148 research outputs found
Sequence based DNA markers and genotyping for cereal genomics and breeding
No full textThe last three decades has seen the rapid evolution of a variety of DNA-based molecular markers that are powerful tools for genome analysis and marker-trait association (MTA) studies. Recently, high-throughput sequence-based methods have been developed for use in plant breeding. Sequence-based markers include simple sequence repeats (SSRs; also known as microsatellites) and single nucleotide polymorphisms (SNPs), which now dominate applications in modern genetic analysis. Insertion site-based polymorphisms (ISBPs), copy number variations (CNVs) and presence and absence variations (PAVs) constitute another group of markers that are being applied in a variety of plant systems. Markers may be used for a variety of purposes including diversity analysis, linkage-based QTL mapping, LD-based association mapping and marker assisted selection (MAS). Large sequence datasets (including both, genomic sequences and expressed sequences) are available for many cereals, enabling the mining for large numbers of SSRs, SNPs, ISBPs and CNVs/PAVs. Recombination bins are being used as markers for genotyping mapping populations and QTL analysis in crops such as rice, where reference genome sequences are available. In this chapter we describe the discovery and application of molecular markers using automated sequencing platforms including those based on next generation sequencing (NGS)
Organization of retrotransposons and microsatellites in cereal genomes
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Single-molecule DNA sequencing technologies for future genomics research
Get PDFDuring the current genomics revolution, the genomes of a large number of living organisms have been fully sequenced. However, with the advent of new sequencing technologies, genomics research is now at the threshold of a second revolution. Several second-generation sequencing platforms became available in 2007, but a further revolution in DNA resequencing technologies is being witnessed in 2008, with the launch of the first single-molecule DNA sequencer (Helicos Biosciences), which has already been used to resequence the genome of the M13 virus. This review discusses several single-molecule sequencing technologies that are expected to become available during the next few years and explains how they might impact on genomics research
Assessment of genetic diversity and population structure in a selected germplasm collection of 292 jute genotypes by microsatellite (SSR) markers
No full textGenetic diversity within the available jute germplasm has not been characterised in detail. Therefore, using 172 SSRs developed in our laboratory, we assessed genetic diversity and population structure in 292 genotypes (including both indigenous and exotic accessions) of two cultivated species (C. capsularis L. and C. olitorius L.). Altogether, as many as 596 alleles (3.46 alleles per locus) were detected. The average values of PIC calculated over all the loci did not differ significantly in the two species (0.198 in C. capsularis and 0.203 in C. olitorius). In C. capsularis, 112 markers (2.55 alleles per locus) and in C. olitorius 140 markers (2.75 alleles per locus) were polymorphic. During both distance based cluster analyses and model based structure analyses, most of the indigenous and exotic genotypes of the two species clearly delineated into separate groups. Basic statistics (Ne, I and He) revealed that the exotic genotypes were slightly more diverse than the indigenous genotypes in C. olitorius while the reverse was true in case of C. capsularis. In each of the two species, low level of population differentiation (Fst) was observed between the indigenous and exotic genotypes, which are also congruent with the results of AMOVA and Nei’s genetic distance, suggesting incidence of gene flow through germplasm exchange across countries. Seven pairs of most divergent genotypes of the two species were identified by pair-wise genetic distance analysis which could be useful for development of jute genotypes with improved fibre yield and fibre quality traits
Linkage disequilibrium and association studies in higher plants: Present status and future prospects
No full textDuring the last two decades, DNA-based molecular markers have been extensively utilized for a variety of studies in both plant and animal systems. One of the major uses of these markers is the construction of genome-wide molecular maps and the genetic analysis of simple and complex traits. However, these studies are generally based on linkage analysis in mapping populations, thus placing serious limitations in using molecular markers for genetic analysis in a variety of plant systems. Therefore, alternative approaches have been suggested, and one of these approaches makes use of linkage disequilibrium (LD)-based association analysis. Although this approach of association analysis has already been used for studies on genetics of complex traits (including different diseases) in humans, its use in plants has just started. In the present review, we first define and distinguish between LD and association mapping, and then briefly describe various measures of LD and the two methods of its depiction. We then give a list of different factors that affect LD without discussing them, and also discuss the current issues of LD research in plants. Later, we also describe the various uses of LD in plant genomics research and summarize the present status of LD research in different plant genomes. In the end, we discuss briefly the future prospects of LD research in plants, and give a list of softwares that are useful in LD research, which is available as electronic supplementary material (ESM)
Two molecular probes characterizing the A and C genomes in the genus Avena (oats)
No full textTwo clones were isolated from oat (Avena sativa cv. Hinoat) genomic DNA. Restriction analysis and cross-hybridization studies revealed that these clones represent two different families of repeated DNA. Single accessions of 10 Avena species, representing three ploidy levels (2x, 4x, and 6x; x=7) and comprising all available genomic constitutions (AA, CC, AABB, AACC, and AACCDD), were analyzed with these probes. Differences were observed among single representatives of the 10 species in the relative abundance of each probe and between the probes in relative abundance in each species. In slot-blot experiments, for each of the two probes, hybridization intensities were independent of genome composition. Southern blots of HindIII DNA digests from the 10 species, using each of the two probes, allowed classification of these species into two groups: the three diploid species with a CC genomic constitution had one specific pattern and the remaining seven species having different genomic constitutions (AA, AABB, AACC, AACCDD, the A genome being in common) had a different pattern. Therefore, these probes will distinguish the C-genome diploid species from the diploid and polyploid species carrying the A genome
Taxonomic examination of Triticale (×Triticosecale)
No full textA detailed study of inflorescence, glume, lemma, and lodicule characters was conducted in 108 accessions of triticales (2n=6x=42; 2n=8x=56), in 102 herbarium specimens representing 21 species of Triticum and Aegilops, and in 30 herbarium specimens representing 12 species of Secale. The differences observed justify in our opinion generic status for triticales. A key has been provided for distinguishing the genera Secale, Triticum, and Aegilops and the nothogenus ×Triticosecale. In addition to morphological differences, cytological differences and other differences in starch granules and glutenin morphology, known from other studies, provide further support for the generic status of triticale
Genetic and molecular basis of grain size and grain number and its relevance to grain productivity in higher plants
Get PDFGrain size and grain number constitute 2 important components of grain yield. In particular, the grain size also influences the end-use quality (e.g., flour yield and protein content) and attracts consumer preference. These 2 traits are also the components of the domestication syndrome of crop plants. A number of important studies have recently been conducted to understand the genetic and molecular basis of these 2 important yield-contributing traits. Information generated from these studies was collected and synthesized for the benefit of plant biologists, particularly plant breeders. In the present article, this information is briefly reviewed and the prospects of using this information for improvement of grain productivity in crop plants are discussed
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