Plants produce a range of carbohydrates to meet their growth and developmental needs. Protein reversible phosphorylation plays key roles in coordinating multiple metabolic pathways and integrating diverse internal and external cues. Understanding such regulatory metabolism will provide novel resources for breeding and crop management by modulating metabolic pathways for control of growth and stress response. In this review, we summarize the complex, multifaceted functions of protein phosphorylation and their connections to plant metabolism. We focus particularly on carbohydrate metabolic pathways that are controlled by key kinases and discuss how they are linked to downstream changes in physiology, important agronomic traits and crop quality.

Increasing tiller number is a target of high-yield rice breeding. Identification of tiller-defect mutants and their corresponding genes is helpful for clarifying the molecular mechanism of rice tillering. Summarizing research progress on the two processes of rice tiller formation, namely the formation and growth of axillary meristem, this paper reviews the effects of genetic factors, endogenous hormones, and exogenous environment on rice tillering, finding that multiple molecular mechanisms and signal pathways regulating rice tillering cooperate rice tillering, and discusses future research objectives and application of its regulatory mechanism. Elucidation of theis mechanism will be helpful for breeding high-yielding rice cultivars with ideal plant type via molecular design breeding.

Acquisition of plant phenotypic information facilitates plant breeding, sheds light on gene action, and can be applied to optimize the quality of agricultural and forestry products. Because leaves often show the fastest responses to external environmental stimuli, leaf phenotypic traits are indicators of plant growth, health, and stress levels. Combination of new imaging sensors, image processing, and data analytics permits measurement over the full life span of plants at high temporal resolution and at several organizational levels from organs to individual plants to field populations of plants. We review the optical sensors and associated data analytics used for measuring morphological, physiological, and biochemical traits of plant leaves on multiple scales. We summarize the characteristics, advantages and limitations of optical sensing and data-processing methods applied in various plant phenotyping scenarios. Finally, we discuss the future prospects of plant leaf phenotyping research. This review aims to help researchers choose appropriate optical sensors and data processing methods to acquire plant leaf phenotypes rapidly, accurately, and cost-effectively.

Although a few cases of genetic epistasis in plants have been reported, the combined analysis of genetically phenotypic segregation and the related molecular mechanism remains rarely studied. Here, we have identified a gene (named GaPC) controlling petal coloration in Gossypium arboreum and following a heritable recessive epistatic genetic model. Petal coloration is controlled by a single dominant gene, GaPC. A loss-of-function mutation of GaPC leads to a recessive gene Gapc that masks the phenotype of other color genes and shows recessive epistatic interactions. Map-based cloning showed that GaPC encodes an R2R3-MYB transcription factor. A 4814-bp long terminal repeat retrotransposon insertion at the second exon led to GaPC loss of function and disabled petal coloration. GaPC controlled petal coloration by regulating the anthocyanin and flavone biosynthesis pathways. Expression of core genes in the phenylpropanoid and anthocyanin pathways was higher in colored than in white petals. Petal color was conferred by flavonoids and anthocyanins, with red and yellow petals rich in anthocyanin and flavonol glycosides, respectively. This study provides new insight on molecular mechanism of recessive epistasis, also has potential breeding value by engineering GaPC to develop colored petals or fibers for multi-functional utilization of cotton.

The role of phot1 in triggering hypocotyl phototropism and optimizing growth orientation has been well-characterized in Arabidopsis, whereas the role of Zmphot1 in maize remains largely unclear. Here, we show that Zmphot1 is involved in blue light-induced phototropism. Compared with Atphot1, Zmphot1 exhibited a weaker phototropic response to very low-fluence rates of blue light (< 0.01 μmol m^?2 s^?1), but stronger phototropic response to high-fluence rates of blue light (> 10 μmol m^?2 s^?1) than Atphot1. Notably, blue light exposure induced Zmphot1-green fluorescent protein (GFP), but not Atphot1-GFP, to form the aggregates in the cytoplasm of Nicotiana benthamiana cells. Furthermore, by generating the chimeric phot1 proteins, we found that the serine-threonine kinase (STK) domain at the C-terminus is responsible for a more volatile membrane association of Zmphot1. Consistently, the chimeric phot1 protein fusing the STK domain of Zmphot1 with other domains of Atphot1 responded similarly as Zmphot1 to both low and high fluence rates of blue light. Interestingly, although both Zmphot1 and Atphot1 interact with AtNPH3, Zmphot1 induced weaker dephosphorylation of NON-PHOTOTROPIC HYPOCOTYL 3 (NPH3) than Atphot1. Together, our findings indicate that Zmphot1 and Atphot1 exhibit different photosensory function during phototropic response and that the STK domain may play a key role in determining their properties.

Lesion mimic mutants (LMMs) are advantageous materials for studying programmed cell death (PCD). Although some rice LMM genes have been cloned, the diversity of functions of these genes indicates that the mechanism of cell death regulation in LMMs needs further study. In this study, we identified a rice light-dependent leaf lesion mimic mutant 4 (llm4) that showed abnormal chloroplast structure, photoinhibition, reduced photosynthetic protein levels, massive accumulation of reactive oxygen species (ROS), and PCD. Map-based cloning and complementation testing revealed that LLM4 encodes zeaxanthin epoxidase (ZEP), an enzyme involved in the xanthophyll cycle, which functions in plant photoprotection, ROS scavenging, and carotenoid and abscisic acid (ABA) biosynthesis. The ABA content was decreased, and the contents of 24 carotenoids differed between the llm4 mutant and the wild type (WT). The llm4 mutant showed reduced dormancy and greater sensitive to ABA than the WT. We concluded that the mutation of LLM4 resulted in the failure of xanthophyll cycle, in turn causing ROS accumulation. The excessive ROS accumulation damaged chloroplast structure and induced PCD, leading eventually to the formation of lesion mimics.

In higher plants, the chloroplast is the most important organelle for photosynthesis and for numerous essential metabolic processes in the cell. Although many genes involved in chloroplast development have been identified, the mechanisms underlying such development are not fully understood. In this study, a rice (Oryza sativa) mutant exhibiting pale green color and seedling lethality was isolated from a mutant library. The mutated gene was identified as an ortholog of THA8 (thylakoid assembly 8) in Arabidopsis and maize. This gene is designated as OsTHA8 hereafter. OsTHA8 showed a typical pentatricopeptide repeat (PPR) characteristic of only four PPR motifs. Inactivation of OsTHA8 led to a deficiency in chloroplast development in the rice seedling stage. OsTHA8 was expressed mainly in young leaves and leaf sheaths. The OsTHA8 protein was localized to the chloroplast. Loss of function of OsTHA8 weakened the editing efficiency of ndhB-611/737 and rps8-182 transcripts under normal conditions. Y2H and BiFC indicated that OsTHA8 facilitates RNA editing by forming an editosome with multiple organellar RNA editing factor (OsMORF8) and thioredoxin z (OsTRXz), which function in RNA editing in rice chloroplasts. Defective OsTHA8 impaired chloroplast ribosome assembly and resulted in reduced expression of PEP-dependent genes and photosynthesis-related genes. Abnormal splicing of the chloroplast gene ycf3 was detected in ostha8. These findings reveal a synergistic regulatory mechanism of chloroplast biogenesis mediated by RNA, broaden the function of the PPR family, and shed light on the RNA editing complex in rice.

Although several pentatricopeptide repeat (PPR) proteins are involved in post-transcriptional processing of mitochondrial RNA, it is unclear which specific protein is involved in the RNA editing of ccmC in maize (Zea mays). Here we report the identification of the maize empty pericarp 601 (emp601) mutant and the map-based cloning of the Emp601 gene, which encodes an E2-type PPR protein that is targeted to mitochondria. A single-nucleotide deletion in the emp601 mutant caused a frameshift and introduced a premature stop codon into the predicted EMP601. This mutation was associated with reduced accumulation of mitochondrial complex III as well as with inhibition of growth and differentiation of basal endosperm transfer layer cells, leading to final degeneration of the embryo and endosperm. We determine that loss of EMP601 function prevents the C-to-U RNA editing of the mitochondrial transcript ccmC at position 358. EMP601 binds to the ccmC transcript and directly interacts with Multiple organellar RNA editing factor 8 and may be a component of the plant mitochondrial editosome. We conclude that EMP601 functions in RNA editing of mitochondrial ccmC transcripts and influences mitochondrial function and seed development.

Flowering time (FT) is a key maize domestication trait, variation in which allows maize to grow in a wide range of latitudes. Although previous studies have investigated the genetic control of FT-related traits per se, few studies of FT hybrid performance have been published. We characterized the genomic architecture associated with hybrid performance for FT in a hybrid panel by testcrossing Chang 7-2 with 328 Ye478 × Qi319 recombinant inbred lines (RILs). We identified 11 quantitative trait loci (QTL) for hybrid performance in FT-related traits, including a major QTL qFH10 that controls hybrid performance and heterosis in a summer maize-growing region. However, this locus acts in regulating FT traits per se only in a spring maize-growing region. We validated ZmCCT10 as a candidate gene for qFH10 and found that differences between hybrids and their parental lines in DNA methylation in the differentially methylated region (DMR, -700 to -1520) of the ZmCCT10 promoter affected gene expression pattern and thereby FT in the summer maize-growing region.

Grain filling influences grain size and quality in cereal crops. The molecular mechanisms that regulate grain endosperm development remain elusive. In this study, we characterized a filling-defective and grain width mutant, fgw1, whose mutation increased rice seed width mainly via cell division and expansion in grains. Sucrose contents were higher but starch contents lower in the fgw1 mutant during the grain-filling stage, resulting in inferior endosperm of opaque, white appearance with loosely packed starch granules. Map-based cloning revealed that FGW1 encoded a protein containing DUF630/DUF632 domains, localized in the plasma membrane with preferential expression in the panicle. RNA interference in FGW1 resulted in increased grain width and weight, whereas overexpression of FGW1 led to slightly narrower kernels and better grain filling. In a yeast two-hybrid assay, FGW1 interacted directly with the 14-3-3 protein GF14f, bimolecular fluorescence complementation verified that the site of interaction was the membrane, and the mutated FGW1 protein failed to interact with GF14f. The expression of GF14f was down-regulated in fgw1, and the activities of AGPase, StSase, and SuSase in the endosperm of fgw1 increased similarly to those of a reported GF14f-RNAi. Transcriptome analysis indicated that FGW1 also regulates cellular processes and carbohydrate metabolism. Thus, FGW1 regulated grain formation via the GF14f pathway.

Nitrogen (N) is an essential macronutrient for plant growth and productivity. Leguminous plants establish symbiotic relationships with nitrogen-fixing rhizobial bacteria to use atmospheric dinitrogen gas to meet high N demand under low-N conditions. Nodule formation and N fixation are energy-consuming processes and are inhibited by nitrate present in the environment. Previous studies in model leguminous plants characterized NIN-LIKE PROTEIN (NLP) proteins that mediate nitrate control of root nodule symbiosis, but the mechanism by which nitrate regulates soybean root nodules via NLP remains unclear. In the soybean genome we found four homologs of AtNLP7, named GmNLP7a-GmNLP7d. We showed that the expression of GmNLP7s is responsive to nitrate but not to rhizobial infection and localized GmNLP7a to the nucleus. Downregulation of GmNLP7s increased nodule number, and overexpression of GmNLP7a (GmNLP7aOE) reduced nodule number regardless of nitrate availability, suggesting a negative role for GmNLP7s in nodulation. Nitrogenase activity in the GmNLP7aOE line was comparable to that of the wild type, indicating that GmNLP7a does not affect mature nodule activity. Overexpression of GmNLP7a downregulated the expression of GmNIN1a and GmENOD40-1. GmNLP7a interacted with GmNIN1a via the PB1 domain. Our results reveal a new regulator of GmNLP7 in nodulation and a molecular mechanism by which nitrate affects nodule number in soybean.

Sorghum (Sorghum bicolor (L.) Moench) is a major world crop that is a reliable source of fodder and food grain in arid regions. However, unlike other cereals, sorghum grain has low nutritional value, owing mainly to the resistance of its storage proteins (kafirins) to protease digestion. Changing the composition of kafirins or their primary structure may address this problem. To induce mutations in kafirin-encoding genes that were expected to disturb their accumulation in endosperm cells, we used a genome-editing approach. By Agrobacterium-mediated genetic transformation of immature embryos of cv. Avans, we obtained 14 transgenic plants with genetic constructs for site-directed mutagenesis of the k1C5 and gKAF1 genes encoding 22 kDa α- and 28 kDa γ-kafirins, respectively. Sequencing of 5 regenerants obtained by using k1C5-addressing vector revealed two plants with mutations. T₁ progeny of these mutants had higher in vitro digestibility of endosperm proteins (86%-92%), in comparison with the donor Avans (63%-67%). The kernels of these plants had a thick vitreous endosperm. A mutant with increased in vitro protein digestibility and vitreous endosperm, carrying a mutation in the target sequence, was also obtained by use of the gKAF1-addressing vector. Thus, using genome editing technology, we have obtained mutants with improved kafirin digestibility that can be used in sorghum breeding.

Drought stress impairs plant growth and other physiological functions. MeHDZ14, a homeodomain-leucine zipper I transcription factor, is strongly induced by drought stress in various cassava cultivars. However, the role of MeHDZ14 in cassava growth regulation has remained unclear. Here we report that MeHDZ14 affected plant height, such that a dwarf phenotype and altered internode elongation were observed in transgenic cassava lines. MeHDZ14 was found to negatively regulate the biosynthesis of lignin. Its overexpression resulted in abaxially rolled leaves. The morphogenesis of leaf epidermal cells was inhibited by overexpression of MeHDZ14, with decreased auxin and gibberellin and increased cytokinin contents. MeHDZ14 was found to regulate many drought-responsive genes, including genes involved in cell wall synthesis and expansion. MeHDZ14 bound to the promoter of caffeic acid 3-O-methyltransferase 1 (MeCOMT1), acting as a transcriptional repressor of genes involved in cell wall development. MeHDZ14 appears to act as a negative regulator of internode elongation and epidermal cell morphogenesis during cassava leaf development.

Puccinia triticina (Pt), as the causal agent of wheat leaf rust, employs a plethora of effector proteins to modulate wheat immunity for successful colonization. Understanding the molecular mechanisms underlying Pt effector-mediated wheat susceptibility remains largely unexplored. In this study, an effector Pt_21 was identified to interact with the apoplast-localized wheat thaumatin-like protein TaTLP1 using a yeast two-hybrid assay and the Pt_21-TaTLP1 interaction was characterized. The interaction between Pt_21 and TaTLP1 was validated by in vivo co-immunoprecipitation assay. A TaTLP1 variant, TaTLP1^C71A, that was identified by the site-directed mutagenesis failed to interact with Pt_21. Pt_21 was able to suppress Bax-mediated cell death in leaves of Nicotiana benthamiana and inhibit TaTLP1-mediated antifungal activity. Furthermore, infiltration of recombinant protein Pt_21 into leaves of transgenic wheat line overexpressing TaTLP1 enhanced the disease development of leaf rust compared to that in wild-type leaves. These findings demonstrate that Pt_21 suppresses host defense response by directly targeting wheat TaTLP1 and inhibiting its antifungal activity, which broadens our understanding of the molecular mechanisms underlying Pt effector-mediated susceptibility in wheat.

Fusarium crown rot (FCR) is a soilborne disease causing severe yield losses in many wheat-growing areas of the world. Diseased plants show browning and necrosis of roots and stems causing white heads at maturity. Little is known about the molecular processes employed by wheat roots to respond to the disease. We characterized morphological, transcriptional and hormonal changes in wheat seedling roots following challenge with Fusarium pseudograminearum (Fp), the main pathogen of FCR. The pathogen inhibited root development to various extents depending on plants’ resistance level. Many genes responsive to FCR infection in wheat roots were enriched in plant hormone pathways. The contents of compounds involved in biosynthesis and metabolism of jasmonic acid, salicylic acid, cytokinin and auxin were drastically changed in roots at five days post-inoculation. Presoaking seeds in methyl jasmonate for 24 h promoted FCR resistance, whereas presoaking with cytokinin 6-benzylaminopurine made plants more susceptible. Overexpression of TaOPR3, a gene involved in jasmonic acid biosynthesis, enhanced plant resistance as well as root and shoot growth during infection.

Base editors of the Cas9 system have been widely used for precise nucleotide substitution in crops. In this study, Cas12a was applied to construct plant cytosine base editors (CBEs). The main elements of Cas12a-CBEs were engineered and their efficiency was evaluated in stably transformed rice cells. An optimized ttCas12a-hyA3Bctd editor, consisting of a LbCas12a variant carrying catalytic inactive D832A and temperature-tolerance D156R double mutations, a truncated human APOBEC3B deaminase, a human RAD51 single-stranded DNA-binding domain, and double copies of UGI, outperformed other Cas12a-CBEs in base editing efficiency. In T₀ transgenic rice plants, ttCas12a-hyA3Bctd edited an average of 42.01% and a maximum of 68.75% of lines at six genomic targets. A-to-G conversions were generated in rice by an adenine base editor with a similar architecture to the optimized CBE. Our results provide preliminary evidence for the feasibility of robust and efficient plant Cas12a base editing systems, which could be useful for precise crop breeding.

Physical dormancy (PY) commonly present in the seeds of higher plants is believed to be responsible for the germination failure by impermeable seed coat in hard seeds of legume species, instead of physiological dormancy (PD). In this study, a non-destructive approach involving multispectral imaging was used to successfully identify hard seeds from non-hard seeds in Medicago sativa, with accuracy as high as 96.8%-99.0%. We further adopted multiple-omics strategies to investigate the differences of physiology, metabolomics, methylomics, and transcriptomics in alfalfa hard seeds, with non-hard seeds as control. The hard seeds showed dramatically increased antioxidants and 125 metabolites of significant differences in non-targeted metabolomics analysis, which are enriched in the biosynthesis pathways of flavonoids, lipids and hormones, especially with significantly higher ABA, a hormone known to induce dormancy. In our transcriptomics results, the enrichment pathway of “response to abscisic acid” of differential expressed genes (DEG) supported the key role of ABA in metabolomics results. The methylome analysis identified 54,899, 46,216 and 54,452 differential methylation regions for contexts of CpG, CHG and CHH, and 344 DEGs might be regulated by hypermethylation and hypomethylation of promoter and exon regions, including four ABA- and JA-responsive genes. Among 8% hard seeds in seed lots, 24.5% still did not germinate after scarifying seed coat, and were named as non-PY hard seeds. Compared to hard seeds, significantly higher contents of ABA/IAA and ABA/JA were identified in non-PY hard seeds, which indicated the potential presence of PD. In summary, the significantly changed metabolites, gene expressions, and methylations all suggested involvement of ABA responses in hard seeds, and germination failure of alfalfa hard seeds was caused by combinational dormancy (PY + PD), rather than PY alone.

The nuclear factor Y (NF-Y) gene family is a class of transcription factors that are widely distributed in eukaryotes and are involved in various biological processes. However, the NF-Y gene family members in watermelon, a valued and nutritious fruit, remain largely unknown and their functions have not been characterized. In the present study, 22 ClNF-Y genes in watermelon, 29 CsNF-Y genes in cucumber, and 24 CmNF-Y genes in melon were identified based on the whole-genome investigation and their protein properties, gene location, gene structure, motif composition, conserved domain, and evolutionary relationship were investigated. ClNF-YB9 from watermelon and its homologs in cucumber and melon were expressed specifically in seeds. Its expression remained low in the early stages of watermelon seed development, increased at 20 days after pollination (DAP), and peaked at 45-50 DAP. Moreover, the knockout mutant Clnf-yb9 exhibited abnormal leafy cotyledon phenotype, implying its critical role during seed formation. Finally, protein interaction assays showed that ClNF-YB9 interacts with all ClNF-YCs and the ClNF-YB9-YC4 heterodimer was able to recruit a ClNF-YA7 subunit to assemble a complete NF-Y complex, which may function in seed development. This study revealed the structure and evolutionary relationships of the NF-Y gene family in Cucurbitaceae and the novel function of ClNF-YB9 in regulating seed development in watermelon.

Many genetic loci for wheat plant height (PH) have been reported, and 26 dwarfing genes have been catalogued. To identify major and stable genetic loci for PH, here we thoroughly summarized these functionally or genetic verified dwarfing loci from QTL linkage analysis and genome-wide association study published from 2003 to 2022. A total of 332 QTL, 270 GWAS loci and 83 genes for PH were integrated onto chromosomes according to their locations in the IWGSC RefSeq v2.1 and 65 QTL-rich clusters (QRC) were defined. Candidate genes in each QRC were predicted based on IWGSC Annotation v2.1 and the information on functional validation of homologous genes in other species. A total of 38 candidate genes were predicted for 65 QRC including three GA2ox genes in QRC-4B-IV, QRC-5A-VIII and QRC-6A-II (Rht24) as well as GA 20-oxidase 2 (TaSD1-3A) in QRC-3A-IV. These outcomes lay concrete foundations for map-based cloning of wheat dwarfing genes and application in breeding.

Thousand-kernel weight (TKW) is a measure of grain weight, a target of wheat breeding. The object of this study was to fine-map a stable quantitative trait loci (QTL) for TKW and identify its candidate gene in a recombinant inbred line (RIL) population derived from the cross of Kenong 9204 (KN9204) and Jing 411 (J411). On a high-density genetic linkage map, 24, 26 and 25 QTL were associated with TKW, kernel length (KL), and kernel width (KW), respectively. A major and stable QTL, QTkw-2D, was mapped to an 8.3 cM interval on chromosome arm 2DL. By saturation of polymorphic markers in its target region, QTkw-2D was confined to a 9.13 Mb physical interval using a secondary mapping population derived from a residually heterozygous line (F_6:7). This interval was further narrowed to 2.52 Mb using QTkw-2D near-isogenic lines (NILs). NILs^KN9204 had higher fresh and dry weights than NILs^J411 at various grain-filling stages. The TKW and KW of NILs^KN9204 were much higher than those of NILs^J411 in field trials. By comparison of both DNA sequence and expression between KN9204 and J411, TraesCS2D02G460300.1 (TraesKN2D01HG49350) was assigned as a candidate gene for QTkw-2D. This was confirmed by RNA sequencing (RNA-seq) of QTkw-2D NILs. These results provide the basis of map-based cloning of QTkw-2D, and DNA markers linked to the candidate gene may be used in marker-assisted selection.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), threatens wheat production worldwide, and resistant varieties tend to become susceptible after a period of cultivation owing to the variation of pathogen races. In this study, a new resistance gene against Pst race CYR34 was identified and predicted using the descendants of a cross between AS1676, a highly resistant Chinese landrace, and Avocet S, a susceptible cultivar. From a heterozygous plant from a F₇ recombinant inbred line (RIL) population lacking the Yr18 gene, a near-isogenic line (NIL) population was developed to map the resistance gene. An all-stage resistance gene, YrAS1676, was identified on chromosome arm 1AL via bulked-segregant exome-capture sequencing. By analyzing a large NIL population consisting of 6537 plants, the gene was further mapped to the marker interval between KA1A_485.36 and KA1A_490.13, spanning 485.36-490.13 Mb on 1AL. A total of 66 annotated genes have been reported in this region. To characterize and predict the candidate gene(s), an RNA-seq was performed using NIL-R and NIL-S seedlings 3 days after CYR34 inoculation. Compared to NIL-S plants, NIL-R plants showed stronger immune reaction and higher expression levels of genes encoding pathogenesis-associated proteins. These differences may help to explain why NIL-R plants were more resistant to Pst race CYR34 than NIL-S plants. By combining fine-mapping and transcriptome sequencing, a calcium-dependent protein kinase gene was finally predicted as the potential candidate gene of YrAS1676. This gene contained a single-nucleotide polymorphism. The candidate gene was more highly expressed in NIL-R than in NIL-S plants. In field experiments with Pst challenge, the YrAS1676 genotype showed mitigation of disease damage and yield loss without adverse effects on tested agronomic traits. These results suggest that YrAS1676 has potential use in wheat stripe rust resistance breeding.

Wheat sharp eyespot, a stem disease caused by the soilborne fungus Rhizoctonia cerealis van der Hoeven, has become a threat to wheat production worldwide. Exploiting resistance resources from wild relatives of wheat is a promising strategy for controlling this disease. In this study, a new wheat-Dasypyrum villosum T2DS·2V#4L translocation line in the background of Chinese Spring (CS) showed stable resistance to R. cerealis. Introgression of the T2DS·2V#4L chromosome into wheat cultivar Aikang 58 by backcrossing produced a marked increase in sharp eyespot resistance in NIL-T2DS·2V#4L in comparison with NIL-T2DS·2DL, and no detrimental effects of 2V#4L on agronomic traits were observed in the BC₂F₂, BC₂F_2:3, and BC₂F_2:4 generations. Flow-sorted sequencing of 2V#4L yielded 384.3 Mb of assembled sequence, and 8836 genes were predicted of which 6154 had orthologs in at least one of the 2AL, 2BL, and 2DL arms of CS, whereas 1549 genes were unique to 2V#4L. About 100,000 SNPs were detected in genes of 2V#4L and 2DL in 10 sequenced bread wheat cultivars. A Kompetitive Allele Specific Polymerase chain reaction and 30 conserved ortholog sequence markers were developed to trace the 2V#4L chromatin in wheat backgrounds. T2DS·2V#4L compensating translocation lines represent novel germplasm with sharp eyespot resistance and the markers will allow rapid detection in breeding programs.

To break the narrow diversity bottleneck of the wheat D genome, a set of Aegilops tauschii-wheat introgression (A-WI) lines was developed by crossing Ae. tauschii accession T015 with common wheat elite cultivar Zhoumai 18 (Zhou18). A high-density genetic map was constructed based on Single Nucleotide Polymorphism (SNP) markers and 15 yield-related traits were evaluated in 11 environments for detecting quantitative trait loci (QTL). A total of 27 environmentally stable QTL were identified in at least five environments, 20 of which were derived from Ae. tauschii T015, explaining up to 24.27% of the phenotypic variations. The major QTL for kernel length (KL), QKl-2D.5, was delimited to a physical interval of approximately 2.6 Mb harboring 52 candidate genes. Three Kompetitive Allele Specific PCR (KASP) markers were successfully developed based on nonsynonymous nucleotide mutations of candidate gene AetT093_2Dv1G100900.1 and showed that A-WI lines with the T015 haplotype had significantly longer KL than the Zhou18 haplotype across all 11 environments. Four primary valuable A-WIs with good trait performance and carrying yield-related QTL were selected for breeding improvement. The results will facilitate the efficient transfer of beneficial genes from Ae. tauschii into wheat cultivars to improve wheat yield and other traits.

High yield is a major objective for peanut (Arachis hypogaea L.) breeding worldwide. However, fewer yield-related quantitative trait loci (QTL) have been reported in peanut than in other staple food crops such as rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). This study aimed to identify stable major-effect QTL associated with pod yield per plant, hundred-pod weight for double-seeded pods, hundred-seed weight, shelling percentage, and pod number per plant, allowing us to predict candidate genes by means of transcriptome and genome sequencing. To this end, we used a population of recombinant inbred lines comprising 192 F_9:11 families derived from a JH6 × KX01-6 cross to construct a high-resolution genetic map (1705.7 cM) consisting of 2273 polymorphic SNPs, with 0.75 cM (on average) between adjacent SNPs. We identified two high-confidence, yield-related QTL, qHYF_A08 and qHYF_B06, explaining 5.78%-31.40% of phenotypic variation and with LOD values of 5.10-24.48, in six environments. qHYF_A08 mainly explained the variation in shelling percentage, whereas qHYF_B06 explained variation in hundred-pod weight and hundred-seed weight and accounted for 8.77%-31.40% of the variation in effective pod number per plant, pod number per plant, and shelling percentage. We narrowed down qHYF_B06 to an 890-kb interval using an advanced mapping population. Transcriptome and genome analyses revealed that only Arahy.129FS0 and Arahy.3R9A5K in the candidate mapping interval were differentially expressed between JH6 and KX01-6, with substantial structural variations in their promoter and coding regions. Genotypes of 208 peanut accessions determined using a diagnostic CAPS marker suggested that the two haplotypes of Arahy.3R9A5K were highly associated with hundred-seed weight and hundred-pod weight; this diagnostic CAPs marker could therefore be useful for selecting high-yielding lines during peanut breeding. Overall, our results provide valuable information for cloning alleles with favorable effects on peanut yield.

As a natural genetic reservoir, wild rice contains many favorable alleles and mutations conferring high yield and resistance to biotic and abiotic stresses. However, there are few reports describing favorable genes or QTL from the AA genome wild rice O. longistaminata, which is characterized by tall and robust habit and long tassels and anthers and shows high potential for use in cultivated rice improvement. We constructed a stable BC₂F₂₀ backcross inbred line (BIL) population of 152 lines from the cross of 9311 × O. longistaminat. Some BILs showed large panicles, large seeds, and strong resistance to rice false smut, bacterial leaf blight, rice blast spot, and brown planthopper. Genomic resequencing showed that the 152 BILs covered about 99.6% of the O. longistaminata genome. QTL mapping with 2432 bin markers revealed 13 QTL associated with seven yield traits and eight with resistance to brown planthopper and to four diseases. Of these QTL, 12 for grain yield and 11 for pest and disease resistance are novel in Oryza species. A large-panicle NIL1880 line containing QTL qPB8.1 showed a nearly 50% increase in spikelet number and 27.5% in grain yield compared to the recurrent parent 9311. These findings support the potential value of O. longistaminata for cultivated rice improvement.

Autopolyploidy and allopolyploidy may represent an evolutionary advantage and are more common in plants than assumed. However, less attention has been paid to autopolyploidy than to allopolyploidy, and its evolutionary consequences are largely unclear, especially for plants with high ploidy levels. In this study, we developed oligonucleotide (oligo)-based chromosome painting probes to identify individual chromosomes in S. spontaneum. Using fluorescence in situ hybridization (FISH), we investigated chromosome behavior during pachytene, metaphase, anaphase, and telophase of meiosis I (MI) in autotetraploid, autooctoploid, and autodecaploid S. spontaneum clones. All autopolyploid clones showed stable diploidized chromosome behavior; so that homologous chromosomes formed almost exclusively bivalents during MI. Two copies of homologous chromosome 8 with similar sizes in the autotetraploid clone showed preferential pairing with each other with respect to the other copies. However, sequence variation analysis showed no apparent differences among homologs of chromosome 8 and all other chromosomes. We suggest that either the stable diploidized pairing or the preferential pairing between homologous copies of chromosome 8 in the studied autopolyploid sugarcane are accounted for by unknown mechanisms other than DNA sequence similarity. Our results reveal evolutionary consequences of stable meiotic behavior in autopolyploid plants.

Temperature compensatory effect, which quantifies the increase in cumulative air temperature from soil temperature increase caused by mulching, provides an effective method for incorporating soil temperature into crop models. In this study, compensated temperature was integrated into the AquaCrop model to investigate the capability of the compensatory effect to improve assessment of the promotion of maize growth and development by plastic film mulching (PM). A three-year experiment was conducted from 2014 to 2016 with two maize varieties (spring and summer) and two mulching conditions (PM and non-mulching (NM)), and the AquaCrop model was employed to reproduce crop growth and yield responses to changes in NM, PM, and compensated PM. A marked difference in soil temperature between NM and PM was observed before 50 days after sowing (DAS) during three growing seasons. During sowing-emergence and emergence-tasseling, the increase in air temperature was proportional to the compensatory coefficient, with spring maize showing a higher compensatory temperature than summer maize. Simulation results for canopy cover (CC) were generally in good agreement with the measurements, whereas predictions of aboveground biomass and grain yield under PM indicated large underestimates from 60 DAS to the end of maturity. Simulations of spring maize biomass and yield showed general increase based on temperature compensation, accompanied by improvement in modeling accuracy, with RMSEs decreasing from 2.5 to 1.6 t ha^?1 and from 4.1 t to 3.4 t ha^?1. Improvement in biomass and yield simulation was less pronounced for summer than for spring maize, implying that crops grown during low-temperature periods would benefit more from the compensatory effect. This study demonstrated the effectiveness of the temperature compensatory effect to improve the performance of the AquaCrop model in simulating maize growth under PM practices.

Automatic collecting of phenotypic information from plants has become a trend in breeding and smart agriculture. Targeting mature soybean plants at the harvesting stage, which are dense and overlapping, we have proposed the SPP-extractor (soybean plant phenotype extractor) algorithm to acquire phenotypic traits. First, to address the mutual occultation of pods, we augmented the standard YOLOv5s model for target detection with an additional attention mechanism. The resulting model could accurately identify pods and stems and could count the entire pod set of a plant in a single scan. Second, considering that mature branches are usually bent and covered with pods, we designed a branch recognition and measurement module combining image processing, target detection, semantic segmentation, and heuristic search. Experimental results on real plants showed that SPP-extractor achieved respective R2 scores of 0.93-0.99 for four phenotypic traits, based on regression on manual measurements.

Accurate estimation of crop evapotranspiration (ETc) and soil water balance, which is vital for optimizing water management strategy in crop production, can be performed by simulation. But existing software has many deficiencies, including complex operation, limited scalability, lack of batch processing, and a single ETc model. Here we present simET, an open-source software package written in the R programming language. Many concepts involved in crop ETc simulation are condensed into functions in the package. It includes three widely used crop ETc models built on these functions: the single-crop coefficient, double-crop coefficient, and Shuttleworth-Wallace models, along with tools for preparing model data and comparing estimates. SimET supports ETc simulation in crops with repeated growth cycles such as alfalfa, a perennial forage crop that is cut multiple times annually.

Rice is a major food crop and is planted worldwide. Climatic deterioration, population growth, farmland shrinkage, and other factors have necessitated the application of cutting-edge technology to achieve accurate and efficient rice production. In this study, we mainly focus on the precise counting of rice plants in paddy field and design a novel deep learning network, RPNet, consisting of four modules: feature encoder, attention block, initial density map generator, and attention map generator. Additionally, we propose a novel loss function called RPloss. This loss function considers the magnitude relationship between different sub-loss functions and ensures the validity of the designed network. To verify the proposed method, we conducted experiments on our recently presented URC dataset, which is an unmanned aerial vehicle dataset that is quite challenged at counting rice plants. For experimental comparison, we chose some popular or recently proposed counting methods, namely MCNN, CSRNet, SANet, TasselNetV2, and FIDTM. In the experiment, the mean absolute error (MAE), root mean squared error (RMSE), relative MAE (rMAE) and relative RMSE (rRMSE) of the proposed RPNet were 8.3, 11.2, 1.2% and 1.6%, respectively, for the URC dataset. RPNet surpasses state-of-the-art methods in plant counting. To verify the universality of the proposed method, we conducted experiments on the well-know MTC and WED datasets. The final results on these datasets showed that our network achieved the best results compared with excellent previous approaches. The experiments showed that the proposed RPNet can be utilized to count rice plants in paddy fields and replace traditional methods.

Greenbug (Schizaphis graminum, Rondani) is a serious insect pest in many wheat growing regions and has been infesting cereal crops in the USA for over a century. Continuous occurrence of new greenbug biotypes makes it essential to explore all greenbug resistant sources available to manage this pest. Gb1, a recessive greenbug resistance gene in DS28A, confers resistance to several economically important greenbug biotypes and is the only gene found to be resistant to greenbug biotype F. A set of 174 F_2:3 lines from the cross DS28A × Custer was evaluated for resistance to greenbug biotype F in 2020 and 2022. Selective genotyping of the corresponding F₂ population using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing (GBS) led to the identification of a candidate genomic region for Gb1. Thus, SSR markers previously mapped in this region were used to genotype the entire F₂ population, and kompetitive allele specific PCR (KASP) markers were also developed from SNPs in the target region. Gb1 was placed in the terminal region of the short arm of chromosome 1A, and its location was confirmed in a second population derived from the cross DS28A × PI 697274. The combined data analysis from the two mapping populations delimited Gb1 to a < 1 Mb interval between 13,328,200 and 14,241,426 bp on 1AS.

Lignin is one of the main components of cell walls and is essential for resistance to insect pests in plants. Cotton plants are damaged by aphid (Aphis gossypii) worldwide but resistant breeding is undeveloped due to scarce knowledge on resistance genes and the mechanism. This study reported a lignin biosynthesis-related gene identified in the F₂ population derived from the cross between cotton cultivars Xinluzao 61 (resistant to aphid) and Xinluzao 50 (susceptible to aphid). A quantitative trait locus was mapped on chromosome D04 with a logarithm of odds (LOD) score of 5.99 and phenotypic effect of 27%. RNA-seq analysis of candidate intervals showed that the expression level of GH_D04G1418 was higher in the resistant cultivar than in the susceptible cultivar. This locus is close to AtLAC4 in the phylogenetic tree and contains a conserved laccase domain. Hence, it was designated GhLAC4-3. Silencing of GhLAC4-3 in Xinluzao 61 via virus-induced gene silencing (VIGS) resulted in decreased lignin content and increased susceptibility to aphids. These results suggest that GhLAC4-3 might enhance aphid resistance by regulating lignin biosynthesis in cotton.

Inter- and intra-specific variations in phenotype are common and can be associated with genomic mutations as well as epigenomic variation. Profiling both genomic and epigenomic variants is at the core of dissecting phenotypic variation. However, an efficient targeted genotyping and epigenotyping system is lacking. We describe a new multiplex targeted genotyping and epigenotyping system called improved bulked-PCR sequencing (iBP-seq). We employed iBP-seq for the detection of genotypes and methylation levels of dozens of target regions in mixed DNA samples. iBP-seq can be adapted for the construction of linkage maps, fine mapping of quantitative-trait loci, and detection of genome editing mutations at a cost as low as $0.016 per site per sample. We developed an automated bioinformatics pipeline, including primer design, a series of bioinformatic analyses for genotyping and epigenotyping, and visualization of results. iBP-seq and its bioinformatics pipeline, available at http://zeasystemsbio.hzau.edu.cn/tools/ibp/, can be adapted to a wide variety of species.