This study delves into the genetic mechanisms underlying seed coat color variation in cowpeas [L.] Walp.), a trait with significant implications for nutritional value, consumer preference, and adaptation to environmental stresses. Through a genome-wide association study (GWAS) involving cowpea accessions exhibiting red, green, and blue seed coats, we identified 16 significant single nucleotide polymorphisms (SNPs) distributed across chromosomes 3, 4, 5, 9, 10, and 11. Our analysis highlighted the polygenic nature of seed coat color, emphasizing the shared SNP loci across different colors, suggesting integrated genetic influence or linked inheritance patterns, especially on chromosomes 9 and 10. We highlighted candidate genes, including Pentatricopeptide repeat family (PPR), Lupus La-related protein/La-related protein 1, and Udp-glycosyltransferase 71b2-related genes on chromosome 9, and MYB-like DNA-binding (MYB) genes on chromosome 10, all of which are implicated in pigment biosynthesis and regulatory pathways crucial to seed coat coloration and plant physiological processes. Our results corroborate previous findings linking seed coat color to the anthocyanin biosynthesis pathway and reveal the complex genetic architecture and phenotypic plasticity inherent in cowpeas. The overlap in quantitative trait loci (QTL) regions across different seed coat colors points to a shared genetic basis, potentially enabling the manipulation of seed coat color to enhance the nutritional profile and marketability of cowpeas.

Leaves play a critical role in plant growth and development, directly influencing crop yield through their essential functions in photosynthesis and respiration. This study employed inheritance analysis and gene mapping of an F population derived from a cross between a spontaneous yellow-green leaf tomato mutant and a wild-type tomato line. The findings conclusively demonstrated that the yellow-green leaf trait is controlled by a single recessive gene. Subsequent fine-mapping localized this gene to a 270-kb region on chromosome 12 of the reference Heinz 1706 genome. Annotation and functional characterization of genes within this region indicated () as the primary candidate gene influencing the yellow-green phenotype trait. Sequencing analysis revealed a 49-bp deletion in the first exon of , resulting in suppressed expression. This functional role was further confirmed through gene editing in tomatoes. Moreover, comparative analyses of photosynthetic pigments and chloroplast ultrastructure revealed notable differences between the mutant and the wild-type lines. Furthermore, the mutant exhibited reduced photosynthetic rate and yield-related agronomic traits. These findings provide valuable insights into the molecular mechanisms underlying yellow-green leaf formation in tomatoes.

The sorghum inflorescence is consisted of sessile (SS) and pedicellate spikelets (PS). Commonly, only SS could produce seeds and each spikelet produces one single seed. Here, we identified a sorghum mutant, named (), which can produce twin seeds in each pair of glumes. We characterized the developmental process of inflorescence in and Jinliang 5 (Jin5, a single-seeded variety) using scanning electron microscope (SEM). The results showed that at the stamen and pistil differentiation stage, could develop two sets of stamens and carpels in one sessile floret, which resulted in twin-seeded phenotype in . Two F mapping populations derived from the cross between Jin5 and , and BTx622B and , were constructed, respectively. The genetic analysis showed that trait was controlled by a single dominant gene. Through bulk segregation analysis with whole-genome sequencing (BSA-seq) and linkage analysis, locus was delimited into a region of around 210-kb on chromosome 6, between the markers and , which contained 32 putative genes. Further analysis indicated that or may be responsible for the twin-seeded phenotype. This result will be useful for map-based cloning of the gene and for marker-assisted breeding for increased grain number per panicle in sorghum.

Chrysanthemums are versatile ornamental plants, and improving leaf and flower traits is an important breeding objective. Distant hybridization is a powerful method for plant breeding and genetic improvement, whereas the genetic basis in interspecific F progeny of chrysanthemums needs to be better understood for breeding purposes. In this study, the leaf and floral traits of the 273 reciprocal interspecific F hybrids of diploid (YSJ) and (JHN) were analyzed along with their SNP-derived genetic structure to elucidate the influence of differences in genetic background between the parents on the hybrid performance. We then performed a genome-wide association analysis (GWAS) to reveal the investigated traits' genomic loci and candidate genes. Considerable phenotypic variation (8.81% ~ 55.78%) and heterosis with transgressive segregation in both directions were observed in the reciprocal progenies. We observed a higher level of phenotypic variation in JHN × YSJ rather than in YSJ × JHN. Also, a significant reciprocal effect was observed for most examined traits. Based on the SNP data, we separated the hybrid progenies into three groups (I, II, and III), albeit imperfectly dependent on the cross directions, except for some reciprocal hybrids clustering into group II. Group I from YSJ × JHN and Group III from YSJ × JHN differed with contrasting and π ratios, indicating the genetic changes in the reciprocal populations. The outcome of GWAS via the IIIVmrMLM method detected 339 significant quantitative trait nucleotides (QTNs) and 40 suggestive QTNs, and the phenotypic variation explained by a single QTN ranged from 0.26% to 7.42%. Within 100 kb upstream and downstream of the important QTNs, we discovered 49 known genes and 39 new candidate genes for the investigated leaf and floral traits. Our study provides profound insights into the genetic architecture of reciprocal hybrid progenies of chrysanthemum species, facilitating future breeding activities.

Cabbage is a widely cultivated leafy vegetable, but head rot disease caused by the fungus can seriously reduce its yield and quality. There are currently not any cabbage varieties that are completely immune to the disease, but its wild relative is very resistant. In this study, cabbage resistance was improved by backcrossing a highly resistant accession (C01) with a susceptible cabbage cultivar (F416). Although C01 lacks a leafy head formation, highly resistant plants appeared in the fourth backcrossing generation (BCF) that had a similar leafy head to F416. The individuals with strong resistance were purified by self-pollination. Inbred lines that maintained a relatively stable resistance at BCF were developed and had significantly higher resistance to than F416. In addition, hybrids created from a cross between of BCF and E2 had higher resistances to and similar agronomic characteristics to Xiyuan 4. The results demonstrated that new F416 lines that are resistant to can be developed, and that these lines could be used to create new cabbage varieties with superior head rot resistance.

Citrus Huanglongbing (HLB) is a devastating disease spread by citrus psyllid, causing severe losses to the global citrus industry. The transmission of HLB is mainly influenced by both the pathogen and the citrus psyllid. The unculturable nature of the HLB bacteria ( Liberibacter asiaticus, Las) and the susceptibility of all commercial citrus varieties made it extremely difficult to study the mechanisms of resistance and susceptibility. In recent years, new progress has been made in understanding the virulence factors of Las as well as the defense strategies of citrus host against the attack of Las. This paper reviews the recent advances in the pathogenic mechanisms of Las, the screening of agents targeting the Las, including antimicrobial peptides, metabolites and chemicals, the citrus host defense response to Las, and strategies to enhance citrus defense. Future challenges that need to be addressed are also discussed.

Plant height is one of the most critical factors influencing wheat plant architecture, and the application of Green Revolution genes has led to a reduction in plant height and an increase in yield. Discovering new dwarfing genes and alleles can contribute to enhance the genetic diversity of wheat. Here we obtained an EMS induced dwarf wheat mutant with increased grain weight, which exhibited a reduction in plant height ranging from 46.47% to 49.40%, and its cell length was shorter. The mutant was sensitive to exogenous gibberellin, but its sensitivity was lower than that of its wild type. Genetic analysis on plant height and gene mapping located the target region to a 4.07 cM interval on chr. 4AL. Within this interval, we identified a co-segregated mutation in , which is a novel allele of the Green Revolution gene . We also found large fragment inversions in the genetic map of the mutant. The novel allele diversifies natural allelic variations and could be utilized in future wheat improvement. Furthermore, we demonstrated that chemical mutagen treatment led to large fragment inversion.

Coleoptile length, in wheat, is a significant agronomic trait impacting yield by facilitating the successful establishment of seedlings. In arid regions, varieties possessing longer coleoptile can evade harsh conditions by deep sowing, paving the way for improved yield. However, the study of genes involved in coleoptile development is insufficient. In this study, a high-density 660 K SNP array was used for genome-wide association study (GWAS) on coleoptile length in 150 wheat varieties. The findings revealed the detection of 353 significantly associated SNPs across all environments. The integration of linkage disequilibrium analysis and haplotype analysis mined 23 core QTLs capable responsible for the stable regulating coleoptile length in wheat. In wheat varieties characterized by extended coleoptile length, 6,600, 11,524, and 6,059 genes were found to be differentially expressed at three distinct developmental stages within the coleoptile, respectively. Through GWAS, gene expression levels, and functional annotation, we concluded the identification of two candidate genes (, ) regulating wheat coleoptile length. By employing WGCNA and protein interactions prediction, discovered that the 19 genes were found to interact with candidate genes and participate in plant hormone metabolism and signaling, cell elongation or proliferation, which collectively contributing to coleoptile elongation. Additionally, two KASP markers were developed which can be used in breeding. These results offer a basis for understanding the genetic regulatory network responsible for wheat coleoptile length formation. The QTLs and candidate genes identified in this study can be further utilized for genetic improvement of wheat coleoptile length.

Soybean is an indispensable crop producing the majority of vegetative oils and proteins. China has been importing millions of ton of soy beans in recent years. Developing new varieties with favorable traits in both yield and resilience has great potential to meet the market needs in China. In this study, we bred a new variety (Xiangchun 37) which has been licensed by Ministry of Agriculture and Rural Affairs of the People's Republic of China in 2024. In the field tests, Xiangchun 37 showed medium maturity period (107.4 days from sowing to harvest), high yield (187.3 kg/667m), and high seed oil content (22.19%). Overall assessment showed Xiangchun 37 had other favorable traits including the plant architecture and disease resistance. In conclusion, Xiangchun 37 is a new variety suitable for Hunan Province, China and has promising future for further genetic improvement as a germplasm with multiple favorable traits.

Disease-resistant plants activate immune responses by specifically recognition Candidate Secreted Effector Proteins (CSEPs) through resistance (R) proteins. In research on cucumber powdery mildew resistance breeding, several R genes and CSEPs have been identified; however, the specific interactions between R proteins and CSEPs are still largely unexplored. In this study, we used a luciferase reporter assay to identify six CSEPs from that potentially induce cell death in cucumber. Subsequent yeast two-hybrid analysis revealed that only the mature form of CSEP30 (CSEP30) interacted with the cucumber mutant STAY-GREEN (), a gene previously recognized for its broad-spectrum resistance in genetic studies. This interaction was confirmed using pull-down and co-immunoprecipitation assays. Additionally, to determine if the interaction leads to phenotypic changes, Cssgr and CSEP30 were transiently expressed in tobacco leaves. The infiltration of Cssgr in tobacco resulted in reduced chlorosis compared to the wild-type CsSGR. Co-infiltration of Cssgr with CSEP30 induced distinct dry necrotic lesions, contrasting the effects observed when Cssgr and CSEP30 were infiltrated separately. Additionally, after infection in moderately powdery mildew-resistant Gy14 cucumber, similar necrotic lesions and specific expression of , as along with defense response-related genes (), were observed. This study suggests that the interaction between Cssgr and CSEP30 could trigger cell death and defense response, offering new insights into the molecular function of Cssgr in disease resistance in Gy14 cucumber.

Determinate inflorescence is indeed a pivotal agricultural characteristic in crops, notably impacting the architecture modification of (AACC, 2n = 38). Previous study identified a crucial gene that encodes the transcription factor (). Here by two alleles were cloned and sequenced from indeterminate 2982 and determinate 4769, respectively, we found that harbors two T/C and G/C non-synonymous mutations in exon 1, and contains sixty-six differences in a 1.9 Kb promoter sequence. Subsequently, was introduced into 571 line by genetic complementation and overexpression, transgenic plants 571 lines and 571lines were all restored to the indeterminate inflorescence. Interestingly, after was knocked out in 'Westar', transgenic plants Westar lines were mutated to determinate inflorescences. Additionally, a NIL-4769 line was constructed to evaluate the effect of on agronomic traits of , the results demonstrated that reduced the plant height and increased the branch number and branch thousand grain weight of Finally, we performed RT-qPCR, GUS staining and subcellular localization experiments to analyze the expression pattern of , the results showed that the expression of at shoot apex of NIL-4769 was higher than that of 4769, GUS activity was detected at apical of and was detected in cell membrane, nucleus and cytoplasm. Our findings provide a firm molecular foundation for the study of rapeseed's molecular mechanism of determinate inflorescence formation, as well as theoretical guidance for the application of determinate inflorescence in rapeseed breeding.

The PHOSPHATE STARVATION RESPONSE REGULATOR (PHR) plays a crucial regulatory role in plants during the process of responding to phosphate starvation. In this study, we combined reverse genetics and biotechnology to investigate the function of and , including proteins containing the Myb_DNA_banding and Myb_CC-LHEQLE structural domains, in maize seedlings. Phylogenetic analysis revealed that and have high homology with and , and share the characteristic features of nuclear localisation and transcriptional self-activation. Real-time quantitative PCR analysis showed that low phosphate (Pi) stress significantly induced the expression of and in maize seedling stage, and candidate gene association analysis further revealed the close association of these two genes with root traits under Pi stress conditions. Transgenic plants overexpressing and in show a significant increase in lateral root number, fresh weight and total phosphorus accumulation under low-Pi stress. Besides, CHIP-PCR experiments identified target genes involved in hormone regulation, metal ion transport and homeostasis, phosphatase encoding, and photosynthesis, providing new insights into the biological functions of and . Furthermore, our study showed that ZmPHR1 interacts with six SPX domain-only proteins (ZmSPXs) in maize, while ZmPHR2 interacts with five of these proteins. and expression was repressed in low Pi conditions, but was up-regulated in knockout material, according to our study of transgenic seedlings overexpressing in maize. We identified downstream target genes involved in the phosphorus signaling pathway, which are mainly involved in plant-pathogen interactions, ascorbic acid and arabinose metabolism, and ABC transporter proteins, by RNA-seq analysis of transgenic seedlings grown under low Pi stress for 7 days. Collectively, these results provide important clues to elucidate the role and functional significance of and under low Pi stress and also provide insights into understand the molecular mechanism of phosphorus homeostasis in maize.

Bud endodormancy in deciduous fruit trees is an adaptive trait evolved by selection for the capacity to survive unfavorable environmental conditions. Deciduous trees require a certain amount of winter chill named chilling requirement (CR) to promote bud endodormancy release. In recent decades, global warming has endangered the chill accumulation in deciduous fruit trees. Developing low-CR cultivars is a practical way to neutralize the effect of climate changes on the cultivation and distribution of deciduous fruit trees. In this review, we focus on the effect of chilling accumulation on bud endodormancy release and the genetic mechanisms underlying the chilling requirement in deciduous fruit trees. Additionally, we put forth a regulatory model for bud endodormancy and provide prospective directions for future research in deciduous fruit trees.

Late blight (LB), caused by oomycete , is one of the most destructive diseases of the cultivated tomato, . Since new and aggressive clonal lineages of , many of which overcoming formerly effective fungicides or host resistance genes, have continued to emerge, it is crucial to identify, characterize, and utilize new sources of host resistance in tomato breeding. A recent screening of tomato germplasm identified accession PI 224710 with very strong resistance to several current clonal lineages. The present study aimed to identify and characterize QTLs associated with LB resistance in PI 224710. Disease screening of a large F population ( = 1721), derived from a cross between PI 224710 and LB-susceptible tomato breeding line Fla. 8059, followed by F progeny testing, resulted in the identification of 43 highly-resistant and 27 highly-susceptible F individuals. A selective genotyping approach, using 469 non-identical SNP markers, resulted in the construction of a genetic linkage map and identification of three LB-resistance QTLs on chromosomes 6, 9 and 10 of PI 224710. A comparison of the QTLs genomic locations with the tomato physical map resulted in the identification of several candidate genes, which might be underpinning the LB-resistance QTLs in PI 224710. The identified markers associated with the LB-resistance QTLs can be utilized in breeding programs to transfer resistance from PI 224710 into tomato breeding lines and hybrid cultivars via marker-assisted breeding; they also can be used to develop near-isogenic lines for fine mapping of the QTLs.

Cotton is a widely planted commercial crop in the world. Enhancing fiber yield and quality is a long-term goal for cotton breeders. Our previous work has demonstrated that fine promotion of auxin biosynthesis in ovule epidermis, by overexpressing , has a significant improvement on lint yield and fiber fineness. Lately, transgenic cottons overexpressing variants modify mature fiber length by controlling GhPIN3a-mediated polar auxin transport in ovules. Here, this study showed that all these related cottons displayed unsatisfactory agronomic performance in field conditions. Yet extra auxin supply could promote their fiber development, suggesting inadequate auxin supply in the ovules. Thus, these cottons were integrated with enhanced auxin synthesis by crossing with cotton. All the transgene-stacked cottons exhibited synergetic effects on cotton yield (seedcotton yield, lint yield, and lint percentage) and quality (length, strength, and micronaire). Notably, comparing to the background, the transgene-stacked cotton co-expressing and (constitutively active ) exhibited a 12.6% increase in seedcotton yield and a 19.0% increase in lint yield over a three-year field trial, and simultaneously resulted in further improvement on fiber length, strength, and micronaire. Collectively, our data provide a potential strategy for genetic improvement on cotton fiber yield and quality.

Crispness stands as a pivotal criterion in assessing apple texture, widely cherished by consumers. Yet, owing to its multifaceted nature, crispness remains a formidable challenge in artificial enhancement efforts. To expedite the early and precise evaluation of apple crispness, this study centered on a hybrid population derived from 'Fuji' and 'Pink Lady' cultivars, showcasing segregating crispness traits. We conducted measurements of flesh water content, cellular anatomical morphology, and employed a texture analyzer to assess mechanical properties of the offspring flesh. Integrating these three dimensions, we conducted a comprehensive analysis of quantitative characteristics of apple crispness, juxtaposed with sensory evaluation. Utilizing BSA-seq technology, we scrutinized extreme phenotypic individuals, revealing QTL loci intricately linked to the aforementioned dimensions, and subsequently developed Key Allele-Specific PCR (KASP) markers. These markers underwent validation in hybrid populations of 'Hanfu' x 'Pink Lady' and 'Hanfu' x 'Honey Crisp'. Our findings underscored significant correlations between mechanical properties, water content, and cell size with crispness. Higher mechanical properties and water content, alongside smaller cell size, correlated with firmer flesh texture; moderate mechanical properties, and elevated water content and cell size, with crisper texture; whereas lower mechanical properties, water content, and cell size implied softer flesh.The study yielded KASP markers effectively reflecting flesh mechanical properties (SNP_24399345), water content (SNP_8667563), and cell size (SNP_15566229). Comprehensive analysis of these markers identified CC-CC-TT as an effective identifier of soft flesh individuals; while GG-TC-TT and GG-CC-TT combinations better represented individuals with harder flesh. The Crunchy subclass could be discerned by combinations of GG-TC-TC, GG-TC-CC, GG-TT-TC, and GG-TT-CC. These findings furnish effective molecular markers for the genetic enhancement of apple crispness, bearing significant implications for the cultivation of novel apple varieties.

Deterioration of rice ( L.) affects grain quality and seed viability during storage. Lipoxygenase (LOX), a key enzyme in lipid metabolism, directly affects the rate of ageing. Here, we found that knock-out of lipoxygenase gene 1 by CRISPR/Cas9 delayed loss of seed viability and quality. Transcriptome analysis showed that during storage, affected transcription of multiple genes, including genes related to lipid metabolism and antioxidant pathways such as phosphatase and acetaldehyde dehydrogenase, which may regulate the seed storability. The genes significantly down- and up-regulated only in Ningjing 4 after NA for 13 months and 3 days of AA suggesting that likely promoted seed viability in rice by balancing ageing and storage related genes, and regulated the seed storability through the amino acid synthesis and metabolic pathways. Moreover, knock-out of without CRISPR/Cas9 not only improved the seed viability, but also had little impact on agronomic traits. More importantly, the knock-out lines were approved in 2019 (Agricultural Foundation of China Report No. 770). Collectively, our study showed that knock-out of is beneficial for prolongation of seed viability and can be directly applied to agricultural production.

The ATP-binding cassette (ABC) superfamily is involved in numerous complex biological processes. However, the understanding of ABCs in plant pathogen defense, particularly against , remains limited. In this study, we identified that plays a positive role in apple resistance to . Overexpression of significantly enhanced the resistance of apple calli and fruits to . Our findings revealed that the jasmonic acid (JA) content and the expression of genes associated with JA biosynthesis and signal transduction were higher in stable overexpressing apple calli than that of wild-type after inoculation with . Similar results were obtained for apple fruits with transient overexpression of . Our research indicates that enhances apple resistance to through the JA signaling pathway. We further determined that plays a crucial role in the apple's response to JA signaling. Moreover, exogenous methyl jasmonate (MeJA) treatment significantly enhanced the effectiveness of in boosting apple resistance to . We proposed a positive feedback regulatory loop between -mediated apple resistance to and JA signal. In summary, our study offers new insights into the role of ABC superfamily members in the control of plant disease resistance.

Rice grain size and grain weight, which have a great influence on rice quality and yield, are complex quantitative traits that are mediated by grain length (GL), grain width (GW), length-to-width ratio (LWR), and grain thickness (GT). In this study, the BCF and BCF populations derived from a cross between two rice varieties, Guangzhan 63-4S (GZ63-4S) and Dodda, were used to locate quantitative trait loci (QTL) related to grain size. A total of 30 QTL associated with GL, GW and LWR were detected, of which six QTL were scanned repeatedly in both populations. Two QTL, and , were selected for genetic effect validation and were subsequently fine mapped to 2.359 kb and 176 kb, respectively. (known as ), which encoding an ent-beyerene synthase and as the only gene found in 2.359 kb interval, was proposed to be the candidate for . Moreover, the grains of homozygous mutant plants generated by the CRISPR-Cas9 system became shorter and wider. In addition, the allele from GZ63-4S contributes to the increase of yield per plant. Our study not only laid the foundation for further functional study of and map-based cloning of , but also provided genetic resources for the development of high yield and good quality rice varieties.