Three subfamilies of grasses, the Ehrhartoideae, Panicoideae and Pooideae, provide the bulk of human nutrition and are poised to become major sources of renewable energy. Here we describe the genome sequence of the wild grass Brachypodium distachyon (Brachypodium), which is, to our knowledge, the first member of the Pooideae subfamily to be sequenced. Comparison of the Brachypodium, rice and sorghum genomes shows a precise history of genome evolution across a broad diversity of the grasses, and establishes a template for analysis of the large genomes of economically important pooid grasses such as wheat. The high-quality genome sequence, coupled with ease of cultivation and transformation, small size and rapid life cycle, will help Brachypodium reach its potential as an important model system for developing new energy and food crops.

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Genome sequencing and analysis of the model grass Brachypodium distachyon

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.

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

/pdf/genome-sequencing-and-analysis-of-themodel-grass-3hu9hqmqqm.pdf

Genome sequencing and analysis of themodel grass Brachypodium distachyon

Abiotic stresses are one of the major constraints to crop production and food security worldwide. The situation has aggravated due to the drastic and rapid changes in global climate. Heat and drought stress are undoubtedly the two most important stresses having huge impact on growth and productivity of the crops. It is very important to understand the physiological, biochemical and ecological interventions related to these stresses for better management. A wide range of plant responses to these stresses could be generalized into morphological, physiological and biochemical responses. Interestingly, this review provides a detailed account of plant responses to heat and drought stresses with special focus on highlighting the commonalities and differences. Crop growth and yields are negatively affected by sub-optimal water supply and abnormal temperatures due to physical damages, physiological disruptions and biochemical changes. Both these stresses have multi-lateral impacts and therefore, complex in mechanistic action. A better understanding of plant responses to these stresses has pragmatic implication for remedies and management. A comprehensive account of conventional as well as modern approaches to deal with heat and drought stresses have also been presented here. A side-by-side critical discussion on salient responses and management strategies for these two important abiotic stresses provides a unique insight into the phenomena. A holistic approach taking into account the different management options to deal with heat and drought stress simultaneously could be a win-win approach in future.

/pdf/crop-production-under-drought-and-heat-stress-plant-4citjxbeya.pdf

Crop Production under Drought and Heat Stress: Plant Responses and Management Options

Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.

/pdf/a-physical-genetic-and-functional-sequence-assembly-of-the-4suqnkiymo.pdf

A physical, genetic and functional sequence assembly of the barley genome

NAC proteins: regulation and role in stress tolerance

Abiotic stresses such as drought, high salinity, and cold are common adverse environmental conditions that significantly influence plant growth and productivity worldwide. The phytohormone abscisic acid (ABA) plays an important role in physiological and developmental responses as well as in co-ordinating various stress signal transduction pathways in plants. DREBs (dehydration responsive element binding) are important plant transcription factors (TFs) that regulate the expression of many stress-inducible genes mostly in an ABA-independent manner and play a critical role in improving the abiotic stress tolerance of plants by interacting with a DRE/CRT cis-element present in the promoter region of various abiotic stress-responsive genes. This review summarizes recent studies highlighting the role of the DRE-binding family of TFs in the adaptive responses to different abiotic stresses and their structural and functional characters with emphasis on the expression and regulation of DREBs. The practical and application value of DREBs in crop improvement, such as stress tolerance engineering as well as marker-assisted selection (MAS), has also been discussed.

/pdf/role-of-drebs-in-regulation-of-abiotic-stress-responses-in-1whj5367cl.pdf

Role of DREBs in regulation of abiotic stress responses in plants

Molecular markers are useful for a variety of purposes relevant to crop improvement. The most important of these uses is the indirect marker­ assisted selection (MAS) exercised during plant breeding. For this purpose, molecular markers need to be amenable to automation and high throughput approaches. However, the gel-based assays that are needed for most molecular markers are time con­ suming and expensive, limiting their utility. The new generation molecular markers, called single nucleo­ tide polymorphisms (SNPs) do not always need these gel-based assays. They are also the most abundant of all marker systems known so far, both in animal and plant genomes. A large number of SNPs have already been developed in the human genome, some of them proving useful for diagnosis of diseases. A beginning has also been made in the development and use of SNPs in higher plants, including some crop and tree species. Hopefully in future, they will be used in plants in a big way. Several approaches can be used for discovery of new SNPs and about a dozen different methods are now available for SNP genotyping. Some of these methods are also suitable for automation and high throughput approaches. These methods, in prin­ ciple, make a distinction between a perfect match and a mismatch (at the SNP site) between a probe of known sequence and the target DNA containing the SNP site. The target DNA in most of these methods is a peR product, except in some cases like 'invasive cleavage assay', and 'reduced representation shotgun (RRS)' devised and used recently. The different methods of SNP discovery and detection, along with examples of some known uses of SNPs in plant sys­ tems are described in this article.

Single nucleotide polymorphisms (SNPs): a new paradigm in molecular marker technology and DNA polymorphism detection with emphasis on their use in plants

A set of 20 wheat microsatellite markers was used with 55 elite wheat genotypes to examine their utility (1) in detecting DNA polymorphism, (2)in the identifying genotypes and (3) in estimating genetic diversity among wheat genotypes. The 55 elite genotypes of wheat used in this study originated in 29 countries representing six continents. A total of 155 alleles were detected at 21 loci using the above microsatellite primer pairs (only 1 primer amplified 2 loci; all other primers amplified 1 locus each). Of the 20 primers amplifying 21 loci, 17 primers and their corresponding 18 loci were assigned to 13 different chromosomes (6 chromosomes of the A genome, 5 chromosomes of the B genome and 2 chromosomes of the D genome). The number of alleles per locus ranged from 1 to 13, with an average of 7.4 alleles per locus. The values of average polymorphic information content (PIC) and the marker index (MI) for these markers were estimated to be 0.71 and 0.70, respectively. The (GT)n microsatellites were found to be the most polymorphic. The genetic similarity (GS) coefficient for all possible 1485 pairs of genotypes ranged from 0.05 to 0.88 with an average of 0.23. The dendrogram, prepared on the basis of similarity matrix using the UPGMA algorithm, delineated the above genotypes into two major clusters (I and II), each with two subclusters (Ia, Ib and IIa, IIb). One of these subclusters (Ib) consisted of a solitary genotype (E3111) from Portugal, so that it was unique and diverse with respect to all other genotypes belonging to cluster I and placed in subcluster Ia. Using a set of only 12 primer pairs, we were able to distinguish a maximum of 48 of the above 55 wheat genotypes. The results demonstrate the utility of microsatellite markers for detecting polymorphism leading to genotype identification and for estimating genetic diversity.

http://www.angelfire.com/rnb/rkv/A11_TAG2000.pdf

The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat

An integrated barley transcript map (consensus map) comprising 1,032 expressed sequence tag (EST)-based markers (total 1,055 loci: 607 RFLP, 190 SSR, and 258 SNP), and 200 anchor markers from previously published data, has been generated by mapping in three doubled haploid (DH) populations. Between 107 and 179 EST-based markers were allocated to the seven individual barley linkage groups. The map covers 1118.3 cM with individual linkage groups ranging from 130 cM (chromosome 4H) to 199 cM (chromosome 3H), yielding an average marker interval distance of 0.9 cM. 475 EST-based markers showed a syntenic organisation to known colinear linkage groups of the rice genome, providing an extended insight into the status of barley/rice genome colinearity as well as ancient genome duplications predating the divergence of rice and barley. The presented barley transcript map is a valuable resource for targeted marker saturation and identification of candidate genes at agronomically important loci. It provides new anchor points for detailed studies in comparative grass genomics and will support future attempts towards the integration of genetic and physical mapping information.

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Manoj Prasad

Papers

NAC proteins: regulation and role in stress tolerance

Role of DREBs in regulation of abiotic stress responses in plants

Single nucleotide polymorphisms (SNPs): a new paradigm in molecular marker technology and DNA polymorphism detection with emphasis on their use in plants

The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat

A 1,000-loci transcript map of the barley genome: new anchoring points for integrative grass genomics