and 1017 rapeseed homologs of known genes from other species. Among the 10 modules in this gene coexpression network, modules 1 and 2 were core modules and contained genes involved in source-flow-sink processes such as synthesis and transportation of fatty acid and protein, and photosynthesis. A hub gene SERINE CARBOXYPEPTIDASE-LIKE 19 (SCPL19) was identified by candidate gene association analysis in rapeseed and functionally investigated using Arabidopsis T-DNA mutant and overexpression lines. Our study demonstrates the power of gene coexpression analysis to prioritize candidate genes from large candidate QTG sets and enhances the understanding of molecular mechanism for seed weight at the early developmental stage in rapeseed.

The ability of wheat to adapt to a wide range of environmental conditions is determined mostly by allelic diversity among genes regulating vernalization requirement. Vrn-1 is a major regulator of this requirement. In this study, two novel alleles of Vrn-A1 were discovered in Chinese cultivars: vrn-A1n was identified in two landraces, Jiunong 2 and Ganchun 16, and Vrn-A1o was detected in Duanhongmangmai. Both novel alleles showed a linked duplication in the promoter region. The common copy of these two alleles was identical to the recessive allele vrn-A1. Compared with the recessive allele vrn-A1, the other copy of vrn-A1n contained a 54-bp deletion in the promoter region and the distinct copy of Vrn-A1o contained an 11-bp deletion in the promoter region. In segregating populations in the greenhouse under nonvernalizing (20-25 °C) and long-day (16 h light) conditions, plants with the novel vrn-A1n allele did not head earlier than those with the recessive vrn-A1 allele. However, plants that were either homozygous or heterozygous for the novel Vrn-A1o allele headed earlier than those with the recessive vrn-A1 allele. To identify the novel allele with the small-sized product and facilitate screening, a DNA marker for the novel dominant allele Vrn-A1o was designed. Analysis of the novel-allele distribution showed that two cultivars carrying the vrn-A1n allele were dispersed in the northwestern spring wheat zone, and 12 cultivars carrying the dominant Vrn-A1o allele were widely distributed in the northwestern spring wheat zone, Xinjiang winter and spring wheat zone, Yellow and Huai River valley winter wheat zone, and Qinghai-Tibetan Plateau spring and winter wheat zone. Our study identifies useful germplasm and a DNA marker for wheat breeding.

Pre-harvest sprouting (PHS) is one of the serious global issues in wheat production. Identification of quantitative trait loci (QTL) and closely-linked markers is greatly helpful for wheat improvement. In the present study, a recombinant inbred line (RIL) population derived from the cross of Zhongmai 578 (ZM578)/Jimai 22 (JM22) and parents were phenotyped in five environments and genotyped by the wheat 50 K single-nucleotide polymorphism (SNP) array. Two QTL of germination index (GI), QGI.caas-3A and QGI.caas-5A, were detected, explaining 4.33%-5.58% and 4.43%-8.02% of the phenotypic variances, respectively. The resistant effect of QGI.caas-3A was contributed by JM22, whereas that of QGI.caas.5A was from ZM578. The two QTL did not correspond to any previously identified genes or genetic loci for PHS-related traits according to their locations in the Chinese Spring reference genome, indicating that they are likely to be new loci for PHS resistance. Four kompetitive allele-specific PCR (KASP) markers K_AX-109605367and K_AX-179559687 flanking QGI.caas-3A, and K_AX-111258240 and K_AX-109402944 flanking QGI.caas-5A, were developed and validated in a natural population of 100 wheat cultivars. The distribution frequency of resistance alleles at Qphs.caas-3A and Qphs.caas-5A loci were 82.7% and 57.1%, respectively, in the natural population. These findings provide new QTL and tightly linked KASP markers for improvement of PHS resistance in wheat.

Wheat tiller angle (TA) is an important agronomic trait that contributes to grain production by affecting plant architecture. It also plays a crucial role in high-yield wheat breeding. An association panel and a recombinant inbred line (RIL) population were used to map quantitative trait loci (QTL) for TA. Results showed that 470 significant SNPs with 10.4%-28.8% phenotypic variance explained (PVE) were detected in four replicates by a genome-wide association study (GWAS). Haplotype analysis showed that the TA_Hap_4B1 locus on chromosome 4B was a major QTL to regulate wheat TA. Ten QTL were totally detected by linkage mapping with the RIL population, and QTA.hau-4B.1 identified in six environments with the PVE of 7.88%-18.82% was a major and stable QTL. A combined analysis demonstrated that both TA_Hap_4B1 and QTA.hau-4B.1 were co-located on the same region. Moreover, QTA.hau-4B.1 was confirmed by bulked segregant RNA-Seq (BSR-Seq) analysis. Phenotypic analysis showed that QTA.hau-4B.1 was also closely related to yield traits. Furthermore, TraesCS4B02G049700 was considered as a candidate gene through analysis of gene sequence and expression. This study can be potentially used in cloning key genes modulating wheat tillering and provides valuable genetic resources for improvement of wheat plant architecture.

Agropyron cristatum (2n = 4x = 28, PPPP), which harbours many high-yield and disease-resistance genes, is a promising donor for wheat improvement. Narrow genetic diversity and the trade-off between grain weight and grain number have become bottlenecks for increasing grain yield in wheat. In this study, a novel translocation line, WAT650l, was derived from the chromosome 6P addition line 4844-12, which can simultaneously increase both grain number per spike (GNS) and thousand-grain weight (TGW). Cytological analysis and molecular marker analysis revealed that WAT650l was a 5BL·5BS-6PL (bin 12-17) translocation line. Assessment of agronomic traits and analysis of the BC₄F₂ and BC₅F₂ populations suggested that the 6PL terminal chromosome segment in WAT650l resulted in increased grain number per spike (average increased by 14.07 grains), thousand-grain weight (average increased by 4.31 g), flag leaf length, plant height, spikelet number per spike and kernel number per spikelet during the two growing seasons of 2020-2021 and 2021-2022. Additionally, the increased GNS locus and high-TGW locus of WAT650l were mapped to the bins 16-17 and 12-13, respectively, on chromosome 6PL by genetic population analysis of three translocation lines. In summary, we provide a valuable germplasm resource for broadening the genetic base of wheat and overcoming the negative relationship between GNS and TGW in wheat breeding.

The wild abortive (WA)-type cytoplasmic male sterility (CMS) derived from the wild rice species Oryza rufipogon Griff. is used widely in three-line indica hybrids. The identification and mapping of restorer of fertility (Rf) genes aided in the development of WA-type hybrids. Here we report that testcross F₁ plants from the WA-type CMS line and 9311 exhibited stainable pollen grains with no seed set, indicating that 9311 carries minor-effect Rfs for WA-type CMS. We developed an advanced backcross population consisting of plants harboring small regions of donor chromosomal segments from 9311 in the WA-TianfengA genetic background with moderate seed setting rates. Genetic analysis showed that the pollen fertility levels of the backcross individuals are governed by a single gene from 9311 that we named Rf19(t). By use of the RICE 40 K gene chip, three introduced segments were identified in the fertile lines, and a candidate region spanning 4.37-8.29 Mb on chromosome 1 was identified for Rf19(t). Finally, Rf19(t) was fine-mapped to a region of 90 kb between the DNA marker loci STS1-163 and STS1-183, in which eight ORFs were predicted. Also, using relative expression analyses, comparative sequence analyses and functional domain analyses, we identified LOC_Os01g10530 as the most likely candidate gene for Rf19(t). Furthermore, Rf19(t) was found to function in fertility restoration, most probably by regulating the degradation of mRNA transcribed from the mitochondrial gene WA352. These results increase our knowledge of fertility restoration in WA-type CMS lines and will facilitate the development of high-quality pairs of WA-type CMS and maintainer lines.

Clubroot and herbicide resistance, high oleic acid (OA) content, and early maturity are targets of rapeseed (Brassica napus L.) breeding. The objective of this study was to develop new male-fertility restorer lines by pyramiding favorable genes to improve these traits simultaneously. Seven elite alleles for the four traits were introduced into the restorer line 621R by speed breeding with marker-assisted and phenotypic selection. Six introgression lines (ILs) were developed with four- to seven-gene combinations and crossed with two elite parents to develop hybrids. All ILs and their corresponding hybrids displayed high resistance to both clubroot pathotype 4 and sulfonylurea herbicides. Three ILs and their hybrids showed large increases in OA contents and four showed earlier maturity. These new ILs may be useful in rapeseed hybrid breeding for the target traits.

Rice grain yield and quality are negatively impacted by high temperature stress. Irrigation water temperature significantly affects rice growth and development, thus influencing yield and quality. The role of cooler irrigation water in counteracting high temperature induced damages in rice grain yield and quality are not explored. Hence, in the present study two rice hybrids, Liangyoupeijiu (LYPJ) and IIyou 602 (IIY602) were exposed to heat stress and irrigated with water having different temperatures in a split-split plot experimental design. The stress was imposed starting from heading until maturity under field-based heat tents, over two consecutive years. The maximum day temperature inside the heat tents was set at 38 °C. For the irrigation treatments, two different water sources were used including belowground water with cooler water temperature and pond water with relatively higher water temperature. Daytime mean temperatures in the heat tents were increased by 1.2-2.0 °C across two years, while night-time temperature remained similar at both within and outside the heat tents. Cooler belowground water irrigation did have little effect on air temperature at the canopy level but decreased soil temperature (0.2-1.4 °C) especially under control. Heat stress significantly reduced grain yield (33% to 43%), panicles m⁻² (9% to 10%), spikelets m⁻² (15% to 22%), grain-filling percentage (13% to 26%) and 1000-grain weight (3% to 5%). Heat stress significantly increased chalkiness and protein content and decreased grain length and amylose content. Grain yield was negatively related to air temperature at the canopy level and soil temperature. Whereas grain quality parameters like chalkiness recorded a significantly positive association with both air and soil temperatures. Irrigating with cooler belowground water reduced the negative effect of heat stress on grain yield by 8.8% in LYPJ, while the same effect was not seen in IIY602, indicating cultivar differences in their response to irrigation water temperature. Our findings reveal that irrigating with cooler belowground water would not significantly mitigate yield loss or improve grain quality under realistic field condition. The outcome of this study adds to the scientific knowledge in understanding the interaction between heat stress and irrigation as a mitigation tool. Irrigation water temperature regulation at the rhizosphere was unable to counteract heat stress damages in rice and hence a more integrated management and genetic options at canopy levels should be explored in the future.

Controlled-release urea (CRU) is widely reported to supply crop nitrogen (N) demand with one basal application, thus effectively replacing split applications of urea without diminishing grain yield and N use efficiency (NUE). However, its use for replacement for high-yield split applications of urea (CK) for rice is untested. In addition, the degree to which greenhouse gas (GHG) emissions in rice systems are affected when CRU is substituted for CK remains unclear. During 2017 and 2018, we sampled plant growth and gas emissions in a rice paddy field treated with three CRU types (sulfur-coated urea [SCU], polymer-coated urea [PCU], and bulk blended CRU [BBU]) applied via two methods (surface broadcasting on the soil and subsurface banding at 5 cm depth), with CK as a control. The three CRUs led to different soil NH₄⁺-N dynamics, and the N supply pattern under BBU was more beneficial for rice seedling establishment than under SCU and PCU, resulting in grain yield and NUE comparable to those under CK. CRU type showed no significant effect on either CH₄ emissions or N₂O emissions, and broadcast CRUs exhibited significantly higher total GHG emissions than CK. However, banded CRUs significantly reduced the total GHG emissions in comparison with broadcast CRUs, by 9.2% averaged across the two years. Reduced CH₄ emissions, particularly during the period prior to the middle drainage, contributed largely to the GHG difference. With comparably high grain yield and low total GHG emissions, banded BBU showed a low yield-scaled GHG (GHG emissions divided by grain yield) comparable to that under CK in both years. Overall, our study suggested that N management synchronized with rice demand and contributing to a high NUE tended to minimize yield-scaled GHG. Broadcast CRU can hardly substitute for CK in terms of either grain yield or GHG emissions, but banded BBU is a promising N management strategy for sustaining rice production while minimizing environmental impacts.

Phosphorus (P) is an essential nutrient for maize production, but in temperate areas the P uptake during early growing stages can be limited due to low soil temperature, even though the soil was tested high in P. The objective of this study was to assess the effects of nitrogen and phosphorous (NP) starter fertilisation during early growth stages and its carryover until maize harvest, in mineral-fertilised or manured systems. A field experiment was carried out in north-west Italy during the 2019 and 2020 growing seasons. The trial compared sub-surface placement of NP (diammonium phosphate) or N alone (ammonium nitrate) in bands close to the maize seed furrows, in differing long-term (LT) fertilisation managements: two doses of urea (Min-L and Min-H), two doses of bovine slurry (Slu-L and Slu-H) or two doses of farmyard manure (Fym-L and Fym-H). The two rates, low (L) and high (H), corresponded to 170 and 250 kg N ha⁻¹ year⁻¹ respectively. Compared to N fertilisation, NP starter fertilisation improved early maize growth assessed by leaf area index (LAI) and shoot dry weight (SDW) in all systems. The effects differed between the two years (2019: LAI + 63%, SDW + 67%; 2020: LAI + 36%, SDW + 38%), as 2019 was cool during the first growth. Higher LAI and SDW values were confirmed at crop flowering in the mineral-fertilised systems only. As shoot growth was enhanced by NP starter fertilisation, anthesis occurred 1 day earlier in all systems. However, a response to NP starter fertilisation at harvest was recorded in mineral-fertilised systems only (+1.3 and +3.2 t ha⁻¹ in Min-L and Min-H, respectively). The uptake of P, used as a true indicator of soil nutrient availability, increased with increasing soil Olsen P until 39 mg kg⁻¹. These results suggest that soil test thresholds should be revised for points above which P fertilisation should be suspended.

Verticillium wilt (VW) is a common soilborne disease of cotton. It occurs mainly in the seedling and boll-opening stages and severely impairs the yield and quality of the fiber. Rapid and accurate identification and evaluation of VW severity (VWS) forms the basis of field cotton VW control, which has great significance to cotton production. Cotton VWS values are conventionally measured using in-field observations and laboratory test diagnoses, which require abundant time and professional expertise. Remote and proximal sensing using imagery and spectrometry have great potential for this purpose. In this study, we performed in situ investigations at three experimental sites in 2019 and 2021 and collected VWS values, in situ images, and spectra of 361 cotton canopies. To estimate cotton VWS values at the canopy scale, we developed two deep learning approaches that use in situ images and spectra, respectively. For the imagery-based method, given the high complexity of the in situ environment, we first transformed the task of healthy and diseased leaf recognition to the task of cotton field scene classification and then built a cotton field scenes (CFS) dataset with over 1000 images for each scene-unit type. We performed pretrained convolutional neural networks (CNNs) training and validation using the CFS dataset and then used the networks after training to classify scene units for each canopy. The results showed that the DarkNet-19 model achieved satisfactory performance in CFS classification and VWS values estimation (R² = 0.91, root-mean-square error (RMSE) = 6.35%). For the spectroscopy-based method, we first designed a one-dimensional regression network (1D CNN) with four convolutional layers. After dimensionality reduction by sensitive-band selection and principal component analysis, we fitted the 1D CNN with varying numbers of principal components (PCs). The 1D CNN model with the top 20 PCs performed best (R² = 0.93, RMSE = 5.77%). These deep learning-driven approaches offer the potential of assessing crop disease severity from spatial and spectral perspectives.

Nitrogen (N) fertilization affects grain quality in common buckwheat (Fagopyrum esculentum Moench). But the effects of N fertilizer on various buckwheat protein parameters are not fully understood. This study aimed to investigate the synthesis, accumulation, and quality of buckwheat protein under four N application rates in the Loess Plateau, China. Optimal N application (180 kg N ha⁻¹) improved yield, agronomic traits, and N transport and increased protein yield and protein component accumulation. Prolamin and glutelin accumulation first increased and then decreased with increasing N application. The relationships between the contents of protein components and the amount of applied N generally followed quadratic functions. Nitrate reductase and glutamine synthetase activities first increased and then decreased with increasing N levels. Optimal N fertilizer increased the waterholding capacity and thermal stability of buckwheat protein and reduced its emulsification capacity, but negligibly changed its oil-absorption capacity. Hydrophobic amino acids and glutelin content were the main factors affecting protein quality.

Maize ear development determines the crop yield, and many important transcription factors (TFs) have been identified to function in this process. However, their transcriptional regulation mechanisms are still elusive. In this study, we generated the genome-wide DNA binding sites for 8 TFs which are known to function or highly expressed in inflorescence by applying the tsCUT&Tag method in maize leaf protoplast. We exposed a regulatory grid of 4 WUSCHEL-related homeobox (WOX) genes and revealed their potential regulatory mechanisms. In addition, a hierarchical regulation network for the determinacy and specification of maize inflorescence meristems were also constructed using the binding profiles of a floral development gene INDETERMINATE FLORAL APEX1 (IFA1) and 3 MADS-box genes. Our study provides an in-depth understanding and new insights of the regulatory mechanisms during maize inflorescence development.

Fhb7 is a major gene that was transferred from Thinopyrum ponticum to chromosome 7D of wheat (Triticum aestivum) and confers resistance to both Fusarium head blight (FHB) and Fusarium crown rot (FCR). However, Fhb7 is tightly linked to the PSY-E2 gene, which causes yellow flour, limiting its application in breeding. To break this linkage, marker K-PSY was developed for tagging PSY-E2 and used with Fhb7 markers to identify recombination between the two genes. Screening 21,000 BC₁F₂ backcross progeny (Chinese Spring ph1bph1b*2/SDAU 2028) revealed two Fhb7⁺ wheat-Tp7el₂L lines, Shannong 2-16 and Shannong 16-1, that carry a desired truncated Fhb7⁺ translocation segment without PSY-E2. The two lines show levels of resistance to FHB and FCR similar to those of the original translocation line SDAU 2028, but have white flour. To facilitate Fhb7 use in wheat breeding, STS markers were developed and used to isolate Fhb7 on a truncated Tp7el₂ translocation segment. Near-isogenic lines carrying the Fhb7⁺ segment were generated in the backgrounds of three commercial cultivars, and Fhb7⁺ lines showed increased FHB and FCR resistance without yield penalty. The breakage of the tight linkage between Fhb7 and PSY-E2 via homoeologous recombination provides genetic resources for improvement of wheat resistance to FHB and FCR and permit the large-scale deployment of Fhb7 in breeding using marker-assisted selection.

Sweetpotato (Ipomoea batatas (L.) Lam.) is a widely grown food crop especially in developing countries. Increasing storage-root yield and dry-matter content has been the main breeding objective of the crop, and DNA marker-assisted breeding is needed for this purpose. In this study, using a mapping population of 500 F₁ individuals from a cross between Xushu 18 (female) and Xu 781 (male), we constructed a high-density genetic linkage map of sweetpotato using 601 simple-sequence repeat (SSR) primer pairs. The Xushu 18 map contained 90 linkage groups with 5547 SSR markers and spanned 18,263.5 cM, and the Xu 781 map contained 90 linkage groups with 4599 SSR markers and spanned 18,043.7 cM, representing the highest genome coverage yet reported for sweetpotato. We identified 33 QTL for storage-root yield and 16 QTL for dry-matter content, explaining respectively 6.5%-47.5% and 3.2%-18.9% of variation. These results provide a foundation for fine-mapping and cloning of QTL and for marker-assisted breeding in sweetpotato.