Journal of Integrative Plant Biology最新文献

The past decade has witnessed rapid developments in gene discovery, biological big data (BBD), artificial intelligence (AI)-aided technologies, and molecular breeding. These advancements are expected to accelerate crop breeding under the pressure of increasing demands for food. Here, we first summarize current breeding methods and discuss the need for new ways to support breeding efforts. Then, we review how to combine BBD and AI technologies for genetic dissection, exploring functional genes, predicting regulatory elements and functional domains, and phenotypic prediction. Finally, we propose the concept of intelligent precision design breeding (IPDB) driven by AI technology and offer ideas about how to implement IPDB. We hope that IPDB will enhance the predictability, efficiency, and cost of crop breeding compared with current technologies. As an example of IPDB, we explore the possibilities offered by CropGPT, which combines biological techniques, bioinformatics, and breeding art from breeders, and presents an open, shareable, and cooperative breeding system. IPDB provides integrated services and communication platforms for biologists, bioinformatics experts, germplasm resource specialists, breeders, dealers, and farmers, and should be well suited for future breeding.

Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana, a wild relative of peach with high heterozygosity and diverse stress tolerance, exhibits high resistance against aphids. However, the highly heterozygous genome of P. davidiana makes determining the underlying factors influencing resistance traits challenging. Here, we present the 501.7 Mb haplotype-resolved genome assembly of P. davidiana. Genomic comparisons of the two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1-specific and 2,702 Pda_hap2-specific genes, and 1,118 allele-specific expressed genes. Genome composition indicated 4.1% of the P. davidiana genome was non-peach origin, out of which 94.5% was derived from almond. Based on the haplotype genome, the aphid resistance quantitative trait locus (QTL) was mapped at the end of Pda03. From the aphid resistance QTL, PdaWRKY4 was identified as the major dominant gene, with a 9-bp deletion in its promoter of the resistant phenotype. Specifically, PdaWRKY4 regulates aphid resistance by promoting PdaCYP716A1-mediated anti-aphid metabolite betulin biosynthesis. Moreover, we employed a genome design to develop a breeding workflow for rapidly and precisely producing aphid-resistant peaches. In conclusion, this study identifies a novel aphid resistance gene and provides insights into genome design for the development of resistant fruit cultivars.

Root-knot nematodes (RKNs; Meloidogyne spp.) are a serious threat to crop production. The competition between plants and pathogens for assimilates influences the outcome of their interactions. However, the mechanisms by which plants and nematodes compete with each other for assimilates have not been elucidated. In this study, we demonstrated that miR396a plays a negative role in defense against RKNs and a positive role in sugar accumulation in tomato roots. The overexpression of SlGRF8 (Solanum lycopersicum growth-regulating factor 8), the target of miR396a, decreased the sugar content of the roots and the susceptibility to RKNs, whereas the grf8-cr mutation had the opposite effects. Furthermore, we confirmed that SlGRF8 regulated the sugar content in roots by directly activating the transcription of SlSTP10 (Solanum lycopersicum sugar transporter protein 10) in response to RKN stress. Moreover, SlSTP10 was expressed primarily in the tissues surrounding giant cells, and the SlSTP10 knockout increased both the sugar content in the roots and the plant's susceptibility to RKNs. Overall, this study provides important insight into the molecular mechanism through which the miR396a-SlGRF8-SlSTP10 module regulates sugar allocation in roots under RKN stress.

The fusion of the exonuclease Trex2 with the Cas9 protein significantly enhanced the efficiency of genome editing in hexaploid common wheat, particularly for the simultaneous editing of multiple favorable alleles within a single generation, thereby facilitating genome editing-assisted breeding in polyploid crops.

Flowering time is a crucial rice trait that influences its adaptation to various environments, cropping schedules, and agronomic characteristics. Rice breeders have exploited spontaneous mutations in heading date genes to regulate the flowering time. In the present study, we investigated how breeders in Fukui Prefecture regulated days to heading while developing promising rice varieties. Genome-wide association studies (GWAS) identified Hd1, Hd16, and Hd18 as the major genes controlling days to heading in the population. However, we suspected that this highly bred population might exhibit genomic stratification, which could lead to spurious or false correlations in the GWAS. Thus, we also conducted correlation and partial correlation analyses, which uncovered another key heading date gene, Hd17, that GWAS failed to detect because of its linkage disequilibrium with the major effect gene Hd16. Examination of haplotype frequencies across different breeding periods revealed that the early-heading Hd16 (Hd16(E)) and late-heading Hd17 (Hd17(L)) were increasingly co-selected in the Hd1 functional population. Varieties carrying this Hd16(E)/Hd17(L) combination exhibited days to heading in the range of 70-80, which corresponds to the peak temperature and sunshine period and is also optimal for grain quality and yield components in the Fukui environment. The present study highlights that it is imperative to remain vigilant for Type I (false positives) and Type II (false negatives) errors when performing GWAS on highly bred populations and to implement appropriate countermeasures by accounting for gene-by-gene interactions established through the breeding process. We also discuss the effectiveness of Hd16(E), which is not used outside Japan for subtle days to heading control but is widely used in Japan at certain latitudes.

The loss and gain of OsNAS3 function both positively influence plant disease resistance. Overexpression of OsNAS3 boosts blast resistance by promoting nicotianamine accumulation, thereby enhancing blast resistance. Conversely, knockout of OsNAS3 increases ethylene biosynthesis, also contributing to improved blast resistance.

Cysteine is the precursor for the biosynthesis of glutathione, a key stress-protective metabolite, and methionine, which is imperative for cell growth and protein synthesis. The exact mechanism that governs the routing of cysteine toward glutathione or methionine during stresses remains unclear. Our study reveals that under oxidative stress, methionine and glutathione compete for cysteine and that the increased oxidized glutathione (GSSG) levels under stress hinder methionine biosynthesis. Moreover, we find that inhibition occurs as GSSG binds to and accelerates the degradation of cystathionine γ-synthase, a key enzyme in the methionine synthesis pathway. Consequently, this leads to a reduction in the flux toward methionine-derived metabolites and redirects cysteine utilization toward glutathione, thereby enhancing plant protection. Our study suggests a novel regulatory feedback loop involving glutathione, methionine, and cysteine, shedding light on the plant stress response and the adaptive rerouting of cysteine. These findings offer new insights into the intricate balance of growth and protection in plants and its impact on their nutritional value due to low methionine levels under stress.

Saline-alkaline soils are a major environmental problem that limit plant growth and crop productivity. Plasma membrane H⁺-ATPases and the salt overly sensitive (SOS) signaling pathway play important roles in plant responses to saline-alkali stress. However, little is known about the functional genes and mechanisms regulating the transcription of H⁺-ATPases and SOS pathway genes under saline-alkali stress. In the present study, we identified that the plant AT-rich sequence and zinc-binding (TaPLATZ2) transcription factor are involved in wheat response to saline-alkali stress by directly suppressing the expression of TaHA2/TaSOS3. The knockdown of TaPLATZ2 enhances salt and alkali stress tolerance, while overexpression of TaPLATZ2 leads to salt and alkali stress sensitivity in wheat. In addition, TaWRKY55 directly upregulated the expression of TaPLATZ2 during saline-alkali stress. Through knockdown and overexpression of TaWRKY55 in wheat, TaWRKY55 was shown to negatively modulate salt and alkali stress tolerance. Genetic analyses confirmed that TaPLATZ2 functions downstream of TaWRKY55 in response to salt and alkaline stresses. These findings provide a TaWRKY55-TaPLATZ2-TaHA2/TaSOS3 regulatory module that regulates wheat responses to saline-alkali stress.

Temperature sensitivity and tolerance play a key role in plant survival and production. Perennial ryegrass (Lolium perenne L.), widely cultivated in cool-season for forage supply and turfgrass, is extremely susceptible to high temperatures, therefore serving as an excellent grass for dissecting the genomic and genetic basis of high-temperature adaptation. In this study, expression analysis revealed that LpHsfA2, an important gene associated with high-temperature tolerance in perennial ryegrass, is rapidly and substantially induced under heat stress. Additionally, heat-tolerant varieties consistently display elevated expression levels of LpHsfA2 compared with heat-sensitive ones. Comparative haplotype analysis of the LpHsfA2 promoter indicated an uneven distribution of two haplotypes (HsfA2^Hap1 and HsfA2^Hap2) across varieties with differing heat tolerance. Specifically, the HsfA2^Hap1 allele is predominantly present in heat-tolerant varieties, while the HsfA2^Hap2 allele exhibits the opposite pattern. Overexpression of LpHsfA2 confers enhanced thermotolerance, whereas silencing of LpHsfA2 compromises heat tolerance. Furthermore, LpHsfA2 orchestrates its protective effects by directly binding to the promoters of LpHSP18.2 and LpAPX1 to activate their expression, preventing the non-specific misfolding of intracellular protein and the accumulation of reactive oxygen species in cells. Additionally, LpHsfA4 and LpHsfA5 were shown to engage directly with the promoter of LpHsfA2, upregulating its expression as well as the expression of LpHSP18.2 and LpAPX1, thus contributing to enhanced heat tolerance. Markedly, LpHsfA2 possesses autoregulatory ability by directly binding to its own promoter to modulate the self-transcription. Based on these findings, we propose a model for modulating the thermotolerance of perennial ryegrass by precisely regulating the expression of LpHsfA2. Collectively, these findings provide a scientific basis for the development of thermotolerant perennial ryegrass cultivars.