Pepper (Capsicum annum L.) fruit colours vary from green, ivory, or yellow at the juvenile stage to red, orange, and yellow at the mature stage. Carotenoid accumulation causes fruit colour formation in ripe Capsicum fruits, and capsanthin is a main carotenoid in ripe red pepper fruits. In this study, pepper cultivars with red, yellow, and orange fruits were employed and four key genes named phytoene synthase (Psy), lycopene-β-cyclase (Lcyb), β-carotene hydroxylase (Crtz), and capsanthin/capsorubin synthase (Ccs) in the capsanthin biosynthetic pathway were analyzed. Results show that a clear expression of the Ccs gene in cv. CK7 (yellow) was detected, but the expressions of the Psy and Lcyb genes were low comparing with the other tested cultivars. In addition, the expression of the Ccs gene was not observed in cv. R37-1 (orange). Furthermore, though the four key genes (Psy, Lcyb, Crtz, and Ccs) were detected in red cultivar R15, the expressions of them were low. Sequence analysis further indicated that the Ccs genes in cv. CK7 and cv. R37-1 had a high sequence identity (97.36 %). Interestingly, amino acid sequences coded by the Ccs genes from cv. CK7, cv. R37-1, and cv. R15 were the same. The above results suggest that the genes Psy, Lcyb, Crtz, and Ccs were required for capsanthin synthesis in pepper, and their varied expression patterns resulted in the variety of pepper fruit colours.

The relationship between red fruit colour formation and key genes of capsanthin biosynthesis pathway in Capsicum annuum

Mango is a major fruit crop grown commercially in tropical and subtropical environments globally. It is a highly efficient fruit crop, provides a large supply of fresh fruit and is also a source of timber. Although mango is an economically important tropical fruit, relatively little research has been conducted on its genetics and gene sequence. In the last few decades, conventional breeding attempts have played an important role in mango improvement. There are many problems with mangoes being handled in breeding programs. Mangoes are characterized by having a long juvenile phase, monoembryonic varieties, being highly cross pollinating, having a heavy fruit drop and having alternate crop bearing loads from year to year. All these delay success in mango improvement. Biotechnology can complement conventional breeding and expedite the mango improvement programme. In different mango growing regions, molecular breeding attempts are in progress for creating better cultivars or varieties by selecting attractive, high yielding and good quality mangoes. A few molecular researchers have performed in vitro culture and selection, micro-propagation, embryo rescue, gene cloning, genetic transformation, marker-assisted characterization and DNA fingerprinting. Precise information on the genetic relationship within germplasm diversity is needed for carrying out an efficient breeding programme. In this chapter we described the application of recent molecular biotechniques for the improvement of mango production.

Recent application of biotechniques for the improvement of mango research

Photosynthetic performance is determined by scion/rootstock combination in mango seedling propagation

....................................................................................................................... ii ACKNOWLEDGMENTS .................................................................................................. v DEDICATION ................................................................................................................... vi LIST OF TABLES .............................................................................................................. x LIST OF ILLUSTRATIONS ............................................................................................. xi CHAPTER I – INTRODUCTION ...................................................................................... 1 Background of the Study ................................................................................................ 1 Research Questions ......................................................................................................... 4 Purpose of the Study ....................................................................................................... 5 Hypotheses ...................................................................................................................... 6 Assumptions .................................................................................................................... 7 Delimitations ................................................................................................................... 7 Definitions and Acronyms .............................................................................................. 7 Justification ..................................................................................................................... 9 CHAPTER II – REVIEW OF RELATED LITERATURE .............................................. 11 Soil ................................................................................................................................ 12 Soil Compaction – Indicator of Soil Physical Health ................................................... 14 Soil Organic Matter (SOM) .......................................................................................... 17 Agricultural Soil Ecosystems and Bacterial Diversity.................................................. 19 viii Soil Bacterial Diversity Studies .................................................................................... 21 Soil Bacterial Diversity and Metagenomics ................................................................. 24 Functional Analysis .................................................................................................. 25 Sable Isotope Probing (SIP) ...................................................................................... 25 Denaturing Gradient Gel Electrophoresis (DGGE) and Temperature Gradient Gel Electrophoresis (TGGE) ........................................................................................... 26 Restriction Fragment Length Polymorphism (RFLP)............................................... 26 Next Generation Sequencing (NGS) ......................................................................... 27 Soil Phosphatases .......................................................................................................... 29 Soil Compaction and Soil Biology ............................................................................... 33 Tillage in Agriculture .................................................................................................... 35 Types of Conservation Tillage Practices .................................................................. 38 Zero Tillage (no-till/minimum tillage): ................................................................ 38 Ridge Tillage ......................................................................................................... 38 Mulch Tillage ........................................................................................................ 38 Deoxyribose Nucleic Acid (DNA) ................................................................................ 39 CHAPTER III METHODOLOGY ................................................................................. 41 Collection of Soil Samples............................................................................................ 41 Elemental Analysis of Soil Samples ............................................................................. 42 Soil Compaction Analysis............................................................................................. 44 ix Acid Phosphatase Activity in Soils ............................................................................... 44 Metagenomic Analysis.................................................................................................. 45 CHAPTER IV – ANALYSIS OF DATA ......................................................................... 52 Soil pH .......................................................................................................................... 55 Elemental Analysis of the Soil Samples ....................................................................... 56 Soil Cone Index – Penetration Resistance .................................................................... 58 Acid Phosphatase Activity ............................................................................................ 59 Metagenomic Analysis: Number of Operational Taxonomic Units (OTU). ................ 60 Metagenomic Analysis: Number of Phyla. ................................................................... 61 Metagenomic Analysis: Taxonomic Distribution ......................................................... 62 CHAPTER V – SUMMARY ............................................................................................ 65 Impact of Soil Tillage on Soil ....................................................................................... 65 Effect of Tillage on Soil Compaction ........................................................................... 66 Effect of Tillage on Soil Phosphatase Activity ............................................................. 67 Effect of Tillage on Soil Bacterial Diversity ................................................................ 69 Conclusions ................................................................................................................... 71 APPENDIX A – Data Tables ............................................................................................ 74 REFERENCES ................................................................................................................. 76

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The Influence of Conservation Tillage and Conventional Tillage on Soil Bacterial Diversity in Southern Illinois

Lonicera japonica flos (LJF), the dried flower buds of L. japonica Thunb., have been used in traditional Chinese herbal medicine for thousands of years. Recent studies have reported that LJF has many medicinal properties because of its antioxidative, hypoglycemic, hypolipidemic, anti-allergic, anti-inflammatory, and antibacterial effects. LJF is widely used in China in foods and healthcare products, and is contained in more than 30% of current traditional Chinese medicine prescriptions. Because of this, many Chinese villages cultivate LJF instead of traditional crops due to its high commercial value in the herbal medicine market. Since 2005, the flower buds of L. japonica are the only original LJF parts considered according to the Chinese Pharmacopoeia of the People's Republic of China. However, for historical and commercial reasons, some closely related species of Lonicera Linn. continue to be mislabeled and used as LJF. Currently, there are hundreds of commercial varieties of LJF on the market and it is difficult to choose fine LJF varieties to cultivate. In this study, a total of 21 varieties labeled as LJF on the market were planted in the Hailuogou area. In order to choose the optimum variety, internal transcribed spacer (ITS) sequence alignment analysis was used to test whether the 21 varieties were genuine LJF or not. Cluster analysis of active components based on the content of chlorogenic acid and luteoloside in flower buds, stems and leaves was used to evaluate the quality of the varieties. Results demonstrated that four of the varieties were L. macranthoides Hand.-Mazz., while the other 17 varieties were L. japonica, and genuine LJF. The ITS sequence analysis was proven to be highly effective in identifying LJF and Lonicerae flos. Among the 17 L. japonica varieties, the amounts of chlorogenic acid and luteoloside in flower buds, stems and leaves were significantly different. Based on the cluster analysis method, the variety H11 was observed to have the highest level of active components, and is therefore recommended for large-scale planting in the Hailuogou area.

Identification and evaluation of Lonicera japonica flos introduced to the Hailuogou area based on ITS sequences and active compounds.

High quality genomic DNA is the first step in the development of DNA-based markers for fingerprinting and genetic diversity of crops, including mango (Mangifera indica L.), a woody perennial. Poor quality genomic DNA hinders the successful application of analytical DNA-based tools. Standard protocols for DNA extraction are not suitable for mango since the extracted genomic DNA often contains secondary metabolites that interfere with analytical applications. In this study, we employed an additional step to remove polysaccharides, polyphenols and secondary metabolites from genomic DNA extracted from young or mature leaf tissue; then a modified traditional cetyl trimethyl ammonium bromide (CTAB) method was applied. The use of 0.4 M glucose improved DNA quality and avoided contamination and browning by polyphenolics, relative to the traditional CTAB method. This is an easy and efficient method for genomic DNA extraction from both young and mature leaves of mango. The isolated DNA was free of polysaccharides, polyphenols, RNA and other major contaminants, as judged by its clear colour, its viscosity, A260/A280 ratio and suitability for PCR-based reactions. This modified protocol was also used to extract high quality genomic DNA from other woody perennials, including walnut, guava, lychee, pear, grape and sugarcane.

An improved method to extract DNA from mango Mangifera indica

The amplification of nucleic acid is essential for many analyses requiring DNA. Current techniques require sophisticated equipment or complex experimental procedures whose implementation may be limited to outsourcing to other laboratories, or a continuous electricity supply that is expensive and inaccessible in many regions. In this study, a novel approach, recombinase-aided amplification (RAA), was used to rapidly amplify DNA. Since primer length is one factor that can influenc e the success of DNA amplification, i n this assay, 18 primer pairs were tested between 18 and 28 base pairs in length. Four of these were applied to seven horticultural crops: mango (Mangifera indica L. var. ‘Tainong no.1’), Manchurian walnut (Juglans mandshurica Maxim.), Chinese pear (Pyruspyrifolia (Burm.) Nak), grape (Vitisvinifera L. var. ‘Thompson ’), Cattley guava (Psidium cattleianum Sabine var. ‘Littorale’), lychee (Litchi chinensis Sonn. var.‘Bobaitangbo’) and Chinese sugarcane (Saccharum sinense L.). RAA could successfully and consistently amplify the DNA of all seven horticultural crops.

Successful Amplification of DNA Using Recombinase-Aided Amplification (RAA) and its Application to Seven Horticultural Crops

Black pepper (Piper nigrum) is recognized as "Black Gold" and "King of Spices" because of its widespread use in culinary preparation, food flavoring, and condiment seasoning. It has worldwide fragrance and medical use. The purpose of the conducted research was to investigate growth performance of P. nigrum cuttings in various rooting media and growth regulators concentrations in a low-cost non-mist propagation chamber at the Agroforestry Field Laboratory, Department of Agroforestry and Environmental Science, Sylhet Agricultural University, Sylhet during the period starting from August 2019 to June' 2020. The experiment consisted of two factors: different rooting media and different concentrations of growth regulator, IBA (Indole 3-Butyric Acid). Under the first factor, there were four treatments, namely M1= biochar, M2= vermicompost, M3= well-decomposed cow dung, and M4= field soil as control. Under the second factor, there were four treatments, namely R1= 0.2%, R2= 0.4% and R3= 0.8%, and R4= 0.0% of IBA. The whole experiment was designed in a factorial RCBD (Randomized Complete Block Design) with three replications. Among the different media, M1 treatment (biochar) exhibited superior performance concerning vine length and the number of nodes per vine. On the other hand, R2 treatment (0.4%) concentration of IBA showed better performance regarding the number of roots and vine length. The research found that the growth performance of P. nigrum cuttings are accelerated through integrating rooting media and growth regulators. Consequently, the demand for planting materials could be met.

Mohammad Sorof Uddin

Papers

An improved method to extract DNA from mango Mangifera indica

Recent application of biotechniques for the improvement of mango research

Successful Amplification of DNA Using Recombinase-Aided Amplification (RAA) and its Application to Seven Horticultural Crops

Growth Performance of Black Pepper (P. nigrum) Cuttings in Different Rooting Media and Growth Regulators