Major Crop Plants Research Articles

Technological breakthroughs in generating transgene-free and genetically stable CRISPR-edited plants.

CRISPR/Cas9 gene-editing technologies have been very effective in editing target genes in all major crop plants and offer unprecedented potentials in crop improvement. A major challenge in using CRISPR gene-editing technology for agricultural applications is that the target gene-edited crop plants need to be transgene free to maintain trait stability and to gain regulatory approval for commercial production. In this article, we present various strategies for generating transgene-free and target gene-edited crop plants. The CRISPR transgenes can be removed by genetic segregation if the crop plants are reproduced sexually. Marker-assisted tracking and eliminating transgenes greatly decrease the time and labor needed for identifying the ideal transgene-free plants. Transgenes can be programed to undergo self-elimination when CRISPR genes and suicide genes are sequentially activated, greatly accelerating the isolation of transgene-free and target gene-edited plants. Transgene-free plants can also be generated using approaches that are considered non-transgenic such as ribonucleoprotein transfection, transient expression of transgenes without DNA integration, and nano-biotechnology. Here, we discuss the advantages and disadvantages of the various strategies in generating transgene-free plants and provide guidance for adopting the best strategies in editing a crop plant.

A novel Arabidopsis pathosystem reveals cooperation of multiple hormonal response-pathways in host resistance against the global crop destroyer Macrophomina phaseolina

Dubbed as a “global destroyer of crops”, the soil-borne fungus Macrophomina phaseolina (Mp) infects more than 500 plant species including many economically important cash crops. Host defenses against infection by this pathogen are poorly understood. We established interactions between Mp and Arabidopsis thaliana (Arabidopsis) as a model system to quantitatively assess host factors affecting the outcome of Mp infections. Using agar plate-based infection assays with different Arabidopsis genotypes, we found signaling mechanisms dependent on the plant hormones ethylene, jasmonic acid and salicylic acid to control host defense against this pathogen. By profiling host transcripts in Mp-infected roots of the wild-type Arabidopsis accession Col-0 and ein2/jar1, an ethylene/jasmonic acid-signaling deficient mutant that exhibits enhanced susceptibility to this pathogen, we identified hundreds of genes potentially contributing to a diverse array of defense responses, which seem coordinated by complex interplay between multiple hormonal response-pathways. Our results establish Mp/Arabidopsis interactions as a useful model pathosystem, allowing for application of the vast genomics-related resources of this versatile model plant to the systematic investigation of previously understudied host defenses against a major crop plant pathogen.

Production, characterization, and cross-reactivity of a polyclonal antibody against Arabidopsis TARGET OF RAPAMYCIN

TARGET OF RAPAMYCIN (TOR), a member of the phosphatidylinositol 3-kinase-related family of protein kinases, is encoded by a single, large gene and is evolutionarily conserved in all eukaryotes. TOR plays a role as a master regulator that integrates nutrient, energy, and stress signaling to orchestrate development. TOR was first identified in yeast mutant screens, as its mutants conferred resistance to rapamycin, an antibiotic with immunosuppressive and anticancer activities. In Arabidopsis thaliana, the loss-of-function tor mutant displays embryo lethality, but the precise mechanisms of TOR function are still unknown. Moreover, a lack of reliable molecular and biochemical assay tools limits our ability to explore TOR functions in plants. Here, we produced a polyclonal α-TOR antibody using two truncated variants of TOR (1–200 and 1113–1304 amino acids) as antigens because recombinant full-length TOR is challenging to express in Escherichia coli. Recombinant His-TOR1−200 and His-TOR1113−1304 proteins were individually expressed in E. coli, and a mixture of proteins (at a 1:1 ratio) was used for immunizing rabbits. Antiserum was purified by an antigen-specific purification method, and the purified polyclonal α-TOR antibody successfully detected endogenous TOR proteins in wild-type Arabidopsis and TOR orthologous in major crop plants, including tomato, maize, and alfalfa. Moreover, our α-TOR antibody is useful for coimmunoprecipitation assays. In summary, we generated a polyclonal α-TOR antibody that detects endogenous TOR in various plant species. Our antibody could be used in future studies to determine the precise molecular mechanisms of TOR, which has largely unknown multifunctional roles in plants.

Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage

BackgroundSalinity is a major abiotic stress seriously hindering crop yield. Development and utilization of tolerant varieties is the most economical way to address soil salinity. Upland cotton is a major fiber crop and pioneer plant on saline soil and thus its genetic architecture underlying salt tolerance should be extensively explored.ResultsIn this study, genome-wide association analysis and RNA sequencing were employed to detect salt-tolerant qualitative-trait loci (QTLs) and candidate genes in 196 upland cotton genotypes at the germination stage. Using comprehensive evaluation values of salt tolerance in four environments, we identified 33 significant single-nucleotide polymorphisms (SNPs), including 17 and 7 SNPs under at least two and four environments, respectively. The 17 stable SNPs were located within or near 98 candidate genes in 13 QTLs, including 35 genes that were functionally annotated to be involved in salt stress responses. RNA-seq analysis indicated that among the 98 candidate genes, 13 were stably differentially expressed. Furthermore, 12 of the 13 candidate genes were verified by qRT-PCR. RNA-seq analysis detected 6640, 3878, and 6462 differentially expressed genes at three sampling time points, of which 869 were shared.ConclusionsThese results, including the elite cotton accessions with accurate salt tolerance evaluation, the significant SNP markers, the candidate genes, and the salt-tolerant pathways, could improve our understanding of the molecular regulatory mechanisms under salt stress tolerance and genetic manipulation for cotton improvement.

Resurrection plants: Imperative resources in developing strategies to drought and desiccation pressure

Resurrection plants are the vital assets of nature that have amazing mechanism to restrict the negative impacts of drought or desiccation stress by diminishing cell damage. These surprising plants are in minority on this planet but have the potential to serve as a powerful resource for developing new strategies for major crop plants that are unable to adapt well to the arid climate. In this review, an attempt is made to highlight the potential aspects of these resurrection plants especially the genetic engineering facet which has been done to develop drought tolerance in economically important plants.

Post-transcriptional Regulation of FLOWERING LOCUS T Modulates Heat-Dependent Source-Sink Development in Potato

Understanding tuberization in the major crop plant potato (Solanum tuberosum L.) is of importance to secure yield even under changing environmental conditions. Tuber formation is controlled by a homolog of the floral inductor FLOWERING LOCUS T, referred to as SP6A. To gain deeper insights into its function, we created transgenic potato plants overexpressing a codon-optimized version of SP6A, SP6Acop, to avoid silencing effects. These plants exhibited extremely early tuberization at the juvenile stage, hindering green biomass development and indicating a tremendous shift in the source sink balance. The meristem identity was altered in dormant buds of transgenic tubers. This strong phenotype, not being reported so far for plants overexpressing an unmodified SP6A, could be due to post-transcriptional regulation. In fact, a putative SP6A-specific small regulatory RNA was identified in potato. It was effectively repressing SP6A mRNA accumulation in transient assays as well as in leaves of young potato plants prior to tuber formation. SP6A expression is downregulated under heat, preventing tuberization. The molecular mechanism has not been elucidated yet. We showed that this small RNA is strongly upregulated under heat. The importance of the small RNA was demonstrated by overexpression of a target mimicry construct, which led to an increased SP6A expression, enabling tuberization even under continuous heat conditions, which abolished tuber formation in the wild-type. Thus, our study describes an additional regulatory mechanism for SP6A besides the well-known pathway that integrates both developmental and environmental signals to control tuberization and is therefore apromising target for breeding of heat-tolerant potato.

Modelling G×E with historical weather information improves genomic prediction in new environments.

MotivationInteraction between the genotype and the environment () has a strong impact on the yield of major crop plants. Although influential, taking explicitly into account in plant breeding has remained difficult. Recently has been predicted from environmental and genomic covariates, but existing works have not shown that generalization to new environments and years without access to in-season data is possible and practical applicability remains unclear. Using data from a Barley breeding programme in Finland, we construct an in silico experiment to study the viability of prediction under practical constraints.ResultsWe show that the response to the environment of a new generation of untested Barley cultivars can be predicted in new locations and years using genomic data, machine learning and historical weather observations for the new locations. Our results highlight the need for models of : non-linear effects clearly dominate linear ones, and the interaction between the soil type and daily rain is identified as the main driver for for Barley in Finland. Our study implies that genomic selection can be used to capture the yield potential in effects for future growth seasons, providing a possible means to achieve yield improvements, needed for feeding the growing population.Availability and implementationThe data accompanied by the method code (http://research.cs.aalto.fi/pml/software/gxe/bioinformatics_codes.zip) is available in the form of kernels to allow reproducing the results.Supplementary information Supplementary data are available at Bioinformatics online.

Agrobacterium-Mediated Transformation of Brachypodium distachyon.

Brachypodium distachyon is an excellent model system for the grasses and has been adopted as a research organism by many laboratories around the world. It has all of the biological traits required for a model system, including small stature, short life cycle, small genome, simple growth requirements, and a close relationship to major crop plants (cereals). In addition, numerous resources have been developed for working with this species, including genome sequences for many lines, sequenced mutant collections, and a large, freely available germplasm collection. Fortunately, among grasses B. distachyon is one of the most easily transformed species, an absolute necessity for a model system. Agrobacterium-mediated transformation is the preferred method to transform plants because it usually results in simple insertions of target DNA. In this article, we describe a method for Agrobacterium-mediated transformation of the inbred B. distachyon lines Bd21 and Bd21-3. Embryogenic callus induced from immature embryos is co-cultivated with Agrobacterium tumefaciens strain AGL1 or Agrobacterium rhizogenes strain 18r12v. Hygromycin and paromomycin are used as selective agents, with comparable transformation efficiencies (defined as the percentage of co-cultivated callus that produce transgenic plants) of 40% to 70%. It takes 20 to 30 weeks to obtain T1 seeds starting from the initial step of dissecting out immature embryos. This protocol has been shown to be efficient and facile in several studies that resulted in the creation of over 22,000 T-DNA mutants. © 2019 by John Wiley & Sons, Inc.

Overexpression of MtTdp2α (tyrosyl-DNA phosphodiesterase 2) gene confers salt tolerance in transgenic Medicago truncatula

Soil salinity is one of the main abiotic stresses affecting yield in major crop plants, including legumes. Research carried out on model legumes such as barrel medic (Medicago truncatula Gaertn.) showed that the Tyrosyl-DNA phosphodiesterase 2α (MtTdp2α) DNA repair gene, involved in the removal of topoisomerase-DNA covalent complexes, play a key role in the plant response to osmotic and copper stresses. However, no informations are currently available about the involvement of MtTdp2α in response to salt stress and salt shock. In the present study we investigated the role of MtTdp2α under salinity (0, 50, 100, 150 and 200 mM NaCl) stress conditions in transgenic M. truncatula overexpressing the MtTdp2α gene. The level of salt tolerance of Tdp2-28 selected transgenic line was significantly higher than control as measured by the increase in shoot fresh weight, shoot dry weight and salt sensitivity index, in response to 100 mM NaCl. After salt stress, Tdp2-28 transgenic line showed significantly higher chlorophyll and carotenoid total contents, 2,2-Diphenyl-1-Picrylhydrazyl radical scavenging activity, and significantly lower levels of oxidative DNA damage than the control line. Interestingly, the expression levels of several genes, including genes linked to genome maintenance and regulation of DNA topology (MtTdp1α, MtTop2), base excision repair pathway (MtOGG1) and double strand break sensing/repair (MtMRE11) were enhanced in Tdp2-28 transgenic shoots under salt stress conditions as compared to their controls. These findings suggest that MtTdp2α play an important role in plant tolerance to salt stress. Overexpression of MtTdp2α gene in Medicago truncatula confers salt stress tolerance through better plant growth performances, higher chlorophyll and carotenoid contents, increased antioxidant capacity, reduced oxidative DNA damage, and by up-regulation of several genes involved in DNA metabolism.

Genome-wide identification and expression analyses of WRKY transcription factor family members from chickpea (Cicer arietinum L.) reveal their role in abiotic stress-responses.

WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics. In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome. For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome. We have computationally identified 70 WRKY-encoding non-redundantgenes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2-7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress-response pathways. This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses.

Next generation breeding tools for chamomile: Evaluating genetic diversity, ploidy variation, and identifying marker-trait associations

Chamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous medicinally active compounds. Next generation sequencing (NGS) approaches are applied to exploit genetic resources in the major crop plants to develop genomic resources, and to enhance breeding. Genotyping-by-sequencing (GBS) has been used to evaluate the genetic structure of cultivated populations in the non-model crop chamomile using 6495 SNP markers, and to perform a genome wide association study (GWAS) identifying sequences significantly associated with the medicinally important alpha-bisabolol content. Ploidy variation in chamomile was investigated by high-throughput flow-cytometry. Di-, tri- and tetraploid plants were identified, and in field trials characterized. Since seeds are not needed in the harvested product of chamomile, triploidy could be a way to obtain a sterile chamomile variety, omitting the problems of chamomile seeds lying up to 15 years dormant in the soil and facilitating crop rotation in the fields.

CONSTRUCTION OF THE INFECTIOUS MOLECULE OF BETA SATELLITE ASSOCIATED WITH AGERATUM YELLOW VEIN DISEASE OF AGERATUM CONYZOIDES

Several dicot plant species are mostly infected by the vast variety of begomoviruses in different areas around the globe. Begomoviruses exhibit association with two satellites molecules, alphasatellites and betasatellites which are involved to cause severe viral infection. Whitefly plays a vital role as a vector in the transmission of virus from one plant to another. These viruses use weeds to cause infections when the major crop plants are absent in the field. Ageratum conyzoides is very important weed plant, infected with a unique virus complex. The study is intended to evaluate the satellite molecule diversity associated with yellow vein disease of A.conyzoides. Symptomatic leave samples of field grown ageratum plants were collected from different areas of Faisalabad. Betasatellites were extracted from infected ageratum plants.To amplify the beta satellite component clones, the rolling circular amplification was applied on extracted DNA-β isolated from infectious weed plants.The confirmation of DNA-β was done with the help of restriction by different suitable enzymes. The betasatellites were mainly focused in this study. The DNA-β was completely sequenced and infectious molecule was made.

Combinatorial efficacy of Trichoderma spp. and Pseudomonas fluorescens to enhance suppression of cell wall degrading enzymes produced by Fusarium wilt of Arachis hypogaea.L

Fusarium oxysporum, the soil borne pathogen causes vascular wilt, on majority of crop plants. It has been demonstrated that two different species of Trichoderma and Pseudomonas fluorescens suppress disease by different mechanisms. Therefore, application of a mixture of these biocontrol agents, and thus of several suppressive mechanisms, may represent a viable control strategy. A necessity for biocontrol by combinations of biocontrol agents can be the compatibility of the co-inoculated micro-organisms. Hence, compatibility between Trichoderma spp. and Pseudomonas fluorescens that have the ability to suppress Fusarium oxysporum in vitro on the activity of pectinolytic enzymes of Fusarium oxysporum. The activity of pectinolytic enzymes, i.e. pectin methyl esterase, endo and exo polymethylgalacturonases and exo and endo pectin trans eliminases produced by Fusarium oxysporum (Control) was higher. Maximum inhibition of pectin methylesterase, exo and endo polymethylgalacturonase and exo and endopectin trans eliminase was shown by culture filtrate of Trichoderma viride + Pseudomonas fluorescens (Tv+Pf) (1+2%), followed by Trichoderma harzianum + Pseudomonas fluorescens, (Th +Pf) (1.5+2%) and Trichoderma viride + Trichoderma harzianum (Tv+Th) (1+1.5%). However, pathogenecity suppression of Fusarium oxysporum, a causative of Arachis hypogaea. L by the compatible combination of Trichodema viride + Pseudomonas fluorescens (1+2%) was significantly better as compared to the single bio-agent. This indicates that specific interactions between biocontrol agents influence suppression of pathogenicity factors directly by combinations of these compatible bio-agents.Int. J. Agril. Res. Innov. & Tech. 7 (2): 36-42, December, 2017

The Long Intergenic Noncoding RNA (LincRNA) Landscape of the Soybean Genome.

Long intergenic noncoding RNAs (lincRNAs) are emerging as important regulators of diverse biological processes. However, our understanding of lincRNA abundance and function remains very limited especially for agriculturally important plants. Soybean (Glycine max) is a major legume crop plant providing over a half of global oilseed production. Moreover, soybean can form symbiotic relationships with Rhizobium bacteria to fix atmospheric nitrogen. Soybean has a complex paleopolyploid genome and exhibits many vegetative and floral development complexities. Soybean cultivars have photoperiod requirements restricting its use and productivity. Molecular regulators of these legume-specific developmental processes remain enigmatic. Long noncoding RNAs may play important regulatory roles in soybean growth and development. In this study, over one billion RNA-seq read pairs from 37 samples representing nine tissues were used to discover 6,018 lincRNA loci. The lincRNAs were shorter than protein-coding transcripts and had lower expression levels and more sample specific expression. Few of the loci were found to be conserved in two other legume species (chickpea [Cicer arietinum] and Medicago truncatula), but almost 200 homeologous lincRNAs in the soybean genome were detected. Protein-coding gene-lincRNA coexpression analysis suggested an involvement of lincRNAs in stress response, signal transduction, and developmental processes. Positional analysis of lincRNA loci implicated involvement in transcriptional regulation. lincRNA expression from centromeric regions was observed especially in actively dividing tissues, suggesting possible roles in cell division. Integration of publicly available genome-wide association data with the lincRNA map of the soybean genome uncovered 23 lincRNAs potentially associated with agronomic traits.

The role of silicon (Si) in increasing plant resistance against insect pests review article

Silicon (Si) is reported to improve plant resistance to a range of biotic and abiotic stresses, with consequent yield increases. Silicon plays an important role in providing defense for crops of great economic importance against insect pests attack. In this study, the interaction between plants treated with silicon and reduced insect damage was reviewed. The current review presents the agronomic importance of silicon in plants, the control of insect pests in different major crop plants by silicon treatment, the different mechanisms of silicon- enhanced resistance, and the absence of silicon effects on insect pests. By integrating the data presented in this paper, a good knowledge of the association between silicon treatment, increasing plant resistance, and decreasing insect pest damage could be attainted.

Influence of aspartic acid and lysine on the uptake of gold nanoparticles in rice

The interactions between plants and nanomaterials (NMs) can shed light on the environmental consequences of nanotechnology. We used the major crop plant rice (Oryza sativa L.) to investigate the uptake of gold nanoparticles (GNPs) coated with either negatively or positively charged ligands, over a 5-day period, in the absence or presence of one of two amino acids, aspartic acid (Asp) or lysine (Lys), acting as components of rice root exudates. The presence of Asp or Lys influenced the uptake and distribution of GNPs in rice, which depended on the electrical interaction between the coated GNPs and each amino acid. When the electrical charge of the amino acid was the same as that of the surface ligand coated onto the GNPs, the GNPs could disperse well in nutrient solution, resulting in increased uptake of GNPs into rice tissue. The opposite was true where the charge on the surface ligand was different from that on the amino acid, resulting in agglomeration and reduced Au uptake into rice tissue. The behavior of GNPs in the hydroponic nutrient solution was monitored in terms of agglomeration, particle size distribution, and surface charge in the presence and absence of Asp or Lys, which depended strongly on the electrostatic interaction. Results from this study indicated that the species of root exudates must be taken into account in assessing the bioavailability of nanomaterials to plants.

Molecular genetics and functional genomics of abiotic stress-responsive genes in oilseed rape (Brassica napus L.): a review of recent advances and future

Abiotic stresses are the key factors which negatively influence plant development and productivity and are the main cause of extensive agricultural production losses worldwide. Brassica napus is an oilseed crop of global economic significance and major contributor to the total oilseed production, quite often encounters abiotic stresses, resulting in reduced agricultural productivity. Hence, there is an immediate need being felt to raise B. napus cultivars which would be more suitable for various abiotic stress conditions presently and in the years to come. Biotechnology and molecular plant breeding has emerged as an important tool for molecular understanding of plant response to various abiotic stresses. Currently, various stress-responsive genes and mechanisms have been identified and functionally characterized in model plant Arabidopsis and other major crop plants such as Oryza sativa and Zea mays. However, very inadequate success has been achieved in this direction in a major oilseed crop such as B. napus. In this review, we present the latest methods and approaches of studying abiotic stress in B. napus. In this review, we describe the genes functioning as markers for crop breeding and discuss the recent progress and advances in genome editing by break through CRISPR/Cas9 multigene–multiplex approaches for developing multiple abiotic stress tolerance with our on-going research as a scheme. We also throw some light on molecular genetics, plant breeding and abiotic stress biotechnology of B. napus which offer a new prospective on the research directions for the practical plant breeding and functional genomics of B. napus in response to different abiotic stress conditions.

A cooperative governance network for crop genome editing: The success of governance networks in other areas could help to find common ground for applying genome editing in agriculture.

Emerging biotechnologies, such as genome editing, may revolutionize agricultural development through rapid and precise genetic manipulation of a wide range of crop traits without having to transfer foreign DNA [1]. If so, these new genetic‐engineering (GE) technologies can help to generate crop varieties to address critical challenges in agricultural development, such as climate resilience or nutrient uptake, or diet‐related problems in nutrition and health in poorer countries. However, society must also be protected from potential harmful effects of genetically manipulated crops on the environment, human health, or social welfare. Governance of these crops must therefore balance agricultural developments with risk assessment and prevention of potential harm. > …genome editing is being used to improve the characteristics of major crop plants, but the governance of crop genome editing is poorly defined and developed Presently, genome editing is being used to improve the characteristics of major crop plants, but the governance of crop genome editing is poorly defined and developed. Influential groups concerned with the potential hazards of such crops view this situation with growing alarm, which has created tensions with the academic community and regulatory agencies [2]. Both the USA and the European Commission are currently reviewing the governance of crops produced by genome editing and other new technologies. On the US side, at least, the review process appears unlikely to result in governance approaches that will satisfy parties that are concerned with either over‐ or under‐regulation of such crops, and tension and conflicts about them are likely to heighten. We propose an alternative approach for governance of these crops that may help to defuse tensions and enable exploration of genome editing technologies’ potential while protecting society from harm: a cooperative governance network. Such networks have performed well in …

Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile, and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping

BackgroundChamomile (Matricaria recutita L.) has a long history of use in herbal medicine with various applications, and the flower heads contain numerous secondary metabolites which are medicinally active.In the major crop plants, next generation sequencing (NGS) approaches are intensely applied to exploit genetic resources, to develop genomic resources and to enhance breeding. Here, genotyping-by-sequencing (GBS) has been used in the non-model medicinal plant chamomile to evaluate the genetic structure of the cultivated varieties/populations, and to perform genome wide association study (GWAS) focusing on genes with large effect on flowering time and the medicinally important alpha-bisabolol content.ResultsGBS analysis allowed the identification of 6495 high-quality SNP-markers in our panel of 91 M. recutita plants from 33 origins (2–4 genotypes each) and 4 M. discoidea plants as outgroup, grown in the greenhouse in Gatersleben, Germany. M. recutita proved to be clearly distinct from the outgroup, as was demonstrated by different cluster and principal coordinate analyses using the SNP-markers. Chamomile genotypes from the same origin were mostly genetically similar. Model-based cluster analysis revealed one large group of tetraploid genotypes with low genetic differentiation including 39 plants from 14 origins. Tetraploids tended to display lower genetic diversity than diploids, probably reflecting their origin by artificial polyploidisation from only a limited set of genetic backgrounds.Analyses of flowering time demonstrated that diploids generally flowered earlier than tetraploids, and the analysis of alpha-bisabolol identified several tetraploid genotypes with a high content. GWAS identified highly significant (P < 0.01) SNPs for flowering time (9) and alpha-bisabolol (71). One sequence harbouring SNPs associated with flowering time was described to play a role in self-pollination in Arabidopsis thaliana, whereas four sequences harbouring SNPs associated with alpha-bisabolol were identified to be involved in plant biotic and abiotic stress response in various plants species.ConclusionsThe first genomic resource for future applications to enhance breeding in chamomile was created, andanalyses of diversity will facilitate the exploitation of these genetic resources. The GWAS data pave the way for future research towards the genetics underlying important traits in chamomile, the identification of marker-trait associations, and development of reliable markers for practical breeding.

Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice.

Molecular mapping studies which aim to identify genetic basis of diverse agronomic traits are vital for marker-assisted crop improvement. Numerous Quantitative Trait Loci (QTLs) mapped in rice span long genomic intervals with hundreds to thousands of genes, which limits their utilization for marker-assisted genetic enhancement of rice. Although potent, fine mapping of QTLs is challenging task as it requires screening of large number of segregants to identify suitable recombination events. Association mapping offers much higher resolution as compared to QTL mapping, but detects considerable number of spurious QTLs. Therefore, combined use of QTL and association mapping strategies can provide advantages associated with both these methods. In the current study, we utilized meta-analysis approach to identify metaQTLs associated with grain size/weight in diverse Indian indica and aromatic rice accessions. Subsequently, attempt has been made to narrow-down identified grain size/weight metaQTLs through individual SNP- as well as haplotype-based regional association analysis. The study identified six different metaQTL regions, three of which were successfully revalidated, and substantially scaled-down along with GS3 QTL interval (positive control) by regional association analysis. Consequently, two potential candidate genes within two reduced metaQTLs were identified based on their differential expression profiles in different tissues/stages of rice accessions during seed development. The developed strategy has broader practical utility for rapid delineation of candidate genes and natural alleles underlying QTLs associated with complex agronomic traits in rice as well as major crop plants enriched with useful genetic and genomic information.