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Showing papers on "Molecular breeding published in 2015"


Journal ArticleDOI
TL;DR: The present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.
Abstract: Climate change affects agricultural productivity worldwide. Increased prices of food commodities are the initial indication of drastic edible yield loss, which is expected to increase further due to global warming. This situation has compelled plant scientists to develop climate change-resilient crops, which can withstand broad-spectrum stresses such as drought, heat, cold, salinity, flood, submergence and pests, thus helping to deliver increased productivity. Genomics appears to be a promising tool for deciphering the stress responsiveness of crop species with adaptation traits or in wild relatives toward identifying underlying genes, alleles or quantitative trait loci. Molecular breeding approaches have proven helpful in enhancing the stress adaptation of crop plants, and recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding (GAB). In view of this, the present review elaborates the progress and prospects of GAB for improving climate change resilience in crops, which is likely to play an ever increasing role in the effort to ensure global food security.

231 citations


Journal ArticleDOI
TL;DR: This review provides an overview of the latest developments in root phenotyping and describes the environmental and genetic factors influencing root phenotype and heritability and intends to give direction to future phenotypesing and breeding strategies for optimizing root system functioning.
Abstract: In the last decade cheaper and faster sequencing methods have resulted in an enormous increase in genomic data. High throughput genotyping, genotyping by sequencing and genomic breeding are becoming a standard in plant breeding. As a result, the collection of phenotypic data is increasingly becoming a limiting factor in plant breeding. Genetic studies on root traits are being hampered by the complexity of these traits and the inaccessibility of the rhizosphere. With an increasing interest in phenotyping, breeders and scientists try to overcome these limitations, resulting in impressive developments in automated phenotyping platforms. Recently, many such platforms have been thoroughly described, yet their efficiency to increase genetic gain often remains undiscussed. This efficiency depends on the heritability of the phenotyped traits as well as the correlation of these traits with agronomically relevant breeding targets. This review provides an overview of the latest developments in root phenotyping and describes the environmental and genetic factors influencing root phenotype and heritability. It also intends to give direction to future phenotyping and breeding strategies for optimizing root system functioning. A quantitative framework to determine the efficiency of phenotyping platforms for genetic gain is described. By increasing heritability, managing effects caused by interactions between genotype and environment and by quantifying the genetic relation between traits phenotyped in platforms and ultimate breeding targets, phenotyping platforms can be utilized to their maximum potential.

147 citations


Book ChapterDOI
26 Oct 2015

127 citations


Journal ArticleDOI
TL;DR: This review includes examples of how advanced molecular method have been used in breeding programs for improving blast resistance, allowing rapid introgression of disease resistance genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more durable blast resistance.
Abstract: Rice is a staple and most important security food crop consumed by almost half of the world's population. More rice production is needed due to the rapid population growth in the world. Rice blast caused by the fungus, Magnaporthe oryzae is one of the most destructive diseases of this crop in different part of the world. Breakdown of blast resistance is the major cause of yield instability in several rice growing areas. There is a need to develop strategies providing long-lasting disease resistance against a broad spectrum of pathogens, giving protection for a long time over a broad geographic area, promising for sustainable rice production in the future. So far, molecular breeding approaches involving DNA markers, such as QTL mapping, marker-aided selection, gene pyramiding, allele mining and genetic transformation have been used to develop new resistant rice cultivars. Such techniques now are used as a low-cost, high-throughput alternative to conventional methods allowing rapid introgression of disease resistance genes into susceptible varieties as well as the incorporation of multiple genes into individual lines for more durable blast resistance. The paper briefly reviewed the progress of studies on this aspect to provide the interest information for rice disease resistance breeding. This review includes examples of how advanced molecular method have been used in breeding programs for improving blast resistance. New information and knowledge gained from previous research on the recent strategy and challenges towards improvement of blast disease such as pyramiding disease resistance gene for creating new rice varieties with high resistance against multiple diseases will undoubtedly provide new insights into the rice disease control.

124 citations


Journal ArticleDOI
TL;DR: The design and validation of a unique genic-SNP genotyping chip for genetic and evolutionary studies as well as molecular breeding applications in rice showed high success rate and reproducibility and its efficacy was validated for analysing background recovery in improved mega rice varieties with submergence tolerance developed through marker-assisted backcross breeding.
Abstract: Single nucleotide polymorphism (SNP) is the most abundant DNA sequence variation present in plant genomes. Here, we report the design and validation of a unique genic-SNP genotyping chip for genetic and evolutionary studies as well as molecular breeding applications in rice. The chip incorporates 50,051 SNPs from 18,980 different genes spanning 12 rice chromosomes, including 3,710 single-copy (SC) genes conserved between wheat and rice, 14,959 SC genes unique to rice, 194 agronomically important cloned rice genes and 117 multi-copy rice genes. Assays with this chip showed high success rate and reproducibility because of the SC gene based array with no sequence redundancy and cross-hybridisation problems. The usefulness of the chip in genetic diversity and phylogenetic studies of cultivated and wild rice germplasm was demonstrated. Furthermore, its efficacy was validated for analysing background recovery in improved mega rice varieties with submergence tolerance developed through marker-assisted backcross breeding.

116 citations


Journal ArticleDOI
TL;DR: Dongxiang wild rice is phylogenetically close totemperate japonica and contains multiple cold resistance loci conferring its adaptation to high-latitude habitat, and is most closely related to cold-tolerant Japonica rice rather than to the Indica cultivars that are predominant in the habitat where DXWR grows.
Abstract: Dongxiang wild rice is phylogenetically close to temperate japonica and contains multiple cold resistance loci conferring its adaptation to high-latitude habitat. Understanding the nature of adaptation in wild populations will benefit crop breeding in the development of climate-resilient crop varieties. Dongxiang wild rice (DXWR), the northernmost common wild rice known, possesses a high degree of cold tolerance and can survive overwintering in its native habitat. However, to date, it is still unclear how DXWR evolved to cope with low-temperature environment, resulting in limited application of DXWR in rice breeding programs. In this study, we carried out both QTL mapping and phylogenetic analysis to discern the genetic mechanism underlying the strong cold resistance. Through a combination of interval mapping and single locus analysis in two genetic populations, at least 13 QTLs for seedling cold tolerance were identified in DXWR. A phylogenetic study using both genome-wide InDel markers and markers associated with cold tolerance loci reveals that DXWR belongs to the Or-III group, which is most closely related to cold-tolerant Japonica rice rather than to the Indica cultivars that are predominant in the habitat where DXWR grows. Our study paves the way toward an understanding of the nature of adaptation to a northern habitat in O. rufipogon. The QTLs identified in DXWR in this study will be useful for molecular breeding of cold-tolerant rice.

82 citations


BookDOI
01 Jan 2015
TL;DR: Through case studies from the Pampa Biome, the valorization of plant genetic resources through new domestication, the promotion of the use of scientifi cally developed best management practices for in situ conservation, the widening of the germplasm base for breeding programs, plant breeding for stress tolerance, the development of participatory plant breeding programs and theDevelopment of high quality products are discussed.
Abstract: The domestication of plants, as a bio-cultural process, is a continuous phenomenon intrinsically associated with the use of plants. Traditional and scientifi c knowledge constitute the basis of the various uses of plants from in situ harvesting to complete domestication of crops. One of the most important challenges of our time is to achieve the conservation and sustainable use of plant genetic resources of landraces, species in the process of domestication and species used in situ. The in situ conservation of agricultural biodiversity is a basic element for the development of more sustainable agroecosystems, the adaptation to climate change, the conservation of ecosystem services and to ensure local food security—a conception that is strongly linked to the local development and the protection of cultural and biological diversity. Through case studies from the Pampa Biome we will discuss the valorization of plant genetic resources through new domestication, the promotion of the use of scientifi cally developed best management practices for in situ conservation, the widening of the germplasm base for breeding programs, plant breeding for stress tolerance, the development of participatory plant breeding programs and the development of high quality products.

76 citations


Journal ArticleDOI
TL;DR: A review of marker-assisted breeding from a historical perspective, the road from crop sequencing to breeding, and how sequencing facilitates the application of markers in breeding practice are described.
Abstract: Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding. The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.

72 citations


Journal ArticleDOI
TL;DR: Genetic maps and markers have contributed to potato breeding, and genome information further elucidates questions in potato evolution and supports comprehensive potato breeding.
Abstract: Potato has a variety of reproductive uniquenesses besides its clonal propagation by tubers. These traits are controlled by a different kind of genetic control. The reproductive information has been applied to enable interspecific hybridization to enhance valuable traits, such as disease and pest resistances, from the tuber-bearing Solanum gene pool. While progress has been made in potato breeding, many resources have been invested due to the requirements of large populations and long time frame. This is not only due to the general pitfalls in plant breeding, but also due to the complexity of polyploid genetics. Tetraploid genetics is the most prominent aspect associated with potato breeding. Genetic maps and markers have contributed to potato breeding, and genome information further elucidates questions in potato evolution and supports comprehensive potato breeding. Challenges yet remain on recognizing intellectual property rights to breeding and germplasm, and also on regulatory aspects to incorporate modern biotechnology for increasing genetic variation in potato breeding.

62 citations


Journal ArticleDOI
TL;DR: The current understanding of the potential roles of environmental stress, ROS, and aflatoxin in the interaction between Aspergillus flavus and its host plants are reviewed, and the current status in molecular breeding and marker discovery for resistance to A. flavus colonization and a flatoxin contamination in maize and peanut is reviewed.
Abstract: The colonization of maize (Zea mays L.) and peanut (Arachis hypogaea L.) by the fungal pathogen Aspergillus flavus results in the contamination of kernels with carcinogenic mycotoxins known as aflatoxins leading to economic losses and potential health threats to humans. The regulation of aflatoxin biosynthesis in various Aspergillus spp. has been extensively studied, and has been shown to be related to oxidative stress responses. Given that environmental stresses such as drought and heat stress result in the accumulation of reactive oxygen species (ROS) within host plant tissues, host-derived ROS may play an important role in cross-kingdom communication between host plants and A. flavus. Recent technological advances in plant breeding have provided the tools necessary to study and apply knowledge derived from metabolomic, proteomic, and transcriptomic studies in the context of productive breeding populations. Here, we review the current understanding of the potential roles of environmental stress, ROS, and aflatoxin in the interaction between A. flavus and its host plants, and the current status in molecular breeding and marker discovery for resistance to A. flavus colonization and aflatoxin contamination in maize and peanut. We will also propose future directions and a working model for continuing research efforts linking environmental stress tolerance and aflatoxin contamination resistance in maize and peanut.

59 citations



Journal ArticleDOI
TL;DR: Progress on identifying and verifying QTLs for such traits as growth, disease and stress resistance and sex in recent decades is summarized and the potential applications in marker-assisted selection and molecular breeding are discussed.
Abstract: The traits of cultured fish must continually be genetically improved to supply high-quality animal protein for human consumption. Economically important fish traits are controlled by multiple gene quantitative trait loci (QTL), most of which have minor effects, but a few genes may have major effects useful for molecular breeding. In this review, we chose relevant studies on some of the most intensively cultured fish and concisely summarize progress on identifying and verifying QTLs for such traits as growth, disease and stress resistance and sex in recent decades. The potential applications of these major-effect genes and their associated markers in marker-assisted selection and molecular breeding, as well as future research directions are also discussed. These genetic and genomic analyses will be valuable for elucidating the mechanisms modulating economically important traits and to establish more effective molecular breeding techniques in fish.

Journal ArticleDOI
TL;DR: A glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny is presented to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches to enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.
Abstract: Medicinal plants have long been utilized in traditional medicine and ethnomedicine worldwide. This review presents a glimpse of the current status of and future trends in medicinal plant genomics, evolution, and phylogeny. These dynamic fields are at the intersection of phytochemistry and plant biology and are concerned with the evolution mechanisms and systematics of medicinal plant genomes, origin and evolution of the plant genotype and metabolic phenotype, interaction between medicinal plant genomes and their environment, the correlation between genomic diversity and metabolite diversity, and so on. Use of the emerging high-end genomic technologies can be expanded from crop plants to traditional medicinal plants, in order to expedite medicinal plant breeding and transform them into living factories of medicinal compounds. The utility of molecular phylogeny and phylogenomics in predicting chemodiversity and bioprospecting is also highlighted within the context of natural-product-based drug discovery and development. Representative case studies of medicinal plant genome, phylogeny, and evolution are summarized to exemplify the expansion of knowledge pedigree and the paradigm shift to the omics-based approaches, which update our awareness about plant genome evolution and enable the molecular breeding of medicinal plants and the sustainable utilization of plant pharmaceutical resources.

Journal ArticleDOI
TL;DR: Role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops.
Abstract: Salinity is one of the important abiotic factors for any crop management in irrigated as well as rainfed areas, which leads to poor harvests. This yield reduction in salt affected soils can be overcome by improving salt tolerance in crops or by soil reclamation. Salty soils can be reclaimed by leaching the salt or by cultivation of salt tolerance crops. Salt tolerance is a quantitative trait controlled by several genes. Poor knowledge about mechanism of its inheritance makes slow progress in its introgression into target crops. Brassica is known to be a good reclamation crop. Inter and intra specific variation within Brassica species shows potential of molecular breeding to raise salinity tolerant genotypes. Among the various molecular markers, SSR markers are getting high attention, since they are randomly sparsed, highly variable and show co-dominant inheritance. Furthermore, as sequencing techniques are improving and softwares to find SSR markers are being developed, SSR markers technology is also evolving rapidly. Comparative SSR marker studies targeting Arabidopsis thaliana and Brassica species which lie in the same family will further aid in studying the salt tolerance related QTLs and subsequent identification of the “candidate genes” and finding out the origin of important QTLs. Although, there are a few reports on molecular breeding for improving salt tolerance using molecular markers in Brassica species, usage of SSR markers has a big potential to improve salt tolerance in Brassica crops. In order to obtain best harvests, role of SSR marker driven breeding approaches play important role and it has been discussed in this review especially for the introgression of salt tolerance traits in crops.


Journal ArticleDOI
TL;DR: This manuscript focuses on the study of abiotic stress, in particular drought, salinity and low temperature, during this century, and focuses on studies that investigate confer of stress tolerance and the identification of responsible factors, including wild relatives.
Abstract: Global warming has become a major issue within the last decade. Traditional breeding programs for potato have focused on increasing productivity and quality and disease resistance, thus, modern cultivars have limited tolerance of abiotic stresses. The introgression of abiotic stress tolerance into modern cultivars is essential work for the future. Recently, many studies have investigated abiotic stress using transgenic techniques. This manuscript focuses on the study of abiotic stress, in particular drought, salinity and low temperature, during this century. Dividing studies into these three stress categories for this review was difficult. Thus, based on the study title and the transgene property, transgenic studies were classified into five categories in this review; oxidative scavengers, transcriptional factors, and above three abiotic categories. The review focuses on studies that investigate confer of stress tolerance and the identification of responsible factors, including wild relatives. From a practical application perspective, further evaluation of transgenic potato with abiotic stress tolerance is required. Although potato plants, including wild species, have a large potential for abiotic stress tolerance, exploration of the factors responsible for conferring this tolerance is still developing. Molecular breeding, including genetic engineering and conventional breeding using DNA markers, is expected to develop in the future.

Journal ArticleDOI
Kang Xu1, Wei Duan1, Jun Xiao1, Min Tao1, Chun Zhang1, Yun Liu1, Shaojun Liu1 
TL;DR: This review discusses the progress the laboratory has made in the field of chromosomal ploidy breeding of fish, including distant hybridization, gynogenesis, and androgenesis and systematically summarizes the research status and known problems associated with each technology.
Abstract: Fish genetic breeding is a process that remolds heritable traits to obtain neotype and improved varieties. For the purpose of genetic improvement, researchers can select for desirable genetic traits, integrate a suite of traits from different donors, or alter the innate genetic traits of a species. These improved varieties have, in many cases, facilitated the development of the aquaculture industry by lowering costs and increasing both quality and yield. In this review, we present the pertinent literatures and summarize the biological bases and application of selection breeding technologies (containing traditional selective breeding, molecular marker-assisted breeding, genome-wide selective breeding and breeding by controlling single-sex groups), integration breeding technologies (containing cross breeding, nuclear transplantation, germline stem cells and germ cells transplantation, artificial gynogenesis, artificial androgenesis and polyploid breeding) and modification breeding technologies (represented by transgenic breeding) in fish genetic breeding. Additionally, we discuss the progress our laboratory has made in the field of chromosomal ploidy breeding of fish, including distant hybridization, gynogenesis, and androgenesis. Finally, we systematically summarize the research status and known problems associated with each technology.

Book
16 Sep 2015
TL;DR: Diversity, Intellectual Property and Plant Variety Protection Plant Genetic Resources The Question of Derivatives Multinational Private and Public Seed Sectors Managing Agro-biotechnology Intellectual Property Rights.
Abstract: Contents 1. Introduction to Plant Breeding Plant Breeding and Society Genetics, Omics and Plant Breeding Populations Genetic Diversity Distances Measures Grouping Germplasm Quantitative Variation Mapping Traits Genotype-by-Environment Interaction Phenotyping Phenomics References 2. Plant Genetic Resources for Food and Agriculture Crop Evolution and Plant Species Feeding the World Genebanks Gene Pools Describing Variation and Identifying Redundancy Germplasm Evaluation Descriptors Documentation and Bioinformatics Geo-documentation to Identify Germplasm Genebank Sampling and Core Subsets Genomics of Plant Genetic Resources Putting Genes into Usable Forms References 3. Inbred Development DNA markers for Mapping Quantitative Trait Loci (QTL) and Aided Breeding Inbreeding and Line Development Doubled Haploids Adaptability: Learning for Model Plant Systems Breeding for Stress-prone Environments and Resource-use Efficiency Host-plant Resistance Breeding Participatory and Client-driven Plant Breeding References 4. Population Improvement Recurrent Selection and Breeding Populations Genome-wide Association and Quantitative Trait Variation Plant Genomics and Marker-assisted Selection Genomic Selection and Prediction of Breeding Values References 5. Heterosis and Inter-Specific Hybridization Heterotic Groups Hybrid Vigor Heterosis in Plant Breeding Understanding Hybrid Vigor in Model Plants and Crops Omics Research on Heterosis Hybrids in Selfing Species Polyploid Heterosis Interspecific hybridization References 6. Mutations and Epigenetics Induced Mutations and Plant Breeding Induced Mutations and Genomics-led Plant Breeding Targeting Induced Local Lesions IN Genomes (TILLING) Epigenetics References 7. Genetic Engineering and Transgenic Breeding Plant Genetic Engineering "Issues" Transgenic Crops "Risks" Transgene Flow Pest Resistance and Impacts on Non-target Organisms Detecting Genetically Modified Organisms and Other Safety Assessments Transgenic Agriculture and Co-existence Plant Genetic Engineering Impacts Transgenic Agriculture Outlook New Plant Breeding Techniques References 8. DNA Sequencing, other Omics and Synthetic Biology DNA Sequencing Next Generation Sequencing Genotyping-by-Sequencing Other Relevant Omics for Plant Breeding Breeding Informatics Case Study: Omics-led Legume Breeding Pl ant Synthetic Biology: Another Tool for Plant Breeding? References 9. Breeding Self-fertilizing Plants: From Inbred to Hybrid Cultivars Rice Domestication Genetic Enhancement Genomics Marker-aided Selection (MAS) Stress Breeding Interspecific Hybridization and Participatory Breeding Hybrid Cultivars Phenotyping Genetic Engineering Wheat Evolution and Diversity Germplasm Enhancement Resynthesizing Wheat Shuttle Breeding and Mega-environments Grain Yield Potential Perennial Wheat Biotechnology Ex ante and in silico Breeding Tomato References 10. Breeding Open Pollinated, Hybrid and Transgenic Outcrossing Species Maize Domestication and Diversity Germplasm Enhancement Breeding Inbred Line Development and Hybrids Doubled Haploids Genomics-led Improvement for Enhancing Genetic Gains Developing Stress-resilient Germplasm Nutritious Maize Prediction of Breeding Values Genetic Engineering Cotton Cassava Case Study: Cassava Breeding in sub-Saharan Africa References 11. Polyploidy and Plant Breeding Potato Origin, Diversity and Taxonomy Ploidy Manipulations Genetic Resources and Breeding True Potato Seed Genomics Genetic Engineering Banana/Plantain References 12. Seeds, Clones and Perennials Seed Development: Learning from a Model Plant System Inbred and Open Pollinated Seed Cultivars Hybrid Seed Rapid Multiplication of Healthy and Improved Planting Material of Vegetatively Propagated Crops Seed Health Apomixis: Procreation without Recreation Perennial Crops References 13. Diversity, Intellectual Property and Plant Variety Protection Plant Genetic Resources The Question of Derivatives Multinational Private and Public Seed Sectors Managing Agro-biotechnology Intellectual Property Rights References


Book ChapterDOI
01 Jan 2015
TL;DR: From a plant breeder’s point of view, this chapter addresses the general procedures, theoretical and practical considerations of MAB in plants, including marker-assisted selection (MAS), Marker-assisted backcrossing (MABC), marker- assisted gene pyramiding (MAGP), markers-assisted recurrent selection (MARS) and genomewide selection (GWS).
Abstract: A plant breeder faces the challenge of how to more effectively and efficiently perform selection and accelerate the breeding progress to satisfy the requirements of changing markets for crop cultivars. Molecular marker-assisted breeding (MAB), the application of molecular biotechnologies (DNA markers) to practical breeding and selection, is a novel strategy and a powerful methodology for plant improvement. It has significant advantages compared with conventional breeding methods. Since the 1990s MAB has received increasingly attention and has been extensively used in different crop species. From a plant breeder’s point of view, this chapter addresses the general procedures, theoretical and practical considerations of MAB in plants, including marker-assisted selection (MAS), marker-assisted backcrossing (MABC), marker-assisted gene pyramiding (MAGP), marker-assisted recurrent selection (MARS) and genomewide selection (GWS). Applications of individual MAB methods to practical breeding as well as widely used DNA markers are briefly reviewed, and the challenges and perspectives of MAB are discussed. As a new technology, MAB is not a replacement for but a valued supplement to conventional breeding. Integration of MAB into conventional breeding programs represents an optimistic strategy for future crop improvement.

Journal ArticleDOI
TL;DR: This study establishes an important platform for rice gene functional research and rice molecular breeding by genomic selection by establishing a comprehensive SNP and InDel sub-database for the Rice Functional Genomics-based Breeding (RFGB) Database.
Abstract: Rice is an important food crop worldwide. Genomic research on global germplasm has theoretical and practical significances in the mining of favorable alleles and on genome-based molecular breeding, which are related to Chinese and global food security. Through the 3000 (3K) Rice Genome Project, we collected single nucleotide polymorphism (SNP) and insertion and deletion (InDel) genomic variation data for the 2859 rice genomes, and establish a comprehensive SNP and InDel sub-database for the Rice Functional Genomics-based Breeding (RFGB) Database. This sub-database is a global resource containing a polymorphism information retrieval function, a genome browser visualization system and a data export system for specific genomic regions, along with other tools. This study establishes an important platform for rice gene functional research and rice molecular breeding by genomic selection.

Journal ArticleDOI
TL;DR: The most recent understanding of miR156 function in plants is reviewed, and the major impact the authors are now seeing from its application to crop germplasm improvement and its prospects for future use in plant molecular breeding are highlighted.
Abstract: The discovery of small RNAs in plants has opened a new field in the study of gene regulation, and its application in plant genetic engineering and crop improvement. Of small RNAs, plant microRNAs have been used to increase crop productivity and enhance other traits, such as crop quality and stress tolerance. MicroRNA156 (miR156) and its target SPL genes are highly conserved in the plant kingdom, and together they form an extensive gene regulatory network that controls various aspects of plant growth and development. These include strong impacts on crop yield and quality, flowering time, root development and nodulation, reproduction capacity, secondary metabolism, and plant stress. Here, we review the most recent understanding of miR156 function in plants, and highlight the major impact we are now seeing from its application to crop germplasm improvement and its prospects for future use in plant molecular breeding.

Journal ArticleDOI
TL;DR: The starch metabolism genes with high expression levels will be sequenced in a wheat germplasm set to develop single nucleotide polymorphism markers for improvement of yield- and starch-related traits through molecular breeding approaches.
Abstract: In agricultural crops, seed growth is important for high grain yield. Starch contributes about 50–80 % of the dry weight of seed, and its quality affects both processing and nutrition quality. Despite the wider importance of starch metabolism, the genes involved have not been given much attention or exploited for their use in molecular breeding. Therefore, it is of great interest to analyze the expression of genes involved in starch metabolism for improvement of starch-related traits through molecular breeding. In this study, a quantitative gene expression analysis of 25 starch metabolism genes was conducted in three bread wheat (Triticum aestivum) genotypes differing in yield- and starch-related traits at five seed developmental stages, i.e., 7, 14, 21, 28, and 35 days after anthesis. Their sequences were physically mapped to chromosomes using the wheat genome sequence data through in silico analysis. Their expression data showed dynamic variation during seed development in wheat genotypes. The 25 genes were divided into four groups depending on their expression patterns during seed development. For example, one group was characterized by a high level of expression at early and middle stages as exhibited by different isoforms of starch synthases, starch-branching enzymes, isoamylase, and transcription factors (TaRSR1 and SPA). The enzymes of these genes are key factors in starch biosynthesis. The starch metabolism genes with high expression levels will be sequenced in a wheat germplasm set to develop single nucleotide polymorphism markers for improvement of yield- and starch-related traits through molecular breeding approaches.

Journal ArticleDOI
TL;DR: It will be shown how network analysis can reinforced the discovery of candidate genes/loci more rapidly and with higher confidence as modern agriculture confronts the challenging times ahead, with the increase of abiotic stresses for crops as drought, heat, soil high salinity or waterlogging.

Journal ArticleDOI
TL;DR: Genetic diversity analysis using SSR data was more consistent with pedigrees compared to analysis with SNP data indicating that more than 384 SNPs are required when elite indica breeding material is used and that SSRs could still be used to complement fixed-SNP genotyping platforms for some molecular breeding applications.
Abstract: Simple sequence repeats (SSRs) have been the marker of choice for rice molecular breeding due to the high level of polymorphism, technical simplicity and low cost. Recent advances in rice genomics have led to the discovery of abundant single nucleotide polymorphism (SNPs) which have enormous potential for rice molecular breeding. To assess both marker systems for molecular breeding in rice, SSR and SNP markers were evaluated on a set of 23 genotypes representing indica germplasm for their usefulness in molecular research and breeding program. Seven hundred SSR and sequence tagged sites (STS) markers and 384 SNPs were screened for polymorphism. Highly polymorphic markers based on polymorphic information content (PIC) values were identified, which will be useful for molecular breeding. Data was used to identify an "indica genotyping set" based on high level of polymorphism, chromosome position and marker quality which will provide kits of markers for marker assisted selection (MAS). Genetic diversity analysis using SSR data was more consistent with pedigrees compared to analysis with SNP data indicating that more than 384 SNPs are required when elite indica breeding material is used. The results also indicated that there were polymorphic "blind spots" for the fixed SNP set suggesting that SSRs could still be used to complement fixed-SNP genotyping platforms for some molecular breeding applications.

Journal ArticleDOI
TL;DR: The results indicated thatSFNB resistance is controlled by a large number of QTL varying in effect size with large effects QTL on chromosome 7H, suggesting that phenotypic selection for SFNB resistance performed at either growth stage could achieve adequate levels of resistance.
Abstract: Key message: Evaluation of resistance toPyrenophora teresf.maculatain barley breeding populations via association mapping revealed a complex genetic architecture comprising a mixture of major and minor effect genes. Abstract: In the search for stable resistance to spot form of net blotch (Pyrenophora teres f. maculata, SFNB), association mapping was conducted on four independent barley (Hordeum vulgare L.) breeding populations comprising a total of 898 unique elite breeding lines from the Northern Region Barley Breeding Program in Australia for discovery of quantitative trait loci (QTL) influencing resistance at seedling and adult plant growth stages. A total of 29 significant QTL were validated across multiple breeding populations, with 22 conferring resistance at both seedling and adult plant growth stages. The remaining 7 QTL conferred resistance at either seedling (2 QTL) or adult plant (5 QTL) growth stages only. These 29 QTL represented 24 unique genomic regions, of which five were found to co-locate with previously identified QTL for SFNB. The results indicated that SFNB resistance is controlled by a large number of QTL varying in effect size with large effects QTL on chromosome 7H. A large proportion of the QTL acted in the same direction for both seedling and adult responses, suggesting that phenotypic selection for SFNB resistance performed at either growth stage could achieve adequate levels of resistance. However, the accumulation of specific resistance alleles on several chromosomes must be considered in molecular breeding selection strategies.

Journal ArticleDOI
TL;DR: It is concluded that GS has the potential to significantly improve the efficiency of selection for essential oil yield and the factors that affect the accuracy of genomic estimated breeding values, such as linkage disequilibrium (LD), heritability, relatedness and the genetic architecture of desirable traits.
Abstract: The yield of essential oil in commercially harvested perennial species (e.g. 'Oil Mallee' eucalypts, Tea Trees and Hop) is dependent on complex quantitative traits such as foliar oil concentration, biomass and adaptability. These often show large natural variation and some are highly heritable, which has enabled significant gains in oil yield via traditional phenotypic recurrent selection. Analysis of transcript abundance and allelic diversity has revealed that essential oil yield is likely to be controlled by large numbers of quantitative trait loci that range from a few of medium/large effect to many of small effect. Molecular breeding techniques that exploit this information could increase gains per unit time and address complications of traditional breeding such as genetic correlations between key traits and the lower heritability of biomass. Genomic selection (GS) is a technique that uses the information from markers genotyped across the whole genome in order to predict the phenotype of progeny well before they reach maturity, allowing selection at an earlier age. In this review, we investigate the feasibility of genomic selection (GS) for the improvement of essential oil yield. We explore the challenges facing breeders selecting for oil yield, and how GS might deal with them. We then assess the factors that affect the accuracy of genomic estimated breeding values, such as linkage disequilibrium (LD), heritability, relatedness and the genetic architecture of desirable traits. We conclude that GS has the potential to significantly improve the efficiency of selection for essential oil yield.

Journal ArticleDOI
TL;DR: The use of next-generation sequencing technology to generate molecular markers tightly linked to Potyvirus resistance 4 (Pvr4) locus in pepper, which confers resistance to three pathotypes of potato virus Y and to pepper mottle virus, is described.
Abstract: It is imperative to identify highly polymorphic and tightly linked markers of a known trait for molecular marker-assisted selection. Potyvirus resistance 4 (Pvr4) locus in pepper confers resistance to three pathotypes of potato virus Y and to pepper mottle virus. We describe the use of next-generation sequencing technology to generate molecular markers tightly linked to Pvr4. Initially, comparative genomics was carried out, and a syntenic region of tomato on chromosome ten was used to generate PCR-based markers and map Pvr4. Subsequently, the genomic sequence of pepper was used, and more than 5000 single-nucleotide variants (SNVs) were identified within the interval. In addition, we identified nucleotide binding site–leucine-rich repeat-type disease resistance genes within the interval. Several of these SNVs were converted to molecular markers desirable for large-scale molecular breeding programmes.

Journal ArticleDOI
TL;DR: Meta-analysis of reported quantitative trait loci and selective signals with nucleotide fixation identifies a series of putative candidate genes responsible for 13 agronomically important traits, which would facilitate future QTL mapping and molecular breeding practice.
Abstract: Plant domestication involves complex morphological and physiological modification of wild species to meet human needs. Artificial selection during soybean domestication and improvement results in substantial phenotypic divergence between wild and cultivated soybeans. Strong selective pressure on beneficial phenotypes could cause nucleotide fixations in the founder population of soybean cultivars in quite a short time. Analysis of available sequencing accessions estimates that ~5.3 million single nucleotide variations reach saturation in cultivars, and then ~9.8 million in soybean germplasm. Selective sweeps defined by loss of genetic diversity reveal 2,255 and 1,051 genes were involved in domestication and subsequent improvement, respectively. Both processes introduced ~0.1 million nucleotide fixations, which contributed to the divergence of wild and cultivated soybeans. Meta-analysis of reported quantitative trait loci (QTL) and selective signals with nucleotide fixation identifies a series of putative candidate genes responsible for 13 agronomically important traits. Nucleotide fixation mediated by artificial selection affected diverse molecular functions and biological reactions that associated with soybean morphological and physiological changes. Of them, plant-pathogen interactions are of particular relevance as selective nucleotide fixations happened in disease resistance genes, cyclic nucleotide-gated ion channels and terpene synthases. Our analysis provides insights into the impacts of nucleotide fixation during soybean domestication and improvement, which would facilitate future QTL mapping and molecular breeding practice.

Journal ArticleDOI
TL;DR: The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs.
Abstract: Simple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%), amplicons were successfully generated with high quality. Seventeen (89.5%) showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.