Genome Mapping

The taxonomy of the genus Vigna has been primarily based on morphological attributes. We have used 27 genomic clones from soybean, common bean, mungbean and cowpea to examine restriction fragment length polymorphism (RFLP) among 44 accessions of different species belonging to four subgenera of the genus Vigna. One accession each of common bean (Phaseolus vulgaris) and soybean (Glycine max) was

In this paper we describe a new approach to the construction of data management systems for genomic mapping applications in molecular biology, genetics, and plant breeding. We discuss the architecture of such systems and propose an incremental approach to the development of such systems. We illustrate the proposed approach and architecture with a case study of a prototype data management

In the present study, sixty-seven JNPT (Jawahar New Plant Type) lines were evaluated for twenty-eight morphological and quality traits planted in Randomized Complete Block Design with three replications. The experiment was conducted during Kharif seasons of 2018 at Seed Breeding Farm, Department of Plant Breeding and Genetics, College of Agriculture, JNKVV, Jabalpur (M.P.), India. Observations were recorded on the basis of middle five random competitive plants selected from each line in every replication for yield and quality traits to study the genetic variability parameters, correlation coefficient and path coefficient for yield and its attributing traits. The values of PCV for all the traits were found to be more than GCV and the very small difference was present in between GCV and PCV revealing little influence of environment for their expression. High heritability accompanied with high genetic advance was observed for the traits thousand grain weight (g), head rice recovery (%), spikelet fertility (%), harvest index (%), number of spikelets/panicle, fertile spikelets/panicle, spikelet density, grain yield /plant (g), panicle weight/plant (g), number of tillers/plant and number of productive tillers/plant. Based on the results from correlation and path coefficient analysis, it is concluded that number of tillers/plant, spikelet fertility and panicle weight/plant showed a positive correlation with grain yield and at same time exhibited high positive direct effect towards yield. Therefore, they seem to be primary yield contributing character and thus can be used as direct selection to improve genetic yield potential of rice.

Eggplant (Solanum melongena L.) is an important vegetable crop grown in various tropical and temperate parts of the world. There is a wide genetic diversity in the cultivated as well as the wild species of eggplant. Cultivated varieties of eggplant are susceptible to a wide array ...

Chickpea is a cool season grain legume of exceptionally high nutritive value and most versatile food use. It is mostly grown under rain fed conditions in arid and semi-arid areas around the world. Despite growing demand and high yield potential, chickpea yield is unstable and productivity is stagnant at unacceptably low levels. Major yield increases could be achieved by development and use of cultivars that resist/tolerate abiotic and biotic stresses. In recent years the wide use of early maturing cultivars that escape drought stress led to significant increases in chickpea productivity. In the Mediterranean region, yield could be increased by shifting the sowing date from spring to winter. However, this is hampered by the sensitivity of the crop to low temperatures and the fungal pathogen Ascochyta rabiei. Drought, pod borer (Helicoverpa spp.) and the fungus Fusarium oxysporum additionally reduce harvests there and in other parts of the world. Tolerance to rising salinity will be a future advantage in many regions. Therefore, chickpea breeding focuses on increasing yield by pyramiding genes for resistance/tolerance to the fungi, to pod borer, salinity, cold and drought into elite germplasm. Progress in breeding necessitates a better understanding of the genetics underlying these traits. Marker-assisted selection (MAS) would allow a better targeting of the desired genes. Genetic mapping in chickpea, for a long time hampered by the little variability in chickpea’s genome, is today facilitated by highly polymorphic, co-dominant microsatellite-based markers. Their application for the genetic mapping of traits led to inter-laboratory comparable maps. This paper reviews the current situation of chickpea genome mapping, tagging of genes for ascochyta blight, fusarium wilt resistance and other traits, and requirements for MAS. Conventional breeding strategies to tolerate/avoid drought and chilling effects at flowering time, essential for changing from spring to winter sowing, are described. Recent approaches and future prospects for functional genomics of chickpea are discussed.

Over the past few decades, plant genomics research has been studied extensively bringing about a revolution in the field of plant biotechnology. Molecular markers, useful for plant genome analysis, have now become an important tool in crop improvement. The development and use of molecular markers for the detection and exploitation of DNA polymorphism is one of the most significant developments in the field of molecular genetics. The presence of various types of molecular markers, and differences in their principles, methodologies and applications require careful consideration in choosing one or more of such methods. No molecular markers are available yet that fulfill all requirements needed by researchers. In this article we attempt to review most of the available DNA markers that can be routinely employed in various aspects of plant genome analysis such as characterization of genetic variability, genome fingerprinting, genome mapping, gene localization, analysis of genome evolution, population genetics, taxonomy, plant breeding, and diagnostics. The emerging patterns make up a unique feature of the analyzed individual and are currently considered to be the ultimate tool for biological individualization.

Stripe rust, leaf rust, and Barley Yellow Dwarf Virus (BYDV) are important diseases of barley (Hordeum vulgare L). Using 94 doubled-haploid lines (DH) from the cross of Shyri x Galena, multiple disease phenotype datasets, and a 99-marker linkage map, we determined the number, genome location, and effects of genes conferring resistance to these diseases. We also mapped Resistance Gene Analog Polymorphism (RGAP) loci, based on degenerate motifs of cloned disease resistance genes, in the same population. Leaf rust resistance was determined by a single gene on chromosome 1 (7H). QTLs on chromosomes 2 (2H), 3 (3H), 5 (1H), and 6 (6H) were the principal determinants of resistance to stripe rust. Two- locus QTL interactions were significant determinants of resistance to this disease. Resistance to the MAV and PAV serotypes of BYDV was determined by coincident QTLs on chromosomes 1 (7H), 4 (4H), and 5 (1H). QTL interactions were not significant for BYDV resistance. The associations of molecular markers with qualitative and quantitative disease resistance loci will be a useful information for marker-assisted selection.

The present study was conducted in collaboration with Department of Animal Genetics and Breeding, OUAT and WBUAFS to review on new class of advanced molecular marker techniques derived from combination of earlier basic molecular marker for the genetic improvement of livestock from December, 2016 to June, 2017. In the protein coding region of mtDNA, the cytochrome oxidase I gene has recently gained more attention in developing DNA barcodes for species identification and biodiversity analysis. Among, nuclear marker techniques, RAPD and AFLP are being applied to cDNA based templates to study patterns of gene expression through advanced technique like ESTs and SSCP. While RFPL and microsatellites techniques are used for detecting marker-QTL linkages that accomplished by the use of MAS, genetic fingerprinting and mixture models based on segregation analysis principle. The present study objective was to review the utility of advanced molecular marker technology for selection and genetic improvement of animals.

The first linkage map of the olive (Olea europaea L.) genome has been constructed using random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphisms (AFLP) as dominant markers and a few restriction fragment length polymorphisms (RFLP) and simple-sequence repeats (SSR) as codominant markers. Ninety-five individuals of a cross progeny derived from two highly heterozygous olive cultivars, Leccino and Dolce Agogia, were used by applying the pseudo test-cross strategy. From 61 RAPD primers 279 markers were obtained – 158 were scored for Leccino and 121 for Dolce Agogia. Twenty-one AFLP primer combinations gave 304 useful markers – 160 heterozygous in Leccino and 144 heterozygous in Dolce Agogia. In the Leccino map 249 markers (110 RAPD, 127 AFLP, 8 RFLP and 3 SSR) were linked. This resulted in 22 major linkage groups and 17 minor groups with fewer than four markers. In the Dolce Agogia map, 236 markers (93 RAPD, 133 AFLP, 6 RFLP and 4 SSR) were linked; 27 major linkage groups and three minor groups were obtained. Codominant RFLPs and SSRs, as well as few RAPDs in heteroduplex configuration, were used to establish homologies between linkage groups of both parents. The total distance covered was 2,765 cM and 2,445 cM in the Leccino and Dolce Agogia maps, respectively. The mean map distance between adjacent markers was 13.2 cM in Leccino and 11.9 cM in Dolce Agogia, respectively. Both AFLP and RAPD markers were homogeneously distributed in all of the linkage groups reported. The stearoyl-ACP desaturase gene was mapped on linkage group 4 of cv. Leccino.

Bipolar disorder (BPD) is characterised by episodes of excitement interspersed with periods of depression. The role of genetic factors in BPD is indicated by studies in monozygotic twins showing 40–70 % of concordance. Studies using genetic markers showed linkage of genes for affective disorders in different chromosome regions, emphasising the polygenic and multifactorial traits. The main goal of our research is to search non-synonymous SNPs (those that result in modifications in protein sequence) in genes that can be associated with psychiatric diseases as suggested by genomic mapping and/or by physiological function of the protein. Using DNA sequencing we could confirm a new non-synonymous SNP in the conservative domain of the ALOX12 gene (17p13.1), suggested by EST alignment. This SNP is an alteration from G to A that leads to a change of an arginine (A) to a glutamine in one of the most important domains of the protein. This SNP was evaluated by DNA sequencing in 182 patients with BPD and 160 control individuals. An increased presence of allele A among patients (60 % in controls and 73.1 % in cases; χ2 = 6.581, P = 0.010; OR = 1.8095, 95 % CI = 1.1477–2.853) was found, suggesting an association of this polymorphism with the BPD in this Brazilian sample.

We have constructed a 1736-locus maize genome map containing1156 loci probed by cDNAs, 545 probed by random genomic clones, 16 by simple sequence repeats (SSRs), 14 by isozymes, and 5 by anonymous clones. Sequence information is available for 56% of the loci with 66% of the sequenced loci assigned functions. A total of 596 new ESTs were mapped from a B73 library of 5-wk-old shoots. The map contains 237 loci probed by barley, oat, wheat, rice, or tripsacum clones, which serve as grass genome reference points in comparisons between maize and other grass maps. Ninety core markers selected for low copy number, high polymorphism, and even spacing along the chromosome delineate the 100 bins on the map. The average bin size is 17 cM. Use of bin assignments enables comparison among different maize mapping populations and experiments including those involving cytogenetic stocks, mutants, or quantitative trait loci. Integration of nonmaize markers in the map extends the resources available fo...

Key message A major dwarfing region for plant height, asd1, was identified employing the next-generation sequenc-ing-based QTL-Seq approach from a dwarf mutant and is demonstrated to be responsible for the dwarf nature with least penalty on yield in rice. Abstract The yield plateauing of modern rice is witnessed since many decades due to the narrow genetic base owing to the usage of a single recessive gene, i.e., semi-dwarf-1 (sd-1) for development of short-statured varieties throughout the world. This calls for the searching of alternate sources for short stature in rice. To this end, we made an attempt to uncover yet another, but valuable dwarfing gene employing next-generation sequencing (NGS)-based QTL-Seq approach. Here, we have identified a major QTL governing plant height on chromosome 1, i.e., alternate semi-dwarf 1 (asd1) from an F 2 mapping population derived from a cross between a dwarf mutant, LND384, and a tall landrace, INRC10192. Fine mapping of asd1 region employing sequence-based indel markers delimited the QTL region to 67.51 Kb. The sequencing of the QTL region and gene expression analysis predicted a gene that codes for IWS1 (C-terminus family protein). Furthermore, marker-assisted introgression of the asd1 into tall landrace, INRC10192, reduced its plant height substantially while least affecting the yield and its component traits. Hence, this novel dwarfing gene, asd1, has profound implications in rice breeding.

Molecular markers are routinely used in various crop improvement programmes, ecological, physiological, genetic studies of plants and to improve the efficiency and precision of conventional plant breeding through marker assisted selection. In more than last ten years molecular markers have been developed based on the vast knowledge of genome structure. Considerable emphasis has been laid on the use of molecular markers in practical breeding and genotype identification. Development and constantly modification of molecular markers are being used to enhance their utility and bring about automation in the process of genome analysis. The invention of PCR (Polymerase chain reaction) was a landmark in this direction and proved to be a unique process that brought about a new class of DNA profiling markers. In this article detail review of fundamental principles, mechanism, applications with their considerable merits and demerits are given for 12 different molecular marker techniques: restri...

Background Ependymin (Epd), the predominant protein in the cerebrospinal fluid of teleost fishes, was originally associated with neuroplasticity and regeneration. Ependymin-related proteins (Epdrs) have been identified in other vertebrates, including amphibians and mammals. Recently, we reported the identification and characterization of an Epdr in echinoderms, showing that there are ependymin family members in non-vertebrate deuterostomes. We have now explored multiple databases to find Epdrs in different metazoan species. Using these sequences we have performed genome mapping, molecular phylogenetic analyses using Maximum Likelihood and Bayesian methods, and statistical tests of tree topologies, to ascertain the phylogenetic relationship among ependymin proteins. Results Our results demonstrate that ependymin genes are also present in protostomes. In addition, as a result of the putative fish-specific genome duplication event and posterior divergence, the ependymin family can be divided into four groups according to their amino acid composition and branching pattern in the gene tree: 1) a brain-specific group of ependymin sequences that is unique to teleost fishes and encompasses the originally described ependymin; 2) a group expressed in non-brain tissue in fishes; 3) a group expressed in several tissues that appears to be deuterostome-specific, and 4) a group found in invertebrate deuterostomes and protostomes, with a broad pattern of expression and that probably represents the evolutionary origin of the ependymins. Using codon-substitution models to statistically assess the selective pressures acting over the ependymin protein family, we found evidence of episodic positive Darwinian selection and relaxed selective constraints in each one of the postduplication branches of the gene tree. However, purifying selection (with among-site variability) appears to be the main influence on the evolution of each subgroup within the family. Functional divergence among the ependymin paralog groups is well supported and several amino acid positions are predicted to be critical for this divergence. Conclusion Ependymin proteins are present in vertebrates, invertebrate deuterostomes, and protostomes. Overall, our analyses suggest that the ependymin protein family is a suitable target to experimentally test subfunctionalization in gene copies that originated after gene or genome duplication events.

Drought, low temperature and salinity are the most important abiotic stress factors limiting crop productivity. A genomic map of major loci and QTLs affecting stress tolerance in Triticeae identified the crucial role of the group 5 chromosomes, where the highest concentration of QTLs and major loci controlling plant's adaptation to the environment (heading date, frost and salt tolerance) has been found. In addition, a conserved region with a major role in drought tolerance has been localized to the group 7 chromosomes. Extensive molecular biological studies have led to the cloning of many stress-related genes and responsive elements. The expression of some stress-related genes was shown to be linked to stress-tolerant QTLs, suggesting that these genes may represent the molecular basis of stress tolerance. The development of suitable genetic tools will allow the role of stress-related sequences and their relationship with stress-tolerant loci to be established in the near future.

IntroductionIt has existed for several millennia, in the form of commentaries on religious books, law andliterature. We see it today in concordances, citation indexes and genome maps. You probablyhave created some of it, as a bookmark file in your web browser. The "it" we refer to issuperimposed information: data "placed over" existing information sources to help organize,access, connect and reuse

Drought is a major abiotic stress factor limiting crop production. Identification of genetic factors involved in plant responses to drought stress will provide a solid foundation to improve drought resistance. Sorghum is well adapted to hot dry environments and regarded as a model for studying drought resistance among the grasses. Significant progress in genome mapping of this crop has also been made. In sorghum, rapid premature leaf death generally occurs when water is limited during the grain filling period. Premature leaf senescence, in turn, leads to charcoal rot, stalk lodging, and significant yield loss. More than 80% of commercial sorghum hybrids in the United States are grown under non-irrigated conditions and although most of them have pre-flowering drought resistance, many do not have any significant post-flowering drought resistance. Stay-green is one form of drought resistance mechanism, which gives sorghum resistance to premature senescence under soil moisture stress du...

Eggplant (Solanum melongena L.) is an important vegetable crop grown in various tropical and temperate parts of the world. There is a wide genetic diversity in the cultivated as well as the wild species of eggplant. Cultivated varieties of eggplant are susceptible to a wide array ...