La arveja (Pisum sativum L.) es uno de los cultivos domesticados mas antiguos, altamente valorados y ampliamente cultivados en todo el mundo. Sin embargo, en Colombia esta especie carece de estudios geneticos que permitan establecer la variabilidad total. Se estudio la estructura y diversidad genetica en una coleccion de 50 introducciones de arveja arbustiva provenientes del departamento de Narino con 16 marcadores de repeticion de secuencia simple (SSR). El promedio del contenido de informacion polimorfica (PIC) fue 0,62 con un total de 28 alelos y un promedio de 4 alelos por locus, siendo el locus AB71 y D21 los que amplificaron el mayor numero de alelos (6). La Heterocigosidad observada (Ho) fue 0.09± 0.08 y la esperada (He) 0.42± 0.33, indicando un alto nivel de endogamia (Fis= 0.60) demostrando la naturaleza homocigota de P. sativum. Se infirieron las relaciones geneticas por medio de un analisis de similitud y un analisis Bayesiano (STRUCTURE) detectando dos agrupaciones para los genotipos de arveja analizados, con una alta similitud con las caracteristicas agromorfologicas de cada genotipo. A pesar de la baja heterocigosis, los valores de heterocigosidad espera de la poblacion total (He = 0.60) y de la agrupacion 2 (He = 0.70) asi como la presencia de alelos unicos y raros, muestran un nivel de variabilidad genetica en la coleccion. Los resultados del presente estudio seran utiles para programas de pre - mejoramiento de la misma.

Caracterización molecular de arveja arbustiva (Pisum sativum L) en la zona cerealista del departamento de Nariño, Colombia

Genetic improvement in industrially important guar (Cyamopsis tetragonoloba, L. Taub.) crop has been hindered due to the lack of sufficient genomic or transcriptomic resources. In this study, RNA-Seq technology was employed to characterize the transcriptome of leaf tissues from two guar varieties, namely, M-83 and RGC-1066. Approximately 30 million high-quality pair-end reads of each variety generated by Illumina HiSeq platform were used for de novo assembly by Trinity program. A total of 62,146 non-redundant unigenes with an average length of 679 bp were obtained. The quality assessment of assembled unigenes revealed 87.50 % of complete and 97.18 % partial core eukaryotic genes (CEGs). Sequence similarity analyses and annotation of the unigenes against non-redundant protein (Nr) and Gene Ontology (GO) databases identified 175,882 GO annotations. A total of 11,308 guar unigenes were annotated with various enzyme codes (EC) and categorized in six categories with 55 subclasses. The annotation of biochemical pathways resulted in a total of 11,971 unigenes assigned with 145 KEGG maps and 1,759 enzyme codes. The species distribution analysis of the unigenes showed highest similarity with Glycine max genes. A total of 5,773 potential simple sequence repeats (SSRs) and 3,594 high-quality single nucleotide polymorphisms (SNPs) were identified. Out of 20 randomly selected SSRs for wet laboratory validation, 13 showed consistent PCR amplification in both guar varieties. In silico studies identified 145 polymorphic SSR markers in two varieties. To the best of our knowledge, this is the first report on transcriptome analysis and SNPs identification in guar till date.

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RNA-Seq of Guar (Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources.

Biotechnology and Plant Genetic Resources. Conservation and Use

The studies on genetic variation, diversity and population structure of rice germplasm of North East India could be an important step for improvements of abiotic and biotic stress tolerance in rice. Genetic diversity and genetic relatedness among 114 rice genotypes of North East India were assessed using genotypic data of 65 SSR markers and phenotypic data. The phenotypic diversity analysis showed the considerable variation across genotypes for root, shoot and drought tolerance traits. The principal component analysis (PCA) revealed the fresh shoot weight, root volume, dry shoot weight, fresh root weight and drought score as a major contributor to diversity. Genotyping of 114 rice genotypes using 65 SSR markers detected 147 alleles with the average polymorphic information content (PIC) value of 0.51. Population structure analysis using the Bayesian clustering model approach, distance-based neighbor-joining cluster and principal coordinate analysis using genotypic data grouped the accession into three sub-populations. Population structure analysis revealed that rice accession was moderately structured based on FST value estimates. Analysis of molecular variance (AMOVA) and pairwise FST values showed significant differentiation among all the pairs of sub-population ranging from 0.152 to 0.222 suggesting that all the three subpopulations were significantly different from each other. AMOVA revealed that most of the variation in rice accession mainly occurred among individuals. The present study suggests that diverse germplasm of NE India could be used for the improvement of root and drought tolerance in rice breeding programmes.

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Variability Assessment for Root and Drought Tolerance Traits and Genetic Diversity Analysis of Rice Germplasm using SSR Markers.

Knowledge of genetic diversity within crop species and the nature of their breeding systems are critical for crop improvement. These determine the appropriate species specific breeding methodologies to deploy. Genetic diversity analysis is an ongoing process in the breeding programmes of ‘major crops’, which is used to direct or re-direct breeding objectives (especially selection of parental lines). In this regard, the importance of such information in ‘underutilised’ or ‘minor’ crop species, which largely exist as landraces with little information about their genetic diversity and breeding systems, becomes very important. One such important underutilized crop species which could contribute positively to global food security is Bambara groundnut (Vigna subterranea (L.) Verdc.). We present here an overview of the past two decades of genetic diversity analysis of Bambara groundnut landraces. Various genetic diversity analyses of the available germplasm for the crop using phenotypic descriptors and molecular marker technologies have been reported. Generally, most of these studies lack adequate representation of the available global germplasm. For those studies that involved relatively a large germplasm collections (above 100; sampled from different agro-ecologies) the marker density employed in these analyses has been so far relatively low. Specifically, for breeding systems, high genetic diversity and low heterozygosity have been reported across the germplasm analysed in this highly cleistogamous species. In terms of population structure, the West African and the Southern African accessions appear as distinct clusters. This raises the possibility of the southern African region a secondary centre of domestication or diversity for the crop.

/pdf/genetic-diversity-and-population-structure-of-bambara-ukt9vbzh0f.pdf

Genetic diversity and population structure of Bambara groundnut (Vigna subterranea (L.) Verdc.): synopsis of the past two decades of analysis and implications for crop improvement programmes

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.

Basanta Das Kumar

Papers

Molecular Markers: It's Application in Crop Improvement