Selection of Pyramided Barley Advanced Lines for Stripe Rust, Leaf Rust and Crown Rust Diseases Using Molecular Markers

Barley diseases are the major yield limiting factors for barley cultivation in Nepal. Stripe/Yellow rust (P. striformis f.sp. hordei and P. striformis f.sp. tritici), leaf rust (Puccinia hordei), and crown rust (P. coronata) are the major rust diseases in Nepal. Pyramiding resistance genes against all these rust diseases are possible through molecular marker assisted breeding. Sweden originated barley variety ‘Bonus’ is found resistant to stripe rust and having linked microsatellite markers for stripe rust and crown rust resistance. Similarly, Nepalese hull-less barley variety ‘Solu Uwa’ and Nepalese awn-less barley landrace NPGR Acc# 2478 have linked microsatellite markers for leaf rust resistance. Therefore, one polymorphic sequence tagged sites (STS) marker (ABG054) for stripe rust resistance, two polymorphic simple sequence repeats (SSR) markers (Bmac0144h and HVM049) for leaf rust and one polymorphic SSR marker (Bmag0006) for crown rust resistance were used to select the advanced barley lines (at F8 stage) from above parents. Field screening of stripe rust resistance was also conducted. Among 51 advanced and field disease resistance lines from Bonus/Solu Uwa cross, we have selected 10 pyramided lines for all three types of barley rust resistance. Similarly, among 39 advanced and field disease resistance lines from Bonus/NPGR Acc#2478 cross we have selected three pyramided lines and advanced for further yield testing for general cultivation purpose. The chances of losing the desired gene are high in late generation selection using molecular marker assisted selection (MAS); but the chances of getting agronomically superior varietal output will also increase

Genetic diversity analysis of commercial Arabica coffee in Nepal using Molecular markers

Coffee is an established plant for its flavor and has high commercial use. In Nepal, the popularity of coffee is increasing for its high economic value. However, its diversity and the status of its genetic mapping have not been studied in Nepal. In the present study, the genetic diversity of 28 coffee accessions was assessed by using twenty-four SSR markers with the aim of studying the variation of coffee in accord with the genetic markers from a molecular approach. With the use of DNA extraction and marker selection for its amplification using PCR tools, a total of 81 loci from SSR were identified. Of all SSR 63.22% showed for mean polymorphism. The mean polymorphic information content of SSR was 0.38, which showed low genetic diversity of SSR markers among Coffea genotypes.  On the basis of the SSR marker, the unweighted pair group method with arithmetic mean (UPGMA) dendrogram constructed showed a similar group of distribution among 28 accessions, which was further supported by a principle coordinate analysis scatter plot. The phylogenetic relationships among the accessions were assessed by SSR marker, which also showed low diversity in coffee genotypes. Our study demonstrated the use of SSR markers in diversity analysis as the data were informative and highly reproducible for evaluating relationships among coffee cultivars in Nepal. The use of more markers systems and a high genotype pool would have been beneficial in accessing more accurately. Regardless, the information from the phylogenetic relationship study could be useful for breeding, varietal improvement, and for conservation programs

Molecular Identification and Antioxidant Activity Determination among Coffee Varieties Cultivated in Nepal

Coffee is the most popular beverage containing numerous phytochemical components that have antioxidant activity capable of scavenging free radicals. Antioxidant and phenolic contents have considerable benefits for human health. The aim of this study was the molecular identification of 9 coffee samples from the Nepal Agricultural Research Council, Lalitpur, Nepal, and the determination of the antioxidant activity and total phenolic content of green and roasted coffee beans. Molecular identification was performed using ITS-specific PCR followed by sequencing and phylogenetic tree construction using the maximum parsimony method. The DPPH assay was used to determine the antioxidant activity, and the Folin–Ciocalteu (F-C) assay was used to determine the total phenolic content. All the samples belonged to the taxa Coffea arabica. The antioxidant activity in roasted beans varied from 2.49 to 4.62 AAE mg/g and from 1.4 to 3.9 AAE mg/g in green beans. The total phenolic content varied from 2.58 to 3.38 GAE mg/g and from 4.16 to 5.36 GAE mg/g for the roasted beans and green beans, respectively. The data revealed that the highest antioxidant content (4.62 AAE mg/g) was found in roasted coffee and that the highest phenolic content (5.36 GAE mg/g) was found in green coffee. The study concludes that roasting increases the antioxidant activity but decreases the phenolic content of coffee