Towards molecular breeding of reproductive traits in cereal crops

The transition from vegetative to reproductive phase, flowering per se , floral organ development, panicle structure and morphology, meiosis, pollination and fertilization, cytoplasmic male sterility (CMS) and fertility restoration, and grain development are the main reproductive traits. Unlocking their genetic insights will enable plant breeders to manipulate these traits in cereal germplasm enhancement. Multiple genes or quantitative trait loci (QTLs) affecting flowering (phase transition, photoperiod and vernalization, flowering per se ), panicle morphology and grain development have been cloned, and gene expression research has provided new information about the nature of complex genetic networks involved in the expression of these traits. Molecular biology is also facilitating the identification of diverse CMS sources in hybrid breeding. Few Rf (fertility restorer) genes have been cloned in maize, rice and sorghum. DNA markers are now used to assess the genetic purity of hybrids and their parental lines, and to pyramid Rf or tms (thermosensitive male sterility) genes in rice. Transgene(s) can be used to create de novo CMS trait in cereals. The understanding of reproductive biology facilitated by functional genomics will allow a better manipulation of genes by crop breeders and their potential use across species through genetic transformation.     

Combining population genomics and quantitative genetics: finding the genes underlying ecologically important traits

A central challenge in evolutionary biology is to identify genes underlying ecologically important traits and describe the fitness consequences of naturally occurring variation at these loci. To address this goal, several novel approaches have been developed, including 'population genomics,' where a large number of molecular markers are scored in individuals from different environments with the goal of identifying markers showing unusual patterns of variation, potentially due to selection at linked sites. Such approaches are appealing because of (1) the increasing ease of generating large numbers of genetic markers, (2) the ability to scan the genome without measuring phenotypes and (3) the simplicity of sampling individuals without knowledge of their breeding history. Although such approaches are inherently applicable to non-model systems, to date these studies have been limited in their ability to uncover functionally relevant genes. By contrast, quantitative genetics has a rich history, and more recently, quantitative trait locus (QTL) mapping has had some success in identifying genes underlying ecologically relevant variation even in novel systems. QTL mapping, however, requires (1) genetic markers that specifically differentiate parental forms, (2) a focus on a particular measurable phenotype and (3) controlled breeding and maintenance of large numbers of progeny. Here we present current advances and suggest future directions that take advantage of population genomics and quantitative genetic approaches - in both model and non-model systems. Specifically, we discuss advantages and limitations of each method and argue that a combination of the two provides a powerful approach to uncovering the molecular mechanisms responsible for adaptation.     

From plant genomics to breeding practice

New alleles are constantly accumulated during intentional crop selection. The molecular understanding of these alleles has stimulated new genomic approaches to mapping quantitative trait loci (QTL) and haplotype multiplicity of the genes concerned. A limited number of quantitative trait nucleotides responsible for QTL variation have been described, but an acceleration in their rate of discovery is expected with the adoption of linkage disequilibrium and candidate gene strategies for QTL fine mapping and cloning. Additional layers of regulatory variation have been studied that could also contribute to the molecular basis of quantitative genetics of crop traits. Despite this progress, the role of marker-assisted selection in plant breeding will ultimately depend on the genetic model underlying quantitative variation.     

Recent progression and future perspectives in cotton genomic breeding

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content.Progress in cotton genomics promotes the advancement of cotton genetics,evolutionary studies,functional genetics,and breeding,and has ushered cotton research and breeding into a new era.Here,we summarize high-impact genomics studies for cotton from the last 10 years.The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studi...     

Converging phenomics and genomics to study natural variation in plant photosynthetic efficiency

In recent years developments in plant phenomic approaches and facilities have gradually caught up with genomic approaches. An opportunity lies ahead to dissect complex, quantitative traits when both genotype and phenotype can be assessed at a high level of detail. This is especially true for the study of natural variation in photosynthetic efficiency, for which forward genetics studies have yielded only a little progress in our understanding of the genetic layout of the trait. High‐throughput phenotyping, primarily from chlorophyll fluorescence imaging, should help to dissect the genetics of photosynthesis at the different levels of both plant physiology and development. Specific emphasis should be directed towards understanding the acclimation of the photosynthetic machinery in fluctuating environments, which may be crucial for the identification of genetic variation for relevant traits in food crops. Facilities should preferably be designed to accommodate phenotyping of photosynthesis‐related traits in such environments. The use of forward genetics to study the genetic architecture of photosynthesis is likely to lead to the discovery of novel traits and/or genes that may be targeted in breeding or bio‐engineering approaches to improve crop photosynthetic efficiency. In the near future, big data approaches will play a pivotal role in data processing and streamlining the phenotype‐to‐gene identification pipeline.     

European plant science: a field of opportunities

Plants have a pivotal role in eco- and agricultural systems.Genomics is driving a rapid expansion of our understanding ofhow genes, individually and in networks, determine plant function.Technological developments in breeding and genomics are providingstrategies to translate this knowledge into crop improvement.The possibilities range from improvement of existing crops andthe systematic use of natural diversity through to the domesticationof completely new species. As examples of possible goals, itis discussed how profiling of composition will integrate plantbreeding and agronomic practice with emerging knowledge aboutnutrition and health, how improved and novel crops will contributeto the creation of new bio-based economies revolving aroundplant products, and how advances in our knowledge about plant–environmentand plant–pathogen interactions will provide novel strategiesto stabilize agricultural yield in a fluctuating environmentand contribute to integrated approaches in which modern agricultureis carried out in concert with the environment. In addition,knowledge generated by plant science will be needed to monitor,understand, and cope with climate change and its impact on agricultureand ecosystems. Realization of these goals will require closeinteractions with related disciplines including agronomy andecology. Further, it will be important to continue and deepenopen support for research in the developing world. Key words: Agronomic practice, biodiversity, domestication, ecosystems, environment, genomics, novel crops, plant breeding, plant products, yield     

Seed traits and genes important for translational biology--highlights from recent discoveries

Seeds provide food, feed, fiber and fuel. They are also an important delivery system of genetic information, which is essential for the survival of wild species in ecosystems and the production of agricultural crops. In this review, seed traits and genes that are potentially important for agricultural applications are discussed. Over the long period of crop domestication, seed traits have been modified through intentional or unintentional selections. While most selections have led to seed traits favorable for agricultural consumption, such as larger seeds with higher nutritional value than the wild type, other manipulations in modern breeding sometimes led to negative traits, such as vivipary, precocious germination on the maternal plant or reduced seed vigor, as a side effect during the improvement of other characteristics. Greater effort is needed to overcome these problems that have emerged as a consequence of crop improvement. Seed biology researchers have characterized the function of many genes in the last decade, including those associated with seed domestication, which may be useful in addressing critical issues in modern agriculture, such as the prevention of vivipary and seed shattering or the enhancement of yields. Recent discoveries in seed biology research are highlighted in this review, with an emphasis on their potential for translational biology.     

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.     

高等植物基因组测序回顾与展望

全基因组序列测定为揭示植物重要性状形成的分子和遗传机制提供了强大工具,基因组学研究正开始指引着农作物新品种培育向定向化和精确化转变.在新一代测序技术的带动下,植物全基因组测序的热潮已经到来.对迄今开展的高等植物基因组测序工作进行简要回顾,并对未来的研究热点进行展望.     

From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants

The dissection of gene-trait associations and its translation into practice through plant breeding is a central aspect of modern plant biology. The identification of genes underlying simply inherited traits has been very successful. However, the identification of gene-trait associations for complex (multi-genic) traits in crop plants with large, often polyploid genomes has been limited by the absence of appropriate genetic resources that allow quantitative trait loci (QTL) and causal genes to be identified and localised. There has also been a tendency for genetic resources to be developed in germplasm not directly relevant to the breeding community limiting effective implementation. In this review, we discuss approaches to mapping genes and the development of Multi-parent Advanced Generation Inter-cross (MAGIC) populations derived from breeder-relevant germplasm as a platform for a new generation of gene-trait analysis in crop species.     

Linking plant genes to insect communities: Identifying the genetic bases of plant traits and community composition

Community genetics aims to understand the effects of intraspecific genetic variation on community composition and diversity, thereby connecting community ecology with evolutionary biology. Thus far, research has shown that plant genetics can underlie variation in the composition of associated communities (e.g., insects, lichen and endophytes), and those communities can therefore be considered as extended phenotypes. This work, however, has been conducted primarily at the plant genotype level and has not identified the key underlying genes. To address this gap, we used genome‐wide association mapping with a population of 445 aspen (Populus tremuloides) genets to identify the genes governing variation in plant traits (defence chemistry, bud phenology, leaf morphology, growth) and insect community composition. We found 49 significant SNP associations in 13 Populus genes that are correlated with chemical defence compounds and insect community traits. Most notably, we identified an early nodulin‐like protein that was associated with insect community diversity and the abundance of interacting foundation species (ants and aphids). These findings support the concept that particular plant traits are the mechanistic link between plant genes and the composition of associated insect communities. In putting the “genes” into “genes to ecosystems ecology”, this work enhances understanding of the molecular genetic mechanisms that underlie plant–insect associations and the consequences thereof for the structure of ecological communities.     

Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana

A major challenge in evolutionary biology and plant breeding is to identify the genetic basis of complex quantitative traits, including those that contribute to adaptive variation. Here we review the development of new methods and resources to fine-map intraspecific genetic variation that underlies natural phenotypic variation in plants. In particular, the analysis of 107 quantitative traits reported in the first genome-wide association mapping study in Arabidopsis thaliana sets the stage for an exciting time in our understanding of plant adaptation. We also argue for the need to place phenotype-genotype association studies in an ecological context if one is to predict the evolutionary trajectories of plant species.     

Exploring Complex Ornamental Genomes: The Rose as a Model Plant

Despite its high economic importance, little is known about rose genetics, genome structure, and the function of rose genes. Reasons for this lack of information are polyploidy in most cultivars, simple breeding strategies, high turnover rates for cultivars, and little public funding. Molecular and biotechnological tools developed during the genomics era now provide the means to fill this gap. This will be facilitated by a number of model traits as e.g., a small genome, a large genetic diversity including diploid genotypes, a comparatively short generation time and protocols for genetic engineering. A deeper understanding of genetic processes and the structure of the rose genome will serve several purposes: Applications to the breeding process including marker-assisted selection and direct manipulation of relevant traits via genetic engineering will lead to improved cultivars with new combinations of characters. In basic research, unique characters, e.g., the biosynthesis and emission of particular secondary metabolites will provide new information not available in model species. Furthermore comparative genomics will link information about the rose genome to ongoing projects on other rosaceous crops and will add to our knowledge about genome evolution and speciation. This review is intended as a presentation and is the compilation of the current knowledge on rose genetics and genomics, including functional genomics and genetic engineering. Furthermore, it is intended to show ways how knowledge on rose genetics and genomics can be linked to other species in the Rosaceae in order to utilize this information across genera.     

Genome-wide identification and analysis of rice genes to elucidate morphological agronomic traits

Molecular understanding of morphological agronomic traits is very important to improve grain yield and quality. According to the literature information summarized in Overview of Functionally Characterized Genes in Rice online database, 430 genes related to these traits have been functionally characterized in rice, while the functions of other genes remain to be elucidated. Gene indexed mutants are available for at least half of the genes identified in the rice genome, and are very useful resources to study gene function. To suggest candidate genes for functional studies associated with morphological agronomic traits, we identified genes with tissue/organ-preferred expression patterns through meta-analysis of microarray data, and identified 781 genes for roots, 1,084 for leaves, 1,029 for calluses, 927 for anthers, 241 for embryos, and 343 for endosperms. Additionally, 4,243 genes expressed in all tissue types were allocated to a ubiquitously-expressed gene group (‘housekeeping’ genes). The estimated tissue/organ-preferred and housekeeping genes accounted for 40% of the characterized genes associated with morphological agronomic traits, indicating that identification of tissue/organ-preferred genes is an effective way to provide putative gene function. In this study, we reported the information of gene-indexed mutants for 84% of the identified candidate genes. Our candidate genes and relating indexed mutant resources can potentially be used to improve morphological agronomic traits in rice.