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.

Molecular breeding of farm animals through gene editing

The rapid development of biotechnology has facilitated our understanding of the biological functions of candidate genes for important economic traits in farm animals.Molecular breeding by gene editing has greatly revolutionized the breeding of farm animals.Through gene editing and embryo manipulation,breeds with designed economic or disease-resistant traits can be readily generated.Along with this fast progress,the safety assessment of gene-edited farm animals has attracted public and regulatory attention.This review summarizes the research progress of gene editing in farm animals,focusing on performance improvement,disease resistance,bioreactors,animal welfare,and environmental friendliness.The limitations and future development of gene editing technology in farm animal breeding are also discussed.

Tree Genetics and Molecular Breeding(TGMB)

Tree Genetics and Molecular Breeding(ISSN 1927-5781)is an international,open access,peer reviewed journal,committed to serve for tree genetics and molecular breeding,particularly publishing innovative research findings in the basic and applied fields of tree molecular genetics and novel techniques for fruit/forest/ornamental/

Animal Molecular Breeding(AMB)

Animal Molecular Breeding(ISSN 1927-5609)is an open access,peer reviewed journal published online by Bio Publisher.The journal is publishing all the latest and outstanding research articles,letters and reviews in all areas of animal molecular breeding,containing transgenic breeding and marker assisted breeding,particularly publishing innovative

Animal Molecular Breeding(AMB)

Animal Molecular Breeding(ISSN 1927-5609)is an open access,peer reviewed journal published online by Bio Publisher.The journal is publishing all the latest and outstanding research articles,letters and reviews in all areas of animal molecular breeding,containing transgenic breeding and marker assisted breeding,

Genetic study and molecular breeding for high phosphorus use efficiency in maize

Phosphorus is the second most important macronutrient after nitrogen and it has many vital functions in the life of plants.Most soils have a low available P content,which has become a key limiting factor for increasing crop production.Also,low P use efficiency(PUE)of crops in conjunction with excessive application of P fertilizers has resulted in serious environmental problems.Thus,dissecting the genetic architecture of crop PUE,mining related quantitative trait loci(QTL)and using molecular breeding methods to improve high PUE germplasm are of great significance and serve as an efficient approach for the development of sustainable agriculture.In this review,molecular and phenotypic characteristics of maize inbred lines with high PUE,related QTL and genes as well as low-P responses are summarized.Based on this,a breeding strategy applying genomic selection as the core,and integrating the existing genetic information and molecular breeding techniques is proposed for breeding high PUE maize inbred lines and hybrids.

Genetics,resistance mechanism,and breeding of powdery mildew resistance in cucumbers(Cucumis sativus L.)

Cucumber is an important vegetable worldwide,and powdery mildew(PM)is a common and serious disease of cucumbers.Breeding disease-resistant cucumber varieties is the most advantageous strategy to control this disease.In recent years,exploration and identification of cucumber PM resistance genes have achieved great advancement,and many genes have been cloned and verified using different methods.However,the resistance mechanism of cucumber PM is still unclear,and many ambiguities need to be elucidated urgently.In this review,we summarized the research advances in PM resistance in cucumbers,including genetic analysis,quantitative trait locus mapping,map-based cloning,transcriptomics,mlo-mediated PM resistance,and mining of noncoding RNAs involved in resistance.Finally,the research directions and the problems that need to be solved in the future were discussed.

Rice3K56 is a high-quality SNP array for genome-based genetic studies and breeding in rice(Oryza sativa L.)

Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide,which was then tested extensively in 192 representative rice samples.Printed on the Gene Titan chips of Affymetrix Axiom each containing 56,606 SNP markers,the Rice3K56 array has a high genotyping reliability(99.6%),high and uniform genome coverage(an average of 6.7-kb between adjacent SNPs),abundant polymorphic information and easy automation,compared with previously developed rice SNP arrays.When applied in rice varietal differentiation,population diversity analysis,gene mapping of 13 complex traits by a genome-wide association study analysis(GWAS),and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations,these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding.

Increasing Fusarium verticillioides resistance in maize by genomicsassisted breeding:Methods,progress,and prospects

Maize(Zea mays L.)is an indispensable crop worldwide for food,feed,and bioenergy production.Fusarium verticillioides(F.verticillioides)is a widely distributed phytopathogen and incites multiple destructive diseases in maize:seedling blight,stalk rot,ear rot,and seed rot.As a soil-,seed-,and airborne pathogen,F.verticillioides can survive in soil or plant residue and systemically infect maize via roots,contaminated seed,silks,or external wounds,posing a severe threat to maize production and quality.Infection triggers complex immune responses:induction of defense-response genes,changes in reactive oxygen species,plant hormone levels and oxylipins,and alterations in secondary metabolites such as flavonoids,phenylpropanoids,phenolic compounds,and benzoxazinoid defense compounds.Breeding resistant maize cultivars is the preferred approach to reducing F.verticillioides infection and mycotoxin contamination.Reliable phenotyping systems are prerequisites for elucidating the genetic structure and molecular mechanism of maize resistance to F.verticillioides.Although many F.verticillioides resistance genes have been identified by genome-wide association study,linkage analysis,bulkedsegregant analysis,and various omics technologies,few have been functionally validated and applied in molecular breeding.This review summarizes research progress on the infection cycle of F.verticillioides in maize,phenotyping evaluation systems for F.verticillioides resistance,quantitative trait loci and genes associated with F.verticillioides resistance,and molecular mechanisms underlying maize defense against F.verticillioides,and discusses potential avenues for molecular design breeding to improve maize resistance to F.verticillioides.

CmMYB3-like negatively regulates anthocyanin biosynthesis and flower color formation during the post-flowering stage in Chrysanthemum morifolium

Color fading caused by a decrease in anthocyanin accumulation during the post-flowering stage significantly affects postharvest quality of chrysanthemum.However,the underlying mechanism by which anthocyanin accumulation decreases during the post-flowering stage still unclear,which greatly restricts design of molecular breeding in chrysanthemum.Here,a chrysanthemum SG7 R2R3 MYB transcription factor(TF),CmMYB3-like,was identified to have a function in regulating anthocyanin biosynthesis during the post-flowering stage.Quantitative real time PCR(qRT-PCR)assays showed that the expression of CmMYB3-like was gradually downregulated when anthocyanin content increased during the flowering stage and was significantly upregulated during the post-flowering stage.Genetic transformation of chrysanthemum and dual-luciferase assays in N.benthamiana leaves showed that CmMYB3-like suppressed anthocyanin accumulation by inhibiting the transcription of CmCHS and CmANS directly and that of CmF3H indirectly.However,overexpression or suppression of CmMYB3-like did not affect the biosynthesis of flavones or flavonols.Genetic transformation of chrysanthemum revealed that the overexpression of CmMYB3-like inhibited anthocyanin accumulation,but its suppression prevented the decrease in anthocyanin accumulation during the post-flowering stage.Our results revealed a crucial role of CmMYB3-like in regulating the color of petals during the post-flowering stage and provided a target gene for molecular design breeding to improve the postharvest quality of chrysanthemum.

Antioxidant lignans sesamin and sesamolin in sesame(Sesamum indicum L.):a comprehensive review and future prospects

Sesame(Sesamum indicum L.)is a significantly lucrative cash crop for millions of small-holder farmers.Its seeds are an important source of a highly appreciated vegetable oil globally and two clinically essential antioxidant lignans,sesamin and sesamolin.Accordingly,many countries import millions of tons of sesame seed every year.The demand for lignan-rich sesame seeds has been increasing in recent years due to the continuous discovery of several pharmacological attributes of sesamin and sesamolin.To meet this demand,the sesame breeder’s primary objective is to release sesame cultivars that are enriched in oil and lignans.Thus,it is necessary to summarize the information related to the sesamin and sesamolin contents in sesame in order to promote the joint efforts of specialized research teams on this important oilseed crop.In this article,we present the current knowledge on the sesamin and sesamolin contents in S.indicum L.with respect to the updated biosynthesis pathway,associated markers,governing loci,available variability in sesame germplasm,the in planta potential roles of these compounds in sesame,and the newly discovered pharmacological attributes.In addition,we propose and discuss some required studies that might facilitate genomics-assisted breeding of high lignan content sesame varieties.

Genetic dissection of drought resistance for trait improvement in crops

Reliance on agriculture for food security is a constant in all modern societies.Global climate change and population growth have put immense pressure on sustainable agriculture,exacerbating the effects of environmental stresses.Drought is one of the most pressing abiotic stresses that farmers face,presenting an annual threat to crop growth and yield.Crops have evolved extensive morphological,physiological,and molecular mechanisms to combat drought stress.Drought resistance is a polygenic trait,controlled by a complex genetic network and an array of genes working together to ensure plant survival.Many studies have aimed at dissecting the genetic mechanisms underlying drought resistance.Recent studies using linkage and association mapping have made progress in identifying genetic variations that affect drought-resistance traits.These loci may potentially be engineered by genetic transformation and genome editing aimed at developing new,stress-resistant crop cultivars.Here we summarize recent progress in elucidating the genetic basis of crop drought resistance.Molecular-breeding technologies such as marker-assisted selection,genome selection,gene transformation,and genome editing are currently employed to develop drought-resistant germplasm in a variety of crops.Recent advances in basic research and crop biotechnology covered in this review will facilitate delivery of drought-resistant crops with unprecedented efficiency.

Exploration of rice yield potential: Decoding agronomic and physiological traits

Rice grain yield is determined by three major"visible"morphological traits:grain weight,grain number per panicle,and effective tiller number,which are affected by a series of"invisible"physiological factors including nutrient use efficiency and photosynthetic efficiency.In the past few decades,substantial progress has been made on elucidating the molecular mechanisms underlying grain yield formation,laying a solid foundation for improving rice yield by molecular breeding.This review outlines our current understanding of the three morphological yield-determining components and summarizes major progress in decoding physiological traits such as nutrient use efficiency and photosynthetic efficiency.It also discusses the integration of current knowledge about yield formation and crop improvement strategies including genome editing with conventional and molecular breeding.

Achievements and prospects of grass pea(Lathyrus sativus L.) improvement for sustainable food production

Grass pea offers an attractive choice for sustainable food production, owing to its intrinsic properties including limited water requirement and drought tolerance. However, low productivity and the presence of a neurotoxin(ODAP) have posed major obstacles to its genetic improvement. Also, biotechnological investments remain limited and the genome is complex and not well understood. Strategies that allow identification of genotypes with reduced ODAP content, coupling of low ODAP content with enhanced yield, and effective seed detoxification methods merit immediate attention. Breeder-friendly genomic tools are being increasingly made available to improve the efficiency of breeding protocols. To this end, the application of next-generation sequencing has provided a means of leveraging the repertoire of genomic resources for this somewhat neglected crop. In this review, we describe progress achieved in Lathyrus genetic improvement. We also explore potential opportunities in Lathyrus research and identify urgent research needs.

Intron-targeted gene insertion in rice using CRISPR/Cas9: A case study of the Pi-ta gene

Intron-targeted gene insertion strategy using CRISPR/Cas9(clustered regularly interspaced short palindromic repeats/CRISPR-associated Cas9) has been shown to be a potential tool for crop genetic improvement by targeted mutagenesis or gene replacement of an elite allele into widely cultivated rice varieties. The rice blast resistant protein Pi-ta, differs from its susceptible counterpart, pi-ta, by a single amino acid in exon 2. To create new materials resistant to the rice blast disease, we inserted a genomic fragment containing the exon 2 and 3′ untranslated region(3′ UTR) of Pi-ta into intron 1 of pi-ta in rice materials susceptible to rice blast using the intron-targeted insertion strategy. The gene insertion frequency was3.8%. Several novel transgene-free progeny with stably inherited homozygous insert were identified in the T_1 generation, which have been crossed to rice germplasm bearing other resistance gene(R gene) for pyramiding of R genes. This work verified the feasibility of using the genome editing technology in improvement of qualitative agronomic trait in crops.

Current strategies and advances in wheat biology

The characterization of agronomically important genes has great potential for the improvement of wheat.However,progress in wheat genetics and functional genomics has been impeded by the high complexity and enormous size of the wheat genome.Recent advances in genome sequencing and sequence assembly have produced a high-quality genome sequence for wheat.Here,we suggest that the strategies used to characterize biological mechanisms in model species,including mutant preparation and characterization,gene cloning methods,and improved transgenic technology,can be applied to wheat biology.These strategies will accelerate progress in wheat biology and promote wheat breeding program development.We also outline recent advances in wheat functional genomics.Finally,we discuss the future of wheat functional genomics and the rational design-based molecular breeding of new wheat varieties to contribute to world food security.

Vegetable biology and breeding in the genomics era

Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize,thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.

Functional Role of miRNAs: Key Players in Soybean Improvement

Soybean(Glycine max(L.)Merr)is an agro-economic crop growing across the world to cater nutrition for both human and animal feed due to the high oil and protein content in its edible seeds.The genes and QTLs associated with important agronomic traits in this crop have already been identified and validated for soybean cyst nematode(SCN),Phytophthora root and stem rot,Pythium root rot and aphid resistance,seed quality,nutrient values,and also employed for genetic improvement in soybean.In the last decade,micro RNAs(miRNAs)have been considered the effector molecules,so the detection and characterization of novel miRNAs in soybean have been taken up by several workers.The advancement in the strategy of sequencing and tools of bioinformatics during last decade has contributed to the discovery of many soybean miRNAs,thus miRNA can be used as a tool in molecular breeding studies,and this has opened new vistas for miRNA mediated genetic improvement of soybean to augment crop productivity as well as nutritional quality.This review addresses the current state of understanding of miRNAmediated stress responses,nutrient acquisition,plant development and crop production processes in soybean.

Genetic Improvement of Betula platyphylla Suk.in China:A Review

Birch(Betula platyphylla Suk.),distributed in Eurasia,North America,and Australia,is a kind of cold-resistant,fast-growing,and vital pulpwood tree species.It is also one of the most important ecological restoration tree species with high values of economic benefits in Northeast China.To improve the genetic gain and expand the economic benefit of B.platyphylla,many genetic improvements have been carried out.In China,B.platyphylla is widely distributed and varied,and there are many varieties with excellent genetic characteristics.In this paper,the genetic improvement of B.platyphylla was reviewed,and the previous research results were discussed from two aspects:conventional breeding and molecular breeding.Some problems and corresponding solutions in the genetic improvement were put forward to provide ideas for B.platyphylla breeding in the future.