Shaping polyploid wheat for success: Origins,domestication, and the genetic improvement of agronomic traits

Bread wheat (Triticum aestivum L., AABBDD, 2n = 6x = 42), which accounts for most of the cultivated wheat crop worldwide, is a typical allohexaploid with a genome derived from three diploid wild ancestors. Bread wheat arose and evolved via two sequential allopolyploidization events and was further polished through multiple steps of domestication. Today, cultivated allohexaploid bread wheat has numerous advantageous traits, including adaptive plasticity, favorable yield traits, and extended end-use quality, which have enabled its cultivation well beyond the ranges of its tetraploid and diploid progenitors to become a global staple food crop. In the past decade, rapid advances in wheat genomic research have considerably accelerated our understanding of the bases for the shaping of complex agronomic traits in this polyploid crop. Here, we summarize recent advances in characterizing major genetic factors underlying the origin, evolution, and improvement of polyploid wheats. We end with a brief discussion of the future prospects for the design of gene cloning strategies and modern wheat breeding.     

A Genomic Resource for the Development,Improvement, and Exploitation of Sorghum for Bioenergy

With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production.     

Miscanthus: A fast‐growing crop for environmental remediation and biofuel production

As an herbaceous perennial, Miscanthus has attracted extensive attention in bioenergy refinery and ecological remediation due to its high yield and superior environmental adaptability. This review summarizes current research advances of Miscanthus in several aspects including biological properties, biofuels production, and phytoremediation of contaminated soil. Miscanthus has relatively high biomass yield, calorific value, and cellulose content compared with other lignocellulosic bioenergy crops, which make it one of the most promising feedstocks for the production of second‐generation biofuels. Moreover, Miscanthus can endure soil pollutions caused by various heavy metals and survive in a variety of adverse environmental conditions. Therefore, it also has potential applications in ecological remediation of contaminated soil, and reclamation of polluted soil and water resources. Nevertheless, more endeavors are still needed in the genetic improvement and elite cultivar breeding, large‐scale cultivation on marginal land, and efficient conversion to biofuels, when utilizing Miscanthus as a bioenergy crop. Furthermore, more efforts should also be undertaken to translate Miscanthus into a bioenergy crop with the phytoremediation potential.     

Genomic-based-breeding tools for tropical maize improvement

Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions. Heterosis breeding introduced in early 90 s improved maize yields significantly, but genetic gains is still a mirage, particularly for crop growing under marginal environments. Application of molecular markers has accelerated the pace of maize breeding to some extent. The availability of array of sequencing and genotyping technologies offers unrivalled service to improve precision in maize-breeding programs through modern approaches such as genomic selection, genome-wide association studies, bulk segregant analysis-based sequencing approaches, etc. Superior alleles underlying complex traits can easily be identified and introgressed efficiently using these sequence-based approaches. Integration of genomic tools and techniques with advanced genetic resources such as nested association mapping and backcross nested association mapping could certainly address the genetic issues in maize improvement programs in developing countries. Huge diversity in tropical maize and its inherent capacity for doubled haploid technology offers advantage to apply the next generation genomic tools for accelerating production in marginal environments of tropical and subtropical world. Precision in phenotyping is the key for success of any molecular-breeding approach. This article reviews genomic technologies and their application to improve agronomic traits in tropical maize breeding has been reviewed in detail.     

Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China

Crop improvement is a multifaceted micro-evolutionary process, involving changes in breeding approaches, planting configurations and consumption preferences of human beings. Recent research has started to identify the specific genes or genomic regions correlate to improved agronomic traits, however, an apparent blank between the genetic structure of crop elite varieties and their improving histories in diverse modern breeding programs is still in existence. Foxtail millet (Setaria italica) was one of the earliest cereal crops to be domesticated and served as a staple crop for early civilizations in China, where it is still widely grown today. In the present trial, a panel of foxtail millet elite varieties, which were released in the last sixty years in different geographical regions of China, was characterized using microsatellite markers (SSRs). A clear separation of two subpopulations corresponding to the two eco-geographical regions of foxtail millet production in China was identified by the dataset, which also indicated that in more recently released elite varieties, large quantities of accessions have been transferred from spring-sowing to summer-sowing ecotypes, likely as a result of breeding response to planting configurations. An association mapping study was conducted to identify loci controlling traits of major agronomic interest. Furthermore, selective sweeps involved in improvement of foxtail millet were identified as multi-diverse minor effect loci controlling different agronomic traits during the long-term improvement of elite varieties. Our results highlight the effect of transition of planting configuration and breeding preference on genetic evolvement of crop species.     

Making the most of 'omics' for crop breeding

Adoption of new breeding technologies is likely to underpin future gains in crop productivity. The rapid advances in 'omics' technologies provide an opportunity to generate new datasets for crop species. Integration of genome and functional omics data with genetic and phenotypic information is leading to the identification of genes and pathways responsible for important agronomic phenotypes. In addition, high-throughput genotyping technologies enable the screening of large germplasm collections to identify novel alleles from diverse sources, thus offering a major expansion in the variation available for breeding. In this review, we discuss these advances, which have opened the door to new techniques for construction and screening of breeding populations, to increase ultimately the efficiency of selection and accelerate the rates of genetic gain.     

The ecology and agronomy of Miscanthus sinensis, a species important to bioenergy crop development, in its native range in Japan: a review

Among several candidate perennial taxa, Miscanthus × giganteus has been evaluated and promoted as a promising bioenergy crop. Owing to several limitations, however, of the sterile hybrid, both at the taxon and agronomic production levels, other options need to be explored to not only improve M . × giganteus , which was originally collected in Japan, but to also consider the development of other members of its genus, including Miscanthus sinensis , as bioenergy crops. Indeed, there is likely much to be learned and applied to Miscanthus as a bioenergy crop from the long history of intensive interaction between humans and M. sinensis in Japan, which in some regions of the country spans several thousand years. Combined with its high amount of genetic variation, stress tolerance, biotic interactions with fauna, and function as a keystone species in diverse grasslands and other ecosystems within its native range, the unique and extensive management of M. sinensis in Japan as a forage grass and building material provides agronomists, agroecologists, and plant breeders with the capability of better understanding this species in terms of potential contribution to bioenergy crop development. Moreover, the studies described in this review may serve as a platform for future research of Miscanthus as a bioenergy crop in other parts of the world.     

Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits

For lignocellulosic bioenergy to become a viable alternative to traditional energy production methods, rapid increases in conversion efficiency and biomass yield must be achieved. Increased productivity in bioenergy production can be achieved through concomitant gains in processing efficiency as well as genetic improvement of feedstock that have the potential for bioenergy production at an industrial scale. The purpose of this review is to explore the genetic and genomic resource landscape for the improvement of a specific bioenergy feedstock group, the C4 bioenergy grasses. First, bioenergy grass feedstock traits relevant to biochemical conversion are examined. Then we outline genetic resources available bioenergy grasses for mapping bioenergy traits to DNA markers and genes. This is followed by a discussion of genomic tools and how they can be applied to understanding bioenergy grass feedstock trait genetic mechanisms leading to further improvement opportunities.     

Allele mining in crops: Prospects and potentials

Enormous sequence information is available in public databases as a result of sequencing of diverse crop genomes. It is important to use this genomic information for the identification and isolation of novel and superior alleles of agronomically important genes from crop gene pools to suitably deploy for the development of improved cultivars. Allele mining is a promising approach to dissect naturally occurring allelic variation at candidate genes controlling key agronomic traits which has potential applications in crop improvement programs. It helps in tracing the evolution of alleles, identification of new haplotypes and development of allele-specific markers for use in marker-assisted selection. Realizing the immense potential of allele mining, concerted allele mining efforts are underway in many international crop research institutes. This review examines the concepts, approaches and applications of allele mining along with the challenges associated while emphasizing the need for more refined ‘mining’ strategies for accelerating the process of allele discovery and its utilization in molecular breeding.     

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.

     

Cassava genetic transformation and its application in breeding

As a major source of food, cassava (Manihot esculenta Crantz) is an important root crop in the tropics and subtropics of Africa and Latin America, and serves as raw material for the production of starches and bioethanol in tropical Asia. Cassava improvement through genetic engineering not only overcomes the high heterozygosity and serious trait separation that occurs in its traditional breeding, but also quickly achieves improved target traits. Since the first report on genetic transformation in cassava in 1996, the technology has gradually matured over almost 15 years of development and has overcome cassava genotype constraints, changing from mode cultivars to farmer-preferred ones. Significant progress has been made in terms of an increased resistance to pests and diseases, biofortification, and improved starch quality, building on the fundamental knowledge and technologies related to planting, nutrition, and the processing of this important food crop that has often been neglected. Therefore, cassava has great potential in food security and bioenergy development worldwide.     

Molecular Improvement of Tropical Maize for Drought Stress Tolerance in Sub-Saharan Africa

The C4 grass Zea mays (maize or corn) is the third most important food crop globally after wheat and rice in terms of production and the second most widespread genetically modified (GM) crop, after soybean. Its demand is predicted to increase by 45% by the year 2020. In sub-Saharan Africa, tropical maize has traditionally been the main staple of the diet, 95% of the maize grown is consumed directly as human food and as an important source of income for the resource—poor rural population. However, its growth, development and production are greatly affected by environmental stresses such as drought and salinization. In this respect, food security in tropical sub-Saharan Africa is increasingly dependent on continuous improvement of tropical maize through conventional breeding involving improved germplasm, greater input of fertilizers, irrigation, and production of two or more crops per year on the same piece of land. Integration of advances in biotechnology, genomic research, and molecular marker applications with conventional plant breeding practices opens tremendous avenues for genetic modifications and fundamental research in tropical maize. The ability to transfer genes into this agronomically important crop might enable improvement of the species with respect to enhanced characteristics, such as enriched nutritional quality, high yield, resistance to herbicides, diseases, viruses, and insects, and tolerance to drought, salt, and flooding. These improvements in tropical maize will ultimately enhance global food production and human health. Molecular approaches to modulate drought stress tolerance are discussed for sub-Saharan Africa, but widely applicable to other tropical genotypes in Central and Latin America. This review highlights abiotic constraints that affect growth, development and production of tropical maize and subsequently focuses on the mechanisms that regulate drought stress tolerance in maize. Biotechnological approaches to manage abiotic stress tolerance in maize will be discussed. The current status of tropical maize transformation using Agrobacterium as a vehicle for DNA transfer is emphasized. This review also addresses the present status of genetically modified organisms (GMOs) regulation in sub-Saharan Africa.     

microRNA在玉米生长发育及非生物胁迫响应中的调控功能

microRNA（miRNA）是一类广泛存在于真核生物中长度为20~24 nt的内源非编码小RNA，它们通过对靶基因mRNA进行切割或翻译抑制，在转录后水平调控靶基因的表达。近期研究表明，miRNA参与植物生长发育与逆境胁迫响应的多个重要生物学过程，对作物的农艺性状也起到重要的调控作用。玉米作为重要的粮食、饲料和工业原料，提高其产量和品质对于保障世界粮食安全至关重要，然而与模式植物拟南芥和水稻相比，玉米中miRNA的研究仍然相对较少，理解miRNA在玉米中的功能和调控机理有助于通过分子育种对关键农艺性状进行遗传改良。本文综述了玉米中miRNA的发现与鉴定，系统总结了参与玉米miRNA代谢途径的关键蛋白DCL、AGO和HEN1的研究进展，重点阐述了在玉米生长发育和非生物胁迫响应过程中已开展功能研究miRNA的调控作用，并对玉米miRNA研究当前存在的问题和未来的发展趋势进行了讨论。     

Landraces of maize in Central Mexico: an altitudinal transect

Conservation of crop genetic resources is now considered an important component of sustainable agricultural development. If conservation of genetic resources for agriculture is to be successful, a more complete understanding of the dynamics affecting traditional (landrace) crop populations is needed. We conducted a study of maize-based agriculture in the Central Highlands of Mexico in communities at 2400, 1700, 1400, and 1200 masl to assess the status of traditional varieties in an area characterized by thorough integration into the national economy. Our research contradicts the view that modern varieties persist because of marginal conditions, deficient infrastructure, weaker markets, or traditional attitudes. One or two landraces dominated highland maize populations and farmers appeared to be more conservative in terms of their emphasis on traditional maize varieties than at lower elevations. The dominance of traditional varieties in the highlands is well known but poorly explained, and the coexistence of traditional and modern varieties in the mid-elevations was unexpected. Our highland study area has good roads, is near Mexico City, and is less than 50 km away from four major crop research institutes that have done maize breeding since 1950’s. We suggest that in situ conservation of maize genetic resources in the highlands is sustained because the landraces there have good agronomic performance and are highly valued by farmers for their end-use qualities. At the mid-elevations, competition between local and modern maize was sharpest, and farmers have found that both landraces and improved varieties suit their needs, hence enhancing genetic diversity. Interventions and incentives would appropriately be carried out here to assure in situ conservation of locally adapted landraces of maize.     

Transmission of important chromosomal regions under selection revealed in rice pedigree breeding programs

Genetic analysis across a whole plant genome based on pedigree information offers considerable potential for enhancing genetic gain from plant breeding programs through quantitative trait loci (QTL) mapping and marker-assisted selection. Here, we report its application for graphically genotyping varieties used in Chinese japonica rice (Oryza sativa L.) pedigree breeding programs. We identified 34 important chromosomal regions from the founder parent that are under selection in the breeding programs, and by comparing donor genomic regions that are under selection with QTL locations of agronomic traits, we found that QTL clustered in important genomic regions, in accordance with association analyses of natural populations and other previous studies. The convergence of genomic regions under selection with QTL locations suggests that donor genomic regions harboring key genes/QTL for important agronomic traits have been selected by plant breeders since the 1950s from the founder rice plants. The results provide better understanding of the effects of selection in breeding programs on the traits of rice cultivars. They also provide potentially valuable information for enhancing rice breeding programs through screening candidate parents for targeted molecular markers, improving crop yield potential and identifying suitable genetic material for use in future breeding programs.     

A global barley panel revealing genomic signatures of breeding in modern Australian cultivars

The future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Today’s gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact that breeding had on the genetic diversity of Hordeum vulgare (barley) released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined data set and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.     

Transgenic Populus Trees for Forest Products,Bioenergy, and Functional Genomics

Species within the genus Populus are among the fastest growing trees in regions with a temperate climate. Not only are they an integral component of ecosystems, but they are also grown commercially for fuel, fiber, and forest products in rural areas of the world. In the late 1970s, they were designated as a bioenergy crop by the U.S. Department of Energy, as a result of research following the oil embargo. Populus species also serve as model trees for plant molecular biology research. In this article, we will review recent progress in the genetic improvement of Populus, considering both classical breeding and genetic engineering for bioenergy, as well as in using transgenics to elucidate gene functionality. A perspective for future improvement of Populus via functional genomics will also be presented.     

Cell Wall Composition and Bioenergy Potential of Rice Straw Tissues Are Influenced by Environment,Tissue Type,and Genotype

Breeding has transformed wild plant species into modern crops, increasing the allocation of their photosynthetic assimilate into grain, fiber, and other products for human use. Despite progress in increasing the harvest index, much of the biomass of crop plants is not utilized. Potential uses for the large amounts of agricultural residues that accumulate are animal fodder or bioenergy, though these may not be economically viable without additional efforts such as targeted breeding or improved processing. We characterized leaf and stem tissue from a diverse set of rice genotypes (varieties) grown in two environments (greenhouse and field) and report bioenergy-related traits across these variables. Among the 16 traits measured, cellulose, hemicelluloses, lignin, ash, total glucose, and glucose yield changed across environments, irrespective of the genotypes. Stem and leaf tissue composition differed for most traits, consistent with their unique functional contributions and suggesting that they are under separate genetic control. Plant variety had the least influence on the measured traits. High glucose yield was associated with high total glucose and hemicelluloses, but low lignin and ash content. Bioenergy yield of greenhouse-grown biomass was higher than field-grown biomass, suggesting that greenhouse studies overestimate bioenergy potential. Nevertheless, glucose yield in the greenhouse predicts glucose yield in the field (ρ?=?0.85, p?<?0.01) and could be used to optimize greenhouse (GH) and field breeding trials. Overall, efforts to improve cell wall composition for bioenergy require consideration of production environment, tissue type, and variety.     

Research Progress and Application of Plant Branching

Plant branching development plays an important role in plant morphogenesis (aboveground plant type), the number and angle of branches are important agronomic characters that determine crop plant type. Effective branches determine the number of panicles or pods of crops and then control the yield of crops. With the rapid development of plant genomics and molecular genetics, great progress has been made in the study of branching development. In recent years, a series of important branching-related genes have been validated from Arabidopsis thaliana, rice, pea, tomato and maize mutants. It is reviewed that plant branching development is controlled by genetic elements and plant hormones, such as auxin, cytokinin and lactones (or lactone derivatives), as well as by environment and genetic elements. Meanwhile, shoot architecture in crop breeding was discussed in order to provide theoretical basis for the study of crop branching regulation.