Utilizing resequencing big data to facilitate Brassica vegetable breeding:tracing introgression pedigree and developing highly specific markers for clubroot resistance

Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable species B.rapa and B.oleracea,several commercial cultivars with unclear CR pedigrees have been intensively used as CR donors in breeding.However,the continuous occurrence of CR-breaking makes the CR pedigree underlying these cultivars one of the breeders'most urgent concerns.The complex intraspecific diversity of these two major Brassica vegetables has also limited the applicability of CR markers in different breeding programs.Here we first traced the pedigree underlying two kinds of CR that have been widely applied in breeding by linkage and introgression analyses based on public resequencing data.In B.rapa,a major locus CRzi8 underlying the CR of the commercial CR donor‘DegaoCR117’was identified.CRzi8 was further shown to have been introgressed from turnip(B.rapa ssp.rapifera)and that it carried a potential functional allele of Crr1a.The turnip introgression carried CRb^(c),sharing the same coding sequence with the CRb that was also identified from chromosome C07 of B.oleracea CR cultivars with different morphotypes.Within natural populations,variation analysis of linkage intervals of CRzi8,PbBa8.1,CRb,and CRb^(c)yielded easily resolved InDel markers(>20 bp)for these fundamental CR genes.The specificity of these markers was tested in diverse cultivars panels,and each exhibited high reliability in breeding.Our research demonstrates the value of the practice of applying resequencing big data to solve urgent concerns in breeding programs.

Genome Analysis in Wheat Breeding for Disease Resistance

A brief review on the development of wheat germplasm with introduced powdery mildew and scab resistance from Haynaldia villosa Sch. and Leymus racemosus Lam., Roegneria ciliaris (Trin.) Nevski as well as R. kamoji C. Koch respectively was made. In the course of germplasm development, genome analysis by means of chromosome banding, genomic in situ hybridization (GISH) or fluorescence in situ hybridization (FISH), molecular markers, particularly restriction fragment length polymorphism (RFLP) coupled with aneuploid analysis was employed for the purpose of improving breeding efficiency. Potential use of such germplasm in wheat breeding practice, basic studies and some related problems were also discussed.

Breeding wheat for resistance to Fusarium head blight in the Global North: China, USA, and Canada

The objective of this paper is to review progress made in wheat breeding for Fusarium head blight(FHB) resistance in China, the United States of America(USA), and Canada. In China,numerous Chinese landraces possessing high levels of FHB resistance were grown before the 1950 s. Later, pyramiding multiple sources of FHB resistance from introduced germplasm such as Mentana and Funo and locally adapted cultivars played a key role in combining satisfactory FHB resistance and high yield potential in commercial cultivars.Sumai 3, a Chinese spring wheat cultivar, became a major source of FHB resistance in the USA and Canada, and contributed to the release of more than 20 modern cultivars used for wheat production, including the leading hard spring wheat cultivars Alsen, Glenn, Barlow and SY Ingmar from North Dakota, Faller and Prosper from Minnesota, and AAC Brandon from Canada. Brazilian wheat cultivar Frontana, T. dicoccoides and other local germplasm provided additional sources of resistance. The FHB resistant cultivars mostly relied on stepwise accumulation of favorable alleles of both genes for FHB resistance and high yield,with marker-assisted selection being a valuable complement to phenotypic selection. With the Chinese Spring reference genome decoded and resistance gene Fhb1 now cloned, new genomic tools such as genomic selection and gene editing will be available to breeders, thus opening new possibilities for development of FHB resistant cultivars.

Creating large EMS populations for functional genomics and breeding in wheat

Wheat germplasm is a fundamental resource for basic research,applied studies,and wheat breeding,which can be enriched normally by several paths,such as collecting natural lines,accumulating breeding lines,and introducing mutagenesis materials.Ethyl methane sulfonate(EMS)is an alkylating agent that can effectively introduce genetic variations in a wide variety of plant species.In this study,we created a million-scale EMS population(MEP)that started with the Chinese wheat cultivars‘Luyan 128’,‘Jimai 38’,‘Jimai 44’,and‘Shannong 30’.In the M1 generation,the MEP had numerous phenotypical variations,such as>3,000 chlorophyll-deficient mutants,2,519 compact spikes,and 1,692 male sterile spikes.There were also rare mutations,including 30 independent tillers each with double heads.Some M1 variations of chlorophyll-deficiency and compact spikes were inheritable,appearing in the M2 or M3 generations.To advance the entire MEP to higher generations,we adopted a single-seed descendent(SSD)approach.All other seed composites of M2 were used to screen other agronomically important traits,such as the tolerance to herbicide quizalofop-P-methyl.The MEP is available for collaborative projects,and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.

Rice Heat Tolerance Breeding: A Comprehensive Review and Forward Gaze

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

Advances in Cotton Breeding for Resistance to Fusarium and Verticillium Wilt in the Last Fifty Years in China

This review summarizes the main advances in cotton breeding for resistance to fusarium and verticillium wilt in the last fifty years in China. The topics discussed include main achievements, experiences, problems and countermeasures for solving.

Combining Ability and Breeding Potential of Rapeseed Elite Lines for Pod Shatter Resistance

Pod shatter resistance of rapeseed is of great importance for modem farming practice. In order to determine the combining ability of elite inbred lines and the breeding potential of rapeseed hybrids in terms of pod shatter resistance, analysis of a 6×6 incomplete diallel cross was conducted at two locations. Results showed that a significant variation existed among breeding lines and their F1 hybrids for pod shatter resistant index （SRI）, pod length and width. Pod shatter resistance was significantly positively correlated with pod length. The general combining ability （GCA） effects （GCA=l.58） played a more important role than specific combining ability （SCA） effects （SCA=0.20） for pod shatter trait. The elite lines R1, 1019B and 1055B displayed significant positive GCA effects for pod shatter resistance. Four crosses （1019B×R1, 1015B×R1, 6098B×R1, and 8908B×R1） with high mean performance and positive SCA effects were recommended for developing new hybrids for mechanical harvest in the middle reaches of the Yangtze River.

Reversal of tamoxifen resistance by artemisinin in ER+breast cancer:bioinformatics analysis and experimental validation

Breast cancer is the leading cause of cancer-related deaths in women worldwide,with Hormone Receptor(HR)+being the predominant subtype.Tamoxifen(TAM)serves as the primary treatment for HR+breast cancer.However,drug resistance often leads to recurrence,underscoring the need to develop new therapies to enhance patient quality of life and reduce recurrence rates.Artemisinin(ART)has demonstrated efficacy in inhibiting the growth of drug-resistant cells,positioning art as a viable option for counteracting endocrine resistance.This study explored the interaction between artemisinin and tamoxifen through a combined approach of bioinformatics analysis and experimental validation.Five characterized genes(ar,cdkn1a,erbb2,esr1,hsp90aa1)and seven drug-disease crossover genes(cyp2e1,rorc,mapk10,glp1r,egfr,pgr,mgll)were identified using WGCNA crossover analysis.Subsequent functional enrichment analyses were conducted.Our findings confirm a significant correlation between key cluster gene expression and immune cell infiltration in tamoxifen-resistant and-sensitized patients.scRNA-seq analysis revealed high expression of key cluster genes in epithelial cells,suggesting artemisinin’s specific impact on tumor cells in estrogen receptor(ER)-positive BC tissues.Molecular target docking and in vitro experiments with artemisinin on LCC9 cells demonstrated a reversal effect in reducing migratory and drug resistance of drug-resistant cells by modulating relevant drug resistance genes.These results indicate that artemisinin could potentially reverse tamoxifen resistance in ER-positive breast cancer.

Biomass-enhanced Janus sponge-like hydrogel with salt resistance and highstrength for efficient solar desalination

Interfacial solar-driven evaporation technology shows great potential in the field of industrial seawater desalination, and the development ofefficient and low-cost evaporation materials is key to achieving large-scale applications. Hydrogels are considered to be promising candidates;however, conventional hydrogel-based interfacial solar evaporators have difficulty in simultaneously meeting multiple requirements, including ahigh evaporation rate, salt resistance, and good mechanical properties. In this study, a Janus sponge-like hydrogel solar evaporator (CPAS) withexcellent comprehensive performance was successfully constructed. The introduction of biomass agar (AG) into the polyvinyl alcohol (PVA)hydrogel backbone reduced the enthalpy of water evaporation, optimized the pore structure, and improved the mechanical properties. Meanwhile, by introducing hydrophobic fumed nano-silica aerogel (SA) and a synergistic foaming-crosslinking process, the hydrogel spontaneouslyformed a Janus structure with a hydrophobic surface and hydrophilic bottom properties. Based on the reduction of the evaporation enthalpy andthe modulation of the pore structure, the CPAS evaporation rate reached 3.56 kg m^(-2) h^(-1) under one sun illumination. Most importantly, owingto the hydrophobic top surface and 3D-interconnected porous channels, the evaporator could work stably in high concentrations of salt-water(25 wt% NaCl), showing strong salt resistance. Efficient water evaporation, excellent salt resistance, scalable preparation processes, and low-costraw materials make CPAS extremely promising for practical applications.

Strategy for Use of Rice Blast Resistance Genes in Rice Molecular Breeding

Rice blast is one of the most destructive diseases affecting rice production worldwide.The development and rational use of resistant varieties has been the most effective and economical measure to control blast.In this review,we summarized the cloning and utilization of rice blast resistance genes,such as Pi1,Pi2,Pi9,Pi54,Pigm and Piz-t.We concluded that three main problems in the current breeding of rice blast resistance are:availability of few R(resistance)genes that confer resistance to both seedling and panicle blast,the resistance effect of pyramided lines is not the result of a simple accumulation of resistance spectrum,and only a few R genes have been successfully used for molecular breeding.Therefore,novel utilization strategies for rice blast R genes in molecular breeding were proposed,such as accurately understanding the utilization of R genes in main modern rice varieties,creating a core resistant germplasm with excellent comprehensive traits,screening and utilizing broadspectrum and durable resistance gene combinations.Lastly,the trends and possible development direction of blast resistance improvement were also discussed,including new genes regulating resistance identified via GWAS(genome-wide association study)and improving rice blast resistance using genetic editing.

Greatly enhanced corrosion/wear resistances of epoxy coating for Mg alloy through a synergistic effect between functionalized graphene and insulated blocking layer

The poor corrosion and wear resistances of Mg alloys seriously limit their potential applications in various industries.The conventional epoxy coating easily forms many intrinsic defects during the solidification process,which cannot provide sufficient protection.In the current study,we design a double-layer epoxy composite coating on Mg alloy with enhanced anti-corrosion/wear properties,via the spin-assisted assembly technique.The outer layer is functionalized graphene(FG)in waterborne epoxy resin(WEP)and the inner layer is Ce-based conversion(Ce)film.The FG sheets can be homogeneously dispersed within the epoxy matrix to fill the intrinsic defects and improve the barrier capability.The Ce film connects the outer layer with the substrate,showing the transition effect.The corrosion rate of Ce/WEP/FG composite coating is 2131 times lower than that of bare Mg alloy,and the wear rate is decreased by~90%.The improved corrosion resistance is attributed to the labyrinth effect(hindering the penetration of corrosive medium)and the obstruction of galvanic coupling behavior.The synergistic effect derived from the FG sheet and blocking layer exhibits great potential in realizing the improvement of multi-functional integration,which will open up a new avenue for the development of novel composite protection coatings of Mg alloys.

Breeding Soybeans for Resistance to Physiological Race 4 of Cyst Nematode

Soybean cyst nematode causes serious damage to soybean production. In 1991, we started breeding studies on the resistance of soybeans to the cyst nematode. We found that near the Beijing area the dominant race of the cyst nematode was race 4. We made more than 50 combinations of cross. The best combination was Dan 8 X PI 437654 which resulted in marked segregation in plant height, pod habit, resistance to cyst nematode and maturity. We obtained many new soybean lines highly resistant to the cyst nematode through the pedigree method of selection, enlarging the number of plants of good combinations, alternative breeding in the North and in the South, and identification at an early generation. We now have released three soybean cultivars, Zhonghuang 12, Zhonghuang 13 and Zhonghuang 17 with moderate resistance to the cyst nematode in Beijing, Anhui, Tianjin and Northern China. In addition, we obtained many lines which were highly resistant to the cyst nematode.

Multi Location Field Evaluation of BC1F2 Sorghum Populations for Striga Resistance in Niger

In Niger, a landlocked country, sorghum is the second staple food cultivated over the country by smallholder farmer. The crop is important for human and animal consumption. Despite its importance, the crop is affected by biotic and abiotic constraints. Among those constraints, striga has a high impact on yield. In fact, to survive, farmers are growing their local preferred sorghum varieties wish is highly sensible to the weed. Striga management is a challenge that requires a permanent solution. In addition, the development of high-yielding Striga resistant genotypes will be appreciated by farmers. The development of striga resistance will be based on the breeding population performances under farmer’s diverse environmental conditions adaptation. The main objective of this study is to evaluate two breeding populations for striga resistance in two different environments at Boulke and Dibissou in Tahoua region, to identify the early and high-yielding striga tolerant genotypes under natural infestation.

Evaluation of maize inbred lines currently used in Chinese breeding programs for resistance to six foliar diseases

Foliar diseases are common in most maize-producing regions and have caused serious yield reduction in China. To evaluate genetic resistance of parental lines actively used in maize breeding programs to major foliar diseases, 152 maize inbred lines were tested against northern corn leaf blight(NCLB), southern corn leaf blight(SCLB), Curvularia leaf spot(CLS),gray leaf spot(GLS), common rust, and southern rust from 2003 to 2005. A small number of lines exhibited highly resistant reactions to common rust and southern rust, but none were highly resistant to NCLB, SCLB, CLS, and GLS. Although 53.3%, 40.8%, and 80.7% of lines were resistant to NCLB, SCLB, and common rust, the resistance in most lines was moderate.Resistance to CLS, GLS, and southern rust was rare in this collection of maize lines. Five lines,313, Chang 7-2, Qi 319, Qi 318, and Shen 137, were resistant to five diseases tested. Lines belonging to heterotic subgroup PB exhibited better resistance to the foliar diseases than lines from other heterotic subgroups, such as BSSS, PA, Lancaster, LRC, and PA. The results will be of benefit to breeders for selecting lines in disease resistance breeding programs.

Cross Breeding of Populus and Its Hybrids for Cold Resistance

Populus tomentosa was crossed with P.tremuloidis, P.grandidentata, P.alba×P.grandidentata and P.alba×Ulmuspumila in order to maintain its rapid growth and high wood quality and improve its resistance to cold. Two methods were used to increase the germination rate from 1.5% to 41.1% and the remaining rate from 1.7% to 44.2%. Forty crossing combinations were conducted and 2744 hybrid seedlings were obtained. MX4×P.grandidentata （G-1-58）, MX3×P.tremuloidis （T-44-60）, MX2×P.tremuloidis （1-13-87-37） and MX2×（P.alba×P.grandidentata） were regarded as superior combinations after analysis and selection. Thirty seedlings of these combinations and 11 triploid seedlings identified by counting their chromosomes were selected as super plants.

Breeding for FHB Resistance via Fusarium Damaged Kernels and Deoxynivalenol Accumulation as Well as Inoculation Methods in Winter Wheat

FHB is one of the most destructive diseases of wheat. Resistance testing depends strongly on inoculation methods, and on measured traits. Therefore a four-year (2009-2012) study was performed using spray inoculation + polyethylene (PE) bag cover, spray inoculation + mist irrigation, and spawn method supported by mist irrigation on 40 genotypes, 20 from Hungary and 20 from IFA Tulln, Austria. Each year four isolates were used in artificial inoculations except the spawn method where stalk debris served the inoculum. Visual Fusarium head blight (FHB) scores, Fusarium damaged kernels (FDK) and deoxynivalenol (DON) contamination were checked. 7680 FHB and FDK, as well as 3840 DON analyses served as the background for the statistical evaluation. The most reliable method used was the spray + polyethylene (PE) bag;the other two were significantly poorer being valid for all traits. The FHB scores were the least reliable, whereas the FDK was much more consequent and the DON gave the best results. The FDK gave much better predictions for DON contamination than FHB. The cultivars responses correlated well at different epidemic severities. The presence of the kernel resistance was confirmed and a new trait as extra kernel susceptibility was described. Presence of DON resistance was confirmed again, and extra DON susceptibility was described as a new trait. DON performance varied on the most sensitive cultivar between 0.32 and 143 mg/kg (mean 17.52 mg/kg) and on the most resistant genotype between 0.00 and 18.19 mg/kg (mean 1.87 mg/kg). Correlations between stability and resistance level are r = 0.85 for FHB, 0.78 for FDK, and 0.88 for DON, all at a significance level of p = 0.001. The very close correlation between FDK and DON contamination (r = 0.81, p = 0.001) proves that control of DON contamination needs appropriate resistance. In the breeding program evaluation of FDK is the most important, and then DON will be decided. Variety registration must be updated;otherwise no improvement on the field will occur.

Progress Towards Genetics and Breeding for Minor Genes Based Resistance to Ug99 and Other Rusts in CIMMYT High-Yielding Spring Wheat

Wheat rusts continue to cause significant losses worldwide despite major efforts given to their genetic control. This is due to frequent evolution and selection of virulence in pathogen overcoming the deployed race-specific resistance genes. Although the life of effective race-specific resistance genes can be prolonged by using gene combinations, an alternative approach being implemented at CIMMYT is to deploy varieties that posses adult plant resistance （APR） based on combinations of minor, slow rusting genes. When present alone, the APR genes do not confer adequate resistance especially under high disease pressure; however, combinations of 4 or 5 minor genes usually result in ＂near-immunity＂ or a high level of resistance. Although only a few APR genes are catalogued, various APR QTLs are now known and could lead to further characterization of additional genes. Four characterized genes have pleiotropic effects in conferring partial APR to all 3 rusts and powdery mildew, thus simplifying the task of breeding wheat varieties that are resistant to multiple diseases. Significant progress was made recently in developing high-yielding wheat germplasm that possesses high levels of APR to all three rusts by implementing a Mexico- Kenya shuttle breeding scheme. Parents with APR to Ug99 were hybridized with high-yielding parents that had adequate to high levels of APR to leaf rust and yellow rust. Segregating populations and advanced lines from these crosses were selected under high rust pressures in Mexico （leaf rust and yellow rust） and Kenya （Ug99 stem rust and yellow rust） to identify high- yielding progenies that possess high to adequate APR to all three rusts. International distribution of these high-yielding wheats is underway through CIMMYT intemational yield trials and screening nurseries. It is expected that several wheat varieties with APR to three rusts will be released and grown in various countries in the near-future that will allow determining the durability of resistance.

Status and strategies in breeding for rust resistance in wheat

Wheat along with rice and maize is fulfilling half of the calories demands of the world. Global Wheat production has increased tremendously since green revolution in 1960’s and helped in minimizing hunger and malnutrition. Developing countries, which consume 60% of the global wheat production, have shown a higher yield increase than the developed countries in the past [1]. It was driven by the hunger prevalence in these countries and was attributable to the introduction of high yielding and rusted resistant semi dwarf varieties developed under the collaborative efforts of International and National research systems during the last 50 years. Whereas, climate change and the emergence of new pests and diseases are threatening the food sustainability. The evolution of new races of disease pathogens like stem rust (Ug 99) is of serious concern. In order to feed the ever increasing population we have to increase wheat production at the rate 1.6% which can be achieved by developing high yielding varieties having a good tolerance level for biotic and abiotic stresses.

Conventional Breeding and Molecular Markers for Blast Disease Resistance in Rice (Oryza sativa L.)

Monogenic lines,which carried 23 genes for blast resistance were tested and used donors to transfer resistance genes by crossing method.The results under blast nursery revealed that 9 genes from 23 genes were susceptible to highly susceptible under the three locations(Sakha,Gemmeza,and Zarzoura in Egypt);Pia,Pik,Pik-p,Piz-t,Pita,Pi b,Pi,Pi 19 and Pi 20.While,the genes Pii,Pik-s,Pik-h,Pi z,Piz-5,Pi sh,Pi 3,Pi 1,Pi 5,Pi 7,Pi 9,Pi 12,Pikm and Pita-2 were highly resistant at the same locations.Clustering analysis confirmed the results,which divided into two groups;the first one included all the susceptible genes,while the second one included the resistance genes.In the greenhouse test,the reaction pattern of five races produced 100%resistance under artificial inoculation with eight genes showing complete resistance to all isolates.The completely resistant genes:Pii,Pik-s,Piz,Piz-5(=bi2)(t),Pita(=Pi4)(t),Pita,Pi b and Pi1 as well as clustering analysis confirmed the results.In the F1 crosses,the results showed all the 25 crosses were resistant for leaf blast disease under field conditions.While,the results in F2 population showed seven crosses with segregation ratio of 15(R):1(S),two cross gave segregated ratio of 3 R:1 S and one gave 13:3.For the identification of blast resistance genes in the parental lines,the marker K3959,linked to Pik-s gene and the variety IRBLKS-F5 carry this gene,which was from the monogenic line.The results showed that four genotypes;Sakha 105,Sakha 103,Sakha 106 and IRBLKS-F5 were carrying Pik-s gene,while was absent in the Sakha 101,Sakha 104,IRBL5-M,IRBL9-W,IRBLTACP1 and IRBL9-W(R)genotypes.As for Pi 5 gene,the results showed that it was present in Sakha 103 and Sakha 104 varieties and absent in the rest of the genotypes.In addition,Pita-Pita-2 gene was found in the three Egyptian genotypes(Sakha 105,Sakha 101 and Sakha 104)plus IRBLTACP1 monogenetic.In F2 generation,six populations were used to study the inheritance of blast resistance and specific primers to confirm the ratio and identify the resistance genes.However,the ratios in molecular markers were the same of the ratio under field evaluation in the most population studies.These findings would facilitate in breeding programs for gene pyramiding and gene accumulation to produce durable resistance for blast using those genotypes.

Breeding and Application Techniques of a New Rice Variety Liliang-you 3822 with High Yield and Disease Resistance

Liliangyou 3822 is a novel indica hybrid rice variety that exhibits disease resistance,high yield,lodging resistance,and late maturity.It employs a self-selected two-line sterile line,Li 38S,and a self-selected restorer line,R22.This variety was subjected to a regional test of indica late-maturing groups in the middle and lower reaches of the Yangtze River in 2020.The results demonstrated that the average yield of the variety was 9.95 t/hm 2,which was 10.67%higher than that of the control Fengliangyou 4,indicating a highly significant yield increase.In the continuous test in 2021,the average yield was 9.74 t/hm 2,representing a 6.52%increase over the control,which also exhibited a significant increase.Finally,the average yield of the two years regional test was 9.84 t/hm 2,which was 8.58%higher than that of the control.In the 2021 production test,the average yield of the variety was 9.32 t/hm 2,which was 12.19%higher than that of the control,indicating a remarkably significant yield increase.In 2022,the variety was validated by the National Crop Variety Approval Committee(GSD 20220143).