Academic literature on the topic 'Barley Disease and pest resistance Genetic aspects'

Landraces play a key role in crop breeding by providing beneficial trait for improvement of related crops and their genetic diversity studies are very important for breeding program and identification of parental lines. In this study, 585 barley (Hordeum vulgare L.) landraces collected from 13 agro-ecological zones of Ethiopia were evaluated along with 10 cultivars for their phenotypic diversity and population structure in relation to agronomic traits, resistance to major diseases and barley shoot fly. Data on 22 agronomic traits, three major diseases and barley shoot fly resistance-related traits were recorded. Univariate and multivariate approaches such as principal component and cluster analyses were applied to assess the genetic diversity and population structure. The analysis of variance indicated significant genotypic main, accessions x year and accession x environment interaction effects for almost all the traits evaluated. However, the accessions x environment interactions were mainly due to changes in magnitude rather than crossover types of interactions. The diversity analysis indicated that the population was highly structured according to kernel row-type, region (geographic) origin and altitude classes. Since the population is highly structured, appropriate statistical models will be needed when this population is used for association mapping studies. Eight principal components (PCs) in principal component analysis (PCA) accounted for the variation of 83.01%. The most related traits were included in the same PC, implying that results from PCA could give clues as to the relationship among traits. Though variability existed within and among clusters, useful germplasm clustered together. These materials are important sources of germplasm for the improvement of agronomic, disease and insect pest resistance traits. Keywords: Barley, diseases, genetic diversity, landraces, multivariate, shoot fly

Landraces play a key role in crop breeding by providing beneficial trait for improvement of related crops and their genetic diversity studies are very important for breeding program and identification of parental lines. In this study, 585 barley (Hordeum vulgare L.) landraces collected from 13 agro-ecological zones of Ethiopia were evaluated along with 10 cultivars for their phenotypic diversity and population structure in relation to agronomic traits, resistance to major diseases and barley shoot fly. Data on 22 agronomic traits, three major diseases and barley shoot fly resistance-related traits were recorded. Univariate and multivariate approaches such as principal component and cluster analyses were applied to assess the genetic diversity and population structure. The analysis of variance indicated significant genotypic main, accessions x year and accession x environment interaction effects for almost all the traits evaluated. However, the accessions x environment interactions were mainly due to changes in magnitude rather than crossover types of interactions. The diversity analysis indicated that the population was highly structured according to kernel row-type, region (geographic) origin and altitude classes. Since the population is highly structured, appropriate statistical models will be needed when this population is used for association mapping studies. Eight principal components (PCs) in principal component analysis (PCA) accounted for the variation of 83.01%. The most related traits were included in the same PC, implying that results from PCA could give clues as to the relationship among traits. Though variability existed within and among clusters, useful germplasm clustered together. These materials are important sources of germplasm for the improvement of agronomic, disease and insect pest resistance traits. Keywords: Barley, diseases, genetic diversity, landraces, multivariate, shoot fly

The aim of the programme started at ARDI-Fundulea in 1999 is to improve the pest and disease resistance of cultivated barley (H. vulgare L.) by introgressing valuable genes from the wild species H. bulbosum L. The paper presents results on the development and cytogenetical characterization of primary genetic stocks represented by diploid, triploid and tetraploid interspecific hybrids and first backcrossed generation descendants. several sterile diploid hybrids were found during the phenotypic screening and cytological analysis of haploid progeny from H. vulgare 2x × H. bulbosum 2x crosses. These hybrids were treated with colchicine and fertile tetraploid hybrids were obtained. Significant improvements in the seed setting and in vitro triploid hybrid regeneration were obtained using doubled haploid lines (DHLs), previously selected for high interspecific crossability, in crosses with a tetraploid cytotype of H. bulbosum. Meiosis analysis of triploid hybrids provided compelling evidence that relatively high intergenomic allosyndetic pairing had occurred in some of the triploids with increased potential for crossing over and genetic recombination. High mean values for hybrid stability, multivalent associations in MI, higher chiasma frequency per PMC and partial pollen fertility were considered by far the most important criteria in the cytogenetic selection of triploid hybrids. Selected triploids were backcrossed to barley DHLs. Among the in vitro regenerated backcrossed progeny several putative substitution lines (SLs) were identified by preliminary cytological screening. The complete phenotypic and cytogenetic characterization and disease resistance tests of tetraploid hybrids and putative SLs or RLs are now in progress.

Ingestion of wheat, barley, or rye triggers small intestinal inflammation in patients with celiac disease. Specifically, the storage proteins of these cereals (gluten) elicit an adaptive Th1-mediated immune response in individuals carrying HLA-DQ2 or HLA-DQ8 as major genetic predisposition. This well-defined role of adaptive immunity contrasts with an ill-defined component of innate immunity in celiac disease. We identify the α-amylase/trypsin inhibitors (ATIs) CM3 and 0.19, pest resistance molecules in wheat, as strong activators of innate immune responses in monocytes, macrophages, and dendritic cells. ATIs engage the TLR4–MD2–CD14 complex and lead to up-regulation of maturation markers and elicit release of proinflammatory cytokines in cells from celiac and nonceliac patients and in celiac patients’ biopsies. Mice deficient in TLR4 or TLR4 signaling are protected from intestinal and systemic immune responses upon oral challenge with ATIs. These findings define cereal ATIs as novel contributors to celiac disease. Moreover, ATIs may fuel inflammation and immune reactions in other intestinal and nonintestinal immune disorders.

Proteinase inhibitors and thionins are among the many proteins thought to have a role in plant defence against pests and pathogens. Complementary DNA clones encoding the precursors of a multi-domain proteinase inhibitor from Nicotiana alata Link et Otto (NA-PI) (Mr approximately 43 000) and a β-hordothionin (β-HTH) (Mr approximately 13 000) from barley, were linked to constitutive promoters and subsequently transferred by Agrobacterium-mediated transformation into tobacco. The NA-PI and β-HTH precursor proteins were synthesised and post-translationally processed in transgenic tobacco and accumulated as polypeptides of apparent size Mr approximately 6000 and Mr approximately 8500, respectively. The na-pi and β-hth genes were stably inherited for at least two generations. Transgenic tobacco plants containing the highest amounts of NA-PI and β-HTH were crossed to produce plants containing both genes. Helicoverpa armigera (tobacco budworm) larvae that ingested transgenic tobacco leaves expressing both NA-PI and β-HTH, exhibited higher mortality and slower development relative to larvae fed on non-transgenic tobacco. NA-PI and β-HTH, either alone, or in combination, also conferred protection against the fungal pathogen, Botrytis cinerea (grey mould) and the bacterial pathogen, Pseudomonas solanacearum (bacterial wilt). The effect of the two proteins depended upon the organism tested and the contribution of each gene to the protective effects was not necessarily equal. The genetic engineering of plants with proteinase inhibitors or thionins, therefore, has potential for improving crop productivity by simultaneously increasing resistance to both pests and pathogens.

This study reviews published information on the tactical management decisions needed to maximise economic grain yield in winter-dominant rainfall regions of the Mediterranean type. Tactical decisions are defined as those relating to the period from immediately before sowing to harvest. Tactical management is the principal means by which farmers respond to changing environmental and short-term economic conditions as the season progresses. The review considers published evidence that underpins these decisions and relates to cereal crops (wheat, barley and oats), pulse crops (field pea, faba bean, chickpea and narrow-leaved lupin) and canola. The criteria used to guide management decisions during the season involve soil and tissue tests for nutrients, knowledge of weed numbers and resistance status in the current and previous seasons, weather conditions that favour disease development, and knowledge of thresholds and biology of insect pests that may warrant control measures. All of these decisions can be related to the timing of the opening rains and the length of the growing season; the crop, pasture or weeds present in the previous two seasons; the presence of pest- and disease-bearing crop residues; and the type of tillage in use. Most of these indicators require further refinement through research across environments, soil types, crop types and production systems. The likely interactions between tactical or short-term management decisions, longer term or strategic decisions, and genetic factors are discussed. The prevalent use of chemicals in the management of biotic factors that can impact the crops is noted, as is progress towards various systems of ‘integrated’ management of these threats to crop production. Most tactical decisions in rainfed cropping systems appear to be supported by adequate evidence, although some decisions are still based on practical experience and observations. Application of tactical management practices together with strategic management and use of improved genotypes provides the possibility of achieving rainfall-limited potential grain yield at a regional scale. The papers reviewed have been selected partly on the basis that the experimental treatments achieved the estimated potential grain yield. Where the potential grain yields are not being achieved in commercial crops, it remains unclear whether this is due to inadequate adoption of existing information or inadequate research to identify and address the underlying causes. We highlight the need to devise a simple decision aid to assist farmers and their advisers to respond to the variable seasonal conditions evident since the turn of the Century.

White clover (Trifolium repens L.) and red clover (T. pratense L.) are the most important legumes of temperate pastures. The former is used largely in systems based around sheep or cattle grazing and is grown together with a companion grass. Breeding aims to optimize the white clover contribution to the sward. This means that yield per se is not the aim but rather to take full advantage of the benefits of white clover; in particular, nitrogen fixation, high protein content, digestibility, mineral content and high intake. The objective is an agronomically and, as far as possible, nutritionally balanced sward, thus persistence of white clover and yield stability over a number of years are key goals. A considerable focus of germplasm improvement has therefore been overcoming biotic and abiotic stresses to clover performance. The former include not only pests and diseases but also the impact of the ruminant animal and the competitive interaction with the companion grass, while abiotic stress could be loosely defined as ‘winter hardiness’ and ‘summer survival’ depending on the site. In recent years the focus of many breeding efforts has shifted to give more consideration to the effects of variation within white clover germplasm on animal performance and the environment. Beneficial effects on productivity have been known for many years, but recent studies of the impact of forage diets on meat and milk quality have opened up new opportunities for improvement. Diffuse pollution of nitrogen and phosphorus from agricultural sources is high on the environmental protection agenda of many governments. Breeding efforts are now being made to reduce the contribution of clovers to both direct (leaching) and indirect (through animal returns) pollution. In particular, recent insights into mechanisms affecting protein breakdown in the rumen and silo offer new prospects for breeding interventions to reduce environmental impacts.Molecular marker methods are being developed in white clover and the transfer and use of resources and information accumulating in the model legumes Medicago truncatula and Lotus japonicus is likely to be a major route by which the power of genomic approaches is translated into forage legume improvement. Hybrids of white clover and related species have been developed to introgress key traits; namely, drought tolerance, grazing tolerance of large leaf types and enhanced seed yield, for which only limited genetic variation is present within the white clover gene pool.Red clover is less persistent than white clover, is typically cut three or more times in a season and is used to make silage for winter feed. Although it is often grown with a companion grass, monocultures are common and yield per se as well as persistency and pest and disease resistance are major breeding aims. Fewer agronomic studies and less germplasm improvement have been carried out in this species and molecular studies are not as well advanced although, as with white clover, future developments are likely to benefit greatly from a close relationship to model legumes. Red clover brings considerable benefits in terms of animal production and meat and milk quality. These aspects, alongside approaches to reduce nitrogenous pollution from the silo, represent considerable opportunities for variety development.

Agriculture production is directly dependent on climate change and weather. Possible changes in temperature, precipitation and CO2 concentration are expected to significantly impact crop growth and ultimately we lose our crop productivity and indirectly affect the sustainable food availability issue. The overall impact of climate change on worldwide food production is considered to be low to moderate with successful adaptation and adequate irrigation. Climate change has a serious impact on the availability of various resources on the earth especially water, which sustains life on this planet. The global food security situation and outlook remains delicately imbalanced amid surplus food production and the prevalence of hunger, due to the complex interplay of social, economic, and ecological factors that mediate food security outcomes at various human and institutional scales. Weather aberration poses complex challenges in terms of increased variability and risk for food producers and the energy and water sectors. Changes in the biosphere, biodiversity and natural resources are adversely affecting human health and quality of life. Throughout the 21st century, India is projected to experience warming above global level. India will also begin to experience more seasonal variation in temperature with more warming in the winters than summers. Longevity of heat waves across India has extended in recent years with warmer night temperatures and hotter days, and this trend is expected to continue. Strategic research priorities are outlined for a range of sectors that underpin global food security, including: agriculture, ecosystem services from agriculture, climate change, international trade, water management solutions, the water-energy-food security nexus, service delivery to smallholders and women farmers, and better governance models and regional priority setting. There is a need to look beyond agriculture and invest in affordable and suitable farm technologies if the problem of food insecurity is to be addressed in a sustainable manner. Introduction Globally, agriculture is one of the most vulnerable sectors to climate change. This vulnerability is relatively higher in India in view of the large population depending on agriculture and poor coping capabilities of small and marginal farmers. Impacts of climate change pose a serious threat to food security. “Food security exists when all people, at all times, have physical and economic access to sufficient, safe and nutritious food that meets their dietary needs and food preferences for an active and healthy life” (World Food Summit, 1996). This definition gives rise to four dimensions of food security: availability of food, accessibility (economically and physically), utilization (the way it is used and assimilated by the human body) and stability of these three dimensions. According to the United Nations, in 2015, there are still 836 million people in the world living in extreme poverty (less than USD1.25/day) (UN, 2015). And according to the International Fund for Agricultural Development (IFAD), at least 70 percent of the very poor live in rural areas, most of them depending partly (or completely) on agriculture for their livelihoods. It is estimated that 500 million smallholder farms in the developing world are supporting almost 2 billion people, and in Asia and sub-Saharan Africa these small farms produce about 80 percent of the food consumed. Climate change threatens to reverse the progress made so far in the fight against hunger and malnutrition. As highlighted by the assessment report of the Intergovernmental Panel on Climate change (IPCC), climate change augments and intensifies risks to food security for the most vulnerable countries and populations. Few of the major risks induced by climate change, as identified by IPCC have direct consequences for food security (IPCC, 2007). These are mainly to loss of rural livelihoods and income, loss of marine and coastal ecosystems, livelihoods loss of terrestrial and inland water ecosystems and food insecurity (breakdown of food systems). Rural farmers, whose livelihood depends on the use of natural resources, are likely to bear the brunt of adverse impacts. Most of the crop simulation model runs and experiments under elevated temperature and carbon dioxide indicate that by 2030, a 3-7% decline in the yield of principal cereal crops like rice and wheat is likely in India by adoption of current production technologies. Global warming impacts growth, reproduction and yields of food and horticulture crops, increases crop water requirement, causes more soil erosion, increases thermal stress on animals leading to decreased milk yields and change the distribution and breeding season of fisheries. Fast changing climatic conditions, shrinking land, water and other natural resources with rapid growing population around the globe has put many challenges before us (Mukherjee, 2014). Food is going to be second most challenging issue for mankind in time to come. India will also begin to experience more seasonal variation in temperature with more warming in the winters than summers (Christensen et al., 2007). Climate change is posing a great threat to agriculture and food security in India and it's subcontinent. Water is the most critical agricultural input in India, as 55% of the total cultivated areas do not have irrigation facilities. Currently we are able to secure food supplies under these varying conditions. Under the threat of climate variability, our food grain production system becomes quite comfortable and easily accessible for local people. India's food grain production is estimated to rise 2 per cent in 2020-21 crop years to an all-time high of 303.34 million tonnes on better output of rice, wheat, pulse and coarse cereals amid good monsoon rains last year. In the 2019-20 crop year, the country's food grain output (comprising wheat, rice, pulses and coarse cereals) stood at a record 297.5 million tonnes (MT). Releasing the second advance estimates for 2020-21 crop year, the agriculture ministry said foodgrain production is projected at a record 303.34 MT. As per the data, rice production is pegged at record 120.32 MT as against 118.87 MT in the previous year. Wheat production is estimated to rise to a record 109.24 MT in 2020-21 from 107.86 MT in the previous year, while output of coarse cereals is likely to increase to 49.36 MT from 47.75 MT. Pulses output is seen at 24.42 MT, up from 23.03 MT in 2019-20 crop year. In the non-foodgrain category, the production of oilseeds is estimated at 37.31 MT in 2020-21 as against 33.22 MT in the previous year. Sugarcane production is pegged at 397.66 MT from 370.50 MT in the previous year, while cotton output is expected to be higher at 36.54 million bales (170 kg each) from 36.07. This production figure seem to be sufficient for current population, but we need to improve more and more with vertical farming and advance agronomic and crop improvement tools for future burgeoning population figure under the milieu of climate change issue. Our rural mass and tribal people have very limited resources and they sometime complete depend on forest microhabitat. To order to ensure food and nutritional security for growing population, a new strategy needs to be initiated for growing of crops in changing climatic condition. The country has a large pool of underutilized or underexploited fruit or cereals crops which have enormous potential for contributing to food security, nutrition, health, ecosystem sustainability under the changing climatic conditions, since they require little input, as they have inherent capabilities to withstand biotic and abiotic stress. Apart from the impacts on agronomic conditions of crop productions, climate change also affects the economy, food systems and wellbeing of the consumers (Abbade, 2017). Crop nutritional quality become very challenging, as we noticed that, zinc and iron deficiency is a serious global health problem in humans depending on cereal-diet and is largely prevalent in low-income countries like Sub-Saharan Africa, and South and South-east Asia. We report inefficiency of modern-bred cultivars of rice and wheat to sequester those essential nutrients in grains as the reason for such deficiency and prevalence (Debnath et al., 2021). Keeping in mind the crop yield and nutritional quality become very daunting task to our food security issue and this can overcome with the proper and time bound research in cognizance with the environment. Threat and challenges In recent years, climate change has become a debatable issue worldwide. South Asia will be one of the most adversely affected regions in terms of impacts of climate change on agricultural yield, economic activity and trading policies. Addressing climate change is central for global future food security and poverty alleviation. The approach would need to implement strategies linked with developmental plans to enhance its adaptive capacity in terms of climate resilience and mitigation. Over time, there has been a visible shift in the global climate change initiative towards adaptation. Adaptation can complement mitigation as a cost-effective strategy to reduce climate change risks. The impact of climate change is projected to have different effects across societies and countries. Mitigation and adaptation actions can, if appropriately designed, advance sustainable development and equity both within and across countries and between generations. One approach to balancing the attention on adaptation and mitigation strategies is to compare the costs and benefits of both the strategies. The most imminent change is the increase in the atmospheric temperatures due to increase levels of GHGs (Green House Gases) i.e. carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O) and chlorofluorocarbons (CFCs) etc into the atmosphere. The global mean annual temperatures at the end of the 20th century were almost 0.7 degree centigrade above than those recorded at the end of the 19th century and likely to increase further by 1.8- 6.4ºC by 2100 AD. The quantity of rainfall and its distribution will be affected to a great extent resulting in more flooding. The changes in soil properties such as loss of organic matter, leaching of soil nutrients, salinization and erosion are a likely outcome of climate change in many cases. Water crisis can be a serious problem with the anticipated global warming and climate change. With increasing exploitation of natural resources and environmental pollution, the atmospheric temperature is expected to rise by 3-5 0C in next 75-100 years (www.ipcc.ch/sr15/chapter/chapter-1). If it happens most of the rivers originating from the Himalayas may dry up and cause severe shortage of water for irrigation, suppressing agriculture production by 40-50%. There has been considerable concern in recent years about climatic changes caused by human activities and their effects on agriculture. Surface climate is always changing, but at the beginning of industrial revolution these changes have been more noticeable due to interference of human beings activity. Studies of climate change impacts on agriculture initially focused on increasing temperature. Many researchers, including reported that changes in temperature, radiation and precipitation need to be studied in order to evaluate the impact of climate change. Temperature changes can affect crop productivity. Higher temperatures may increase plant carboxilation and stimulate higher photosynthesis, respiration, and transpiration rates. Meanwhile, flowering may also be partially triggered by higher temperatures, while low temperatures may reduce energy use and increased sugar storage. Changes in temperature can also affect air vapor pressure deficits, thus impacting the water use in agricultural landscapes. This coupling affects transpiration and can cause significant shifts in temperature and water loss (Mukherjee, 2017). In chickpea and other pulse crop this increase in temperature due to climate change affects to a greater extent flower numbers, pod production, pollen viability, and pistilfunction are reduced and flower and pod abortion increased under terminal heat stress which ultimately leads to hamper its productivity on large scale. There is probability of 10-40% loss in crop production in India with the expected temperature increase by 2080-2100. Rice yields in northern India during last three decades are showing a decreasing trend (Aggarwal et al., 2000). Further, the IPCC (2007) report also projected that cereal yields in seasonally dry and tropical regions like India are likely to decrease for even small local temperature increases. wheat production will be reduced by 4-5 million tonnes with the rise of every 10C temperature throughout the growing period that coincides in India with 2020-30. However, grain yield of rice declined by 10% for each 1ºC increase in growing season. A 1ºC increase in temperature may reduce rapeseed mustard yield by 3-7%. Thus a productivity of 2050-2562 kg/ha for rapeseed mustard would have to be achieved by 2030 under the changing scenario of climate, decreasing and degrading land and water resources, costly inputs, government priority of food crops and other policy imperatives from the present level of nearly 1200 kg/ha. Diseases and pest infestation In future, plant protection will assume even more significance given the daunting task before us to feed the growing population under the era of shifting climate pattern, as it directly influence pest life cycle in crop calendar (Mukherjee, 2019). Every year, about USD 8.5 billion worth of crops are lost in India because of disease and insects pests and another 2.5 billion worth of food grains in storages. In the scenario of climate change, experts believe that these losses could rise as high as four folds. Global warming and climate change would lead to emergence of more aggressive pests and diseases which can cause epidemics resulting in heavy losses (Mesterhazy et al., 2020). The range of many insects will change or expand and new combinations of diseases and pests may emerge. The well-known interaction between host × pathogen × environment for plant disease epidemic development and weather based disease management strategies have been routinely exploited by plant pathologists. However, the impact of inter annual climatic variation resulting in the abundance of pathogen populations and realistic assessment of climatic change impacts on host-pathogen interactions are still scarce and there are only handful of studies. Further emerging of new disease with climate alteration in grain crop such as wheat blast, become challenging for growers and hamper food chain availability (Mukherjee et al., 2019). Temperature increase associated with climatic changes could result in following changes in plant diseases: Extension of geographical range of pathogens Changes in population growth rates of pathogens Changes in relative abundance and effectiveness of bio control agents Changes in pathogen × host × environment interactions Loss of resistance in cultivars containing temperature-sensitive genes Emergence of new diseases/and pathogen forms Increased risk of invasion by migrant diseases Reduced efficacy of integrated disease management practices These changes will have major implications for food and nutritional security, particularly in the developing countries of the dry-tropics, where the need to increase and sustain food production is most urgent. The current knowledge on the main potential effects of climate change on plant patho systems has been recently summarized by Pautasso et al. (2012). Their overview suggests that maintaining plant health across diversified environments is a key requirement for climate change mitigation as well as the conservation of biodiversity and provisions of ecosystem services under global change. Changing in weed flora pattern under different cropping system become very challenging to the food growers, and threat to our food security issue. It has been estimated that the potential losses due to weeds in different field crops would be around 180 million tonnes valued Rs 1,05,000 crores annually. In addition to the direct effect on crop yield, weeds result in considerable reduction in the efficiency of inputs used and food quality. Increasing atmospheric CO2 and temperature have the potential to directly affect weed physiology and crop-weed interactions vis-à-vis their response to weed control methods. Many of the world’s major weeds are C4 plants and major crops are C3 plants (Mandal and Mukherjee, 2018). The differential effects of CO2 on C3 and C4 plants may have implications on crop-weed interactions. Weed species have a greater genetic diversity than most crops and therefore, under the changing scenario of resources (eg., light, moisture, nutrients, CO2), weeds will have the greater capacity for growth and reproductive response than most crops. Differential response to seed emergence with temperature could also influence species establishment and subsequent weed-crop competition. Increasing temperature might allow some sleeper weeds to become invasive (Mukherjeee, 2020; Science Daily, 2009). Studies suggest that proper weed management techniques if adopted can result in an additional production of 103 million tonnes of food grains, 15 million tonnes of pulses,10 million tonnes of oilseeds, and 52 million tonnes of commercial crops per annum, which in few cases are even equivalent to the existing annual production (Rao and Chauhan, 2015). There is tremendous scope to increase agricultural productivity by adopting improved weed management technologies that have been developed in the country. Conclusion The greatest challenge before us is to enhance the production of required amount of food items viz., cereals, pulses, oilseeds, vegetable, underutilized fruit etc to keep pace with population growth through employing suitable crop cultivars, biotechnological approaches, conserving natural resources and protecting crops from weeds, insects pests and diseases eco-friendly with climate change. Research is a continuous process that has to be pursued vigorously and incessantly in the critical areas viz., evolvement of new genotype, land development and reclamation, soil and moisture conservation, soil health care, seeds and planting material, enhancing fertilizer and water use efficiencies, conservation agriculture, eco-friendly plant protection measures etc. Due to complexity of crop environment interaction under different climate situation, a multidisciplinary approach to the problem is required in which plant breeders, agronomists, crop physiologists and agrometeorologists need to interact for finding long term solutions in sustaining crop production. References: Abbade, E. B. 2017. Availability, access and utilization: Identifying the main fragilities for promoting food security in developing countries. World Journal of Science, Technology and Sustainable Development, 14(4): 322–335. doi:10.1108/WJSTSD-05-2016-0033 Aggrawal, P.K., Bandyopadhyay, S. and Pathak, S. 2020. Analysis of yield trends of the Rice-Wheat system in north-western India. Outlook on Agriculture, 29(4):259-268. Christensen, J.H., Hewitson, B., Busuioc, A., Chen, A. and Gao, X, 2007. Regional Climate Projections. In: Climate Change 2007: The Physical Science Basis. Cambridge University Press. Cambridge, United Kingdom. Debnath, S., Mandal, B., Saha, S., Sarkar, D., Batabyal, K., Murmu, S., Patra, B.C., Mukherjee, and Biswas, T. 2021. Are the modern-bred rice and wheat cultivars in India inefficient in zinc and iron sequestration?. Environmental and Experimental Botany,189:1-7. (https://doi.org/10.1016/j.envexpbot.2021.104535) 2007. Climate Change 2007- Impacts, Adaptation and Vulnerability. Contribution of Working Group II to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change, M.L. Parry, O.F. Canziani, J.P. Palutikof, P.J. van der Linden and C.E. Hanson, Eds., Cambridge University Press, Cambridge, UK, 976pp. Mandal, B and Mukherjee, D. 2018. Influenced of different weed management Practices for Higher Productivity of Jute (Corchorus olitorius) in West Bengal. International Journal of Bioresource Science, 5 (1): 21-26. Mesterhazy, A., Olah, J. and Popp, J. 2020. Losses in the grain supply chain: causes and solutions. Sustainability, 12, 2342; doi:10.3390/su12062342. Mukherjee D. 2019. Effect of various crop establishment methods and weed management practices on growth and yield of rice. Journal of Cereal Research, 11(3): 300-303. http://doi.org/10.25174/2249-4065/2019/95811. Mukherjee, D. 2014. Climate change and its impact on Indian agriculture. In : Plant Disease Management and Microbes (eds. Nehra, S.). Aavishkar Publishers, Jaipur, India. Pp 193-206. Mukherjee, D. 2017. Rising weed problems and their effects on production potential of various crops under changing climate situation of hill. Indian Horticulture Journal, 7(1): 85-89. Mukherjee, D., Mahapatra, S., Singh, D.P., Kumar, S., Kashyap , P.L. and Singh, G.P. 2019. Threat assessment of wheat blast like disease in the West Bengal". 4th International Group Meeting on Wheat production enhancement through climate smart practices. at CSK HPKV, Palampur, HP, India, February, 14-16, 2019. Organized by CSK HPKV, Palampur and Society of Advancement of Wheat and Barley Research (SAWBAR). Journal of Cereal Research, 11 (1): 78. Mukherjee, D. 2020. Herbicide combinations effect on weeds and yield of wheat in North-Eastern plain. Indian Journal of Weed Science, 52 (2): 116–122. Pautasso, M. 2012. Observed impacts of climate change on terrestrial birds in Europe: an overview. Italian Journal of Zoology, 38:56-74. .Doi:10.1080/11250003.2011.627381 Rao, A.N. and Chauhan, B.S. 2015. Weeds and weed management in India -A Review. 25 Asian Pacific Weed Science Society Conference, at Hyderabad, India, Volume: 1 (A.N. Rao and N.T. Yaduraju (eds.). pp 87-118.

Barley yellow dwarf virus (BYDV), an aphid transmitted luteovirus, is the most widespread and economically damaging virus of cereal crops. The work in this thesis aims to characterise the basis of the naturally occurring resistance to BYDV in cereals in three ways: Firstly, by facilitating the isolation of the Yd2 gene for BYDV resistance from barley by a map-based approach. Secondly, by determining if a BYDV resistance gene in rice is orthologous to Yd2. Thirdly, by establishing if other BYDV resistance genes in non- Ethiopian barleys are allelic to Yd2. It is hoped that the information generated in this study will ultimately assist in the production of BYDV resistant cereal cultivars. A detailed genetic map of the Yd2 region of barley chromosome 3 was constructed, containing 19 RFLP loci, the centromere and the Yd2 gene. Yd2 mapped on the long arm, 0.5 cM from the centromere, and in the mapping population of 106 F2 individuals, perfectly cosegregated with the RFLP loci XYlp, and Xwg889. This map represents the first stage in a project to isolate the Yd2 gene by a map-based approach. The isolation of Yd2 could help to elucidate the molecular mechanism of the Yd2-mediated BYDV resistance, and may allow the production of BYDV resistant cereals by genetic transformation. The RFLP markers mapped closest to Yd2 could also be useful in barley breeding, by enabling selection for both the presence of Yd2 and the absence of agronomically undesirable traits known to be closely linked to Yd2. Genetically Directed Representational Difference Analysis (GDRDA) is a technique based on subtractive hybridisation, which can be used to identify RFLP markers closely linked to a gene of interest. Two GDRDA experiments were performed with the intention of generating additional RFLP markers close to Yd2. However, the first experiment yielded RFLP probes that were not derived from the barley genome, while the second experiment yielded probes that detected repetitive sequences. It was concluded that GDRDA is of limited use in generating further markers close to Yd2. To isolate the Yd2 gene by a map-based approach, a much larger mapping population will need to be analysed to genetically resolve markers tightly linked to Yd2. If the two morphological markers uzu dwarf and white stripe,,j flank Yd2, then they could assist in this task by enabling the visual identification of F2 seedlings resulting from recombination close to Yd2. However, in this study, both morphological markers were found to be located distal to Yd2. Therefore, these two morphological markers can not be used together to facilitate high resolution genetic mapping of the Yd2 locus. It may be possible to use large-insert genomic DNA clones from the relatively small genome of rice to generate further RFLP markers close to the Yd2 gene in barley, provided that the order of orthologous sequences in barley and rice is conserved close to the Yd2 locus. To assess the feasibility of this approach, RFLP probes used to identify loci close to Yd2 were mapped in rice using a segregating rice F2 population. Five of the RFLP loci mapped together and in the same order as RFLP loci mapped close to Yd2 in barley using the same probes. By comparing the location of RFLPs mapped by other researchers in rice using probes mapped close to Yd2, the region of conserved linkage between rice and the Yd2 region was tentatively identified as the central portion of rice chromosome 1. The collinearity shown by orthologous sequences in barley and rice indicated that it may indeed be possible to use rice to assist in generating RFLP markers close to Yd2. Of all the cereals, rice is the most amenable to map-based gene isolation, due to its small genome, well developed physical and genetic maps, and its ability to be genetically transformed with high efficiency. If a BYDV resistance gene that is orthologous to Yd2 could be identified in rice, this gene could be isolated with relative ease, and then used to identify barley cDNA clones corresponding to Yd2 gene by virtue of the sequence homology expected between these genes. To test if a BYDV resistance gene from an Italian rice line is orthologous to Yd2, recombinant-inbred rice lines previously characterised for this gene were analysed using probes mapped close to Yd2 in barley. No genetic linkage was detected between the RFLP loci and the BYDV resistance gene, indicating that the gene is unlikely to be orthologous to Yd2. BYDV resistance alleles at the Yd2 locus which are of a non-Ethiopian origin may show interesting differences to Ethiopian Yd2 resistance alleles. To identify barleys which may contain resistance alleles of Yd2, ten BYDV resistant barleys not known to contain Yd2 were assessed for their resistance to the PAVadel isolate of BYDV in the glasshouse. CI 1179, Rojo, Perry, Hannchen, Post and CI 4228 were found to be the most resistant under these conditions, and were analysed further. If the resistance from these barleys is controlled by alleles of Yd2, RFLP markers close to Yd2 will be expected to cosegregate with the resistance in F2 families derived from crosses between these resistant barleys and the BYDV susceptible barleys Atlas and Proctor. RFLPs suitable for use in these allelism tests were identified using probes mapped close to Yd2. However, time did not permit the analysis of these F2 populations.
Thesis (Ph.D.) -- University of Adelaide, Dept. of Plant Science, 1996

Bibliography: leaves 118-132. This thesis examines the structure and gene expression of barley yellow dwarf viruses (BYDVs)-PAV in order to gain a better understanding of the interaction between the virus and the Yd2 resistance gene. The protein products of open reading frame (ORF)3, ORF4 and ORF5 are expressed in bacterial cells, in order to characterise the BYDV-PAV virion-associated proteins. The effect of the Yd2 resistance gene on the expression of the BYDV-PAV viral proteins in infected cells is also studied.

Doctor of Philosophy
The responses of 92 barley genotypes to selected P. hordei pathotypes was assessed in greenhouse tests at seedling growth stages and in the field at adult plant growth stages to determine known or unknown resistances. On the basis of multipathotype tests, 35 genotypes were postulated to carry Rph2, Rph4, Rph5, Rph12, RphCantala alone or combinations of Rph2 + Rph4 and Rph1 + Rph2, whereas 52 genotypes lacked detectable seedling resistance to P. hordei. Five genotypes carried seedling resistance that was effective to all pathotypes tested, of which four were believed to carry uncharacterised resistance based on pedigree information. Field tests at adult plant growth stages indicated that while 28 genotypes were susceptible, 57 carried uncharacterised APR to P. hordei. Pedigree analysis indicated that APR in the test genotypes could have been derived from three different sources. The resistant responses of seven cultivars at adult plant growth stages were believed to be due to the presence of seedling resistance effective against the field pathotypes. Genetic studies conducted on 10 barley genotypes suggested that ‘Vada’, ‘Nagrad’, ‘Gilbert’, ‘Ulandra (NT)’ and ‘WI3407’ each carry one gene providing adult plant resistance to P. hordei. Genotypes ‘Patty’, ‘Pompadour’ ‘Athos’, ‘Dash’ and ‘RAH1995’ showed digenic inheritance of APR at one field site and monogenic inheritance at a second. One of the genes identified in each of these cultivars provided high levels of APR and was effective at both field sites. The second APR gene was effective only at one field site, and it conferred low levels of APR. Tests of allelism between resistant genotypes confirmed a common APR gene in all genotypes with the exception of ‘WI3407’, which based on pedigree information was genetically distinct from the gene common in ‘Vada’, ‘Nagrad’, ‘Patty’, ‘RAH1995’ and ‘Pompadour’. An incompletely dominant gene, Rph14, identified previously in an accession of Hordeum vulgare confers resistance to all known pathotypes of P. hordei in Australia. The inheritance of Rph14 was confirmed using 146 and 106 F3 lines derived from the crosses ‘Baudin’/ ‘PI 584760’ (Rph14) and ‘Ricardo’/‘PI 584760’ (Rph14), respectively. Bulk segregant analysis on DNA from the parental genotypes and resistant and susceptible DNA bulks from F3 lines using diversity array technology (DArT) markers located Rph14 to the short arm of chromosome 2H. Polymerase chain reaction (PCR) based marker analysis identified a single simple sequence repeat (SSR) marker, Bmag692, linked closely to Rph14 at a map distance of 2.1 and 3.8 cM in the populations ‘Baudin’/ ‘PI 584760’and ‘Ricardo’/‘PI 584760’, respectively. Seedlings of 62 Australian and two exotic barley cultivars were assessed for resistance to a variant of Puccinia striiformis, referred to as BGYR, which causes stripe rust on several wild Hordeum species and some genotypes of cultivated barley. With the exception of six Australian barley cultivars and an exotic cultivar, all displayed resistance to the pathogen. Genetic analyses of six Australian barley cultivars and the Algerian barley ‘Sahara 3771’, suggested that they carried either one or two major seedling resistance genes to the pathogen. A single recessive seedling resistance gene, Bgyr1, identified in ‘Sahara 3771’ was located on the long arm of chromosome 7H and flanked by restriction fragment length polymorphism (RFLP) markers wg420 and cdo347 at genetic distances of 12.8 and 21.9 cM, respectively. Mapping resistance to BGYR at adult plant growth stages using a doubled haploid population derived from the cross ‘Clipper’/‘Sahara 3771’ identified two major QTLs on the long arms of chromosomes 3H and 7H that explained 26 and 18% of total phenotypic variation, respectively. The QTL located on chromosome 7HL corresponded to the seedling resistance gene Bgyr1. The second QTL was concluded to correspond to a single adult plant resistance gene designated Bgyr2, originating from cultivar ‘Clipper’.

Little is known about the mechanism of virus disease resistance in plants. The aim of the work presented here was to answer whether disease resistance is offered within the cell or at the level of intercellular movement of the virus. The protoplast system was used for this purpose. Conditions were optimized to isolate viable protoplasts from the leaves of Lactuca sativa cultivars. Protoplasts and leaves from resistant and susceptible Lactuca sativa cultivars were inoculated separately with turnip mosaic virus (TuMV) and lettuce mosaic virus (LMV), Virus multiplication was examined over time using enzyme-linked immunosorbent assay. Resistant cv. Kordaat did not support TuMV multiplication in protoplasts as well as in leaves. The results indicated that resistance to TuMV is available within the cell. The results ruled out the possibility of involvement of cell to cell movement and resistance to TuMV seems to be constitutive. On the other hand, protoplasts and leaves from both resistant and susceptible lettuce cultivars supported LMV multiplication. This suggested that resistance to LMV may not be offered within the cell. The results also indicated that the resistance to LMV was partly due to a hypersensitive response though virus was still able to spread systemically. To contribute towards mapping of the Tu resistance gene, the genotype of F$ sb2$ individuals was determined by screening an F$ sb3$ population from 71 F$ sb2$ individuals of a cross between cv. Calmar and cv. Kordaat for TuMV-infection. These data were useful for the production of bulks around the Tu locus to facilitate the search for new molecular markers linked to the Tu gene.

To study resistance (R) genes that are expressed when Sophrolaeliacattleya Ginny Champion 'Riverbend' orchid tissue was infected with the tobacco mosaic virus (TMV0), a subtraction library of cDNA clones was previously constructed using mRNA isolated before and after infection (Shuck, unpublished). From 200 clones collected, 5 clones were randomly selected, DNA was isolated, and the cDNA insert was sequenced. These sequences were imported into BLAST to search for homology to other R genes. This search revealed clone 4A to have an 84% homology to a 54 nucleotide region from the Arabidopsis thaliana oligouridylate binding protein which is highly expressed and known to bind RNA Polymerase III transcripts and adenovirus associated RNAs. Further bioinformatics analysis was performed utilizing databases and analysis packages available on the Internet, software such as Vector NTI (Informax, Bethesda, MD), and manual searches. However, no additional domains or motifs indicative of pathogen resistance genes were located in any of the 5 clones. Subsequently, total proteins expressed at various time points following infection were examined on denaturing 5-20% gradient polyacrylamide gels stained with the ProteoSilver Plus TM silver stain kit (Sigma, St. Louis, MO) in order to examine the timing and duration of expression of proteins involved in TMV-O resistance. One protein of-18 kDa was highly expressed at 4 hr after infection that was not seen in the negative control. By 8 hr the band was no longer expressed, it was expressed again from 30 - 48 hr, but was not seen again in later time points. Finally, total mRNA isolated from pooled time points and subjected to in vitro translation indicated a reduction in translation products after infection, providing evidence of posttranscriptional gene silencing (PTGS) following TMV-O infection.
Department of Biology