Rapid Breeding Research Articles

Large invasive herbaceous plants decrease the taxonomic, functional and phylogenetic diversity of birds via their reproductive traits

Abstract Birds are among the organisms most impacted by plant invasions, the effects of which are particularly conspicuous during the breeding season. Birds can incorrectly assess the suitability of large, invasive hogweeds Heracleum sp. in south‐eastern Poland when selecting nesting sites early in spring when the developing invaders do not yet differ substantially in form from the rest of the vegetation. One would expect lower bird breeding success in areas with invasive hogweeds. Furthermore, this may shift bird community composition towards species with filtered traits, which may then be reflected in various measures of diversity. To assess these expectations, we conducted bird surveys at 74 sites, arranged as 37 pairs (with invasive Heracleum vs. control). The presence of Heracleum was associated with lower bird taxonomic and phylogenetic diversity. Functional richness (calculated based on species' reproductive traits) was also lower at sites with these invaders. The species detected at Heracleum sites were characterised by traits associated with rapid breeding, for example, small clutches, short incubation periods and short fledging periods. We show that the bird community at sites with hogweeds became less diverse and composed of random species sharing similar reproductive traits. Bird communities with low diversity at Heracleum sites tended to exhibit a common trait syndrome. These patterns provide insights into the mechanisms of how invasive plants may lead to the loss of some traits and species in bird communities. Read the free Plain Language Summary for this article on the Journal blog.

Rapid breeding of an early maturing, high-quality, and high-y.ielding rice cultivar using marker‑assisted selection coupled with optimized anther culture.

The online version contains supplementary material available at 10.1007/s11032-024-01495-4.

Optimizing protein content prediction in rice bean (Vigna umbellata L.) by integrating near-infrared reflectance spectroscopy, MPLS, deep learning, and key wavelengths selection algorithms

Rice bean, a potential protein-rich underutilized crop, can serve as a valuable source for food and feed, contributing to sustainable food and nutrition security. However, traditional methods for measuring protein content are laborious, tedious, and expensive. This study evaluates the performance of Modified Partial Least Squares (MPLS) and 1D Convolutional Neural Network (1D CNN) models in predicting protein content in rice bean using Near-Infrared Reflectance Spectroscopy (NIRS) data. Both models were validated with whole spectra, key wavelengths, and spectral segments derived from Genetic Algorithm (GA), Ant Colony Optimization (ACO), Particle Swarm Optimization (PSO), and Competitive Adaptive Reweighted Sampling (CARS). The 1D CNN model demonstrated superior predictive performance, with an 11 % increase in R² and an 18 % increase in RPD using the whole spectra compared to the MPLS model. Specifically, the 1D CNN model with CARS-selected wavelengths achieved an R² of 0.82 and an RPD of 2.15, while the MPLS model achieved an R² of 0.84 and an RPD of 2.25. The segmented spectra approach further enhanced the 1D CNN model's performance, achieving the highest R² of 0.84 and an RPD of 2.28 with CARS-selected segments. These results highlight that the 1D CNN model with CARS-selected wavelengths provides the best predictive performance for protein content in rice bean. The optimized method can lead to rapid early-phase breeding practices and improved quality assessments in leguminous crops, emphasizing the importance of integrating advanced modeling techniques with NIRS for agricultural applications.

Research on the rapid tissue breeding technology of the endangered plant Cibotium barometz (L.) J. Sm.

Cibotium barometz (L.) J. Sm., a fern, holds significant value in traditional Chinese medicine. This research aimed to establish a rapid tissue breeding technology for Cibotium barometz (L.) and provide a theoretical basis for its artificial breeding and industrial planting. The optimum conditions for spores germination were selected, including both the best sterilization time and the ideal spore germination medium. Subsequently, the optimal medium for proliferation and differentiation were chosen, and the optimal concentration of plant hormones was screened to determine the optimal medium. The rooting experiment was performed in two single-factor experiments by using differentiated sporophytes as materials. These experiments showed that the optimal sterilization time was 11 min and the best medium for germination was 1/8MS + 0.02 mg/L IAA. MS medium was suitable for proliferation, while WPM medium was suitable for sporophyte differentiation. The best medium for growth was MS + 1.0 mg/L IAA + 0.5 mg/L 6-BA. In the absence of sucrose, the seedlings barely grew and failed to differentiate into sporophytes. They showed optimal growth and differentiation at a sucrose concentration of 20 g/L. The plant growth regulators plant growth regulators used, including IAA, NAA, 6-BA, and GA3, showed more effective differentiation, wherease KT had a slightly weaker effect. The rooting rate reached the maximum when the concentrations of ABT and IBA were at 1.5 mg•L− 1 and IAA was at 1.0 mg•L− 1. The IBA had a significant effect on the average and the longest root length, while the three PGRs had no obvious effect on the average or maximum diameter. Plant tissue culture seedlings still have good genetic stability after subsequent generation. In this study, the optimal cultivation conditions for rapid breeding technology in tissue culture, covering stages from germination and growth to differentiation and rooting, were obtained. Moreover, sporophytes were successfully transplanted to the external environment. This study provided a theoretical reference for the industrial planting of C. barometz.

Integrating high-throughput phenotyping and genome-wide association studies for enhanced drought resistance and yield prediction in wheat.

Drought, especially terminal drought, severely limits wheat growth and yield. Understanding the complex mechanisms behind the drought response in wheat is essential for developing drought-resistant varieties. This study aimed to dissect the genetic architecture and high-yielding wheat ideotypes under terminal drought. An automated high-throughput phenotyping platform was used to examine 28 392 image-based digital traits (i-traits) under different drought conditions during the flowering stage of a natural wheat population. Of the i-traits examined, 17 073 were identified as drought-related. A genome-wide association study (GWAS) identified 5320 drought-related significant single-nucleotide polymorphisms (SNPs) and 27 SNP clusters. A notable hotspot region controlling wheat drought tolerance was discovered, in which TaPP2C6 was shown to be an important negative regulator of the drought response. The tapp2c6 knockout lines exhibited enhanced drought resistance without a yield penalty. A haplotype analysis revealed a favored allele of TaPP2C6 that was significantly correlated with drought resistance, affirming its potential value in wheat breeding programs. We developed an advanced prediction model for wheat yield and drought resistance using 24 i-traits analyzed by machine learning. In summary, this study provides comprehensive insights into the high-yielding ideotype and an approach for the rapid breeding of drought-resistant wheat.

Accelerated breeding strategies for biochemical marker-assisted backcross breeding and mapping population development in bread wheat (Triticum aestivum L.)

In order to rapidly adapt to the evolving climate and sustainably nourish the growing global population, plant breeders are actively investigating more efficient strategies to enhance crop yields. In this study, we present the development of a bread wheat mapping population and backcross breeding program, serving as a valuable genetic resource for mapping the effects of different alleles on trait performance. We employed innovative methodologies to rapidly introgress traits into the bread wheat cultivar. Specifically, we utilized two parents, including Tosunbey x Tahirova2000, in a recombinant inbred line population, in addition, a backcross strategy was applied with line 148 (obtained by crossing Tosunbey x Tahirova2000 with high gluten quality) as the recipient parent of the Nevzatbey cv., known for its awnless feature. The two most important applications of the rapid breeding method are extending the light period and breaking dormancy in early harvested seeds. Both applications were successfully implemented in our study. Our vegetation periods ranging from approximately 50–60 days. Additionally, an early genotype in our developed population was harvested in 40 days. Considering that the genotype underwent a 15-day vernalization period, the generation cycle, including vernalization, drying, and refrigeration, was completed in a total of 64 days. Notably, we employed not only biochemical markers for selection but also incorporated the rapid generation advance technology known as ‘speed breeding’, allowing us to develop BC5F1 within a span of two years. We posit that this approach proves instrumental in swiftly transferring genes for multiple target traits into adapted wheat cultivars or in pyramiding desirable traits within elite breeding material.

Synergizing breeding strategies via combining speed breeding, phenotypic selection, and marker-assisted backcrossing for the introgression of Glu-B1i in wheat.

Wheat is a major food crop that plays a crucial role in the human diet. Various breeding technologies have been developed and refined to meet the increasing global wheat demand. Several studies have suggested breeding strategies that combine generation acceleration systems and molecular breeding methods to maximize breeding efficiency. However, real-world examples demonstrating the effective utilization of these strategies in breeding programs are lacking. In this study, we designed and demonstrated a synergized breeding strategy (SBS) that combines rapid and efficient breeding techniques, including speed breeding, speed vernalization, phenotypic selection, backcrossing, and marker-assisted selection. These breeding techniques were tailored to the specific characteristics of the breeding materials and objectives. Using the SBS approach, from artificial crossing to the initial observed yield trial under field conditions only took 3.5 years, resulting in a 53% reduction in the time required to develop a BC2 near-isogenic line (NIL) and achieving a higher recurrent genome recovery of 91.5% compared to traditional field conditions. We developed a new wheat NIL derived from cv. Jokyoung, a leading cultivar in Korea. Milyang56 exhibited improved protein content, sodium dodecyl sulfate-sedimentation value, and loaf volume compared to Jokyoung, which were attributed to introgression of the Glu-B1i allele from the donor parent, cv. Garnet. SBS represents a flexible breeding model that can be applied by breeders for developing breeding materials and mapping populations, as well as analyzing the environmental effects of specific genes or loci and for trait stacking.

Genome-Wide Identification and Expression Analysis of the DMP and MTL Genes in Sweetpotato (Ipomoea batatas L.).

Sweetpotato (Ipomoea batatas L.) is a strategic crop with both economic and energy value. However, improving sweetpotato varieties through traditional breeding approaches can be a time-consuming and labor-intensive process due to the complex genetic nature of sweetpotato as a hexaploid species (2n = 6x = 90). Double haploid (DH) breeding, based on in vivo haploid induction, provides a new approach for rapid breeding of crops. The success of haploid induction can be achieved by manipulating specific genes. Two of the most critical genes, DMP (DUF679 membrane proteins) and MTL (MATRILINEAL), have been shown to induce haploid production in several species. Here, we identified and characterized DMP and MTL genes in sweetpotato using gene family analysis. In this study, we identified 5 IbDMPs and 25 IbpPLAs. IbDMP5 and IbPLAIIs (IbPLAIIκ, IbPLAIIλ, and IbPLAIIμ) were identified as potential haploid induction (HI) genes in sweetpotato. These results provide valuable information for the identification and potential function of HI genes in sweetpotato and provide ideas for the breeding of DH lines.

Tomato: Breeding and Genomics

Tomato is an important vegetable of the human diet. In tomatoes, through conventional breeding methods, many cultivars with desirable traits have been developed. With the advancement in sequencing technologies combined with reducing cost per sample, high-throughput genotyping platforms and bioinformatics pipelines have revolutionized tomato improvement. After the tomato genome sequencing in 2012, thousands of cultivated and wild species have been sequenced with respect to studies on population structure, genetic diversity, high-density maps and structural variants analysis so on. Now, genomics-assisted research would aim to discover of QTLs/genes and associated single nucleotide polymorphisms (SNP) markers by genome-wide association studies (GWAS) using high-throughput genotyping (SNP array or genotyping-by-sequencing) for rapid breeding. Moreover, genome editing and genomics selection tools would increase breeding efficiency and higher genetic gain in tomatoes.

A MADS-box gene-induced early flowering pear (Pyrus communis L.) for accelerated pear breeding.

There have been a considerable number of studies that have successfully sped up the flowering cycle in woody perennial horticultural species. One particularly successful study in apple (Malus domestica) accelerated flowering using a silver birch (Betula pendula) APETALA1/FRUITFULL MADS-box gene BpMADS4, which yielded a good balance of vegetative growth to support subsequent flower and fruit development. In this study, BpMADS4 was constitutively expressed in European pear (Pyrus communis) to establish whether this could be used as a tool in a rapid pear breeding program. Transformed pear lines flowered within 6-18 months after grafting onto a quince (Cydonia oblonga) rootstock. Unlike the spindly habit of early flowering apples, the early flowering pear lines displayed a normal tree-like habit. Like apple, the flower appearance was normal, and the flowers were fertile, producing fruit and seed upon pollination. Seed from these transformed lines were germinated and 50% of the progeny flowered within 3 months of sowing, demonstrating a use for these in a fast breeding program.

Ag/ZnO core–shell NPs boost photosynthesis and growth rate in wheat seedlings under simulated full sun spectrum

Breeding programs rely on light wavelength, intensity, and photoperiod for rapid success. In this study, we investigated the ability of Ag/ZnO nanoparticles (NPs) to improve the photosynthesis and growth of wheat under simulated full solar spectrum conditions. The world population is increasing rapidly, it is necessary to increase the number of crops in order to ensure the world’s food security. Conventional breeding is time-consuming and expensive, so new techniques such as rapid breeding are needed. Rapid breeding shows promise in increasing crop yields by controlling photoperiod and environmental factors in growth regulators. However, achieving optimum growth and photosynthesis rates is still a challenge. Here, we used various methods to evaluate the effects of Ag/ZnO NPs on rice seeds. Using bioinformatics simulations, we evaluated the light-harvesting efficiency of chlorophyll a in the presence of Ag/ZnO NPs. Chemically synthesized Ag/ZnO nanoparticles were applied to rice grains at different concentrations (0–50 mg/L) and subjected to a 12-h preparation time. Evaluation of seed germination rate and growth response in different light conditions using a Light Emitting Diode (LED) growth chamber that simulates a rapid growth system. The analysis showed that the surface plasmon resonance of Ag/ZnO NPs increased 38-fold, resulting in a 160-fold increase in the light absorption capacity of chlorophyll. These estimates are supported by experimental results showing an 18% increase in the yield of rice seeds treated with 15 mg/L Ag/ZnO NPs. More importantly, the treated crops showed a 2.5-fold increase in growth and a 1.4-fold increase in chlorophyll content under the simulated full sun spectrum (4500 lx) and a 16-h light/8-h dark photoperiod. More importantly, these effects are achieved without oxidative or lipid peroxidative damage. Our findings offer a good idea to increase crop growth by improving photosynthesis using Ag/ZnO nanoparticle mixture. To develop this approach, future research should go towards optimizing nanoparticles, investigating the long-term effects, and exploring the applicability of this process in many products. The inclusion of Ag/ZnO NPs in rapid breeding programs has the potential to transform crops by reducing production and increasing agricultural productivity.

Research Progress and a Prospect Analysis of Asexual Bamboo Reproduction

Bamboo possesses various characteristics that make it a promising renewable biomass resource. These include rapid growth, early timber production, strong adaptability, high yield, ease of planting, wide distribution, and ease of processing. With the increasing demand for bamboo resources, rapid propagation, species selection, and breeding have always been the focus of bamboo research. However, the long and unpredictable flowering cycle of bamboo, coupled with the difficulties of obtaining seeds, has made it difficult for mass-scale propagation and the introduction of desirable traits through classical breeding methods, which hinders the genetic improvement of bamboo. Asexual propagation, tissue culture, and genetic transformation present an effective breeding method to hasten the breeding process, improve breeding efficiency, and screen and create superior new varieties, and may significantly enhance the genetic improvement of bamboo and the development of the bamboo industry. This study reviews recent research on the asexual propagation of bamboo, propagation methods, cultivation means, influencing factors, and transgenes. The bamboo species that participated in asexual reproduction were systematically sorted according to the type of explants, the formula of the culture medium, and the results achieved. In addition, the bottlenecks and development trends in each training process were identified. This study provides a reference for the rapid propagation and genetic breeding of bamboo plants.

Rapid breeding of ‘Natsuiro’, a new rice cultivar with resistance to high temperatures and rice blast, using genome-wide marker-assisted selection

我が国の稲作経営においては，生産コストおよび環境負荷を低減しつつ高値販売が安定して実現できるイネ品種が求められている．高温登熟性と病害抵抗性を兼ね備え，稲作経営からのニーズに応えることができる早生品種は，現状ではまだ少ない．「なついろ」は，早生で高温登熟性に優れる「三重23号」の遺伝背景に，「ともほなみ」由来のいもち病圃場抵抗性遺伝子pi21を短期間で導入することにより育成された．連続戻し交雑では，BC1F1からBC3F1の各世代において，pi21を対象としたDNAマーカー選抜に加えゲノムワイドマーカーを用いた背景選抜を実施することにより，最初の人工交配（2013年）から2年2ヶ月で目的の遺伝子型を実現し，その後系統選抜および生産力検定試験等の特性把握調査の後に，6年後の2019年に品種登録出願された．「なついろ」は「三重23号」と比較して，いもち病圃場抵抗性が強いこと，稈長と穂長がやや長いこと，千粒重がやや小さいこと以外は概ね同様の農業形質を有する．また，「コシヒカリ」と比較して，稈長は10 cm短く，穂数はやや少なく，草型は“中間型”である．出穂期，成熟期は「コシヒカリ」よりそれぞれ3日および5日早い．pi21を有し，葉いもち圃場抵抗性は“極強”である．高温登熟性は「三重23号」と同程度の“強”で，「コシヒカリ」より強い．「なついろ」は2020年に三重県の奨励品種として採用された．高温登熟性と病害抵抗性を兼ね備え，稲作経営からのニーズに応えることができる早生品種としての普及が期待される．

Optimization of light/dark cycle in an extended photoperiod‐based speed breeding protocol for grain legumes

AbstractThe use of high‐performing varieties could contribute to increase food legume production and meet the population demand. However, the long process of conventional breeding is a serious limitation that needs further acceleration of genetic improvement. Speed breeding based on extended photoperiod is one of the techniques that allows rapid generation turnover by accelerating the plant life cycle. The present study focused on optimizing the duration of extended photoperiod for lentil, chickpea and faba bean in a growth chamber with light‐emitting diode (LED) light sources. Significant differences in growth rate, biomass production, phenology, physiology, plant injury and yield components were observed depending on light phase durations (22, 18 and 14 h). Twenty‐two hours of light resulted in earlier flowering and maturity, but higher stress symptoms than the other two light treatments. However, vegetative development was almost normal with limited stress under 14 h of light, but late flowering and maturity. Interestingly, good plant establishment with limited stress and shorter vegetative cycle was observed under 18 h of light. Therefore, a photoperiod of 18 h of light/6 h of darkness could be advised for a rapid breeding protocol.

Environmental Simulation Model for Rapid Prediction of Tea Seedling Growth

Accurate and effective monitoring of environmental parameters in tea seedling greenhouses is an important basis for regulating the seedling environment, which is crucial for improving the seedling growth quality. This study proposes a tea seedling growth simulation (TSGS) model based on deep learning. The Internet of Things system was used to measure environmental change during the whole seedling process. The correlation between the environmental parameters and the biomass growth of tea seedlings in various varieties was analyzed. A CNN-LSTM network was proposed to build the TSGS model of light, temperature, water, gas, mineral nutrition, and growth biomass. The results showed that: (1) the average correlation coefficients of air temperature, soil temperature, and soil moisture with the biomass growth of tea seedlings were 0.78, 0.84, and −0.63, respectively, which were three important parameters for establishing the TSGS model. (2) For evaluating the TSGS model of a single variety, the accuracy of ZM’s TSGS based on the CNN-LSTM network was the highest (Rp2 = 0.98, RMSEP = 0.14). (3) For evaluating the TSGS model of multiple varieties, the accuracy of TSGS based on the CNN-LSTM network was the highest (Rp2 = 0.96, RMSEP = 0.17). This study provided effective technical parameters for intelligent control of tea-cutting growth and a new method for rapid breeding.

The Cell Wall Regeneration of Tobacco Protoplasts Based on Microfluidic System

The cell wall, serving as the exoskeleton of plants, is naturally a barrier to resist external stresses. Protoplasts can be obtained by dissolving the cell walls of plant cells without damaging the cell membrane, and are widely used in the rapid propagation, transgenic breeding, and somatic hybridization of plants. However, to regenerate the cell wall is a precondition for cell division. Therefore, to study the culture condition and influencing factors during the cell wall regeneration of protoplasts is vital. Traditionally, culture medium is used to cultivate protoplasts, but it has some disadvantages. Herein, a microfluidic system with crossed channels was constructed to isolate and cultivate the protoplasts of tobacco. Then, the cell wall regeneration of the tobacco protoplasts was also studied based on this microfluidic system. It was found that, compared with the control, benzo-(1, 2, 3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH) could accelerate the regeneration of the cell wall, while Pseudomonas syringae pv. tomato DC3000 (Pst DC3000) could inhibit the regeneration of the cell wall within 24 h. To conclude, this study demonstrated that a crossed microfluidic chip could be an effective tool to study cell wall regeneration or other behavior of plant cells in situ with high resolution. In addition, this study revealed the rate of cell wall regeneration under BTH and Pst DC3000 treatment.

The Establishment of Rapid Propagation System of ‘RED SUN’ Phalaenopsis aphrodite

Phalaenopsis aphrodite Rchb. F. is a plant of great ornamental and economic value, and its growth has strict requirements in terms of environment. In order to establish the rapid propagation of Phalaenopsis aphrodite Rchb. F., this study used the popular large-flowered variety ‘RED SUN’, which is found on the market, as the material, and studied the effects of pedicel taking time, site, plant growth regulators, and organic substances on the establishment of a regeneration system. The results indicated that the best combination of initiation culture was collecting peduncles in January + upper position of peduncles + 0.1% HgCl2 sterilization for 8 min. The best recipe for inducing adventitious buds was MS + TDZ 0.4 mg/L + NAA 0.5 mg/L. The optimal combination for adventitious bud propagation was MS + TDZ 0.2 mg/L + NAA 0.4 mg/L. The best recipe for strong seedling from aseptic seedlings was MS + NAA 0.4 mg/L + banana powder 20 g/L + tryptone 2 g. The best recipe for rooting for aseptic seedlings was 1/2 MS + IBA 0.5 mg/L + charcoal 2 g/L. The best combination of acclimation and transplanting for Phalaenopsis was using sphagnum in the training seedling room, which produced a seedling survival rate of 97%. Our findings, therefore, demonstrate the methods of rapid breeding of the Phalaenopsis orchid, which provide a scientific basis for the conservation of this species.

New cycle, same old mistakes? Overlapping vs. discrete generations in long-term recurrent selection

BackgroundRecurrent selection is a foundational breeding method for quantitative trait improvement. It typically features rapid breeding cycles that can lead to high rates of genetic gain. Usually, generations are discrete in recurrent selection, which means that breeding candidates are evaluated and considered for selection for only one cycle. Alternately, generations can overlap, with breeding candidates considered for selection as parents for multiple cycles. With recurrent genomic selection but not phenotypic selection, candidates can be re-evaluated by using genomic estimated breeding values without additional phenotyping of the candidates themselves. Therefore, it may be that candidates with true high breeding values discarded in one cycle due to underestimation of breeding value could be identified and selected in subsequent cycles. The consequences of allowing generations to overlap in recurrent selection are unknown. We assessed whether maintaining overlapping and discrete generations led to differences in genetic gain for phenotypic, genomic truncation, and genomic optimum contribution recurrent selection by stochastic simulation.ResultsWith phenotypic selection, overlapping generations led to decreased genetic gain compared to discrete generations due to increased selection error bias. Selected individuals, which were in the upper tail of the distribution of phenotypic values, tended to also have high absolute error relative to their true breeding value compared to the overall population. Without repeated phenotyping, these individuals erroneously believed to have high value were repeatedly selected across cycles, leading to decreased genetic gain. With genomic truncation selection, overlapping and discrete generations performed similarly as updating breeding values precluded repeatedly selecting individuals with inaccurately high estimates of breeding values in subsequent cycles. Overlapping generations did not outperform discrete generations in the presence of a positive genetic trend with genomic truncation selection, as individuals from previous breeding cycles typically had truly lower breeding values than candidates from the current generation. With genomic optimum contribution selection, overlapping and discrete generations performed similarly, but overlapping generations slightly outperformed discrete generations in the long term if the targeted inbreeding rate was extremely low.ConclusionMaintaining discrete generations in recurrent phenotypic selection leads to increased genetic gain, especially at low heritabilities, by preventing selection error bias. With genomic truncation selection and genomic optimum contribution selection, genetic gain does not differ between discrete and overlapping generations assuming non-genetic effects are not present. Overlapping generations may increase genetic gain in the long term with very low targeted rates of inbreeding in genomic optimum contribution selection.

Comparative transcriptome analysis reveals different defence responses during the early stage of wounding stress in Chi-Nan germplasm and ordinary Aquilaria sinensis

BackgroundAgarwood is a valuable Chinese medicinal herb and spice that is produced from wounded Aquilaria spp., is widely used in Southeast Asia and is highly traded on the market. The lack of highly responsive Aquilaria lines has seriously restricted agarwood yield and the development of its industry. In this article, a comparative transcriptome analysis was carried out between ordinary A. sinensis and Chi-Nan germplasm, which is a kind of A. sinensis tree with high agarwood-producing capacity in response to wounding stress, to elucidate the molecular mechanism underlying wounding stress in different A. sinensis germplasm resources and to help identify and breed high agarwood-producing strains.ResultsA total of 2427 and 1153 differentially expressed genes (DEGs) were detected in wounded ordinary A. sinensis and Chi-Nan germplasm compared with the control groups, respectively. KEGG enrichment analysis revealed that genes participating in starch metabolism, secondary metabolism and plant hormone signal transduction might play major roles in the early regulation of wound stress. 86 DEGs related to oxygen metabolism, JA pathway and sesquiterpene biosynthesis were identified. The majority of the expression of these genes was differentially induced between two germplasm resources under wounding stress. 13 candidate genes related to defence and sesquiterpene biosynthesis were obtained by WGCNA. Furthermore, the expression pattern of genes were verified by qRT-PCR. The candidate genes expression levels were higher in Chi-Nan germplasm than that in ordinary A. sinensis during early stage of wounding stress, which may play important roles in regulating high agarwood-producing capacity in Chi-Nan germplasm.ConclusionsCompared with A. sinensis, Chi-Nan germplasm invoked different biological processes in response to wounding stress. The genes related to defence signals and sesquiterepene biosynthesis pathway were induced to expression differentially between two germplasm resources. A total of 13 candidate genes were identified, which may correlate with high agarwood-producting capacity in Chi-Nan germplasm during the early stage of wounding stress. These genes will contribute to the development of functional molecular markers and the rapid breeding highly of responsive Aquilaria lines.

Recoloring tomato fruit by CRISPR/Cas9-mediated multiplex gene editing.

Fruit color is an important horticultural trait, which greatly affects consumer preferences. In tomato, fruit color is determined by the accumulation of different pigments, such as carotenoids in the pericarp and flavonoids in the peel, along with the degradation of chlorophyll during fruit ripening. Since fruit color is a multigenic trait, it takes years to introgress all color-related genes in a single genetic background via traditional crossbreeding, and the avoidance of linkage drag during this process is difficult. Here, we proposed a rapid breeding strategy to generate tomato lines with different colored fruits from red-fruited materials by CRISPR/Cas9-mediated multiplex gene editing of three fruit color-related genes (PSY1, MYB12, and SGR1). Using this strategy, the red-fruited cultivar 'Ailsa Craig' has been engineered to a series of tomato genotypes with different fruit colors, including yellow, brown, pink, light-yellow, pink-brown, yellow-green, and light green. Compared with traditional crossbreeding, this strategy requires less time and can obtain transgene-free plants with different colored fruits in less than 1year. Most importantly, it does not alter other important agronomic traits, like yield and fruit quality. Our strategy has great practical potential for tomato breeding and serves as a reference for improving multigene-controlled traits of horticultural crops.