Biotechnology for Conservation and Utilization of Agricultural Plant Genetic Resources in Nepal

Agricultural biodiversity is the basis of human life and food security. Nepal with 577 cultivated species possesses huge diversity at varietal as well as landrace levels. In most agricultural crops the rapid genetic erosion due to several reasons is a common phenomenon. Thus, considering the importance of agricultural biodiversity declared by Convention on Biological Diversity for sustainable food production, National Agriculture Genetic Resources Center (NAGRC) has been established for conservation and sustainable utilization of agricultural biodiversity. This paper thus delineates the application of biotechnological tools adopted by NAGRC for effective and efficient conservation and use of agricultural plant genetic resources (APGRs). Among the adopted technologies, tissue bank using shoot tip culture of vegetatively propagating and recalcitrant crops eg potato, sugarcane, banana, sweet potato, etc are in function. Under the molecular marker technology, currently random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers have been used for developing DNA profiles, identifying duplicates in the collections, assessing genetic diversity and screening accessions against economic traits. DNA bank has also been created for storing DNA of indigenous crops and these DNA can be accessed for research and study. Genotypic database has been developed for chayote, finger millet, wheat and maize for identification and selection of the accessions.Journal of Nepal Agricultural Research Council Vol.3 2017: 49-5

Evaluation of Naked Barley Landraces for Agro-morphological Traits

Naked barley (Hordeum vulgare var. nudum L.) is a traditional, culturally important, climate-resilient winter cereal crop of Nepal. Evaluation of the naked barely genotypes for yield and disease is fundamental for their efficient utilization in plant breeding schemes and effective conservation programs. Therefore, to identify high yielding and yellow rust resistant landraces of naked barley for hilly and mountainous agro-ecosystem, twenty naked barley landraces collected from different locations of Nepal, were evaluated in randomized complete block design (RCBD) with three replications during winter season of 2016 and 2017 at Khumaltar, Lalitpur, Nepal. Combined analysis of variances revealed that NGRC04902 (3.46 t/ha), NGRC00886 (3.28 t/ha), NGRC02309 (3.21 t/ha) and NGRC06026 (3.10 t/ha) were the high yielding landraces and statistically at par with the released variety 'Solu Uwa' (3.15 t/ha). The landraces namely NGRC00837 (ACI Value: 1.86) was found resistant to yellow rust diseases. Landraces NGRC06034 (131.7 days) and NGRC02363 (130.8 days) were found early maturing and NGRC02306 (94.36 cm) was found dwarf landraces among tested genotypes. These landraces having higher yield and better resistance to yellow rust need to be deployed to farmers' field to diversify the varietal options and used in resistant breeding program to improve the productivity of naked barley for Nepalese farmers

Information Theory and Multivariate Techniques for Analyzing DNA Sequence Data: An Example from Tomato Genes

oai:nepjol:article/3867DNA and amino acid sequences are alphabetic symbols having no underlying metric. Use of information theory is one of the solutions for sequence metric problems. The reflection of DNA sequence complexity in phenotype stability might be useful for crop improvement. Shannon-Weaver index (Shannon Entropy, H') and mutual information (MI) index were estimated from DNA sequences of 22 genes, consisted of two gene families of tomato, namely disease resistance and fruit quality. Main objective was use of information theory and multivariate techniques to understand diversity among genes and relate the sequence complexity with phenotypes. The normalized H' value ranged from 0.429 to 0.461. The highest diversity was observed in the gene Crtr-B (beta carotene hydroxylase). Two principal components which accounted for 36.65% variation placed these genes into four groups. Groupings of these genes by both principal component and cluster analyses showed clearly the similarity at phenotypes levels within cluster. Sequences similarity among genes was observed within a family. Diversity assessment of genes applying information theory should link to understand the sequences complexity with respect to gene stability for example stability of resistance gene.Key words: Diversity analysis; DNA sequences; principal component analysis; tomato genesNepal Journal of Biotechnology, 2011, Vol. 1, No. 1 pp.1-

Association Mapping for Improvement of Quantitative Traits in Plant Breeding Populations

DNA-based molecular markers have been extensively utilized for mapping of genes and quantitative trait loci (QTL) of interest based on linkage analysis in mapping populations. This is in contrast to human genetics that use of linkage disequilibrium (LD)-based mapping for fine mapping of QTLs using single nucleotide polymorphisms. LD based association mapping (AM) has promise to be used in plants. Possible use of such approach may be for fine mapping of genes / QTLs, identifying favorable alleles for marker aided selection and cross validation of results from linkage mapping for precise location of genes / QTLs of interest. In the present review, we discuss different mapping populations, approaches, prospects and limitations of using association mapping in plant breeding populations. This is expected to create awareness in plant breeders in use of AM in crop improvement activities.Key words: Association mapping; plant breeding; DNA marker; quantitative trait lociDOI: http://dx.doi.org/10.3126/njb.v2i1.5686  Nepal Journal of Biotechnology Jan.2012, Vol.2(1): 72-8

Genetic Relationship among Nepalese Rice Landraces and Cultivars based on RAPD Markers

Genetic information of any genotype is necessary to manage and utilize them in conservation and breeding program. A total of 28 RAPD markers were used to relate the genetic structure among 50 Nepalese rice genotypes consisting of 29 landraces, 12 breeding lines and 9 released cultivars. Some of them are aromatic and blast resistance. Only four primers (P41, P60, P109 and P141) amplified the DNA of these genotypes with scorable bands. Primer 60 produced the highest number of bands (8). The highest number of present bands (6) was shown by primer 41 in 10 rice genotypes. Grouping of these genotypes based on the adaptation to agro-climatic zone was not observed, probably due to low percentage coverage of genome by four primers.  Most of the genotypes grouped in two clusters. Kali Marsi and IR-24 formed separate individual cluster. Mansara and Jarneli were the most similar landraces (0.96). Churenodhan and Pranpyuri were the most closely related with Masuli. Only one genotype NR-285-18 has fallen in the first quadrant by principal component (PC) analysis and the fourth quadrant was empty. The highest contribution in PC1 was from the second band of primer 41. This RAPD information can be used for selecting lines and for blast resistance breeding.Key words: Genetic distance; rice; RAPDDOI: http://dx.doi.org/10.3126/njb.v2i1.5635Nepal Journal of Biotechnology Jan.2012, Vol.2(1): 16-2

Agro-morphological Diversity of High Altitude Bean Landraces in the Kailash Sacred Landscape of Nepal

Many varieties of bean are widely grown across diverse agro-ecological zones in Nepal. And opportunities exist for improving the crops and enhancing their resilience to various biotic and abiotic stressors. In this context, an experiment was conducted from June to October 2016 in Khar VDC of Darchula district to study the phenotypic traits of nine landraces of bean (Phaseolus vulgaris L.). The bean landraces were planted using randomized complete block design in three sites (Dhamidera, Dallekh and Sundamunda villages), with three replications in each site for their comparative analysis. The study considered the following phenotypic traits: days to emergence, days to 50% flowering, days to 90% pod maturity, number of nodes, pod length, pod width, number of pods, number of seeds per pod and weight and grain yield for 100 seeds. Kruskal-Wallis test showed significant differences in the landraces both within and among locations. KA-17-08-FB and KA-17-04-FB were late  flowering (63 and 65 days respectively) compared to other landraces whereas KA-17-07-FB flowered earliest (within 42 days). In all three sites, three landraces namely KA-17-07-FB, KA-17-04-FB and KA-17-06-FB were found to be relatively more resistant to pest and diseases than other landraces. Eight out of nine landraces in Dhamidera and Dallekh villages and seven out of nine in Sundamunda village produced seeds greater than 1.0 t/ha. Among the nine varieties KA-17-02-FB was the highest yielding variety, with an average yield of 3.8 t/ha. This study is useful for identifying suitable landraces for future promotion based on their maturity, grain yield, diseases resistance and other qualitative and quantitative characteristics

Information Theory and Multivariate Techniques for Analyzing DNA Sequence Data: An Example from Tomato Genes

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Diversity Analysis and Physico-Morphlogical Characteritics of Indigenous Germplasm of Lablab Bean

Germplasm characterization is an important component of crop breeding program. In characterizing indigenous beans lablab which is used for vegetables as well pulses in Nepal. Twenty three lablab beans germplasm were evaluated for different qualitative and quantitive physico-morphological charecteristics for two years during 2011 and 2012 at Horticulture Research Station, Malepatan, Pokhara. The germplasm showed considerable variations in most of the qualitative and quantitative traits. Leaf size, vine color, flower color, pod color, pod shape, pod type and seed color varied among the genotypes. Variation was also observed in yield attributing characters eg, pod length and width, 10 fresh pod weight, seeds per pod and 100-seed weight. Days to 50% flowering ranged from 81 to 130 days indicating the presence of early varieties. Fresh pod weight of 10 pods was ranged from 45.0 g to 162.5 g. Multivariate analysis indicated four groups in these genotypes, among with ML-02 and ML-10 were distinct in comparioson with other genotypes. Simple selection may be considered to develop high yielding, early type varieties from these gentopypes

Genetic Parameters of Common Wheat in Nepal

Knowledge on variation within traits and their genetics are prerequisites in crop improvement program. Thus, in present paper we aimed to estimate genetic and environmental indices of common wheat genotypes. For the purpose, eight quantitative traits were measured from 30 wheat genotypes, which were in randomized complete block design with 3 replicates. Components of variance and covariance were estimated along with heritability, genetic gain, realized heritability, coheritability and correlated response. Differences between phenotypic and genotypic variances in heading days, maturity days and plant height were not large. Grain yield and plant height showed the highest phenotypic (18.189%) and genotypic (12.06%) coefficient of variances, respectively. Phenotypic covariance was higher than genotypic and environmental covariance in most of the traits. The highest heritability and realized heritability were of heading days followed by maturity days. Genetic gain for plant height was the highest. Co-heritability of 1000-grain weight with tillers number was the highest. The highest correlated response was expressed by grain yield with tillers number. This study indicates the possibility of improving wheat genotypes through selection utilizing existing variation in these traits.Journal of Nepal Agricultural Research Council Vol.1 2015 pp.9-1