Edwin Pang

An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts

Recognizing the enormous potential of DNA markers in plant breeding, many agricultural research centers and plant breeding institutes have adopted the capacity for marker development and marker-assisted selection (MAS). However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci (QTLs) and the jargon used by molecular biologists, the utility of DNA markers in plant breeding may not be clearly understood by non-molecular biologists. This review provides an introduction to DNA markers and the concept of polymorphism, linkage analysis and map construction, the principles of QTL analysis and how markers may be applied in breeding programs using MAS. This review has been specifically written for readers who have only a basic knowledge of molecular biology and/or plant genetics. Its format is therefore ideal for conventional plant breeders, physiologists, pathologists, other plant scientists and students.

Transcriptional profiling of chickpea genes differentially regulated in response to high-salinity, cold and drought

BackgroundCultivated chickpea (Cicer arietinum) has a narrow genetic base making it difficult for breeders to produce new elite cultivars with durable resistance to major biotic and abiotic stresses. As an alternative to genome mapping, microarrays have recently been applied in crop species to identify and assess the function of putative genes thought to be involved in plant abiotic stress and defence responses. In the present study, a cDNA microarray approach was taken in order to determine if the transcription of genes, from a set of previously identified putative stress-responsive genes from chickpea and its close relative Lathyrus sativus, were altered in chickpea by the three abiotic stresses; drought, cold and high-salinity. For this, chickpea genotypes known to be tolerant and susceptible to each abiotic stress were challenged and gene expression in the leaf, root and/or flower tissues was studied. The transcripts that were differentially expressed among stressed and unstressed plants in response to the particular stress were analysed in the context of tolerant/susceptible genotypes.ResultsThe transcriptional change of more than two fold was observed for 109, 210 and 386 genes after drought, cold and high-salinity treatments, respectively. Among these, two, 15 and 30 genes were consensually differentially expressed (DE) between tolerant and susceptible genotypes studied for drought, cold and high-salinity, respectively. The genes that were DE in tolerant and susceptible genotypes under abiotic stresses code for various functional and regulatory proteins. Significant differences in stress responses were observed within and between tolerant and susceptible genotypes highlighting the multiple gene control and complexity of abiotic stress response mechanism in chickpea.ConclusionThe annotation of these genes suggests that they may have a role in abiotic stress response and are potential candidates for tolerance/susceptibility.

Lathyrus improvement for resistance against biotic and abiotic stresses: From classical breeding to marker assisted selection

SummarySeveral Lathyrus species and in particular Lathyrus sativus (grass pea) have great agronomic potential as grain and forage legume, especially in drought conditions. Grass pea is rightly considered as one of the most promising sources of calories and protein for the vast and expanding populations of drought-prone and marginal areas of Asia and Africa. It is virtually the only species that can yield high protein food and feed under these conditions. It is superior in yield, protein value, nitrogen fixation, and drought, flood and salinity tolerance than other legume crops. Lathyrus species have a considerable potential in crop rotation, improving soil physical conditions; reducing the amount of disease and weed populations, with the overall reduction of production costs. Grass pea was already in use in Neolithic times, and presently is considered as a model crop for sustainable agriculture. As a result of the little breeding effort invested in it compared to other legumes, grass pea cultivation has shown a regressive pattern in many areas in recent decades. This is due to variable yield caused by sensitivity to diseases and stress factors and above all, to the presence of the neurotoxin β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), increasing the danger of genetic erosion. However, both L. sativus and L. cicera are gaining interest as grain legume crops in Mediterranean-type environments and production is increasing in Ethiopia, China, Australia and several European countries.This paper reviews research work on Lathyrus breeding focusing mainly on biotic and abiotic resistance improvement, and lists current developments in biotechnologies to identify challenges for Lathyrus improvement in the future.

Abiotic Stress Responses in Plants: Present and Future

Drought, cold, high-salinity and heat are major abiotic stresses that severely reduce the yield of food crops worldwide. Traditional plant breeding approaches to improve abiotic stress tolerance of crops had limited success due to multigenic nature of stress tolerance. In the last decade, molecular techniques have been used to understand the mechanisms by which plants perceive environmental signals and further their transmission to cellular machinery to activate adaptive responses. This knowledge is critical for the development of rational breeding and transgenic strategies to impart stress tolerance in crops. Studies on physiological and molecular mechanisms of abiotic stress tolerance have led to characterisation of a number of genes associated with stress adaptation. Techniques like microarrays have proven to be invaluable in generating a list of stress-related genes. Some of these genes are specific for a particular stress while others are shared between various stresses. Interestingly, a number of genes are shared in abiotic and biotic stress responses. This highlights the complexity of stress response and adaptation in plants. There is a whole cascade of genes involved in abiotic stress tolerance; starting from stress perception to transcriptional activation of downstream genes leading to stress adaptation and tolerance. A number of these genes have been discovered but we still do not have the complete list with all interactions. There is also significant number of genes with unknown functions found to be regulated by abiotic stresses. Understanding the function of these genes and their interaction with other known genes to effect stress adaptation is required.

Inhibitions of mast cell-derived histamine release by different Flos Magnoliae species in rat peritoneal mast cells.

Flos Magnoliae (FM) is a commonly used Chinese medicinal herb for symptomatic relief of allergic rhinitis, sinusitis and headache. A number of FM species have been used as substitutes or adulterants for clinical application, although the differences in their pharmacological actions have not been reported. The present study investigated the effects of six identified FM species M. biondii, M. denudata, M. kobus, M. liliflora, M. sargentiana and M. sprengeri, as well as the marker compounds magnolin and fargesin on compound 48/80-induced histamine release in rat peritoneal mast cells (RPMC) in vitro. Ethanolic extracts of all FM species produced a concentration-dependent inhibition of compound 48/80-induced histamine release in RPMC. The rank order of the IC(50)s was M. biondii<M. kobus<M. liliflora<M. denudata<M. sprengeri<M. sargentiana. The marker compound magnolin, but not fargesin, only slightly inhibited the histamine release. The contents of magnolin and fargesin, determined by using RP-HPLC, varied significantly among these FM species. Magnolin was found in M. biondii, M. kobus and M. liliflora, but not in M. denudate, M. sprengeri and M. sargentiana, while fargesin was only found in M. biondii and M. kobus. These findings provide the first evidence of differences in pharmacological actions of different FM species on mast cell-derived histamine release in vitro. In addition, the marker compounds magnolin and fargesin may not play a major role in the observed pharmacological actions of FM species.

Chemistry and bioactivity of Flos Magnoliae, a Chinese herb for rhinitis and sinusitis

Flos Magnoliae (FM, Chinese name: Xin-yi) is one of the most commonly used Chinese medicinal herbs. It has a long history of clinical use for managing rhinitis, sinusitis and headache. More than 20 different FM species have been used clinically, which makes species identification and evaluation of pharmacological effects of individual chemical ingredients difficult. In this review, we have summarized the current knowledge on FM phytochemistry and its bioactivity activities. The bioactive compounds in FM include both lipid and water-soluble components. More than 90% of the essential components of FM species are terpenoids, including monoterpenes and sesquiterpenes. Lignans and neolignans including tetrahydrofurofuran, tetrahydrofuran and aryltetralin are also present in FM species. A small number of water-soluble compounds have been isolated from Magnolia flower buds, including a benzylisoquinoline alkaloid magnoflorine, an ester ethyl-E-p-hydroxyl-cinnamate and a flavonoid biondnoid. A wide range of pharmacological actions of FM have been reported, including anti-allergy, anti-inflammation and anti-microbial activity. The structure-activity relationship analysis revealed the influence of methylation at position 5 on the 3,7-dioxabicyclo-(3,3,0)-octane backbone of six lignans in antagonistic activities against platelet-activating factor. In addition, the trans stereoisomer fargesin had a much lower bioactivity than the cis stereoisomer demethoxyaschantin. Recent studies have been directed towards the isolation of other bioactive compounds. Further studies on FM may help to develop new anti-inflammatory and anti-allergic drugs.

Examination of Pisum and Lathyrus species as sources of ascochyta blight resistance for field pea (Pisum sativum)

Ascochyta blight resistance in Pisum sativum (field pea), P. fulvum and Lathyrus species was examined in glasshouse experiments using an isolate of the fungal pathogen Mycosphaerella pinodes that had been isolated from field pea. In the genus Pisum there was significant variation in stem infection among the primitive field pea lines, the field pea cultivars and the P. fulvum lines. Two P. fulvum lines and one primitive field pea line exhibited significantly less stem infection than the two field pea cultivars. Leaf infection of the primitive field pea lines was not significantly different from that of the field pea cultivars. P. fulvum accession PS1115 had the least stem infection and the least leaf infection among the Pisum germplasm. Examination of stem infection in Lathyrus showed that L. sativus, L. ochrus and L. clymenum accessions were significantly more resistant to stem infection than the field pea cultivars. Six of the eight accessions of Lathyrus were also significantly more resistant to leaf infection than the field pea cultivars. Among ten accessions of L. sativus, there was significant variation in severity of stem infection but not leaf infection. This is the first report comparing ascochyta blight resistance between Lathyrus and Pisum species and among Lathyrus accessions and the results show that Lathyrus species may be a source of resistance alleles that could be exploited to develop ascochyta blight resistance in field pea.

Selection of wild cicer accessions for the generation of mapping populations segregating for resistance to ascochyta blight

In order to determine genetically diverse parents for the generation of mapping populations segregating for resistance to ascochyta blight in wild Cicer species, the genetic diversity between a selection of resistant and susceptible accessions was assessed using molecular markers. Twenty Cicer accessions — comprising eight C. reticulatum accessions, six C. echinospermum accessions, five C. bijugum accessions, and one C. arietinum accession — were compared using a combination of seven RAPD primers and seven ISSR primers. A total of 231 polymorphic bands were scored and used to determine the genetic distances between accessions using Jaccard similarity coefficients. The most genetically diverse parents for the generation of intraspecific and interspecific populations segregating for resistance to ascochyta blight are reported.

The Role of Micro-Ribonucleic Acids in Legumes with a Focus on Abiotic Stress Response

Legumes are special group of N‐fixing plants that are an essential component of cropping system and important source of food and feed for human and animal consumption. Like other crops, the productivity of legumes is threatened by environmental stresses caused due to global climate change. Abiotic stress tolerance is complex trait involving a suite of genes, the expression of which is controlled by transcription factors including gene and/or polypeptide sequences. Recently, micro‐ribonucleic acids (miRNAs) have been increasingly recognized for their role in regulating the synthesis of polypeptides from different messenger ribonucleic acids (mRNAs) including those that act as transcription factors. This review summarizes the current knowledge on the role of different miRNAs in response to main abiotic stresses in legumes. We found consistent as well as conflicting results within and between different legume species. This highlights that we have barely scratched the surface and very comprehensive and targeted experiments will be required in future to underpin the role of miRNAs in controlling the expression of important genes associated with abiotic stress tolerances.

A cDNA microarray approach to decipher lentil (Lens culinaris) responses to Ascochyta lentis.

Ascochyta blight, caused by Ascochyta lentis Vassilievsky, is an important fungal disease of lentil (Lens culinaris subsp. culinaris). Manifestation of disease in plants is due to differential expression of genes in the both host and the pathogen. Identification of genes that are differentially expressed in varieties with resistance to A. lentis will lead to the accurate selection and development of crop varieties with increased resistance. To elucidate the complex network of genes underlying A. lentis resistance in lentil, a targeted genomics approach was utilised. The present study reports for the first time the use of microarray technology to study gene expression in lentil, specifically in response to A. lentis inoculation in a highly resistant (ILL7537) and highly susceptible (ILL6002) lentil variety. Ninety genes were differentially expressed in ILL7537 and 95 genes were differentially expressed in ILL6002. The expression profiles of the two varieties showed substantial difference in type and time of genes that were expressed in response to A. lentis. The resistant variety showed early upregulation of PR4 and 10 proteins and other defence-related genes. The susceptible genotype showed early downregulation of defence-related genes. Real-time RT-PCR was used to verify microarray expression ratios. The resistant and susceptible lentil varieties differ not only in the type of genes expressed but also in the time and level of expression in response to A. lentis inoculation. Different components of the defence mechanism and key putative defence genes were identified by comparing the transcriptional profiles of the susceptible and resistant lentil genotypes. Following further functional characterisation, these candidate ascochyta blight resistance genes may be used in future strategic A. lentis resistance breeding programs.