Genetic analysis of adaptation differences between highland and lowland tropical maize using molecular markers

Molecular-marker loci were used to investigate the adaptation differences between highland and lowland tropical maize. An F2 population from the cross of two inbred lines independently derived from highland and lowland maize germplasm was developed, and extracted F3:4 lines were phenotype in replicated field trials at four thermally diverse tropical testing sites, ranging from lowland to extreme highland (mean growing season temperature range 13.2–24.6°C). Traits closely related with adaptation, such as biomass and grain yield, yield components, days from sowing to male and female flowering, total leaf number, plant height and number of primary tassel branches (TBN), were analyzed. A large line ´ environment interaction was observed for most traits. The genetic basis of this interaction was reflected by significant, but systematic, changes from lowland to highland sites in the correlation between the trait value and genomic composition (designated by the proportion of marker alleles with the same origin). Joint analysis of quantitative trait loci (QTLs) over sites detected 5–8 QTLs for each trait (except disease scores, with data only from one site). With the exception of one QTL for TBN, none of these accounted for more than 15% of the total phenotypic variation. In total, detected QTLs accounted for 24–61% of the variation at each site on average. For yield, yield components and disease scores, alleles generally favored the site of origin. Highland-derived alleles had little effect at lowland sites, while lowland- derived alleles showed relatively broader adaptation. Gradual changes in the estimated QTL effects with increasing mean site temperature were observed, and paralleled the observed patterns of adaptation in high land and lowland germplasm. Several clusters of QTLs for different traits reflected the relative importance in the adaptation differences between the two germplasm types, and pleiotropy is suggested as the main cause for the clustering. Breeding for broad thermal adaptation should be possible by pooling genes showing adaptation to specific thermal regimes, though perhaps at the expense of reduced progress for adaptation to a specific site. Molecular marker-assisted selection would be an ideal tool for this task, since it could greatly reduce the linkage drag caused by the unintentional transfer of undesirable trait

Interpreting genotype × environment interaction in tropical maize using linked molecular markers and environmental covariables

An understanding of the genetic and environmental basis of genotype´environment interaction (GEI) is of fundamental importance in plant breeding. In mapping quantitative trait loci (QTLs), suitable genetic populations are grown in different environments causing QTLs´environment interaction (QEI). The main objective of the present study is to show how Partial Least Squares (PLS) regression and Factorial Regression (FR) models using genetic markers and environmental covariables can be used for studying QEI related to GEI. Biomass data were analyzed from a multi-environment trial consisting of 161 lines from a F3:4 maize segregating population originally created with the purpose of mapping QTLs loci and investigating adaptation differences between highland and lowland tropical maize. PLS and FR methods detected 30 genetic markers (out of 86) that explained a sizeable proportion of the interaction of maize lines over four contrasting environments involving two low-altitude sites, one intermediate-altitude site, and one high-altitude site for biomass production. Based on a previous study, most of the 30 markers were associated with QTLs for biomass and exhibited significant QEI. It was found that marker loci in lines with positive GEI for the highland environments contained more highland alleles, whereas marker loci in lines with positive GEI for intermediate and lowland environments contained more lowland alleles. In addition, PLS and FR models identified maximum temperature as the most-important environmental covariable for GEI. Using a stepwise variable selection procedure, a FR model was constructed for GEI and QEI that exclusively included cross products between genetic markers and environmental covariables. Higher maximum temperature in low- and intermediatealtitude sites affected the expression of some QTLs, while minimum temperature affected the expression of other QTLs

Crop Updates - 2009 Katanning

This session covers seventeen papers from different authors GM canola – How will it affect the way I farm? Murray Scholz, 2008 Nuffield scholar, Southern NSW Eight years of IWM smashes tyegrass seed banks by 98% over 31 focus paddocks, Peter Newman, Glenn Adam & Trevor Bell, Department of Agriculture and Food The global economic climate and impacts on agriculture, profile on Michael Whitehead Rabobank New York Lessons from five years of cropping systems research, W.K. Anderson, Department of Agriculture and Food Case study of a 17year old agricultural lime trial, C. Gazey, Department of Agriculture and Food, J. Andrew, Precision SoilTech and R. Pearce, ConsultAg Fertilising in a changing price environment, Bill Bowden, Wayne Pluske and Jeremy Lemon, Department of Agriculture and Food Fact or Fiction: Who is telling the truth and how to tell the difference? D.C. Edmeades, agKnowledge Ltd, Hamilton Forecast disease resistance profile for the Western Australian barley crop over the next three years, JJ Russell, Department of Agriculture and Food Malting barley varieties differ in their flowering date and their response to change in sowing date, BH Paynter and JJ Russell, Department of Agriculture and Food Decimating weed seed banks within non-crop phases for the benefit of subsequent crops, Dr Davis Ferris, Department of Agriculture and Food Autumn cleaning yellow serradella pastures with broad spectrum herbicides – a novel weed control strategy that exploits delayed germination, Dr Davis Ferris, Department of Agriculture and Food Emerging weeds in changing farming systems, Dr Abul Hashen, Department of Agriculture and Food More glyphosate-resistant annual ryegrass populations within Western Australia, Dr Abul Hashem and Dr Catherine Borger, Department of Agriculture and Food Reasons to use only the full label herbicide rate, Stephen B. Powels, Qin Yu, Mechelle Owen, Roberto Busi, Sudheesh Manalil, University of Western Australia Flaxleaf fleabane – coming to a property near you! Sally Peltzer, Department of Agriculture and Food Glyphosate – the consequences of cutting rates! Sally Peltzer and David Minkey, Department of Agriculture and Food Benefits of crop rotations/break crops in managing soil moisture, soil health, weeds and disease – an overview, Raj Malik, Department of Agriculture and Foo

Association and Linkage Analysis of Aluminum Tolerance Genes in Maize

Aluminum (Al) toxicity is a major worldwide constraint to crop productivity on acidic soils. Al becomes soluble at low pH, inhibiting root growth and severely reducing yields. Maize is an important staple food and commodity crop in acidic soil regions, especially in South America and Africa where these soils are very common. Al exclusion and intracellular tolerance have been suggested as two important mechanisms for Al tolerance in maize, but little is known about the underlying genetics. linkage populations with approximately 200 individuals each were used to study genetic variation in this complex trait. Al tolerance was measured as net root growth in nutrient solution under Al stress, which exhibited a wide range of variation between lines. Comparative and physiological genomics-based approaches were used to select 21 candidate genes for evaluation by association analysis.). These four candidate genes are high priority subjects for follow-up biochemical and physiological studies on the mechanisms of Al tolerance in maize. Immediately, elite haplotype-specific molecular markers can be developed for these four genes and used for efficient marker-assisted selection of superior alleles in Al tolerance maize breeding programs

Enhancing Nutrient Use Efficiencies in Rainfed Systems

Successful and sustained crop production to feed burgeoning population in rainfed areas, facing soil fertility-related degradation through low and imbalanced amounts of nutrients, requires regular nutrient inputs through biological, organic or inorganic sources of fertilizers. Intensification of fertilizer (all forms) use has given rise to concerns about efficiency of nutrient use, primarily driven by economic and environmental considerations. Inefficient nutrient use is a key factor pushing up the cost of cultivation and pulling down the profitability in farming while putting at stake the sustainability of rainfed farming systems. Nutrient use efficiency implies more produce per unit of nutrient applied; therefore, any soil-water-crop management practices that promote crop productivity at same level of fertilizer use are expected to enhance nutrient use efficiency. Pervasive nutrient depletion and imbalances in rainfed soils are primarily responsible for decreasing yields and declining response to applied macronutrient fertilizers. Studies have indicated soil test-based balanced fertilization an important driver for enhancing yields and improving nutrient use efficiency in terms of uptake, utilization and use efficiency for grain yield and harvest index indicating improved grain nutritional quality. Recycling of on-farm wastes is a big opportunity to cut use and cost of chemical fertilizers while getting higher yield levels at same macronutrient levels. Best management practices like adoption of high-yielding and nutrient-efficient cultivars, landform management for soil structure and health, checking pathways of nutrient losses or reversing nutrient losses through management at watershed scale and other holistic crop management practices have great scope to result in enhancing nutrient and resource use efficiency through higher yields. The best practices have been found to promote soil organic carbon storage that is critical for optimum soil processes and improve soil health and enhance nutrient use efficiency for sustainable intensification in the rainfed systems

Genomic-based-breeding tools for tropical maize improvement

Maize has traditionally been the main staple diet in the Southern Asia and Sub-Saharan Africa and widely grown by millions of resource poor small scale farmers. Approximately, 35.4 million hectares are sown to tropical maize, constituting around 59% of the developing worlds. Tropical maize encounters tremendous challenges besides poor agro-climatic situations with average yields recorded <3 tones/hectare that is far less than the average of developed countries. On the contrary to poor yields, the demand for maize as food, feed, and fuel is continuously increasing in these regions. Heterosis breeding introduced in early 90 s improved maize yields significantly, but genetic gains is still a mirage, particularly for crop growing under marginal environments. Application of molecular markers has accelerated the pace of maize breeding to some extent. The availability of array of sequencing and genotyping technologies offers unrivalled service to improve precision in maize-breeding programs through modern approaches such as genomic selection, genome-wide association studies, bulk segregant analysis-based sequencing approaches, etc. Superior alleles underlying complex traits can easily be identified and introgressed efficiently using these sequence-based approaches. Integration of genomic tools and techniques with advanced genetic resources such as nested association mapping and backcross nested association mapping could certainly address the genetic issues in maize improvement programs in developing countries. Huge diversity in tropical maize and its inherent capacity for doubled haploid technology offers advantage to apply the next generation genomic tools for accelerating production in marginal environments of tropical and subtropical world. Precision in phenotyping is the key for success of any molecular-breeding approach. This article reviews genomic technologies and their application to improve agronomic traits in tropical maize breeding has been reviewed in detail